Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold45
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: 1930935
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 50924 characters in sequence are not A, C, G, or T
File 2 of 7
Found at i:235602 original size:137 final size:137
Alignment explanation
Indices: 235401--235671 Score: 440
Period size: 137 Copynumber: 2.0 Consensus size: 137
235391 TTTTTTTGAT
235401 TTTTTTAAAATTGATTTATTTTTTGCGGCGTTTTTTTAATAAAAACGCCGCTATTGCTTATCTTT
1 TTTTTTAAAATTGATTTATTTTTTGCGGCG-TTTTTTAATAAAAACGCCGCTATTGCTTATCTTT
* ** * *
235466 TGCGGTGTTTTTTATAAAAACGCCGCAAAATATTATTTCATTTTGAACAAAA-TGACGCTGTTTT
65 TGCGGCGTTTTCCATAAAAACGCCCCAAAATATTATTTCATTTTGAA-AAAACTGACGCCGTTTT
235530 GCTATTTTA
129 GCTATTTTA
235539 TTTTTTATAAATTGATTTATTTTTTGCGGCG-TTTTT-ATAGAAAACGCCGCTATTGCTTATCTT
1 TTTTTTA-AAATTGATTTATTTTTTGCGGCGTTTTTTAATA-AAAACGCCGCTATTGCTTATCTT
235602 TTGCGGCGTTTTCCATAAAAACGCCCCAAAATATTATTTCATTTTGAAAAAACTGACGCCGTTTT
64 TTGCGGCGTTTTCCATAAAAACGCCCCAAAATATTATTTCATTTTGAAAAAACTGACGCCGTTTT
235667 GCTAT
129 GCTAT
235672 GCTAAAAATT
Statistics
Matches: 125, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
136 7 0.06
137 88 0.70
138 7 0.06
139 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (137 bp):
TTTTTTAAAATTGATTTATTTTTTGCGGCGTTTTTTAATAAAAACGCCGCTATTGCTTATCTTTT
GCGGCGTTTTCCATAAAAACGCCCCAAAATATTATTTCATTTTGAAAAAACTGACGCCGTTTTGC
TATTTTA
Found at i:236702 original size:73 final size:71
Alignment explanation
Indices: 236611--236779 Score: 257
Period size: 73 Copynumber: 2.4 Consensus size: 71
236601 AGCATTAGCA
* * * * *
236611 GCGCCTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATGTT
1 GCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACAGCGTCGTTGGGCTTA--TT
236676 TTTTTGCG
64 TTTTTGCG
*
236684 GCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACAGTGTCGTTGGGCTTATTTT
1 GCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACAGCGTCGTTGGGCTTATTTT
236749 TTTGCG
66 TTTGCG
*
236755 GCGCTTTCTCAAAAACGCCGCTAAA
1 GCGCTTTCTTAAAAACGCCGCTAAA
236780 GCACTAAGCA
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
71 34 0.38
73 55 0.62
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (71 bp):
GCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACAGCGTCGTTGGGCTTATTTT
TTTGCG
Found at i:236910 original size:103 final size:106
Alignment explanation
Indices: 236743--237636 Score: 539
Period size: 115 Copynumber: 7.8 Consensus size: 106
236733 TCGTTGGGCT
* * * *
236743 TATTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCACTAAGCATTAGTGGCGCTTTCTTAA
1 TATTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGCGGCGCTTTCTTAA
*
236808 AAACGCCGCTAAATCCCCAAAAGC-C-C-TCGTTAGGCTTA
66 AAACGCCGCTAAATCCCCAAAAGCACACGTCGTTAGGATTA
236846 TATTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGCGGCGCTTTCTTAA
1 TATTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGCGGCGCTTTCTTAA
* *
236911 AAACGACGCTAAATCCCCAAAAGCCCACAAAACGACGTCGTTGGGATTA
66 AAACGCCGCTAAATCCCCAAAAG----C---AC-ACGTCGTTAGGATTA
* *
236960 TGTTTTTTTTACGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGCGGCGCTTTCTTA
1 T-ATTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGCGGCGCTTTCTTA
* * *
237025 AAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTA
65 AAAACGCCGCTAAATCCCCAAAAG--CAC---A---CGTCGTTAGGATTA
* * * * * *
237075 TGTTTTTTTGCGGCGCTTTCTTAAAAACGTCGCTAAATCCCCAAAAGCCCACAAAACAGT-GTCG
1 TATTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAA-GCCC---TG---AC----CATTAG-CG
* ***** * * * * * ***
237139 TTGGGCTTAT-TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCACTAAG-CATTAGTGGCG
54 --GCGCTT-TCTTAAAAAC-GC-C--GCT--AAATC-CC-CAAAAGCAC-ACGTCGTTAG-GATT
*
237202 C
106 A
**** * * * * *
237203 T-TTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACGCTGCTAAAGCCCTGAGCATTAG
1 TATT-TT-TTTGCGGCGCT---T--------TCTCA-AAAACGCCGCTAAAGCCCTGACCATTAG
* * * *
237267 TGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAACCCACAAAACGGGGTCGTTGGGCTTA
52 CGGCGCTTTCTTAAAAACGCCGCTAAATCCCC-AAAA-GCAC---AC---GTCGTTAGGATTA
* * * * *
237330 TGTTTTTTTGTGGCGCTTTCTCAAAAACGCTGCTAAAGCCCTGAGCATTAGTGGCGCTTTCTTAA
1 TATTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGCGGCGCTTTCTTAA
* *
237395 AAACGCCGCTAAATCCCCAAAAGC-C-C-TCGTTGGGCTTA
66 AAACGCCGCTAAATCCCCAAAAGCACACGTCGTTAGGATTA
* * *
237433 TGTTTTTTTGCGGCGCATTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGCGGCACTTTCTTAA
1 TATTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGCGGCGCTTTCTTAA
*
237498 AAACGCCGCTAAATCCCCAAAAGCCCACAAAACGACGTCGTTGGGATTA
66 AAACGCCGCTAAATCCCCAAAAG----C---AC-ACGTCGTTAGGATTA
*
237547 TGTTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGCGGCGCTTTCTTA
1 T-ATTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGCGGCGCTTTCTTA
237612 AAAACGCCGCTAAATCCCCAAAAGC
65 AAAACGCCGCTAAATCCCCAAAAGC
237637 TCTGAAAACG
Statistics
Matches: 622, Mismatches: 91, Indels: 148
0.72 0.11 0.17
Matches are distributed among these distances:
103 177 0.28
107 3 0.00
110 2 0.00
111 4 0.01
112 2 0.00
113 8 0.01
114 115 0.18
115 186 0.30
118 1 0.00
120 1 0.00
121 7 0.01
122 7 0.01
123 1 0.00
124 4 0.01
125 5 0.01
126 6 0.01
127 22 0.04
128 22 0.04
129 7 0.01
130 4 0.01
131 4 0.01
132 1 0.00
133 7 0.01
134 3 0.00
135 5 0.01
137 1 0.00
140 5 0.01
141 12 0.02
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (106 bp):
TATTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGCGGCGCTTTCTTAA
AAACGCCGCTAAATCCCCAAAAGCACACGTCGTTAGGATTA
Found at i:237055 original size:115 final size:114
Alignment explanation
Indices: 236834--237696 Score: 634
Period size: 115 Copynumber: 7.4 Consensus size: 114
236824 CCAAAAGCCC
* * *
236834 TCGTTAGGCTTATATTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGCG
1 TCGTTGGGATTATGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGCG
236899 GCGCTTTCTTAAAAACGACGCTAAATCCCCAAAAGCCCACAAAACGACG
66 GCGCTTTCTTAAAAACGACGCTAAATCCCCAAAAGCCCACAAAACGACG
*
236948 TCGTTGGGATTATGTTTTTTTTACGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGC
1 TCGTTGGGATTATG-TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGC
* * * *
237013 GGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCG
65 GGCGCTTTCTTAAAAACGACGCTAAATCCCCAAAAGCCCACAAAACGACG
* * * * * *
237063 TCGTTTGGCTTATGTTTTTTTGCGGCGCTTTCTTAAAAACGTCGCTAAATCCCCAAAAGCCCACA
1 TCGTTGGGATTATGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAA-GCCC---TG---AC-
* * ***** * * * * * *
237128 AAACAGT-GTCGTTGGGCTTAT-TTTTTTGCGGCGCT---TTCTCAAAAACGCCGCTAAA-G-C-
58 ---CATTAG-CG--GCGCTT-TCTTAAAAACGACGCTAAATCCCCAAAAGC-CCACAAAACGACG
* ** * *** * * * *
237185 AC-TAAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACGCTGC
1 TCGTTGGGATTA-T---G-TTT-TT--TTGCGGCGCT---T--------TCTCA-AAAACGCCGC
* * * *
237249 TAAAGCCCTGAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAACCCACAAAAC
46 TAAAGCCCTGACCATTAGCGGCGCTTTCTTAAAAACGACGCTAAATCCCCAAAAGCCCACAAAAC
**
237314 GGGG
111 GACG
* * * * *
237318 TCGTTGGGCTTATGTTTTTTTGTGGCGCTTTCTCAAAAACGCTGCTAAAGCCCTGAGCATTAGTG
1 TCGTTGGGATTATGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGCG
*
237383 GCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAG----C----C--C-
66 GCGCTTTCTTAAAAACGACGCTAAATCCCCAAAAGCCCACAAAACGACG
* *
237421 TCGTTGGGCTTATGTTTTTTTGCGGCGCATTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGCG
1 TCGTTGGGATTATGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGCG
* *
237486 GCACTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACGACG
66 GCGCTTTCTTAAAAACGACGCTAAATCCCCAAAAGCCCACAAAACGACG
237535 TCGTTGGGATTATGTTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGC
1 TCGTTGGGATTATG-TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGC
* * ** * *
237600 GGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCTCTGAAAACGGCA
65 GGCGCTTTCTTAAAAACGACGCTAAATCCCCAAAAGCCCACAAAACGACG
* * * * * **
237650 TCGTCGGGCTTA-GGTTTTTTGTGGCGCTTTTTGGAAAACGCCGCTAA
1 TCGTTGGGATTATGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAA
237697 TGCTTATTTT
Statistics
Matches: 595, Mismatches: 96, Indels: 117
0.74 0.12 0.14
Matches are distributed among these distances:
103 94 0.16
106 1 0.00
107 1 0.00
110 1 0.00
111 1 0.00
113 30 0.05
114 121 0.20
115 216 0.36
118 1 0.00
121 7 0.01
122 2 0.00
123 2 0.00
124 9 0.02
125 11 0.02
126 8 0.01
127 16 0.03
128 16 0.03
129 9 0.02
130 11 0.02
131 11 0.02
132 1 0.00
133 2 0.00
134 6 0.01
137 1 0.00
140 5 0.01
141 12 0.02
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (114 bp):
TCGTTGGGATTATGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGACCATTAGCG
GCGCTTTCTTAAAAACGACGCTAAATCCCCAAAAGCCCACAAAACGACG
Found at i:237099 original size:73 final size:71
Alignment explanation
Indices: 237011--237182 Score: 263
Period size: 73 Copynumber: 2.4 Consensus size: 71
237001 CTGACCATTA
* * * *
237011 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTAT
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACAGCGTCGTTGGGCTTA-
237076 GTTTTTTT
65 -TTTTTTT
* *
237084 GCGGCGCTTTCTTAAAAACGTCGCTAAATCCCCAAAAGCCCACAAAACAGTGTCGTTGGGCTTAT
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACAGCGTCGTTGGGCTTAT
237149 TTTTTT
66 TTTTTT
*
237155 GCGGCGCTTTCTCAAAAACGCCGCTAAA
1 GCGGCGCTTTCTTAAAAACGCCGCTAAA
237183 GCACTAAGCA
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
71 33 0.36
73 58 0.64
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.28
Consensus pattern (71 bp):
GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACAGCGTCGTTGGGCTTAT
TTTTTT
Found at i:237217 original size:185 final size:182
Alignment explanation
Indices: 236869--237420 Score: 739
Period size: 185 Copynumber: 3.0 Consensus size: 182
236859 CGCTTTCTCA
* * *
236869 AAAACGCCGCTAAAGCCCTGACCATTAGCGGCGCTTTCTTAAAAACGACGCTAAATCCCCAAAAG
1 AAAACGCTGCTAAAGCCATGAGCATTAGCGGCGCTTTCTTAAAAACGACGCTAAATCCCCAAAAG
* *
236934 CCCACAAAACGACGTCGTTGGGATTATGTTTTTTTTACGGCGCTTTCTCAAAAACGCCGCTAAAG
66 CCCACAAAACG-CGTCGTTGGGCTTA--TTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAG
* * * *
236999 CCCTGACCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAC
128 CCCTGAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCAC
*** * **** * *
237054 AAAACGGC-GTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTCTTAAAAACGTCGCTAAATCCCCA
1 AAAAC-GCTG-C-TAAAGC-CATGAGCATTAGCGGCGCTTTCTTAAAAACGACGCTAAATCCCCA
*
237118 AAAGCCCACAAAACAGTGTCGTTGGGCTTA-TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAA
62 AAAGCCCACAAAAC-GCGTCGTTGGGCTTATTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAA
* *
237182 AGCACTAAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCAC
126 AGCCCTGAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCAC
* * * *
237239 AAAACGCTGCTAAAGCCCTGAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAA
1 AAAACGCTGCTAAAGCCATGAGCATTAGCGGCGCTTTCTTAAAAACGACGCTAAATCCCCAAAAG
* * *
237304 CCCACAAAACGGGGTCGTTGGGCTTATGTTTTTTTGTGGCGCTTTCTCAAAAACGCTGCTAAAGC
66 CCCACAAAAC-GCGTCGTTGGGCTTAT-TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGC
237369 CCTGAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCC
129 CCTGAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCC
237421 TCGTTGGGCT
Statistics
Matches: 320, Mismatches: 39, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
182 63 0.20
183 3 0.01
184 88 0.28
185 96 0.30
186 3 0.01
187 3 0.01
188 63 0.20
189 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (182 bp):
AAAACGCTGCTAAAGCCATGAGCATTAGCGGCGCTTTCTTAAAAACGACGCTAAATCCCCAAAAG
CCCACAAAACGCGTCGTTGGGCTTATTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC
TGAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCAC
Found at i:237251 original size:70 final size:70
Alignment explanation
Indices: 237169--237314 Score: 256
Period size: 70 Copynumber: 2.1 Consensus size: 70
237159 CGCTTTCTCA
*
237169 AAAACGCCGCTAAAGCACTAAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAG
1 AAAACGCCGCTAAAGCACTAAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAA
237234 CCCAC
66 CCCAC
* * *
237239 AAAACGCTGCTAAAGCCCTGAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAA
1 AAAACGCCGCTAAAGCACTAAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAA
237304 CCCAC
66 CCCAC
237309 AAAACG
1 AAAACG
237315 GGGTCGTTGG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.36, C:0.31, G:0.16, T:0.17
Consensus pattern (70 bp):
AAAACGCCGCTAAAGCACTAAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAA
CCCAC
Found at i:237540 original size:217 final size:218
Alignment explanation
Indices: 237239--237636 Score: 681
Period size: 217 Copynumber: 1.8 Consensus size: 218
237229 AAAAGCCCAC
* * * *
237239 AAAACGCTGCTAAAGCCCTGAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAA
1 AAAACGCCGCTAAAGCCCTGACCATTAGCGGCACTTTCTTAAAAACGCCGCTAAATCCCCAAAAA
** * * *
237304 CCCACAAAACGGGGTCGTTGGGCTTATG-TTTTTTTGTGGCGCTTTCTCAAAAACGCTGCTAAAG
66 CCCACAAAACGACGTCGTTGGGATTATGTTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAG
* *
237368 CCCTGAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCTCGTTGGGCTTA
131 CCCTGACCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCTCGTTGGGCTTA
237433 TGTTTTTTTGCGGCGCATTCTCA
196 TGTTTTTTTGCGGCGCATTCTCA
*
237456 AAAACGCCGCTAAAGCCCTGACCATTAGCGGCACTTTCTTAAAAACGCCGCTAAATCCCCAAAAG
1 AAAACGCCGCTAAAGCCCTGACCATTAGCGGCACTTTCTTAAAAACGCCGCTAAATCCCCAAAAA
237521 CCCACAAAACGACGTCGTTGGGATTATGTTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAG
66 CCCACAAAACGACGTCGTTGGGATTATGTTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAG
237586 CCCTGACCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGC
131 CCCTGACCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGC
237637 TCTGAAAACG
Statistics
Matches: 168, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
217 85 0.51
218 83 0.49
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.25
Consensus pattern (218 bp):
AAAACGCCGCTAAAGCCCTGACCATTAGCGGCACTTTCTTAAAAACGCCGCTAAATCCCCAAAAA
CCCACAAAACGACGTCGTTGGGATTATGTTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAG
CCCTGACCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCTCGTTGGGCTTA
TGTTTTTTTGCGGCGCATTCTCA
Found at i:237782 original size:12 final size:12
Alignment explanation
Indices: 237765--237790 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
237755 TTTTTTATCT
237765 AAACGCCGCTAA
1 AAACGCCGCTAA
237777 AAACGCCGCTAA
1 AAACGCCGCTAA
237789 AA
1 AA
237791 GCTTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:238437 original size:2 final size:2
Alignment explanation
Indices: 238425--238461 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
238415 GTTAACAATA
*
238425 AT AT A- AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
238462 TTATCTTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:238979 original size:9 final size:9
Alignment explanation
Indices: 238965--238992 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
238955 TTCGAATTCG
238965 AATTCGAAT
1 AATTCGAAT
238974 AATTCGAAT
1 AATTCGAAT
238983 AATTCGAAT
1 AATTCGAAT
238992 A
1 A
238993 TCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:245044 original size:5 final size:6
Alignment explanation
Indices: 245029--245053 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
245019 TTTGAAATTA
245029 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
245054 TATATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:247898 original size:26 final size:26
Alignment explanation
Indices: 247869--247923 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
247859 AAAAGCGCAA
247869 AAAAACCGCAAAAAAAAAGAAAAAAC
1 AAAAACCGCAAAAAAAAAGAAAAAAC
*
247895 AAAAAGCGCAAAAAAAAAGAAAAAAC
1 AAAAACCGCAAAAAAAAAGAAAAAAC
247921 AAA
1 AAA
247924 GAGTTGTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.78, C:0.13, G:0.09, T:0.00
Consensus pattern (26 bp):
AAAAACCGCAAAAAAAAAGAAAAAAC
Found at i:247919 original size:37 final size:37
Alignment explanation
Indices: 247851--247925 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
247841 TTATTCTTTA
* ** *
247851 AAAAAATAAAAAGCGCAAAAAAACCGCAAAAAAAAAG
1 AAAAAACAAAAAGCGCAAAAAAAAAGAAAAAAAAAAG
*
247888 AAAAAACAAAAAGCGCAAAAAAAAAGAAAAAACAAAG
1 AAAAAACAAAAAGCGCAAAAAAAAAGAAAAAAAAAAG
247925 A
1 A
247926 GTTGTATGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.76, C:0.12, G:0.11, T:0.01
Consensus pattern (37 bp):
AAAAAACAAAAAGCGCAAAAAAAAAGAAAAAAAAAAG
Found at i:250331 original size:3 final size:3
Alignment explanation
Indices: 250323--250366 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
250313 ATCTATCCTT
250323 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
250367 TAACTAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:254394 original size:18 final size:18
Alignment explanation
Indices: 254371--254405 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
254361 ACCGCTTACC
254371 GTCTCCGCCGTGGGAGTG
1 GTCTCCGCCGTGGGAGTG
*
254389 GTCTCCGCCTTGGGAGT
1 GTCTCCGCCGTGGGAGT
254406 AGCGGGCGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.29, G:0.40, T:0.26
Consensus pattern (18 bp):
GTCTCCGCCGTGGGAGTG
Found at i:262631 original size:3 final size:3
Alignment explanation
Indices: 262623--262665 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
262613 GAAATCAAGA
*
262623 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AG AAG CAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
262666 AAAGTAAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:262674 original size:6 final size:6
Alignment explanation
Indices: 262665--262693 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
262655 AAGCAGAAGA
262665 AAAAGT AAAAGT AAAAGT AAAAGT AAAAG
1 AAAAGT AAAAGT AAAAGT AAAAGT AAAAG
262694 GTATTCAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (6 bp):
AAAAGT
Found at i:264327 original size:21 final size:21
Alignment explanation
Indices: 264286--264324 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
264276 GTTTATGTTT
*
264286 TATTATTTTAACCATTATTAA
1 TATTATTATAACCATTATTAA
264307 TATTATTATAA-CATTATT
1 TATTATTATAACCATTATT
264325 TAACATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTATTATAACCATTATTAA
Found at i:265834 original size:12 final size:12
Alignment explanation
Indices: 265817--265869 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 12
265807 CTTATTATGA
265817 ATTTTTATAATT
1 ATTTTTATAATT
*
265829 ATTTTTAATATGTTTT
1 ATTTTT-ATA---ATT
265845 ATTTTTTATAATT
1 A-TTTTTATAATT
265858 ATTTTTATAATT
1 ATTTTTATAATT
265870 TATTATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
12 17 0.50
13 6 0.18
16 6 0.18
17 5 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (12 bp):
ATTTTTATAATT
Found at i:265880 original size:19 final size:19
Alignment explanation
Indices: 265790--265920 Score: 88
Period size: 19 Copynumber: 6.6 Consensus size: 19
265780 TCAATAAATG
* *
265790 ATTATAATTTATTAGAACTT
1 ATTATAATTT-TTATAATTT
265810 ATTATGAATTTTTATAA-TT
1 ATTAT-AATTTTTATAATTT
* **
265829 ATTTTTAATATGTTTTATTTTTT
1 A-TTAT-A-AT-TTTTATAATTT
* *
265852 ATAATTATTTTTATAATTT
1 ATTATAATTTTTATAATTT
* *
265871 ATTATAATTTATATAATAT
1 ATTATAATTTTTATAATTT
265890 -TTATAAGTTTTTATGAATTT
1 ATTATAA-TTTTTAT-AATTT
265910 -TTATAATTTTT
1 ATTATAATTTTT
265921 GTAGGTTTAC
Statistics
Matches: 88, Mismatches: 16, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
18 6 0.07
19 38 0.43
20 26 0.30
21 7 0.08
22 8 0.09
23 3 0.03
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (19 bp):
ATTATAATTTTTATAATTT
Found at i:265881 original size:29 final size:28
Alignment explanation
Indices: 265820--265909 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 28
265810 ATTATGAATT
**
265820 TTTATAATTATTTTTA-ATATGTTTTATTT
1 TTTATAATTATTTTTATA-AT-TTTTATAA
265849 TTTATAATTATTTTTATAATTTATTATAA
1 TTTATAATTATTTTTATAATTT-TTATAA
* *
265878 TTTAT-ATAATATTTATAAGTTTTTATGAA
1 TTTATAATTATTTTTATAA-TTTTTAT-AA
265907 TTT
1 TTT
265910 TTATAATTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
28 17 0.32
29 35 0.66
30 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (28 bp):
TTTATAATTATTTTTATAATTTTTATAA
Found at i:265885 original size:9 final size:9
Alignment explanation
Indices: 265791--265920 Score: 91
Period size: 10 Copynumber: 13.2 Consensus size: 9
265781 CAATAAATGA
265791 TTATAATTT
1 TTATAATTT
* *
265800 ATTAGAACTTA
1 -TTATAA-TTT
265811 TTATGAATTT
1 TTAT-AATTT
265821 TTATAATTAT
1 TTATAATT-T
*
265831 TTTTAATATGT
1 TTATAAT-T-T
*
265842 TT-TATTTT
1 TTATAATTT
265850 TTATAATTATTT
1 TTAT-A--ATTT
265862 TTATAATTT
1 TTATAATTT
265871 ATTATAATTT
1 -TTATAATTT
* *
265881 ATATAATAT
1 TTATAATTT
265890 TTATAAGTTT
1 TTATAA-TTT
265900 TTATGAATTT
1 TTAT-AATTT
265910 TTATAATTT
1 TTATAATTT
265919 TT
1 TT
265921 GTAGGTTTAC
Statistics
Matches: 97, Mismatches: 12, Indels: 23
0.73 0.09 0.17
Matches are distributed among these distances:
8 3 0.03
9 29 0.30
10 47 0.48
11 11 0.11
12 7 0.07
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.62
Consensus pattern (9 bp):
TTATAATTT
Found at i:269531 original size:54 final size:54
Alignment explanation
Indices: 269472--269628 Score: 146
Period size: 54 Copynumber: 3.1 Consensus size: 54
269462 ACTATAACTT
269472 TACTTCAAAATTTAGAGAATATGTCGATATAAAGAACTAATTTAATAAAGAATG
1 TACTTCAAAATTTAGAGAATATGTCGATATAAAGAACTAATTTAATAAAGAATG
* * * *
269526 TACTTC--AA-TT----AATATG-CTGCTTATACAA-AA-TAA-CT-AT--A-ACTT
1 TACTTCAAAATTTAGAGAATATGTC-G-ATATA-AAGAACTAATTTAATAAAGAATG
269568 TACTTCAAAATTTAGAGAATATGTCGATATAAAGAACTAATTTAATAAAGAATG
1 TACTTCAAAATTTAGAGAATATGTCGATATAAAGAACTAATTTAATAAAGAATG
269622 TACTTCA
1 TACTTCA
269629 TTCCTATGAA
Statistics
Matches: 77, Mismatches: 8, Indels: 36
0.64 0.07 0.30
Matches are distributed among these distances:
42 8 0.10
43 1 0.01
44 2 0.03
45 4 0.05
46 2 0.03
47 12 0.16
48 12 0.16
49 12 0.16
50 2 0.03
51 4 0.05
52 2 0.03
53 1 0.01
54 15 0.19
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (54 bp):
TACTTCAAAATTTAGAGAATATGTCGATATAAAGAACTAATTTAATAAAGAATG
Found at i:269547 original size:96 final size:97
Alignment explanation
Indices: 269435--269628 Score: 381
Period size: 96 Copynumber: 2.0 Consensus size: 97
269425 AATAAATTAA
269435 AATTAATATGCTTGCTTATACAAAATAACTATAACTTTACTTCAAAATTTAGAGAATATGTCGAT
1 AATTAATATGCTTGCTTATACAAAATAACTATAACTTTACTTCAAAATTTAGAGAATATGTCGAT
269500 ATAAAGAACTAATTTAATAAAGAATGTACTTC
66 ATAAAGAACTAATTTAATAAAGAATGTACTTC
269532 AATTAATATGC-TGCTTATACAAAATAACTATAACTTTACTTCAAAATTTAGAGAATATGTCGAT
1 AATTAATATGCTTGCTTATACAAAATAACTATAACTTTACTTCAAAATTTAGAGAATATGTCGAT
269596 ATAAAGAACTAATTTAATAAAGAATGTACTTC
66 ATAAAGAACTAATTTAATAAAGAATGTACTTC
269628 A
1 A
269629 TTCCTATGAA
Statistics
Matches: 97, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
96 86 0.89
97 11 0.11
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (97 bp):
AATTAATATGCTTGCTTATACAAAATAACTATAACTTTACTTCAAAATTTAGAGAATATGTCGAT
ATAAAGAACTAATTTAATAAAGAATGTACTTC
Found at i:284228 original size:296 final size:297
Alignment explanation
Indices: 283683--284275 Score: 1170
Period size: 296 Copynumber: 2.0 Consensus size: 297
283673 TCCCAAGCAA
283683 CGAAACCCAGTCAAAGCATCCACAATGGTAGAGAATTCCATCAGGAATCAACCAAGGAGCTCTCC
1 CGAAACCCAGTCAAAGCATCCACAATGGTAGAGAATTCCATCAGGAATCAACCAAGGAGCTCTCC
283748 ATTCCACATCATCCTCTTGAAGATTTTACAGAATTGCTATCCAATTTTCTTTTGATATATCGTCC
66 ATTCCACATCATCCTCTTGAAGATTTTACAGAATTGCTATCCAATTTTCTTTTGATATATCGTCC
283813 CTTCTGGGGGTAGCCACTATTTCCTTTAACGGGGAATAATACTCAGAGAAAACTCGATACGAAAC
131 CTTCTGGGGGTAGCCACTATTTCCTTTAACGGGGAATAATACTCAGAGAAAACTCGATACGAAAC
283878 TTTGTCCACCTTCCAGAAATGTCTATGGAACTAGACTATCAACAGTTGTGCACAACCTATAAATC
196 TTTGTCCACCTTCCAGAAATGTCTATGGAACTAGACTATCAACAGTTGTGCACAACCTATAAATC
283943 TACCTTCACCAGCTCGCCTACACGCATTCAAAGATTT
261 TACCTTCACCAGCTCGCCTACACGCATTCAAAGATTT
*
283980 CGAACCCCAG-CAAAGCATCCACAATGGTAGAGAATTCCATCAGGAATCAACCAAGGAGCTCTCC
1 CGAAACCCAGTCAAAGCATCCACAATGGTAGAGAATTCCATCAGGAATCAACCAAGGAGCTCTCC
284044 ATTCCACATCATCCTCTTGAAGATTTTACAGAATTGCTATCCAATTTTCTTTTGATATATCGTCC
66 ATTCCACATCATCCTCTTGAAGATTTTACAGAATTGCTATCCAATTTTCTTTTGATATATCGTCC
284109 CTTCTGGGGGTAGCCACTATTTCCTTTAACGGGGAATAATACTCAGAGAAAACTCGATACGAAAC
131 CTTCTGGGGGTAGCCACTATTTCCTTTAACGGGGAATAATACTCAGAGAAAACTCGATACGAAAC
284174 TTTGTCCACCTTCCAGAAATGTCTATGGAACTAGACTATCAACAGTTGTGCACAACCTATAAATC
196 TTTGTCCACCTTCCAGAAATGTCTATGGAACTAGACTATCAACAGTTGTGCACAACCTATAAATC
284239 TACCTTCACCAGCTCGCCTACACGCATTCAAAGATTT
261 TACCTTCACCAGCTCGCCTACACGCATTCAAAGATTT
284276 AAACGTTTCA
Statistics
Matches: 295, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
296 286 0.97
297 9 0.03
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.27
Consensus pattern (297 bp):
CGAAACCCAGTCAAAGCATCCACAATGGTAGAGAATTCCATCAGGAATCAACCAAGGAGCTCTCC
ATTCCACATCATCCTCTTGAAGATTTTACAGAATTGCTATCCAATTTTCTTTTGATATATCGTCC
CTTCTGGGGGTAGCCACTATTTCCTTTAACGGGGAATAATACTCAGAGAAAACTCGATACGAAAC
TTTGTCCACCTTCCAGAAATGTCTATGGAACTAGACTATCAACAGTTGTGCACAACCTATAAATC
TACCTTCACCAGCTCGCCTACACGCATTCAAAGATTT
Found at i:287994 original size:17 final size:18
Alignment explanation
Indices: 287972--288009 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
287962 AATCAAAATC
287972 TTCCTATAT-CTGTTATT
1 TTCCTATATGCTGTTATT
* *
287989 TTCCTATTTGCTGTTGTT
1 TTCCTATATGCTGTTATT
288007 TTC
1 TTC
288010 GTGTGTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.11, C:0.18, G:0.11, T:0.61
Consensus pattern (18 bp):
TTCCTATATGCTGTTATT
Found at i:288385 original size:16 final size:16
Alignment explanation
Indices: 288354--288384 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
288344 ACATTTTAAG
288354 ATTTTGGGTTTATTTT
1 ATTTTGGGTTTATTTT
288370 ATTTT-GGTTTATTTT
1 ATTTTGGGTTTATTTT
288385 TGTTTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.13, C:0.00, G:0.16, T:0.71
Consensus pattern (16 bp):
ATTTTGGGTTTATTTT
Found at i:289013 original size:17 final size:17
Alignment explanation
Indices: 288976--289014 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
288966 CTTTTTCTAT
*
288976 TTTTTTCTTTCTTTGAG
1 TTTTTTCTTTCTTTCAG
288993 TTTTTTCTGTTCTTTCA-
1 TTTTTTCT-TTCTTTCAG
289010 TTTTT
1 TTTTT
289015 CGTATACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.05, C:0.13, G:0.08, T:0.74
Consensus pattern (17 bp):
TTTTTTCTTTCTTTCAG
Found at i:289014 original size:18 final size:17
Alignment explanation
Indices: 288969--289014 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
288959 GGTGGTTCTT
288969 TTTCTATTTTTTTCTTTC
1 TTTC-ATTTTTTTCTTTC
* *
288987 TTTGAGTTTTTTCTGTTC
1 TTTCATTTTTTTCT-TTC
289005 TTTCATTTTT
1 TTTCATTTTT
289015 CGTATACATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.07, C:0.13, G:0.07, T:0.74
Consensus pattern (17 bp):
TTTCATTTTTTTCTTTC
Found at i:301463 original size:7 final size:7
Alignment explanation
Indices: 301451--301500 Score: 72
Period size: 6 Copynumber: 7.7 Consensus size: 7
301441 GATTCTGATA
301451 AAAAATC
1 AAAAATC
301458 AAAAATC
1 AAAAATC
301465 AAAAATC
1 AAAAATC
301472 -AAAATC
1 AAAAATC
301478 -AAAATC
1 AAAAATC
301484 -AAAATC
1 AAAAATC
301490 AAAAA-C
1 AAAAATC
301496 AAAAA
1 AAAAA
301501 AGAAAAGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 24 0.57
7 18 0.43
ACGTcount: A:0.74, C:0.14, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATC
Found at i:301513 original size:31 final size:31
Alignment explanation
Indices: 301452--301533 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
301442 ATTCTGATAA
** **
301452 AAAATCAAAAATCAAAAATCAAAATCAAAATC
1 AAAATCAAAAA-CAAAAAAGAAAAGAAAAATC
301484 AAAATCAAAAACAAAAAAGAAAAGAAAAATC
1 AAAATCAAAAACAAAAAAGAAAAGAAAAATC
* *
301515 AAAGTCAAAAGCAAAAAAG
1 AAAATCAAAAACAAAAAAG
301534 GGAAATCAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 33 0.75
32 11 0.25
ACGTcount: A:0.72, C:0.12, G:0.06, T:0.10
Consensus pattern (31 bp):
AAAATCAAAAACAAAAAAGAAAAGAAAAATC
Found at i:303544 original size:44 final size:44
Alignment explanation
Indices: 303483--303887 Score: 246
Period size: 44 Copynumber: 8.8 Consensus size: 44
303473 AGACTGAAGA
* * *
303483 AGAAATCTCATCTCCCTGAGATTATAGCGGAGAAGATTGAAGCT
1 AGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT
* * * * **
303527 AGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAAT
1 AGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT
* * *
303570 A-AAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCACATCAGATTGAAGCC
1 AGAA--ATCTTATCTCCCTGAGA-TTACAG-CG-G-AG-------CAGATTGAAGCT
*
303625 AGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCC
1 AGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT
* * *
303669 AAAAATCTTATCTCACTGAGATTACAGTGGAGCAGATTGAAGCT
1 AGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT
* * * * * * *
303713 AGTAATCCTATCTCCCTTAGATTACAGTGGAGCGGATTAAAAC-
1 AGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT
* * *
303756 A-AAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCACATCAGATTGAAGCC
1 AGAA--ATCTTATCTCCCTGAGA-TTACAG-CG-G-AG-------CAGATTGAAGCT
* * *
303811 AGAAATCTTATCTCCCAGTGATTACAACGGAGCAGATTGAAGCT
1 AGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT
* * *
303855 AGTAATCCTATCTCCCTGAGATTACAGTGGAGC
1 AGAAATCTTATCTCCCTGAGATTACAGCGGAGC
303888 GAATTAAAAC
Statistics
Matches: 278, Mismatches: 51, Indels: 64
0.71 0.13 0.16
Matches are distributed among these distances:
42 2 0.01
43 7 0.03
44 193 0.69
45 2 0.01
46 2 0.01
47 4 0.01
51 4 0.01
52 2 0.01
53 2 0.01
54 50 0.18
55 6 0.02
56 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (44 bp):
AGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT
Found at i:303657 original size:98 final size:98
Alignment explanation
Indices: 303516--303848 Score: 393
Period size: 98 Copynumber: 3.5 Consensus size: 98
303506 ATAGCGGAGA
* * * * *
303516 AGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTA
1 AGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAACAAAGGATCTTA
303581 TCTCTCTGAAGTTACAGTAGAGTAGATCACATC
66 TCTCTCTGAAGTTACAGTAGAGTAGATCACATC
* ** *
303614 AGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAAA-AATCTT
1 AGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATT-AAAACAAAGGATCTT
*
303678 ATCTCACTG-AGATTACAGT-G-G-AG-------C
65 ATCTCTCTGAAG-TTACAGTAGAGTAGATCACATC
* * * * *
303702 AGATTGAAGCTAGTAATCCTATCTCCCTTAGATTACAGTGGAGCGGATTAAAACAAAGGATCTTA
1 AGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAACAAAGGATCTTA
303767 TCTCTCTGAAGTTACAGTAGAGTAGATCACATC
66 TCTCTCTGAAGTTACAGTAGAGTAGATCACATC
* * * *
303800 AGATTGAAGCCAGAAATCTTATCTCCCAGTGATTACAACGGAGCAGATT
1 AGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATT
303849 GAAGCTAGTA
Statistics
Matches: 192, Mismatches: 29, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
87 6 0.03
88 64 0.33
89 3 0.02
90 1 0.01
91 2 0.01
95 2 0.01
96 1 0.01
97 3 0.02
98 105 0.55
99 5 0.03
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (98 bp):
AGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAACAAAGGATCTTA
TCTCTCTGAAGTTACAGTAGAGTAGATCACATC
Found at i:303812 original size:186 final size:186
Alignment explanation
Indices: 303485--303887 Score: 680
Period size: 186 Copynumber: 2.2 Consensus size: 186
303475 ACTGAAGAAG
* * * *
303485 AAATCTCATCTCCCTGAGATTATAGCGGAGAAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
1 AAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
*
303550 ACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCA
66 ACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCA
* *
303615 GATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAA
131 GATTGAAGCCAGAAATCTTATCTCCCAGAGATTACAACGGAGCAGATTGAAGCCAA
* *
303671 AAATCTTATCTCACTGAGATTACAGTGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTTAGATT
1 AAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
303736 ACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCA
66 ACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCA
* * *
303801 GATTGAAGCCAGAAATCTTATCTCCCAGTGATTACAACGGAGCAGATTGAAGCTAG
131 GATTGAAGCCAGAAATCTTATCTCCCAGAGATTACAACGGAGCAGATTGAAGCCAA
* *
303857 TAATCCTATCTCCCTGAGATTACAGTGGAGC
1 AAATCTTATCTCCCTGAGATTACAGTGGAGC
303888 GAATTAAAAC
Statistics
Matches: 202, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
186 202 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (186 bp):
AAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
ACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCA
GATTGAAGCCAGAAATCTTATCTCCCAGAGATTACAACGGAGCAGATTGAAGCCAA
Found at i:303822 original size:142 final size:142
Alignment explanation
Indices: 303657--303962 Score: 513
Period size: 142 Copynumber: 2.2 Consensus size: 142
303647 TACAGCGGAG
* * **
303657 CAGATTGAAGCCAAAAATCTTATCTCACTGAGATTACAGTGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCACAGAGATTACAACGGAGCAGATTGAAGCTAGTAATCCT
* *
303722 ATCTCCCTTAGATTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGAATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAG
303787 AGTAGATCACAT
131 AGTAGATCACAT
* *
303799 CAGATTGAAGCCAGAAATCTTATCTCCCAGTGATTACAACGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCACAGAGATTACAACGGAGCAGATTGAAGCTAGTAATCCT
*
303864 ATCTCCCTGAGATTACAGTGGAGCGAATTAAAACAAAGGATCTTATCTCTTTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGAATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAG
*
303929 AGTAGATCGCAT
131 AGTAGATCACAT
*
303941 CAGATTGAAGCCAGGAATCTTA
1 CAGATTGAAGCCAGAAATCTTA
303963 CTCCCTCAAG
Statistics
Matches: 153, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
142 153 1.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (142 bp):
CAGATTGAAGCCAGAAATCTTATCTCACAGAGATTACAACGGAGCAGATTGAAGCTAGTAATCCT
ATCTCCCTGAGATTACAGTGGAGCGAATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAG
AGTAGATCACAT
Found at i:304313 original size:15 final size:16
Alignment explanation
Indices: 304293--304322 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
304283 TAAATAAACA
304293 AAAATAAA-CCAAAAT
1 AAAATAAACCCAAAAT
304308 AAAATAAACCCAAAA
1 AAAATAAACCCAAAA
304323 CCTTAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.73, C:0.17, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAATAAACCCAAAAT
Found at i:304570 original size:15 final size:15
Alignment explanation
Indices: 304552--304581 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
304542 GTGCGCCACT
304552 GCTACGTGCCATGCC
1 GCTACGTGCCATGCC
304567 GCTACGTGCCATGCC
1 GCTACGTGCCATGCC
304582 TCCATGCGCT
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:0.13, C:0.40, G:0.27, T:0.20
Consensus pattern (15 bp):
GCTACGTGCCATGCC
Found at i:304704 original size:17 final size:18
Alignment explanation
Indices: 304668--304705 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
304658 AAAGACACAC
304668 GAAAACAACAGCAAATAG
1 GAAAACAACAGCAAATAG
* *
304686 GAAAATAACAG-ATATAG
1 GAAAACAACAGCAAATAG
304703 GAA
1 GAA
304706 GATTTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.61, C:0.11, G:0.18, T:0.11
Consensus pattern (18 bp):
GAAAACAACAGCAAATAG
Found at i:315933 original size:129 final size:129
Alignment explanation
Indices: 315709--315943 Score: 303
Period size: 129 Copynumber: 1.8 Consensus size: 129
315699 CATTTATTTC
315709 AATTTAAAAGGATATTCGGCTATTTAGAATTAACGAGAAAAATCGAAGCCCAGTAAGTTAGGGCA
1 AATTTAAAAGGATATTCGGCTATTTAGAATTAACGAGAAAAATCGAAGCCCAGTAAGTTAGGGCA
* * * * * *
315774 CGATTTCTCGAATTTTCTAAATATAGAATATTACCTTTATTTTTTTGAAATTTTATGTATTTGGA
66 CAATTTCTCAAATTTCCAAAATACAAAATATTACC-TTATTTTTTTGAAATTTTATGTATTTGGA
** * ** * *
315839 AATTTAAAAGGATATTTTGCTATTTGGGTTTAACGAG-AAAATCG-AGACCTAGTAAGTTAGGGT
1 AATTTAAAAGGATATTCGGCTATTTAGAATTAACGAGAAAAATCGAAG-CCCAGTAAGTTAGGGC
* *
315902 ACAATTTCTCAAATTTCCAAAATGCAAAATATTGCCTTATTT
65 ACAATTTCTCAAATTTCCAAAATACAAAATATTACCTTATTT
315944 AGCAAAATTC
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
128 8 0.09
129 49 0.55
130 32 0.36
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (129 bp):
AATTTAAAAGGATATTCGGCTATTTAGAATTAACGAGAAAAATCGAAGCCCAGTAAGTTAGGGCA
CAATTTCTCAAATTTCCAAAATACAAAATATTACCTTATTTTTTTGAAATTTTATGTATTTGGA
Found at i:318063 original size:20 final size:18
Alignment explanation
Indices: 318040--318080 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
318030 GCGTATGTAC
318040 ATATTTACAAACGTAAAAAT
1 ATATTT-CAAAC-TAAAAAT
*
318060 ATATTTGAAACTAAAAAT
1 ATATTTCAAACTAAAAAT
318078 ATA
1 ATA
318081 AAAGTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 4 0.20
20 6 0.30
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (18 bp):
ATATTTCAAACTAAAAAT
Found at i:320095 original size:45 final size:45
Alignment explanation
Indices: 320046--320731 Score: 193
Period size: 44 Copynumber: 15.3 Consensus size: 45
320036 CAGTACATGA
*
320046 AGACACGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
1 AGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
* * * * *** *
320091 AGACAAGATCTG-TTTCTTTGATCTACTTCA-CGCCAGTACATGA
1 AGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
*
320134 AGACATGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
1 AGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
* * * * *** *
320179 AGACAAGATCTG-TTTCTTTGATCTACTTCA-CGCCAGTACATGA
1 AGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
** * ** * * * *
320222 AGACAAGATCTACTTTCTTTGATTTGCTTCGCCACCAGTATGGGA
1 AGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
* * * * * * *** *
320267 AGGCAAGATCAACTTTTTTCTGATATTTGATCTACTTCA-CGCCAGTACATGA
1 AGACAAGAT---CTGTTTTC-----TTCGACCTACTCCACCACCAGTATGGGG
* * ** * * *
320319 AGACAAGATCTGCTTTCTTCGATCTGTTTCACCACCAGTACGGGA
1 AGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
* * * * * * *** *
320364 AGACAAGATCTGGTATCTTTGATCTACTTCA-CGCCAGTACATGA
1 AGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
* * * ** * * *
320408 AGACAAGATCCGCTTTCTTCGATCTGTTTCACCACCAGTACGGGA
1 AGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
* * * * * * *** *
320453 AGACAAGATCTGGTATCTTTGATCTACTTCA-CGCCAGTACATGA
1 AGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
* * * ** * * *
320497 AGACAAGATCCGCTTTCTTCGATCTGTTTCACCACCAGTACGGGA
1 AGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
* * * * * * *** *
320542 AGACAAGATCTGGTATCTTTGATCTACTTCA-CGCCAGTACATGA
1 AGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
* * * ** * * *
320586 AGACAAGATCCGCTTTCTTCGATCTGTTTCACCACCAGTACGGGA
1 AGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
* * * * * * *** *
320631 AGACAAGATCTGGTATCTTTGATCTACTTCA-CGCCAGTACATGA
1 AGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
* * * ** * * *
320675 AGACAAGATCCGCTTTCTTCGATCTGTTTCACCACCAGTACGGGA
1 AGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
320720 AGACAAGATCTG
1 AGACAAGATCTG
320732 GTATCTTTGA
Statistics
Matches: 498, Mismatches: 126, Indels: 34
0.76 0.19 0.05
Matches are distributed among these distances:
43 38 0.08
44 211 0.42
45 209 0.42
48 6 0.01
49 6 0.01
52 17 0.03
53 11 0.02
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (45 bp):
AGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGG
Found at i:320443 original size:89 final size:89
Alignment explanation
Indices: 320015--320796 Score: 1190
Period size: 89 Copynumber: 8.7 Consensus size: 89
320005 CAGGACCTAC
* * * * ** *
320015 TATCTTTGATCTACTTCACGCCAGTACATGAAGACACGATCTGTTTTCTTCGACCTACTCCACCA
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCCGCTTTCTTCGATCTGTTTCACCA
* *
320080 CCAGTATGGGGAGACAAGATCT-G
66 CCAGTACGGGAAGACAAGATCTGG
* * * * * ** *
320103 TTTCTTTGATCTACTTCACGCCAGTACATGAAGACATGATCTGTTTTCTTCGACCTACTCCACCA
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCCGCTTTCTTCGATCTGTTTCACCA
* *
320168 CCAGTATGGGGAGACAAGATCT-G
66 CCAGTACGGGAAGACAAGATCTGG
* ** * * * *
320191 TTTCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTTGATTTGCTTCGCCA
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCCGCTTTCTTCGATCTGTTTCACCA
* * **
320256 CCAGTATGGGAAGGCAAGATCAACTTTTTTC
66 CCAGTACGGGAAGACAAGAT---C----TGG
* *
320287 TGATATTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCACC
1 T-ATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCCGCTTTCTTCGATCTGTTTCACC
320352 ACCAGTACGGGAAGACAAGATCTGG
65 ACCAGTACGGGAAGACAAGATCTGG
320377 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCCGCTTTCTTCGATCTGTTTCACCA
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCCGCTTTCTTCGATCTGTTTCACCA
320442 CCAGTACGGGAAGACAAGATCTGG
66 CCAGTACGGGAAGACAAGATCTGG
320466 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCCGCTTTCTTCGATCTGTTTCACCA
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCCGCTTTCTTCGATCTGTTTCACCA
320531 CCAGTACGGGAAGACAAGATCTGG
66 CCAGTACGGGAAGACAAGATCTGG
320555 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCCGCTTTCTTCGATCTGTTTCACCA
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCCGCTTTCTTCGATCTGTTTCACCA
320620 CCAGTACGGGAAGACAAGATCTGG
66 CCAGTACGGGAAGACAAGATCTGG
320644 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCCGCTTTCTTCGATCTGTTTCACCA
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCCGCTTTCTTCGATCTGTTTCACCA
320709 CCAGTACGGGAAGACAAGATCTGG
66 CCAGTACGGGAAGACAAGATCTGG
320733 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCCGCTTTCTTCGATCTGTTTCACC
1 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCCGCTTTCTTCGATCTGTTTCACC
320797 TGGGAGGATA
Statistics
Matches: 658, Mismatches: 27, Indels: 17
0.94 0.04 0.02
Matches are distributed among these distances:
88 160 0.24
89 417 0.63
90 2 0.00
91 1 0.00
94 1 0.00
95 1 0.00
96 1 0.00
97 75 0.11
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (89 bp):
TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCCGCTTTCTTCGATCTGTTTCACCA
CCAGTACGGGAAGACAAGATCTGG
Found at i:325335 original size:26 final size:26
Alignment explanation
Indices: 325299--325349 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
325289 TAGCATCTGG
325299 CTTGTATCCTAAGCCAAAACGGTCCA
1 CTTGTATCCTAAGCCAAAACGGTCCA
*
325325 CTTGTATCCTAAGCCAAAATGGTCC
1 CTTGTATCCTAAGCCAAAACGGTCC
325350 TGCTTGTCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.25
Consensus pattern (26 bp):
CTTGTATCCTAAGCCAAAACGGTCCA
Found at i:325821 original size:40 final size:40
Alignment explanation
Indices: 325766--325841 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
325756 CATAAACAGT
325766 TGGGCCAATTAACAAGGGAATGTCAATTCTTCCCATGACC
1 TGGGCCAATTAACAAGGGAATGTCAATTCTTCCCATGACC
*
325806 TGGGCCAATTAACAAGGGTATGTCAATTCTTCCCAT
1 TGGGCCAATTAACAAGGGAATGTCAATTCTTCCCAT
325842 TACTTTCCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (40 bp):
TGGGCCAATTAACAAGGGAATGTCAATTCTTCCCATGACC
Found at i:335820 original size:21 final size:20
Alignment explanation
Indices: 335794--335833 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
335784 TATTCCATGA
*
335794 AATTAAAATATCATAAAAGAG
1 AATT-AAATAACATAAAAGAG
*
335815 AATTAATTAACATAAAAGA
1 AATTAAATAACATAAAAGA
335834 AAATGATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (20 bp):
AATTAAATAACATAAAAGAG
Found at i:336481 original size:5 final size:5
Alignment explanation
Indices: 336473--336502 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
336463 CCTTACCTTC
*
336473 TAATA TAATA TAATA TAATA CAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA
336503 GGTTAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (5 bp):
TAATA
Found at i:343413 original size:28 final size:28
Alignment explanation
Indices: 343370--343439 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
343360 AAACACAACA
**
343370 GAAAAGAATAATCTTTGTGGCGAACTCT
1 GAAAAGAATAGCCTTTGTGGCGAACTCT
343398 GAAAAGAATAGCCTTTGTGGCGAACTCT
1 GAAAAGAATAGCCTTTGTGGCGAACTCT
343426 GAAAAGAATAGCCT
1 GAAAAGAATAGCCT
343440 GTGTTGAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (28 bp):
GAAAAGAATAGCCTTTGTGGCGAACTCT
Found at i:348992 original size:129 final size:129
Alignment explanation
Indices: 348786--349857 Score: 1588
Period size: 129 Copynumber: 8.3 Consensus size: 129
348776 AGGATTCATC
* * ** * *
348786 GTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAGTCTGCTCCACTGTA
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCA
* *
348851 ACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGTAACTTCAGAGAAATAAGATCTGTG
66 ACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTG
* * *
348915 GTTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTTGTTTCTTCTGTCTGCTCCGCTGCA
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCA
* *
348980 ACTTCAGGGAGATAAGAATGGATGCGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGTG
66 ACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTG
* *
349044 GTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTGCA
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCA
* * * *
349109 ACTTTAGGGAGATAAGACTGGATGCGATCTGTTCTACTACAACTTCAGAGAGATGAGATCTGTG
66 ACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTG
* * * * **
349173 GTTTTAATCCGCTCCACTGTAACTTCAGGAAGATAGGATTGATTTCTTCTGTCTGTTCTGCTGCA
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCA
* * *
349238 ACTTCAGAGAGATAAGACTGGATGCGATATGCTCTACTGCAACTTCAGAGAGATAAGATCTATG
66 ACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTG
* * * * * * *
349302 GTTTTAATCCGCTCCACTGTAATTTTAGGGAGATAAGATTGGTTTCTTTTGTCTGCTCTACTGTA
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCA
* * * * *
349367 ACTTCAGAGAGATGAGACTGGACGCGATCTGCTCTACTGTAACTTCAAAGAGATAAGATCTGTG
66 ACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTG
* * *
349431 GTTTTAATCCGCTCTACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTTTCTGCTCCACTGCA
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCA
* * *
349496 ACTTCAGGGAGATAAGACTGGATGCGATCTGCTTTACTGTAACTTCAGAGAGATAAGATTTGTG
66 ACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTG
* * * *
349560 GTTTTAATCCGCTTCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCTGTTCCGCTGCA
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCA
* *
349625 ACTTTAGGGAGATAAGACTGGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTG
66 ACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTG
* * * * * *
349689 GTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTT-TTTTTTTTACTCCACTACA
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCA
* *
349753 ACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGTG
66 ACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTG
*
349817 GTTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTG
1 GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTG
349858 TAGCTTTACT
Statistics
Matches: 852, Mismatches: 91, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
128 111 0.13
129 741 0.87
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (129 bp):
GTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCA
ACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTG
Found at i:350626 original size:93 final size:96
Alignment explanation
Indices: 350467--350645 Score: 247
Period size: 93 Copynumber: 1.9 Consensus size: 96
350457 GAAAAATGCT
* *
350467 TGAAAAAGATTATCACAATGGACAAAATGAAATTTTATTAAGAACAAAGATCGAAATGAATTAA-
1 TGAAAAAGATTACCACAATGGACAAAATGAAATTTTATTAAGAACAAAGATCGAAATGAATAAAT
350531 T-T-AAGATAGCAAATTTTGTTAAGATAAGA
66 TATCAAGATAGCAAATTTTGTTAAGATAAGA
* * * * * * *
350560 TGAAAAAGATTACCACAATGGATAAGATGAAATTTTGTTGATAGCAAAGCTCGAAATGAATAAAT
1 TGAAAAAGATTACCACAATGGACAAAATGAAATTTTATTAAGAACAAAGATCGAAATGAATAAAT
350625 TAATCAAGATAGCAAATTTTG
66 T-ATCAAGATAGCAAATTTTG
350646 CCAAGATTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
93 55 0.75
94 1 0.01
96 1 0.01
97 16 0.22
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (96 bp):
TGAAAAAGATTACCACAATGGACAAAATGAAATTTTATTAAGAACAAAGATCGAAATGAATAAAT
TATCAAGATAGCAAATTTTGTTAAGATAAGA
Found at i:351407 original size:7 final size:7
Alignment explanation
Indices: 351395--351450 Score: 71
Period size: 7 Copynumber: 8.0 Consensus size: 7
351385 CCCGGTAGAG
351395 GTTTTTT
1 GTTTTTT
351402 GTTTTTT
1 GTTTTTT
351409 GTTTTTT
1 GTTTTTT
*
351416 ATTTTCTT
1 GTTTT-TT
351424 GTTTTTT
1 GTTTTTT
351431 -TTGTTTT
1 GTT-TTTT
351438 -TTTTTT
1 GTTTTTT
351444 GTTTTTT
1 GTTTTTT
351451 TGCCTCCACT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
6 6 0.14
7 32 0.73
8 6 0.14
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.86
Consensus pattern (7 bp):
GTTTTTT
Found at i:351428 original size:20 final size:20
Alignment explanation
Indices: 351404--351451 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
351394 GGTTTTTTGT
*
351404 TTTTTGTTTTTTATTTTCTTG
1 TTTTT-TTTGTTATTTTCTTG
* *
351425 TTTTTTTTGTTTTTTTTTTG
1 TTTTTTTTGTTATTTTCTTG
351445 TTTTTTT
1 TTTTTTT
351452 GCCTCCACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.02, C:0.02, G:0.08, T:0.88
Consensus pattern (20 bp):
TTTTTTTTGTTATTTTCTTG
Found at i:351435 original size:24 final size:22
Alignment explanation
Indices: 351398--351451 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 22
351388 GGTAGAGGTT
351398 TTTTGTTTTTTGTTTTTTATTTTC
1 TTTT-TTTTTTGTTTTTT-TTTTC
*
351422 TTGTTTTTTTTGTTTTTTTTTTG
1 TT-TTTTTTTTGTTTTTTTTTTC
351445 TTTTTTT
1 TTTTTTT
351452 GCCTCCACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 5 0.18
23 6 0.21
24 15 0.54
25 2 0.07
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.87
Consensus pattern (22 bp):
TTTTTTTTTTGTTTTTTTTTTC
Found at i:354208 original size:19 final size:20
Alignment explanation
Indices: 354184--354230 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
354174 TGTGAAAATC
* *
354184 TAATGCATATG-ATGTAATG
1 TAATGCAAATGCATGGAATG
354203 TAATGCAAATGCATGGAATG
1 TAATGCAAATGCATGGAATG
354223 -AATGCAAA
1 TAATGCAAA
354231 AAGAAAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGCATGGAATG
Found at i:358009 original size:15 final size:15
Alignment explanation
Indices: 357960--358010 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
357950 TTACTTCAGA
*
357960 TTACGTTTTAGTCAC
1 TTACGTTTTAGTCAT
* *
357975 TTATG-TTT-GACAT
1 TTACGTTTTAGTCAT
357988 GTTACGTTTTAGTCAT
1 -TTACGTTTTAGTCAT
358004 TTACGTT
1 TTACGTT
358011 ATCGTGTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 3 0.11
14 7 0.25
15 14 0.50
16 4 0.14
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.51
Consensus pattern (15 bp):
TTACGTTTTAGTCAT
Found at i:358640 original size:31 final size:29
Alignment explanation
Indices: 358605--358681 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
358595 TTAATAGCTC
*
358605 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* * ***
358636 AGTGACAAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
358665 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
358682 CTAAGGTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 21 0.55
30 1 0.03
31 16 0.42
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:358833 original size:31 final size:29
Alignment explanation
Indices: 358798--358874 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
358788 TTAATAGCTC
*
358798 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* * ***
358829 AGTGACAAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
358858 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
358875 CTAAGGTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 21 0.55
30 1 0.03
31 16 0.42
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:358833 original size:193 final size:193
Alignment explanation
Indices: 358504--358889 Score: 756
Period size: 193 Copynumber: 2.0 Consensus size: 193
358494 GAAAAAATAT
358504 GGGGATCGATTGTATAATTTACCCTAAAATTTTTGTTTGAAATGATGATTTAACGTGCCACGTCA
1 GGGGATCGATTGTATAATTTACCCTAAAATTTTTGTTTGAAATGATGATTTAACGTGCCACGTCA
358569 ACTTACCGTTATACTGTTAGTGGCAATTAATAGCTCAGTGACTAAAATGTTACAACACGATAACA
66 ACTTACCGTTATACTGTTAGTGGCAATTAATAGCTCAGTGACTAAAATGTTACAACACGATAACA
358634 TAAGTGACAAAAACGTAACATTTCAAACATAAGTGACTAAAATGTAACCTAAGGTAAACAAAA
131 TAAGTGACAAAAACGTAACATTTCAAACATAAGTGACTAAAATGTAACCTAAGGTAAACAAAA
358697 GGGGATCGATTGTATAATTTACCCTAAAATTTTTGTTTTGAAATGA-GATTTAACGTGCCACGTC
1 GGGGATCGATTGTATAATTTACCCTAAAATTTTTG-TTTGAAATGATGATTTAACGTGCCACGTC
358761 AACTTACCGTTATACTGTTAGTGGCAATTAATAGCTCAGTGACTAAAATGTTACAACACGATAAC
65 AACTTACCGTTATACTGTTAGTGGCAATTAATAGCTCAGTGACTAAAATGTTACAACACGATAAC
358826 ATAAGTGACAAAAACGTAACATTTCAAACATAAGTGACTAAAATGTAACCTAAGGTAAACAAAA
130 ATAAGTGACAAAAACGTAACATTTCAAACATAAGTGACTAAAATGTAACCTAAGGTAAACAAAA
358890 ATGACCATGG
Statistics
Matches: 192, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
193 182 0.95
194 10 0.05
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (193 bp):
GGGGATCGATTGTATAATTTACCCTAAAATTTTTGTTTGAAATGATGATTTAACGTGCCACGTCA
ACTTACCGTTATACTGTTAGTGGCAATTAATAGCTCAGTGACTAAAATGTTACAACACGATAACA
TAAGTGACAAAAACGTAACATTTCAAACATAAGTGACTAAAATGTAACCTAAGGTAAACAAAA
Found at i:360603 original size:33 final size:32
Alignment explanation
Indices: 360564--360643 Score: 83
Period size: 34 Copynumber: 2.4 Consensus size: 32
360554 TCTTTCCTTC
* *
360564 CTCTTTTCATTTTTTCTTTCTTTTTCCTT-TTTT
1 CTCTTTTCATTTTATCCTTC-TTTT-CTTCTTTT
*
360597 CTCTTTTTCGTTTTATCCTTCTTTTCTTCTTTT
1 CTC-TTTTCATTTTATCCTTCTTTTCTTCTTTT
360630 CT-TTTTCATCTTTA
1 CTCTTTTCAT-TTTA
360644 CGTCGGTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
31 6 0.15
32 7 0.17
33 13 0.32
34 14 0.35
ACGTcount: A:0.05, C:0.23, G:0.01, T:0.71
Consensus pattern (32 bp):
CTCTTTTCATTTTATCCTTCTTTTCTTCTTTT
Found at i:363351 original size:12 final size:12
Alignment explanation
Indices: 363334--363367 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
363324 AAATACAAAA
363334 TAAAAAAATGCT
1 TAAAAAAATGCT
363346 T-AAAAAATGCT
1 TAAAAAAATGCT
363357 TAAAAAAATGC
1 TAAAAAAATGC
363368 CAGTAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.24
Consensus pattern (12 bp):
TAAAAAAATGCT
Found at i:363933 original size:13 final size:13
Alignment explanation
Indices: 363915--363978 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
363905 TTTTTTATTA
363915 TTTTTTCTTTCCT
1 TTTTTTCTTTCCT
**
363928 TTTTTTCTTTTTTT
1 TTTTTTC-TTTCCT
*
363942 CTTTTTTCTTTCCC
1 -TTTTTTCTTTCCT
* *
363956 CTTTTTCTTTCTT
1 TTTTTTCTTTCCT
363969 TTTTCTTCTT
1 TTTT-TTCTT
363979 CTTCTTCCTT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
13 20 0.51
14 12 0.31
15 7 0.18
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTCTTTCCT
Found at i:363939 original size:21 final size:23
Alignment explanation
Indices: 363915--364002 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 23
363905 TTTTTTATTA
363915 TTTTTTCTTTCCTTT-TT-TTCT
1 TTTTTTCTTTCCTTTCTTCTTCT
* *
363936 TTTTTTCTTT--TTTCTT-TCCC
1 TTTTTTCTTTCCTTTCTTCTTCT
* *
363956 CTTTTTCTTT-CTTTTTTCTTCT
1 TTTTTTCTTTCCTTTCTTCTTCT
* *
363978 TCTTCTTCCTTCCTTTCTTCTTCT
1 T-TTTTTCTTTCCTTTCTTCTTCT
364002 T
1 T
364003 CACTTTAGGG
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
19 3 0.06
20 13 0.25
21 15 0.29
22 2 0.04
23 7 0.13
24 12 0.23
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTTCTTTCCTTTCTTCTTCT
Found at i:363946 original size:28 final size:27
Alignment explanation
Indices: 363906--363978 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
363896 CTGTTTATAT
**
363906 TTTTTATTATTTTTTCTTTCCTTTTTTTC
1 TTTTT-TT-TTTTTTCTTTCCCCTTTTTC
363935 TTTTTTTCTTTTTTCTTTCCCCTTTTTC
1 TTTTTTT-TTTTTTCTTTCCCCTTTTTC
* *
363963 TTTCTTTTTTCTTCTT
1 TTTTTTTTTTTTTCTT
363979 CTTCTTCCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 8 0.21
28 26 0.67
29 5 0.13
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (27 bp):
TTTTTTTTTTTTTCTTTCCCCTTTTTC
Found at i:364114 original size:9 final size:9
Alignment explanation
Indices: 364097--364152 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
364087 TCTTGTCTAT
*
364097 TTTTTTCTC
1 TTTTCTCTC
364106 TTTTCTCTC
1 TTTTCTCTC
*
364115 TTTTCTTTC
1 TTTTCTCTC
*
364124 TTCTCT-TC
1 TTTTCTCTC
*
364132 TTTCTCTCTG
1 TTT-TCTCTC
*
364142 TTTTTTCTC
1 TTTTCTCTC
364151 TT
1 TT
364153 CTATTTTCGA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
8 4 0.11
9 30 0.79
10 4 0.11
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTTCTCTC
Found at i:364120 original size:16 final size:18
Alignment explanation
Indices: 364099--364140 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
364089 TTGTCTATTT
364099 TTTTCTCTT-TTCTC-TC
1 TTTTCTCTTCTTCTCTTC
364115 TTTTCT-TTCTTCTCTTC
1 TTTTCTCTTCTTCTCTTC
364132 TTTCTCTCT
1 TTT-TCTCT
364141 GTTTTTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.09
16 11 0.50
17 5 0.23
18 3 0.14
19 1 0.05
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTCTCTTCTTCTCTTC
Found at i:364145 original size:27 final size:26
Alignment explanation
Indices: 364104--364154 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
364094 TATTTTTTTC
364104 TCTTTTCTCTCTTTTCTT-TCTTCTCT
1 TCTTTTCTCTCTTTT-TTCTCTTCTCT
*
364130 TCTTTCTCTCTGTTTTTTCTCTTCT
1 TCTTT-TCTCTCTTTTTTCTCTTCT
364155 ATTTTCGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (26 bp):
TCTTTTCTCTCTTTTTTCTCTTCTCT
Found at i:364148 original size:25 final size:22
Alignment explanation
Indices: 364096--364149 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 22
364086 CTCTTGTCTA
364096 TTTTT-TTCTCTTTTCTCTCTT
1 TTTTTCTTCTCTTTTCTCTCTT
364117 TTCTTTCTTCTCTTCTTTCTCTCTGT
1 TT-TTTCTTCTC-T-TTTCTCTCT-T
364143 TTTTTCT
1 TTTTTCT
364150 CTTCTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 2 0.07
22 3 0.11
23 5 0.18
24 1 0.04
25 14 0.50
26 3 0.11
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTTCTTCTCTTTTCTCTCTT
Found at i:364160 original size:25 final size:23
Alignment explanation
Indices: 364100--364160 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 23
364090 TGTCTATTTT
364100 TTTCTCTTTTCTCTCTTTTCTTTC
1 TTTCT-TTTTCTCTCTTTTCTTTC
364124 TTCTCTTCTTTCTCTCTGTTT-TTTC
1 TT-TCTT-TTTCTCTCT-TTTCTTTC
364149 TCTTCTATTTTC
1 T-TTCT-TTTTC
364161 GAAAACCCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
24 3 0.09
25 24 0.75
26 5 0.16
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTCTTTTTCTCTCTTTTCTTTC
Found at i:364303 original size:12 final size:12
Alignment explanation
Indices: 364286--364312 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
364276 TTTTCTATTC
364286 TTTGCTTGATTT
1 TTTGCTTGATTT
364298 TTTGCTTGATTT
1 TTTGCTTGATTT
364310 TTT
1 TTT
364313 TTTTGTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.15, T:0.70
Consensus pattern (12 bp):
TTTGCTTGATTT
Found at i:364588 original size:30 final size:30
Alignment explanation
Indices: 364548--364680 Score: 158
Period size: 30 Copynumber: 4.4 Consensus size: 30
364538 ATTTGATGTC
* * ** *
364548 AAAATATAATTTTAGGAATGTTTAGGGGTT
1 AAAATGTAATTTTAAGAAAATTTAAGGGTT
* * **
364578 AAAATGTAATTTCAAGAAAGTTTGTGGGTT
1 AAAATGTAATTTTAAGAAAATTTAAGGGTT
* *
364608 AAAATATAATTTTAGGAAAATTTAAGGGTT
1 AAAATGTAATTTTAAGAAAATTTAAGGGTT
*
364638 AAAATGTAATTTTAAGAAAATTTAAGGGTC
1 AAAATGTAATTTTAAGAAAATTTAAGGGTT
364668 AAAATGTAATTTT
1 AAAATGTAATTTT
364681 TTTTAAAAAT
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 88 1.00
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.38
Consensus pattern (30 bp):
AAAATGTAATTTTAAGAAAATTTAAGGGTT
Found at i:364618 original size:60 final size:60
Alignment explanation
Indices: 364545--364680 Score: 191
Period size: 60 Copynumber: 2.3 Consensus size: 60
364535 AAAATTTGAT
** * * **
364545 GTCAAAATATAATTTTAGGAATGTTTAGGGGTTAAAATGTAATTTCAAGAAAGTTTGTGG
1 GTCAAAATATAATTTTAGGAAAATTTAAGGGTTAAAATGTAATTTCAAGAAAATTTAAGG
* *
364605 GTTAAAATATAATTTTAGGAAAATTTAAGGGTTAAAATGTAATTTTAAGAAAATTTAAGG
1 GTCAAAATATAATTTTAGGAAAATTTAAGGGTTAAAATGTAATTTCAAGAAAATTTAAGG
*
364665 GTCAAAATGTAATTTT
1 GTCAAAATATAATTTT
364681 TTTTAAAAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.41, C:0.02, G:0.19, T:0.38
Consensus pattern (60 bp):
GTCAAAATATAATTTTAGGAAAATTTAAGGGTTAAAATGTAATTTCAAGAAAATTTAAGG
Found at i:365113 original size:152 final size:152
Alignment explanation
Indices: 364861--366165 Score: 1513
Period size: 153 Copynumber: 8.5 Consensus size: 152
364851 GGCCGACGAT
* * * *
364861 CCGAAGCTCAACTCACCTATCGGATTATGAGTTGATATTTG-AAAAACAGAAATTG-AAAATACC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
* * * * **
364924 TC-AGCGTGCGACCTGTGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAA-AGAA
66 TCGA-CATGTG-CCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTAAAAAACAGAA
* * *
364987 TTTGAAAAATACCTGGGCGTGTGAC
129 ATTGAAAAATACCTCGGCATGTG-C
** *
365012 CTAAGGCTCAACTCACCTCTTGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
*
365077 TCGACATGTGCCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTGAAAAACAGAAAT
66 TCGACATGTGCCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTAAAAAACAGAAAT
* *
365141 TAAAAAAAATACCTCAGCATGTGC
131 T--GAAAAATACCTCGGCATGTGC
* * * *
365165 CCGAAGCTCAACTCACCTTTCACATTATGAGTTGAATTTTGAAAAAACAGAAATTGAAAAATACC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
* * * * * *
365230 TTGGCATGTGCTCGAGGCTCAACTAACCTCTCGTATTATGAGTTGATTTTTGAAAAAACAGAAAT
66 TCGACATGTGCCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTAAAAAACAGAAAT
365295 TGAAAAATACCTCGGCATGTGC
131 TGAAAAATACCTCGGCATGTGC
* * * *
365317 CCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTG-AAAAATAGAGATTAAAAAAATAC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATT-GAAAAATAC
* * *
365381 CTCGTCATGTGCCCGAGGCTCAACTCACCTCTCCTCTCGTATTATGAGTTGA-TTTTTAAAAAAT
65 CTCGACATGTGCCCGAGGCTCAACTCA-----CCTCTCGCATTATGAGTTGATTTTTTAAAAAAC
* * *
365445 AGAGATTAAAAAAATACCTCGTCATGTGC
125 AGAAATT-GAAAAATACCTCGGCATGTGC
* *
365474 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAAAAATTGAAAAGTACC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
* * * **
365539 TC-AGCATGTGCCCGAGGCTTAACTCACCTCTCGTATTATGAGTTAATTTTAAAAAAAACAGAAA
66 TCGA-CATGTGCCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTAAAAAACAGAAA
*
365603 TTGAAAAGTACCTCGGCATGTGC
130 TTGAAAAATACCTCGGCATGTGC
* * * * * *
365626 CCAAGGCTCAACTCACCTCTGGCATTATGAGTTGA-TTAT-AAAAAAAATAAATTAAAAAATACC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
* * * * * *
365689 TCGGCACGTGCCCGAGGCTCAACTCACCTATTGCATTATGAGTTGATTTTTGAAAAATCAGAAAT
66 TCGACATGTGCCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTAAAAAACAGAAAT
* * *
365754 TGAAAAATACCTCAGCGTGCGAC
131 TGAAAAATACCTCGGCATGTG-C
* * * * * *
365777 CTGGGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTAAAAAAAATAGAAATTGAAAAATGC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTT-GAAAAAACAGAAATTGAAAAATAC
* * * *
365842 CTCGGCATGTGACCCGAGACTCAACTCACCTCTCAG-ACTATGAGTTGATTTTTGAAAAAAACAG
65 CTCGACATGTG-CCCGAGGCTCAACTCACCTCTC-GCATTATGAGTTGATTTTT-TAAAAAACAG
* *
365906 AAATTGAAAAATACATCGGCGTGTGC
127 AAATTGAAAAATACCTCGGCATGTGC
* * *
365932 CCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTG-AAAACCAGAAACTGAAAAATACC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
* ** *
365996 TC-AGCGTACGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAAACAGA
66 TCGA-CATGTG-CCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTT-TAAAAAACAGA
*
366060 AATTG-AAAATACCTCGGCATGCGAC
128 AATTGAAAAATACCTCGGCATGTG-C
* * * * *
366085 CCGAGGCTCAACTCACCTCTCGGATTATAAGTTGACTTTTGAAAAAATAGAAATTGAAAAATACA
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
* *
366150 TCGGCGTGTGCCCGAG
66 TCGACATGTGCCCGAG
366166 TGTAACACCC
Statistics
Matches: 987, Mismatches: 137, Indels: 58
0.84 0.12 0.05
Matches are distributed among these distances:
150 91 0.09
151 88 0.09
152 229 0.23
153 252 0.26
154 88 0.09
155 72 0.07
156 47 0.05
157 110 0.11
158 10 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (152 bp):
CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
TCGACATGTGCCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTAAAAAACAGAAAT
TGAAAAATACCTCGGCATGTGC
Found at i:366146 original size:77 final size:76
Alignment explanation
Indices: 364861--366165 Score: 1597
Period size: 76 Copynumber: 17.1 Consensus size: 76
364851 GGCCGACGAT
* * * *
364861 CCGAAGCTCAACTCACCTATCGGATTATGAGTTGATATTTG-AAAAACAGAAATTG-AAAATACC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
* * *
364924 TCAGCGTGCGAC
66 TCGGCATGTG-C
* * *** *
364936 CTGTGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAA-AGAATTTGAAAAATACC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
* *
365000 TGGGCGTGTGAC
66 TCGGCATGTG-C
** *
365012 CTAAGGCTCAACTCACCTCTTGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
*
365077 TCGACATGTGC
66 TCGGCATGTGC
*
365088 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTG-AAAAACAGAAATTAAAAAAAATA
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATT--GAAAAATA
*
365152 CCTCAGCATGTGC
64 CCTCGGCATGTGC
* * * *
365165 CCGAAGCTCAACTCACCTTTCACATTATGAGTTGAATTTTGAAAAAACAGAAATTGAAAAATACC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
*
365230 TTGGCATGTGC
66 TCGGCATGTGC
* * *
365241 TCGAGGCTCAACTAACCTCTCGTATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
365306 TCGGCATGTGC
66 TCGGCATGTGC
* * * *
365317 CCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTG-AAAAATAGAGATTAAAAAAATAC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATT-GAAAAATAC
*
365381 CTCGTCATGTGC
65 CTCGGCATGTGC
* * * *
365393 CCGAGGCTCAACTCACCTCTCCTCTCGTATTATGAGTTGATTTTT-AAAAAATAGAGATTAAAAA
1 CCGAGGCTCAACTCA-----CCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATT-GAAA
*
365457 AATACCTCGTCATGTGC
60 AATACCTCGGCATGTGC
* *
365474 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAAAAATTGAAAAGTACC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
*
365539 TCAGCATGTGC
66 TCGGCATGTGC
* * * ** *
365550 CCGAGGCTTAACTCACCTCTCGTATTATGAGTTAATTTTAAAAAAAACAGAAATTGAAAAGTACC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
365615 TCGGCATGTGC
66 TCGGCATGTGC
* * * * * *
365626 CCAAGGCTCAACTCACCTCTGGCATTATGAGTTGA-TTAT-AAAAAAAATAAATTAAAAAATACC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
*
365689 TCGGCACGTGC
66 TCGGCATGTGC
* * *
365700 CCGAGGCTCAACTCACCTATTGCATTATGAGTTGATTTTTGAAAAATCAGAAATTGAAAAATACC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
* * *
365765 TCAGCGTGCGAC
66 TCGGCATGTG-C
* * * * * *
365777 CTGGGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTAAAAAAAATAGAAATTGAAAAATGC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTT-GAAAAAACAGAAATTGAAAAATAC
365842 CTCGGCATGTGAC
65 CTCGGCATGTG-C
* *
365855 CCGAGACTCAACTCACCTCTCAG-ACTATGAGTTGATTTTTGAAAAAAACAGAAATTGAAAAATA
1 CCGAGGCTCAACTCACCTCTC-GCATTATGAGTTGATTTTTG-AAAAAACAGAAATTGAAAAATA
* *
365919 CATCGGCGTGTGC
64 CCTCGGCATGTGC
* * *
365932 CCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTG-AAAACCAGAAACTGAAAAATACC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
* * **
365996 TCAGCGTACGAC
66 TCGGCATGTG-C
366008 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAAACAGAAATTG-AAAATAC
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTG-AAAAAACAGAAATTGAAAAATAC
*
366072 CTCGGCATGCGAC
65 CTCGGCATGTG-C
* * * * *
366085 CCGAGGCTCAACTCACCTCTCGGATTATAAGTTGACTTTTGAAAAAATAGAAATTGAAAAATACA
1 CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
*
366150 TCGGCGTGTGC
66 TCGGCATGTGC
366161 CCGAG
1 CCGAG
366166 TGTAACACCC
Statistics
Matches: 1074, Mismatches: 131, Indels: 49
0.86 0.10 0.04
Matches are distributed among these distances:
74 62 0.06
75 97 0.09
76 487 0.45
77 233 0.22
78 119 0.11
79 1 0.00
81 75 0.07
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (76 bp):
CCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAAATACC
TCGGCATGTGC
Found at i:367711 original size:50 final size:50
Alignment explanation
Indices: 367646--367778 Score: 149
Period size: 50 Copynumber: 2.7 Consensus size: 50
367636 CAATGCGATA
* * ** * * * *
367646 TCCCAGATATGGTCTTACGTGGGAGTTCTTATATCGGTGCCCATGTCATG
1 TCCCAGACATGGTCTTACGGGGGACCTCTCATATCGGTGCCAACGCCATG
*
367696 TCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACGGGGGACCTCTCATATCGGTGCCAACGCCATG
* ** *
367746 TCCCAGACATGATCTTACATGAGACCTCTCATA
1 TCCCAGACATGGTCTTACGGGGGACCTCTCATA
367779 ACCTCAATAA
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.28
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACGGGGGACCTCTCATATCGGTGCCAACGCCATG
Found at i:374187 original size:22 final size:22
Alignment explanation
Indices: 374159--374209 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
374149 CGAGTCTGAC
*
374159 AAATTCACATTCATTCTTGGTT
1 AAATTCACATTCATACTTGGTT
*
374181 AAATTCACGTTCATACTTGGTT
1 AAATTCACATTCATACTTGGTT
*
374203 ACATTCA
1 AAATTCA
374210 TCTTACCCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (22 bp):
AAATTCACATTCATACTTGGTT
Found at i:376059 original size:20 final size:20
Alignment explanation
Indices: 376013--376059 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
376003 ATCATGGTCT
*
376013 TTGCTTACTTCTTTACTTAC
1 TTGCTTAATTCTTTACTTAC
** *
376033 TCACTTAATTGTTTACTTAC
1 TTGCTTAATTCTTTACTTAC
376053 TTGCTTA
1 TTGCTTA
376060 CTTAAACAAC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.53
Consensus pattern (20 bp):
TTGCTTAATTCTTTACTTAC
Found at i:376260 original size:49 final size:49
Alignment explanation
Indices: 376183--376425 Score: 170
Period size: 50 Copynumber: 4.8 Consensus size: 49
376173 TGATAATAAC
* * *
376183 TTGCCAAAGCCATATGCCAGACAAGGTCTTACATGGGATGTT-TCCTAT-G
1 TTGCCAATGCCATAT-CCAGACATGGTCTTACATGGGA-GTTCTCATATCG
*
376232 TTGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATCG
1 TTGCCAATGCCATATCC-AGACATGGTCTTACATGGGAGTTCTCATATCG
* * * * * ** *
376282 GTGCCCATCCCATGTCCGAGACATGGTCTTAC-GGGTGACCTCTCATCTCGG
1 TTGCCAATGCCATATCC-AGACATGGTCTTACATGG-GAGTTCTCATATC-G
* * ** *
376333 TT-CCAATGCCGTGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAA
1 TTGCCAATGCCATAT-CCAGACATGGTCTTACATGGGAGTTCTCAT-A--TC-G
*
376386 TAATGCCAATGCCATGTCTCAGACATGGTCTTACATGGGA
1 T--TGCCAATGCCATATC-CAGACATGGTCTTACATGGGA
376426 TCTCATCCTT
Statistics
Matches: 157, Mismatches: 23, Indels: 21
0.78 0.11 0.10
Matches are distributed among these distances:
48 5 0.03
49 39 0.25
50 70 0.45
51 6 0.04
53 3 0.02
55 2 0.01
56 32 0.20
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.28
Consensus pattern (49 bp):
TTGCCAATGCCATATCCAGACATGGTCTTACATGGGAGTTCTCATATCG
Found at i:386043 original size:24 final size:25
Alignment explanation
Indices: 386016--386063 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
386006 ATTTATTTAA
*
386016 ATTAATAAA-ATAAA-ATAAAATAAC
1 ATTAA-AAATATAAATACAAAATAAC
386040 ATTAAAAATATAAATACAAAATAA
1 ATTAAAAATATAAATACAAAATAA
386064 AAAATGCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.14
24 10 0.48
25 8 0.38
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (25 bp):
ATTAAAAATATAAATACAAAATAAC
Found at i:386280 original size:15 final size:15
Alignment explanation
Indices: 386228--386290 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
386218 CCCTTTTTTT
386228 CTGC-TGTTGGGCTG
1 CTGCTTGTTGGGCTG
* **
386242 CTGCATACTGGGCTGG
1 CTGCTTGTTGGGCT-G
**
386258 GAGCTTGTTGGGCTG
1 CTGCTTGTTGGGCTG
*
386273 CTGCTTGTTGGCCTG
1 CTGCTTGTTGGGCTG
386288 CTG
1 CTG
386291 ACTGCCTGGC
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
14 4 0.11
15 23 0.62
16 10 0.27
ACGTcount: A:0.05, C:0.22, G:0.40, T:0.33
Consensus pattern (15 bp):
CTGCTTGTTGGGCTG
Found at i:386657 original size:25 final size:25
Alignment explanation
Indices: 386624--386675 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
386614 ACTGTGTTTA
386624 TTTTTCTTTCATTTTTTC-CTTTTCT
1 TTTTTCTTTC-TTTTTTCTCTTTTCT
*
386649 TTTTTCTTTCTTTTTTCTTTTTTCT
1 TTTTTCTTTCTTTTTTCTCTTTTCT
386674 TT
1 TT
386676 CCCATTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (25 bp):
TTTTTCTTTCTTTTTTCTCTTTTCT
Found at i:386717 original size:18 final size:17
Alignment explanation
Indices: 386683--386723 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
386673 TTTCCCATTT
*
386683 TTCTTTCTTTTTTCTTC
1 TTCTTCCTTTTTTCTTC
386700 TTCTTCCTTTCTTTCTTC
1 TTCTTCCTTT-TTTCTTC
386718 TTCTTC
1 TTCTTC
386724 TTCACTTCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (17 bp):
TTCTTCCTTTTTTCTTC
Found at i:386830 original size:28 final size:29
Alignment explanation
Indices: 386790--386858 Score: 72
Period size: 31 Copynumber: 2.4 Consensus size: 29
386780 GTCGTCGGTA
*
386790 CTTTCCTT-TTCTC-CCTCTCCTCTTCTCT
1 CTTTTCTTCTTCTCTCCTCTCCT-TTCTCT
*
386818 CTTTT-TTCTTCTCTTTCCTCTCCTTTCTTT
1 CTTTTCTTCTTCTC--TCCTCTCCTTTCTCT
386848 CTTTTCTTCTT
1 CTTTTCTTCTT
386859 TTTCTCTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
27 2 0.06
28 9 0.26
30 10 0.29
31 13 0.38
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (29 bp):
CTTTTCTTCTTCTCTCCTCTCCTTTCTCT
Found at i:386838 original size:19 final size:19
Alignment explanation
Indices: 386816--386867 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
386806 CTCCTCTTCT
386816 CTCTTTTTTC-TTCTCTTTC
1 CTCTTTTTTCTTTCT-TTTC
**
386835 CTCTCCTTTCTTTCTTTTC
1 CTCTTTTTTCTTTCTTTTC
*
386854 TTCTTTTTCTCTTT
1 CTCTTTTT-TCTTT
386868 TTTCTCTTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (19 bp):
CTCTTTTTTCTTTCTTTTC
Found at i:386866 original size:20 final size:21
Alignment explanation
Indices: 386843--386883 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
386833 TCCTCTCCTT
386843 TCTTTCTTT-TCTTCT-TTTTC
1 TCTTT-TTTCTCTTCTATTTTC
386863 TCTTTTTTCTCTTCTATTTTC
1 TCTTTTTTCTCTTCTATTTTC
386884 AAAAACCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 11 0.58
21 5 0.26
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (21 bp):
TCTTTTTTCTCTTCTATTTTC
Found at i:386877 original size:23 final size:24
Alignment explanation
Indices: 386810--386877 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 24
386800 CTCCCTCTCC
386810 TCTTCTCTCTTTTT-TCTTC-TCTT
1 TCTTCTCT-TTTTTCTCTTCTTCTT
* *
386833 TCCTCTCCTTTCTTTCTTTTCTTCTT
1 TCTTCT-CTTT-TTTCTCTTCTTCTT
386859 T-TTCTCTTTTTTCTCTTCT
1 TCTTCTCTTTTTTCTCTTCT
386878 ATTTTCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
23 16 0.43
24 9 0.24
25 7 0.19
26 5 0.14
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (24 bp):
TCTTCTCTTTTTTCTCTTCTTCTT
Found at i:387260 original size:29 final size:29
Alignment explanation
Indices: 387212--387314 Score: 100
Period size: 30 Copynumber: 3.5 Consensus size: 29
387202 CTTCTAGGGC
* **
387212 CAAAGTGTAATTTTGGGAAAATTTGAGGT
1 CAAAATGTAATTTTAAGAAAATTTGAGGT
* * *
387241 CAAATTGTAATTTTAAGAAAGTTTAAGGGT
1 CAAAATGTAATTTTAAGAAAATTTGA-GGT
* *
387271 TAAAATGTAATTTTAA-AAAAGTTTAGGGGT
1 CAAAATGTAATTTTAAGAAAA-TTT-GAGGT
387301 CAAAATGTAATTTT
1 CAAAATGTAATTTT
387315 TAAAAAACAT
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
29 24 0.40
30 36 0.60
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (29 bp):
CAAAATGTAATTTTAAGAAAATTTGAGGT
Found at i:387282 original size:30 final size:30
Alignment explanation
Indices: 387238--387321 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
387228 GAAAATTTGA
* *
387238 GGTCAAATTGTAATTTTAAGAAAGTTTAAG
1 GGTCAAAATGTAATTTTAAAAAAGTTTAAG
* *
387268 GGTTAAAATGTAATTTTAAAAAAGTTTAGG
1 GGTCAAAATGTAATTTTAAAAAAGTTTAAG
387298 GGTCAAAATGTAATTTTTAAAAAA
1 GGTCAAAATGTAA-TTTTAAAAAA
387322 CATGAAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 38 0.79
31 10 0.21
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.36
Consensus pattern (30 bp):
GGTCAAAATGTAATTTTAAAAAAGTTTAAG
Found at i:390278 original size:103 final size:101
Alignment explanation
Indices: 390130--390323 Score: 255
Period size: 103 Copynumber: 1.9 Consensus size: 101
390120 TACACTATTT
** * * * * *
390130 CCATAACCCAGTTATGGTCTTATCATTAGGATGCCATAGCGCAGCTATAGTCTTACA-CGTATAC
1 CCATAACCCAGTTATGGTCTTATCATTAAAATACCATAGCCCAGCTAGAGTCTTACATC-CAAAC
*
390194 ATACTGCCATGGTCCAACCGTGGTCTTATGTTCAAAGTG
65 AT--TGCCATGGTCCAACCATGGTCTTATGTTCAAAGTG
* *
390233 CCATAACCCAGTTATGGTCTTTTCATTAAAATACCATAGCCCAGCTAGGGTCTTACATCCAAACA
1 CCATAACCCAGTTATGGTCTTATCATTAAAATACCATAGCCCAGCTAGAGTCTTACATCCAAACA
*
390298 TTGCCATGGTCCAATCATGGTCTTAT
66 TTGCCATGGTCCAACCATGGTCTTAT
390324 TCATCAATTC
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
101 23 0.29
103 55 0.70
104 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.30
Consensus pattern (101 bp):
CCATAACCCAGTTATGGTCTTATCATTAAAATACCATAGCCCAGCTAGAGTCTTACATCCAAACA
TTGCCATGGTCCAACCATGGTCTTATGTTCAAAGTG
Found at i:398014 original size:91 final size:92
Alignment explanation
Indices: 397849--398031 Score: 359
Period size: 91 Copynumber: 2.0 Consensus size: 92
397839 CATATTGTAG
397849 TAAACATGTAACTATTTTCTATTTATTTGAACGATGAATAAATAAAGTTAATTTTATATTTCATT
1 TAAACATGTAACTATTTTCTATTTATTTGAACGATGAATAAATAAAGTTAATTTTATATTTCATT
397914 ATTATGTCTTTTGTTTTTATGCCTCTT
66 ATTATGTCTTTTGTTTTTATGCCTCTT
397941 TAAACATGT-ACTATTTTCTATTTATTTGAACGATGAATAAATAAAGTTAATTTTATATTTCATT
1 TAAACATGTAACTATTTTCTATTTATTTGAACGATGAATAAATAAAGTTAATTTTATATTTCATT
398005 ATTATGTCTTTTGTTTTTATGCCTCTT
66 ATTATGTCTTTTGTTTTTATGCCTCTT
398032 ATATTTTGCA
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 82 0.90
92 9 0.10
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (92 bp):
TAAACATGTAACTATTTTCTATTTATTTGAACGATGAATAAATAAAGTTAATTTTATATTTCATT
ATTATGTCTTTTGTTTTTATGCCTCTT
Found at i:401090 original size:49 final size:49
Alignment explanation
Indices: 401006--401143 Score: 152
Period size: 49 Copynumber: 2.8 Consensus size: 49
400996 ATGACAGATG
* *
401006 TGATGGACCACTAGTAGGACATGCTAGTTGCTAACTAGGTGGGAGTGCA
1 TGATGGACCACTGGTAGGACATGTTAGTTGCTAACTAGGTGGGAGTGCA
* * * * *
401055 TGATAGACCACTGGTAGGACATGTTAG-TGTTTAACTAGGTTGGCGTGTA
1 TGATGGACCACTGGTAGGACATGTTAGTTG-CTAACTAGGTGGGAGTGCA
* * * * *
401104 TGTTGGCCCACTGGTAAGACATGTTAGTTGTTAACCAGGT
1 TGATGGACCACTGGTAGGACATGTTAGTTGCTAACTAGGT
401144 TGGCAGTCGA
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
48 2 0.03
49 71 0.95
50 2 0.03
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (49 bp):
TGATGGACCACTGGTAGGACATGTTAGTTGCTAACTAGGTGGGAGTGCA
Found at i:410163 original size:21 final size:21
Alignment explanation
Indices: 410137--410176 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
410127 TTGATTAATT
*
410137 TTAACATTTATGTTATTTATC
1 TTAACATTTATATTATTTATC
*
410158 TTAACATTTTTATTATTTA
1 TTAACATTTATATTATTTA
410177 ATTTAAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (21 bp):
TTAACATTTATATTATTTATC
Found at i:410182 original size:21 final size:21
Alignment explanation
Indices: 410131--410182 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
410121 AAATATTTGA
*
410131 TTAATTTTAACATTTATGTTAT
1 TTAA-TTTAACATTTATATTAT
*
410153 TT-ATCTTAACATTTTTATTAT
1 TTAAT-TTAACATTTATATTAT
410174 TTAATTTAA
1 TTAATTTAA
410183 GTTTAAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.04
21 21 0.81
22 4 0.15
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.60
Consensus pattern (21 bp):
TTAATTTAACATTTATATTAT
Found at i:410378 original size:287 final size:288
Alignment explanation
Indices: 409953--410527 Score: 1143
Period size: 287 Copynumber: 2.0 Consensus size: 288
409943 AAAAAAATTA
409953 ATTTAAATAATATTTTTATTTATCCTTAAAATATAGTTCAAAGTTTGAATTTCAAATATAAAGAT
1 ATTTAAATAATATTTTTATTTATCCTTAAAATATAGTTCAAAGTTTGAATTTCAAATATAAAGAT
410018 AAATCATATTTATCTTAATATTTGCATAAAATTAAATAAAATTAAAATATTTAAACATGCACCAT
66 AAATCATATTTATCTTAATATTTGCATAAAATTAAATAAAATTAAAATATTTAAACATGCACCAT
410083 CAATCTATGTATATCTAATTTTGATTAAAAATTATTTCAAATATTTGATTAATTTTAACATTTAT
131 CAATCTATGTATATCTAATTTTGATTAAAAATTATTTCAAATATTTGATTAATTTTAACATTTAT
410148 GTTATTTATCTTAACATTTTTATTATTTAATTTAAGTTTAAGATGATTAGATATATAAATTTTAT
196 GTTATTTATCTTAACATTTTTATTATTTAATTTAAGTTTAAGATGATTAGATATATAAATTTTAT
410213 TTCCTCCATCGTTCGAGGATATTTTTGG
261 TTCCTCCATCGTTCGAGGATATTTTTGG
410241 ATTTAAATAA-ATTTTTATTTATCCTTAAAATATAGTTCAAAGTTTGAATTTCAAATATAAAGAT
1 ATTTAAATAATATTTTTATTTATCCTTAAAATATAGTTCAAAGTTTGAATTTCAAATATAAAGAT
410305 AAATCATATTTATCTTAATATTTGCATAAAATTAAATAAAATTAAAATATTTAAACATGCACCAT
66 AAATCATATTTATCTTAATATTTGCATAAAATTAAATAAAATTAAAATATTTAAACATGCACCAT
410370 CAATCTATGTATATCTAATTTTGATTAAAAATTATTTCAAATATTTGATTAATTTTAACATTTAT
131 CAATCTATGTATATCTAATTTTGATTAAAAATTATTTCAAATATTTGATTAATTTTAACATTTAT
410435 GTTATTTATCTTAACATTTTTATTATTTAATTTAAGTTTAAGATGATTAGATATATAAATTTTAT
196 GTTATTTATCTTAACATTTTTATTATTTAATTTAAGTTTAAGATGATTAGATATATAAATTTTAT
410500 TTCCTCCATCGTTCGAGGATATTTTTGG
261 TTCCTCCATCGTTCGAGGATATTTTTGG
410528 TGACGACCCC
Statistics
Matches: 287, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
287 277 0.97
288 10 0.03
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (288 bp):
ATTTAAATAATATTTTTATTTATCCTTAAAATATAGTTCAAAGTTTGAATTTCAAATATAAAGAT
AAATCATATTTATCTTAATATTTGCATAAAATTAAATAAAATTAAAATATTTAAACATGCACCAT
CAATCTATGTATATCTAATTTTGATTAAAAATTATTTCAAATATTTGATTAATTTTAACATTTAT
GTTATTTATCTTAACATTTTTATTATTTAATTTAAGTTTAAGATGATTAGATATATAAATTTTAT
TTCCTCCATCGTTCGAGGATATTTTTGG
Found at i:410450 original size:21 final size:21
Alignment explanation
Indices: 410424--410463 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
410414 TTGATTAATT
*
410424 TTAACATTTATGTTATTTATC
1 TTAACATTTATATTATTTATC
*
410445 TTAACATTTTTATTATTTA
1 TTAACATTTATATTATTTA
410464 ATTTAAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (21 bp):
TTAACATTTATATTATTTATC
Found at i:410469 original size:21 final size:21
Alignment explanation
Indices: 410418--410469 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
410408 AAATATTTGA
*
410418 TTAATTTTAACATTTATGTTAT
1 TTAA-TTTAACATTTATATTAT
*
410440 TT-ATCTTAACATTTTTATTAT
1 TTAAT-TTAACATTTATATTAT
410461 TTAATTTAA
1 TTAATTTAA
410470 GTTTAAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.04
21 21 0.81
22 4 0.15
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.60
Consensus pattern (21 bp):
TTAATTTAACATTTATATTAT
Found at i:411224 original size:92 final size:90
Alignment explanation
Indices: 411126--411357 Score: 342
Period size: 89 Copynumber: 2.6 Consensus size: 90
411116 TACAGATTAA
*
411126 ATTAAATTTACAGATACAAAAAAAAATACAAACATTCTAAGAAATTAATACGCGAAAATATAAAA
1 ATTAAATTTACAGAT--AAAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAA
*
411191 ATGAAACATTAAATCCTAAACAACTAT
64 ATGAAACATTAAATCCTAAACAACTAC
*
411218 ATTAAATTTACAGAT-ATAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAAAT
1 ATTAAATTTACAGATAAAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAAAT
* *
411282 GATACCTTAAATCCTAAACAACTAC
66 GAAACATTAAATCCTAAACAACTAC
* * *
411307 ATTAAATTTATAGATATAAAAAAAATAAAAACACTCTAAAGAAA-TAATACA
1 ATTAAATTTACAGATA-AAAAAAAATACAAACATTCT-AAGAAATTAATACA
411358 ATTATTTTGA
Statistics
Matches: 128, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
89 83 0.65
91 24 0.19
92 21 0.16
ACGTcount: A:0.58, C:0.12, G:0.05, T:0.25
Consensus pattern (90 bp):
ATTAAATTTACAGATAAAAAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAAAT
GAAACATTAAATCCTAAACAACTAC
Found at i:412589 original size:9 final size:9
Alignment explanation
Indices: 412575--412605 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
412565 GTTAAACGAA
412575 TCGAGTTAT
1 TCGAGTTAT
*
412584 TCGAGTTAA
1 TCGAGTTAT
412593 TCGAGTTAT
1 TCGAGTTAT
412602 TCGA
1 TCGA
412606 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:413824 original size:3 final size:3
Alignment explanation
Indices: 413816--413850 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
413806 ATTCCACCAA
413816 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
413851 AGTATGCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:423623 original size:43 final size:42
Alignment explanation
Indices: 423583--423699 Score: 141
Period size: 41 Copynumber: 2.8 Consensus size: 42
423573 CGTTAAAGAC
*
423583 CATGACCTTTAACGACGCTTTTATCACAAACGCCGCTAAAGGT
1 CATGACCTTTAACGACGCTTTTGTCACAAACGCCGCTAAA-GT
* *
423626 CATGGTCC-TTAACGACGC--TTGTCACAAACGCCACTAAATGT
1 CAT-GACCTTTAACGACGCTTTTGTCACAAACGCCGCTAAA-GT
* *
423667 CATGAACTTTAGCGACGCTTTTGTCACAAACGC
1 CATGACCTTTAACGACGCTTTTGTCACAAACGC
423700 ATGTCCTTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
40 2 0.03
41 32 0.51
43 26 0.41
44 3 0.05
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (42 bp):
CATGACCTTTAACGACGCTTTTGTCACAAACGCCGCTAAAGT
Found at i:423820 original size:16 final size:15
Alignment explanation
Indices: 423776--423821 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
423766 AAAAACACCG
*
423776 TTAAAAACATAACATT
1 TTAAAAA-ATAATATT
423792 TTAAAAAAT--TATT
1 TTAAAAAATAATATT
423805 TTAATAAAATAATATT
1 TTAA-AAAATAATATT
423821 T
1 T
423822 ATTTTTATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 7 0.27
14 5 0.19
15 2 0.08
16 12 0.46
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAAAAATAATATT
Found at i:423844 original size:24 final size:23
Alignment explanation
Indices: 423808--423853 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
423798 AATTATTTTA
423808 ATAAAATAATATTTAT-TTTTATG
1 ATAAAATAATA-TTATGTTTTATG
*
423831 ATAAATATTATATTATGTTTTAT
1 ATAAA-ATAATATTATGTTTTAT
423854 CTTTTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
ATAAAATAATATTATGTTTTATG
Found at i:423846 original size:23 final size:21
Alignment explanation
Indices: 423799--423853 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 21
423789 ATTTTAAAAA
*
423799 ATTATTTTAATAAAATAATAT
1 ATTATTTTTATAAAATAATAT
*
423820 -TTATTTTTATGATAAATATTAT
1 ATTATTTTTAT-A-AAATAATAT
423842 ATTATGTTTTAT
1 ATTAT-TTTTAT
423854 CTTTTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 9 0.32
21 1 0.04
22 8 0.29
23 4 0.14
24 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
ATTATTTTTATAAAATAATAT
Found at i:432973 original size:7 final size:7
Alignment explanation
Indices: 432961--433034 Score: 51
Period size: 7 Copynumber: 10.1 Consensus size: 7
432951 ACTAGTTAAT
432961 CTAAACC
1 CTAAACC
432968 CTAAACC
1 CTAAACC
* *
432975 TTAAAATC
1 CT-AAACC
432983 CTAAACC
1 CTAAACC
*
432990 ATAAAACC
1 CT-AAACC
432998 CTAAACC
1 CTAAACC
* *
433005 CTTAACA
1 CTAAACC
433012 C-ATAACC
1 CTA-AACC
433019 TCTAAACC
1 -CTAAACC
*
433027 TTAAACC
1 CTAAACC
433034 C
1 C
433035 CAGCCTTTAA
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
7 33 0.66
8 16 0.32
9 1 0.02
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:432987 original size:15 final size:15
Alignment explanation
Indices: 432963--433009 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
432953 TAGTTAATCT
432963 AAACCCTAAACCTTA
1 AAACCCTAAACCTTA
* *
432978 AAATCCTAAACCATA
1 AAACCCTAAACCTTA
432993 AAACCCTAAACCCTTA
1 AAACCCTAAA-CCTTA
433009 A
1 A
433010 CACATAACCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 22 0.81
16 5 0.19
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.19
Consensus pattern (15 bp):
AAACCCTAAACCTTA
Found at i:433095 original size:22 final size:21
Alignment explanation
Indices: 433042--433141 Score: 67
Period size: 22 Copynumber: 4.7 Consensus size: 21
433032 CCCCAGCCTT
*
433042 TAAACCGTAAACCATAAATCA
1 TAAACCCTAAACCATAAATCA
* *
433063 TAACCCCTAAACCCATAATTCA
1 TAAACCCTAAA-CCATAAATCA
* ** * *
433085 TAAACCTTAAAATAGTAACTCC
1 TAAACCCTAAACCA-TAAATCA
* *
433107 TAAACCTTAAACTC-TAAACCA
1 TAAACCCTAAAC-CATAAATCA
*
433128 TATACCCTAAACCA
1 TAAACCCTAAACCA
433142 AAAACCTTAA
Statistics
Matches: 59, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
20 1 0.02
21 24 0.41
22 34 0.58
ACGTcount: A:0.46, C:0.29, G:0.02, T:0.23
Consensus pattern (21 bp):
TAAACCCTAAACCATAAATCA
Found at i:433534 original size:41 final size:41
Alignment explanation
Indices: 433477--433761 Score: 285
Period size: 41 Copynumber: 7.0 Consensus size: 41
433467 CGCTAAAATA
*
433477 GAGCATTAGCGGTGCTTCTTCAAAAACGCCGCTAAAGCCCT
1 GAGCATTAGCAGTGCTTCTTCAAAAACGCCGCTAAAGCCCT
* * *
433518 GAGCATTAGCAGTGCTTCATT-AAACACGCCGTTAAAGCCTT
1 GAGCATTAGCAGTGCTTC-TTCAAAAACGCCGCTAAAGCCCT
* * * * *
433559 GAGCATCAGCAGCGCTTCTTAAAAAATGCCGCTAAAACCCT
1 GAGCATTAGCAGTGCTTCTTCAAAAACGCCGCTAAAGCCCT
* * **
433600 GAGCATTAGCAGCGCTTTCAT-AAAAACGCCGCTAAA--AAT
1 GAGCATTAGCAGTGC-TTCTTCAAAAACGCCGCTAAAGCCCT
* * *
433639 AGAGCAATAGCGGTGCTTCTTCAAAAACGCCTCTAAAGCCCT
1 -GAGCATTAGCAGTGCTTCTTCAAAAACGCCGCTAAAGCCCT
* * *
433681 GAGTATTAAC-GACGCTTCTTCAAAAACGCCGCTAAAGCCCT
1 GAGCATTAGCAG-TGCTTCTTCAAAAACGCCGCTAAAGCCCT
* * *
433722 GAGCATTAGCGGTGCGTT-TTAAAAAACTCCGCTAAAGCCC
1 GAGCATTAGCAGTGC-TTCTTCAAAAACGCCGCTAAAGCCC
433762 CATGCATTAG
Statistics
Matches: 201, Mismatches: 33, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
39 5 0.02
40 29 0.14
41 157 0.78
42 10 0.05
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (41 bp):
GAGCATTAGCAGTGCTTCTTCAAAAACGCCGCTAAAGCCCT
Found at i:433719 original size:163 final size:162
Alignment explanation
Indices: 433459--433757 Score: 417
Period size: 163 Copynumber: 1.8 Consensus size: 162
433449 GCGCTTTTTC
* *
433459 AAAAATGCCGCTAAAATAGAGCATTAGCGGTGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCAT
1 AAAAACGCCGCTAAAATAGAGCAATAGCGGTGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCAT
* * * * *
433524 TAGCAGTGCTTCATTAAACACGCCGTTAAAGCCTTGAGCATCAGCAGCGC-TTCTTAAAAAA-TG
66 TAACAGCGCTTCATTAAAAACGCCGCTAAAGCCCTGAGCATCAGCAGCGCGTT-TTAAAAAACT-
433587 CCGCTAAAACCCTGAGCATTAGCAGCGCTTTCAT
129 CCGCTAAAACCCTGAGCATTAGCAGCGCTTTCAT
* *
433621 AAAAACGCCGCTAAAAATAGAGCAATAGCGGTGCTTCTTCAAAAACGCCTCTAAAGCCCTGAGTA
1 AAAAACGCCGCT-AAAATAGAGCAATAGCGGTGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCA
* * *
433686 TTAAC-GACGCTTC-TTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGTGCGTTTTAAAAAAC
65 TTAACAG-CGCTTCATT-AAAAACGCCGCTAAAGCCCTGAGCATCAGCAGCGCGTTTTAAAAAAC
433749 TCCGCTAAA
128 TCCGCTAAA
433758 GCCCCATGCA
Statistics
Matches: 120, Mismatches: 12, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
162 14 0.12
163 103 0.86
164 3 0.03
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (162 bp):
AAAAACGCCGCTAAAATAGAGCAATAGCGGTGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCAT
TAACAGCGCTTCATTAAAAACGCCGCTAAAGCCCTGAGCATCAGCAGCGCGTTTTAAAAAACTCC
GCTAAAACCCTGAGCATTAGCAGCGCTTTCAT
Found at i:433779 original size:82 final size:81
Alignment explanation
Indices: 433477--433761 Score: 317
Period size: 82 Copynumber: 3.5 Consensus size: 81
433467 CGCTAAAATA
* *
433477 GAGCATTAGCGGTGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCAGTGCTTCATTAAA
1 GAGCATTAGCGGTGCTTCTTAAAAAACGCCGCTAAAGCCCTGAGCATTAGCAGCGCTTC-TTAAA
* * *
433542 CACGCCGTTAAAGCCTT
65 AACGCCGCTAAAGCCAT
* * * * * *
433559 GAGCATCAGCAGCGCTTCTTAAAAAATGCCGCTAAAACCCTGAGCATTAGCAGCGCTTTCATAAA
1 GAGCATTAGCGGTGCTTCTTAAAAAACGCCGCTAAAGCCCTGAGCATTAGCAGCGC-TTCTTAAA
*
433624 AACGCCGCTAAA--AAT
65 AACGCCGCTAAAGCCAT
* * * * *
433639 AGAGCAATAGCGGTGCTTCTTCAAAAACGCCTCTAAAGCCCTGAGTATTAAC-GACGCTTCTTCA
1 -GAGCATTAGCGGTGCTTCTTAAAAAACGCCGCTAAAGCCCTGAGCATTAGCAG-CGCTTCTT-A
*
433703 AAAACGCCGCTAAAGCCCT
63 AAAACGCCGCTAAAGCCAT
*
433722 GAGCATTAGCGGTGCGTT-TTAAAAAACTCCGCTAAAGCCC
1 GAGCATTAGCGGTGC-TTCTTAAAAAACGCCGCTAAAGCCC
433762 CATGCATTAG
Statistics
Matches: 167, Mismatches: 29, Indels: 14
0.80 0.14 0.07
Matches are distributed among these distances:
80 6 0.04
81 59 0.35
82 96 0.57
83 6 0.04
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (81 bp):
GAGCATTAGCGGTGCTTCTTAAAAAACGCCGCTAAAGCCCTGAGCATTAGCAGCGCTTCTTAAAA
ACGCCGCTAAAGCCAT
Found at i:440193 original size:14 final size:14
Alignment explanation
Indices: 440174--440201 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
440164 TTATAGATAC
440174 GATTTCAACATATG
1 GATTTCAACATATG
440188 GATTTCAACATATG
1 GATTTCAACATATG
440202 AGTAGATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
GATTTCAACATATG
Found at i:450083 original size:25 final size:25
Alignment explanation
Indices: 450061--450125 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
450051 TATTTTTAAT
450061 TTTATTT-TATCTTTTTATGTTTATG
1 TTTATTTCTAT-TTTTTATGTTTATG
450086 TTTATTTCTA-TTTTTAGTTGTTT-TG
1 TTTATTTCTATTTTTTA--TGTTTATG
*
450111 TTTTATTTTTATTTT
1 -TTTATTTCTATTTT
450126 CTTGTACTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
24 6 0.18
25 9 0.26
26 16 0.47
27 3 0.09
ACGTcount: A:0.14, C:0.03, G:0.08, T:0.75
Consensus pattern (25 bp):
TTTATTTCTATTTTTTATGTTTATG
Found at i:450122 original size:6 final size:6
Alignment explanation
Indices: 450050--450125 Score: 64
Period size: 6 Copynumber: 12.2 Consensus size: 6
450040 TTTATTTGTA
* * * * *
450050 TTATTT TTAATT TTATTT TATCTTT TTATGT TTATGT TTATTT CTATTT
1 TTATTT TTATTT TTATTT T-TATTT TTATTT TTATTT TTATTT TTATTT
450099 TTAGTTGT TT-TGTT TTATTT TTATTT T
1 TTA-TT-T TTAT-TT TTATTT TTATTT T
450126 CTTGTACTTC
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
6 45 0.79
7 9 0.16
8 3 0.05
ACGTcount: A:0.16, C:0.03, G:0.07, T:0.75
Consensus pattern (6 bp):
TTATTT
Found at i:452217 original size:234 final size:235
Alignment explanation
Indices: 451800--452268 Score: 931
Period size: 234 Copynumber: 2.0 Consensus size: 235
451790 TTAATTATGC
451800 AAATTAGTGAATTTGATGCTCCTAATACTTTAAATTCATGTTTATATACTTAGATGAGAATTTGG
1 AAATTAGTGAATTTGATGCTCCTAATACTTTAAATTCATGTTTATATACTTAGATGAGAATTTGG
451865 GAGCGAAACGAGCGAAAAATAAGTCAAAATAAGACAAAAAGAGCTGCTTTCAGGATCTACACGAG
66 GAGCGAAACGAGCGAAAAATAAGTCAAAATAAGACAAAAAGAGCTGCTTTCAGGATCTACACGAG
451930 CTAGGAAAACGTCACACGGGCTGGCCACACGCCCATGTGCCAGCTCATGTCAATTTCACACTCTG
131 CTAGGAAAACGTCACACGGGCTGGCCACACGCCCATGTGCCAGCTCATGTCAATTTCACACTCTG
451995 CTTCTCAAATACGTGGAAAAACCCAATTTTTAGGCTTTGT
196 CTTCTCAAATACGTGGAAAAACCCAATTTTTAGGCTTTGT
452035 AAATTAG-GAATTTGATGCTCCTAATACTTTAAATTCATGTTTATATACTTAGATGAGAATTTGG
1 AAATTAGTGAATTTGATGCTCCTAATACTTTAAATTCATGTTTATATACTTAGATGAGAATTTGG
452099 GAGCGAAACGAGCGAAAAATAAGTCAAAATAAGACAAAAAGAGCTGCTTTCAGGATCTACACGAG
66 GAGCGAAACGAGCGAAAAATAAGTCAAAATAAGACAAAAAGAGCTGCTTTCAGGATCTACACGAG
452164 CTAGGAAAACGTCACACGGGCTGGCCACACGCCCATGTGCCAGCTCATGTCAATTTCACACTCTG
131 CTAGGAAAACGTCACACGGGCTGGCCACACGCCCATGTGCCAGCTCATGTCAATTTCACACTCTG
452229 CTTCTCAAATACGTGGAAAAACCCAATTTTTAGGCTTTGT
196 CTTCTCAAATACGTGGAAAAACCCAATTTTTAGGCTTTGT
452269 GAGCATTCTA
Statistics
Matches: 234, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
234 227 0.97
235 7 0.03
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (235 bp):
AAATTAGTGAATTTGATGCTCCTAATACTTTAAATTCATGTTTATATACTTAGATGAGAATTTGG
GAGCGAAACGAGCGAAAAATAAGTCAAAATAAGACAAAAAGAGCTGCTTTCAGGATCTACACGAG
CTAGGAAAACGTCACACGGGCTGGCCACACGCCCATGTGCCAGCTCATGTCAATTTCACACTCTG
CTTCTCAAATACGTGGAAAAACCCAATTTTTAGGCTTTGT
Found at i:453046 original size:14 final size:14
Alignment explanation
Indices: 453023--453053 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
453013 TATTGTGTCC
*
453023 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
453037 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
453051 TTA
1 TTA
453054 AAAAAAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:472093 original size:27 final size:26
Alignment explanation
Indices: 472047--472097 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
472037 ATGTCGTTGG
*
472047 TTATTTTTTTATCTACATTAATTTCGT
1 TTATTTATTTATCTACATT-ATTTCGT
* *
472074 TTATTTATTTATTTATATTATTTC
1 TTATTTATTTATCTACATTATTTC
472098 TATGTCATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.67
Consensus pattern (26 bp):
TTATTTATTTATCTACATTATTTCGT
Found at i:478241 original size:36 final size:36
Alignment explanation
Indices: 478192--478267 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
478182 GCGGAGCAAA
* * *
478192 TTAAAGCTAAGGGCAGCGAATCTTATCTCCCTGGCG
1 TTAAAGCTAAGGGCAACCAATCTTATATCCCTGGCG
* *
478228 TTAAAGCTGAGGGCAACCAATCTTATATCCCTGGTG
1 TTAAAGCTAAGGGCAACCAATCTTATATCCCTGGCG
478264 TTAA
1 TTAA
478268 GACTTGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (36 bp):
TTAAAGCTAAGGGCAACCAATCTTATATCCCTGGCG
Found at i:478512 original size:169 final size:169
Alignment explanation
Indices: 478228--478762 Score: 867
Period size: 169 Copynumber: 3.2 Consensus size: 169
478218 CTCCCTGGCG
* * * * * *
478228 TTAAAGCTGAGGGCAACCAATCTTATATCCCTGG-TGTTAAGACTTGGAATAGCTGAGGTGGAGT
1 TTAAAGCTGAGGGCAGCGAATCTTATCTTCCTGGCT-TTAAGACTTAGAATAGCTGAGGTGGAGC
* * * *
478292 GGATTAAAGCT-GTGGGCAGTGAATCCTATCTCTTTGGCATTATAGTGGAACAGATTAAAGCTAA
65 AGATTACAG-TGGTGGGCAGCGAATCCTATCTCTTTGGCATTATAATGGAACAGATTAAAGCTAA
*
478356 ACATAGCGAATCTTGTTTCCCTAGCGTTGCAGCGGAGCAGA
129 ACATAGCGAATCTTGTTTCCCTAGCGTTGCAGCAGAGCAGA
*
478397 TTAAAGCTAAGGGCAGCGAATCTTATCTTCCTGGCTTTAAGACTTAGAATAGCTGAGGTGGAGCA
1 TTAAAGCTGAGGGCAGCGAATCTTATCTTCCTGGCTTTAAGACTTAGAATAGCTGAGGTGGAGCA
478462 GATTACAGTGGTGGGCAGCGAATCCTATCTCTTTGGCATTATAATGGAACAGATTAAAGCTAAAC
66 GATTACAGTGGTGGGCAGCGAATCCTATCTCTTTGGCATTATAATGGAACAGATTAAAGCTAAAC
478527 ATAGCGAATCTTGTTTCCCTAGCGTTGCAGCAGAGCAGA
131 ATAGCGAATCTTGTTTCCCTAGCGTTGCAGCAGAGCAGA
* *
478566 TTAAAGCTGAGGGCAGCGAATCTTATCTTTCTGGCTTTAAGACTTAGAATAGCTAAGGTGGAGCA
1 TTAAAGCTGAGGGCAGCGAATCTTATCTTCCTGGCTTTAAGACTTAGAATAGCTGAGGTGGAGCA
* *
478631 GATTACAGCGGTGGGCAGCGAATCCTATCTCTTTGGCATTATAATGGAACAGATTAAAGCTAAAG
66 GATTACAGTGGTGGGCAGCGAATCCTATCTCTTTGGCATTATAATGGAACAGATTAAAGCTAAAC
* *
478696 GTAGCGAATCTTGTTTCCCTAGCGTTGCAACAGAGCAGA
131 ATAGCGAATCTTGTTTCCCTAGCGTTGCAGCAGAGCAGA
*
478735 TTAAAGCTGAGGGCAGCGAGTCTTATCT
1 TTAAAGCTGAGGGCAGCGAATCTTATCT
478763 CACTGGCGTT
Statistics
Matches: 344, Mismatches: 20, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
168 1 0.00
169 342 0.99
170 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (169 bp):
TTAAAGCTGAGGGCAGCGAATCTTATCTTCCTGGCTTTAAGACTTAGAATAGCTGAGGTGGAGCA
GATTACAGTGGTGGGCAGCGAATCCTATCTCTTTGGCATTATAATGGAACAGATTAAAGCTAAAC
ATAGCGAATCTTGTTTCCCTAGCGTTGCAGCAGAGCAGA
Found at i:478883 original size:51 final size:51
Alignment explanation
Indices: 478680--478893 Score: 154
Period size: 51 Copynumber: 4.3 Consensus size: 51
478670 TATAATGGAA
* * * *
478680 CAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCGTTGCAACAGAG
1 CAGATTAAAGCTAAAGGCAGCGAATCTTATCTCCCTAGCGTTGCAGCAGAG
* * * * *
478731 CAGATTAAAGCTGAGGGCAGCGAGTCTTATCTCACTGGCGTTG-AGC---G
1 CAGATTAAAGCTAAAGGCAGCGAATCTTATCTCCCTAGCGTTGCAGCAGAG
*** * ** * * ** **
478778 -A-ATTAAAG-TGGTGGGCAGCGAATCCTATCTCTTTGGCATTATAGTGGAG
1 CAGATTAAAGCT-AAAGGCAGCGAATCTTATCTCCCTAGCGTTGCAGCAGAG
* * *
478827 TAGATTAAAGCTAAAGGTAGCGAATCTTATGTCCCTAGCGTTGCAGCAGAG
1 CAGATTAAAGCTAAAGGCAGCGAATCTTATCTCCCTAGCGTTGCAGCAGAG
478878 CAGATTAAAGCTAAAG
1 CAGATTAAAGCTAAAG
478894 AAAGCGAGCC
Statistics
Matches: 123, Mismatches: 32, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
44 1 0.01
45 31 0.25
46 3 0.02
47 1 0.01
49 1 0.01
50 3 0.02
51 82 0.67
52 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (51 bp):
CAGATTAAAGCTAAAGGCAGCGAATCTTATCTCCCTAGCGTTGCAGCAGAG
Found at i:478907 original size:147 final size:147
Alignment explanation
Indices: 478640--478909 Score: 441
Period size: 147 Copynumber: 1.8 Consensus size: 147
478630 AGATTACAGC
478640 GGTGGGCAGCGAATCCTATCTCTTTGGCATTATAATGGAACAGATTAAAGCTAAAGGTAGCGAAT
1 GGTGGGCAGCGAATCCTATCTCTTTGGCATTATAATGGAACAGATTAAAGCTAAAGGTAGCGAAT
* * * * ** *
478705 CTTGTTTCCCTAGCGTTGCAACAGAGCAGATTAAAGCTGAGGGCAGCGAGTCTTATCTCACTGGC
66 CTTATGTCCCTAGCGTTGCAACAGAGCAGATTAAAGCTAAAGAAAGCGAGCCTTATCTCACTGGC
478770 GTTGAGCGAATTAAAGT
131 GTTGAGCGAATTAAAGT
* **
478787 GGTGGGCAGCGAATCCTATCTCTTTGGCATTATAGTGGAGTAGATTAAAGCTAAAGGTAGCGAAT
1 GGTGGGCAGCGAATCCTATCTCTTTGGCATTATAATGGAACAGATTAAAGCTAAAGGTAGCGAAT
*
478852 CTTATGTCCCTAGCGTTGCAGCAGAGCAGATTAAAGCTAAAGAAAGCGAGCCTTATCT
66 CTTATGTCCCTAGCGTTGCAACAGAGCAGATTAAAGCTAAAGAAAGCGAGCCTTATCT
478910 TTCTGAGCAG
Statistics
Matches: 112, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
147 112 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (147 bp):
GGTGGGCAGCGAATCCTATCTCTTTGGCATTATAATGGAACAGATTAAAGCTAAAGGTAGCGAAT
CTTATGTCCCTAGCGTTGCAACAGAGCAGATTAAAGCTAAAGAAAGCGAGCCTTATCTCACTGGC
GTTGAGCGAATTAAAGT
Found at i:478950 original size:44 final size:44
Alignment explanation
Indices: 478902--479027 Score: 155
Period size: 44 Copynumber: 2.9 Consensus size: 44
478892 AGAAAGCGAG
** *
478902 CCTTATCTTTCTGAGCAGCAGTGGAGTAGGTTGAATATTGA-AGA
1 CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATT-ACAGA
478946 CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGA
1 CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGA
* * * * * *
478990 TCTTATCTCCCTAAGCAGTAGTGTAGCAGATTGAAAAT
1 CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAT
479028 GGTGAATCTT
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
43 1 0.01
44 71 0.99
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (44 bp):
CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGA
Found at i:479167 original size:57 final size:56
Alignment explanation
Indices: 479074--479237 Score: 188
Period size: 57 Copynumber: 2.9 Consensus size: 56
479064 ATTGAACCCA
* *
479074 CTAGTCCTATCTCCCTT-GACAGTAGTGGAATAGATTGAAAATTACAGATCAAAAACC
1 CTAGTCCTATCT-CCTTGGACAGCAGTGGAATGGATTGAAAATTACAGATCAAAAA-C
* * * * * *
479131 CTAGTCCTATCTCCTTGGACAACAGAGGAGTGGATTGAAAATTACAAATCGAAGAC
1 CTAGTCCTATCTCCTTGGACAGCAGTGGAATGGATTGAAAATTACAGATCAAAAAC
* *
479187 CTCAGTCCTATTTCCCTGGACAGCAGTGGAATAGG-TTGAAAATTACAGATC
1 CT-AGTCCTATCTCCTTGGACAGCAGTGGAAT-GGATTGAAAATTACAGATC
479238 TTATCTCCCT
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
56 7 0.08
57 81 0.90
58 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (56 bp):
CTAGTCCTATCTCCTTGGACAGCAGTGGAATGGATTGAAAATTACAGATCAAAAAC
Done.