Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 139 of 167
Found at i:46542897 original size:13 final size:13
Alignment explanation
Indices: 46542879--46542908 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
46542869 AAAAAGAATT
*
46542879 TTTTTTTTAAATA
1 TTTTTTATAAATA
46542892 TTTTTTATAAATA
1 TTTTTTATAAATA
46542905 TTTT
1 TTTT
46542909 GAATTTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTTATAAATA
Found at i:46543468 original size:29 final size:29
Alignment explanation
Indices: 46543410--46543468 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
46543400 TCCACCTTGA
* * * *
46543410 CACGAATTCTCAACAAACAAGTTTTTCAC
1 CACGAACTCTCAACAAACAAATTCTCCAC
*
46543439 CACGAACTCTCAACGAACAAATTCTCCAC
1 CACGAACTCTCAACAAACAAATTCTCCAC
46543468 C
1 C
46543469 TCTTCCACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.37, C:0.34, G:0.07, T:0.22
Consensus pattern (29 bp):
CACGAACTCTCAACAAACAAATTCTCCAC
Found at i:46544505 original size:24 final size:24
Alignment explanation
Indices: 46544478--46544533 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
46544468 AGTAGATATA
46544478 TAAAATAACCATCACTGTTTTTCT
1 TAAAATAACCATCACTGTTTTTCT
46544502 TAAAATAACCATCACTGTTTTTCT
1 TAAAATAACCATCACTGTTTTTCT
46544526 TAAAATAA
1 TAAAATAA
46544534 ACACAACTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (24 bp):
TAAAATAACCATCACTGTTTTTCT
Found at i:46551061 original size:117 final size:116
Alignment explanation
Indices: 46550805--46551303 Score: 601
Period size: 117 Copynumber: 4.5 Consensus size: 116
46550795 AAAAGTAATT
* * * * *
46550805 TTTTTGGGTGATGGCCTGTCAATGGCCGACACCCA--AC--A-GTAAAAAAAATT-GAATTTTTT
1 TTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTTAAAAAAATTCTAATTTTTT
* * * *
46550864 TCGTGTCAGAATCAAATATCAGTATATGAAAAAAGT--AAA-AAAAAAAAAA
66 TCGTGTCAGAATCAGATATAAATATACGAAAAAA-TAAAAATAAAAAAAAAA
**
46550913 ---TT-GGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTTAAAAAAATTCTTTTTTTTT
1 TTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTTAAAAAAATTCTAATTTTTT
46550974 TCGTGTCAGAATCAGATATAAATATACGAAAAAATAAAAATAAAAATAAAAA
66 TCGTGTCAGAATCAGATATAAATATACGAAAAAATAAAAATAAAAA-AAAAA
**
46551026 TTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTTAAAAAAATTCTTTTTTTTT
1 TTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTTAAAAAAATTCTAATTTTTT
46551091 TCGTGTCAGAATCAGATATAAATATACGAAAAAATAAAAATAAAAATAAAAA
66 TCGTGTCAGAATCAGATATAAATATACGAAAAAATAAAAATAAAAA-AAAAA
* *** ***
46551143 TTTTTGGGTGCTGGCCTGTCAATGGCCGGCCCCCAGTACAAA-TTTAAAAAAA-AAAAAAAATTT
1 TTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTTAAAAAAATTCTAATTTTTT
* * *
46551206 TCGTATCAGAATCAGATATAAATAT----AAGAA-AAAAATAATAAAAAAA
66 TCGTGTCAGAATCAGATATAAATATACGAAAAAATAAAAATAAAAAAAAAA
*
46551252 --TTTGGGTACTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTTAAAAAAAT
1 TTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTTAAAAAAAT
46551304 CGTGTCAGAA
Statistics
Matches: 350, Mismatches: 25, Indels: 31
0.86 0.06 0.08
Matches are distributed among these distances:
104 27 0.08
105 2 0.01
106 2 0.01
107 38 0.11
108 11 0.03
109 16 0.05
110 46 0.13
111 7 0.02
112 5 0.01
113 5 0.01
115 27 0.08
116 12 0.03
117 152 0.43
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (116 bp):
TTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTTAAAAAAATTCTAATTTTTT
TCGTGTCAGAATCAGATATAAATATACGAAAAAATAAAAATAAAAAAAAAA
Found at i:46551314 original size:97 final size:94
Alignment explanation
Indices: 46551206--46551562 Score: 396
Period size: 90 Copynumber: 3.8 Consensus size: 94
46551196 AAAAAAATTT
* * *
46551206 TCGTATCAGAATCAGATATAAATATAAGAAAAAAATAATAAAAAAATTTGGGTACTGGCCTGTCA
1 TCGTGTCAGAATCAGATATAAATAT-ACAAAAAAA-AAT--AAAAATTTGGGTGCTGGCCTGTCA
46551271 ATGGCCGGCACCCAGTACAAATTTTAAAA-AAA
62 ATGGCCGGCACCCAGTACAAATTTTAAAATAAA
46551303 TCGTGTCAGAATCAGATATAAATATACAAAAAAAAAT-----TTTGGGTGCTGGCCTGTCAATGG
1 TCGTGTCAGAATCAGATATAAATATACAAAAAAAAATAAAAATTTGGGTGCTGGCCTGTCAATGG
* * ***
46551363 CCGGCACCTAGGACAAATTTTAAAATTTTT
66 CCGGCACCCAGTACAAATTTTAAAA-TAAA
*
46551393 TTGTGTCAGAATCAGATATAAATATACAAAAAAAAAT-----TTTGGGTGCTGGCCTGTCAATGG
1 TCGTGTCAGAATCAGATATAAATATACAAAAAAAAATAAAAATTTGGGTGCTGGCCTGTCAATGG
* * ***
46551453 CCGGCACCTAGGACAAATTTTAAAATTTTT
66 CCGGCACCCAGTACAAATTTTAAAA-TAAA
* * *
46551483 TTGTGTCAGAATCAGATATAAATATACGAAAAAATAAAAAAAAAATTT-GGTGCTGGCCTATCAA
1 TCGTGTCAGAATCAGATATAAATATAC--AAAAA-AAAATAAAAATTTGGGTGCTGGCCTGTCAA
46551547 TGGCCGGCACCCAGTA
63 TGGCCGGCACCCAGTA
46551563 AATTTTTTTT
Statistics
Matches: 237, Mismatches: 13, Indels: 20
0.88 0.05 0.07
Matches are distributed among these distances:
88 45 0.19
90 116 0.49
92 5 0.02
93 4 0.02
95 3 0.01
96 8 0.03
97 53 0.22
98 3 0.01
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (94 bp):
TCGTGTCAGAATCAGATATAAATATACAAAAAAAAATAAAAATTTGGGTGCTGGCCTGTCAATGG
CCGGCACCCAGTACAAATTTTAAAATAAA
Found at i:46551352 original size:88 final size:89
Alignment explanation
Indices: 46551245--46551592 Score: 431
Period size: 90 Copynumber: 3.9 Consensus size: 89
46551235 AAAAAATAAT
* * *** *
46551245 AAAAAAA-TTTGGGTACTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTTAAAA-AAATCGTG
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGGACAAATTTTAAAATTTTTTGTG
46551308 TCAGAATCAGATATAAATATACAA
66 TCAGAATCAGATATAAATATACAA
*
46551332 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCTAGGACAAATTTTAAAATTTTTTTGT
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGGACAAATTTTAAAA-TTTTTTGT
46551397 GTCAGAATCAGATATAAATATACAA
65 GTCAGAATCAGATATAAATATACAA
*
46551422 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCTAGGACAAATTTTAAAATTTTTTTGT
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGGACAAATTTTAAAA-TTTTTTGT
46551487 GTCAGAATCAGATATAAATATACGAAAAAATAA
65 GTCAGAATCAGATATAAATATAC--------AA
* * * **
46551520 AAAAAAAATTT-GGTGCTGGCCTATCAATGGCCGGCACCCA-G-TAAATTTT--TTTTTTTTCGT
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGGACAAATTTTAAAATTTTTT-GT
46551580 GTCAGAATCAGAT
65 GTCAGAATCAGAT
46551593 TGGGTGCCGG
Statistics
Matches: 236, Mismatches: 13, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
87 7 0.03
88 45 0.19
90 116 0.49
92 6 0.03
93 15 0.06
95 7 0.03
96 1 0.00
97 27 0.11
98 12 0.05
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (89 bp):
AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGGACAAATTTTAAAATTTTTTGTG
TCAGAATCAGATATAAATATACAA
Found at i:46551437 original size:90 final size:90
Alignment explanation
Indices: 46551245--46551516 Score: 451
Period size: 90 Copynumber: 3.1 Consensus size: 90
46551235 AAAAAATAAT
* * * *** *
46551245 AAAAAAA-TTTGGGTACTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTTAAAA--AAATCGT
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCTAGGACAAATTTTAAAATTTTTTTGT
46551307 GTCAGAATCAGATATAAATATACAA
66 GTCAGAATCAGATATAAATATACAA
46551332 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCTAGGACAAATTTTAAAATTTTTTTGT
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCTAGGACAAATTTTAAAATTTTTTTGT
46551397 GTCAGAATCAGATATAAATATACAA
66 GTCAGAATCAGATATAAATATACAA
46551422 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCTAGGACAAATTTTAAAATTTTTTTGT
1 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCTAGGACAAATTTTAAAATTTTTTTGT
*
46551487 GTCAGAATCAGATATAAATATACGA
66 GTCAGAATCAGATATAAATATACAA
46551512 AAAAA
1 AAAAA
46551517 TAAAAAAAAA
Statistics
Matches: 174, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
87 7 0.04
88 45 0.26
90 122 0.70
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (90 bp):
AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCTAGGACAAATTTTAAAATTTTTTTGT
GTCAGAATCAGATATAAATATACAA
Found at i:46551572 original size:178 final size:171
Alignment explanation
Indices: 46551245--46551572 Score: 376
Period size: 178 Copynumber: 1.8 Consensus size: 171
46551235 AAAAAATAAT
*
46551245 AAAAAAATTTGGGTACTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTTAAAAAAATCGTGTC
1 AAAAAAATTTGGGTACTGGCCTGTCAATGGCCGGCACCCAGGACAAATTTTAAAAAAATCGTGTC
* *
46551310 AGAATCAGATATAAATATACAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCTAGG
66 AGAATCAGATATAAATATACAAAAAAAAAATTTGGGTGCTGGCCTATCAATGGCCGGCACC----
*
46551375 ACAAATTTTAAAATTTTTTTGTGTCAGAATCAGATATAAATATACAA
127 AC-AA-TGTAAAATTTTTTTGTGTCAGAATCAGATATAAATATACAA
* * *** *
46551422 AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCTAGGACAAATTTTAAAATTTTTTTGT
1 AAAAAAA-TTTGGGTACTGGCCTGTCAATGGCCGGCACCCAGGACAAATTTTAAAA--AAATCGT
46551487 GTCAGAATCAGATATAAATATACGAAAAAATAAAAAAAAAATTT-GGTGCTGGCCTATCAATGGC
63 GTCAGAATCAGATATAAATATAC--------AAAAAAAAAATTTGGGTGCTGGCCTATCAATGGC
*
46551551 CGGCACC-C-A-GTAAATTTTTTTT
120 CGGCACCACAATGTAAAATTTTTTT
46551573 TTTTCGTGTC
Statistics
Matches: 129, Mismatches: 11, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
177 7 0.05
178 56 0.43
180 27 0.21
182 1 0.01
187 26 0.20
188 12 0.09
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (171 bp):
AAAAAAATTTGGGTACTGGCCTGTCAATGGCCGGCACCCAGGACAAATTTTAAAAAAATCGTGTC
AGAATCAGATATAAATATACAAAAAAAAAATTTGGGTGCTGGCCTATCAATGGCCGGCACCACAA
TGTAAAATTTTTTTGTGTCAGAATCAGATATAAATATACAA
Found at i:46552126 original size:29 final size:29
Alignment explanation
Indices: 46552094--46552160 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
46552084 CCTATATATT
*
46552094 TTTTGTAAATTTAA-AATTTAGT-TTGTATA
1 TTTT-TAAATTTAAGAATTTAGTCCT-TATA
**
46552123 TTTTTATTTTTAAGAATTTAGTCCTTATA
1 TTTTTAAATTTAAGAATTTAGTCCTTATA
46552152 TTTTTAAAT
1 TTTTTAAAT
46552161 ATTACGAAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 7 0.23
29 23 0.74
30 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.58
Consensus pattern (29 bp):
TTTTTAAATTTAAGAATTTAGTCCTTATA
Found at i:46553081 original size:104 final size:101
Alignment explanation
Indices: 46552946--46553291 Score: 478
Period size: 104 Copynumber: 3.3 Consensus size: 101
46552936 AGCACCCAAA
46552946 ATTTTTTTCGTATATTTATATCTGATTCTGACACAAAAATTTTTTTTTTTAATTTGTACTGGGTG
1 ATTTTTTTCGTATATTTATATCTGATTCTGACACAAAAATTTTTTTTTTTAATTTGTACTGGGTG
*
46553011 CCGGCCATTGACAGGCTAGCACCCAAATTTTTTATTTTT
66 CCGGCCATTGACAGGCCAGCACCCAAA--TTTT-TTTTT
*
46553050 ATTTTTTGCGTATATTTATATCTGATTCTGACACAAAAATTTTTTTTTTTAATTTGTACTGGGTG
1 ATTTTTTTCGTATATTTATATCTGATTCTGACACAAAAATTTTTTTTTTTAATTTGTACTGGGTG
46553115 CCGGCCATTGACAGGCCAGCACCCAAA-TTTTTTTT
66 CCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTT
* * * *
46553150 ATTTTTTTCGTATATTTATATCTGATTTTGACACGAAAAAAAAAAGAAATTTTCTTTTAAATTTG
1 ATTTTTTTCGTATATTTATATCTGATTCTGACAC--------AAA-AATTTTTTTTTTTAATTTG
46553215 TACTGGGTGCCGGCCATTGACAGGCCAGCACCCATAATTTTTTTTT
57 TACTGGGTGCCGGCCATTGACAGGCCAGCACCCA-AATTTTTTTTT
* * * *
46553261 ACTTTTTTCGTATACTGATATTTGATTCTGA
1 ATTTTTTTCGTATATTTATATCTGATTCTGA
46553292 GTATACTGAT
Statistics
Matches: 219, Mismatches: 12, Indels: 15
0.89 0.05 0.06
Matches are distributed among these distances:
100 37 0.17
101 3 0.01
104 90 0.41
108 3 0.01
109 50 0.23
110 2 0.01
111 34 0.16
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.45
Consensus pattern (101 bp):
ATTTTTTTCGTATATTTATATCTGATTCTGACACAAAAATTTTTTTTTTTAATTTGTACTGGGTG
CCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTT
Found at i:46559350 original size:15 final size:15
Alignment explanation
Indices: 46559327--46559356 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46559317 ATTTAAATGT
*
46559327 TATCTGAATTTATAA
1 TATCCGAATTTATAA
46559342 TATCCGAATTTATAA
1 TATCCGAATTTATAA
46559357 AATACACATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (15 bp):
TATCCGAATTTATAA
Found at i:46565818 original size:4 final size:4
Alignment explanation
Indices: 46565809--46565865 Score: 114
Period size: 4 Copynumber: 14.2 Consensus size: 4
46565799 ATAAAAGGGT
46565809 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
46565857 TGTA TGTA T
1 TGTA TGTA T
46565866 CTTGTCATTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:46570380 original size:15 final size:15
Alignment explanation
Indices: 46570356--46570385 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46570346 TTTGACTGAG
46570356 AGAGGGGGAGGAGAA
1 AGAGGGGGAGGAGAA
*
46570371 AGAGGTGGAGGAGAA
1 AGAGGGGGAGGAGAA
46570386 GGGCAGAGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.57, T:0.03
Consensus pattern (15 bp):
AGAGGGGGAGGAGAA
Found at i:46575498 original size:212 final size:212
Alignment explanation
Indices: 46575068--46575654 Score: 818
Period size: 212 Copynumber: 2.7 Consensus size: 212
46575058 CTCTCAGAAG
* * ** *
46575068 CAGCGGCTTTACCTTCCTGGTTTTTCTTACTAGTCTTCTCTCCAATATTTAGGGTCGAATCAAAA
1 CAGCGGCTTTGCATTCCTGGTTTTTCTTACTAGTCTTCTCTCCTTTATTTAGGGTTGAATCAAAA
*
46575133 TCAAAATCATCCAACCTGCAACAGATACAATGTACAGGCTAATAAATTTAAAAAAAAAATGAATG
66 TCAAAATCATCCAACCTGCAACAGATACAATGTACAGGCTAACAAA--T---AAAAAAATGAATG
* * * * * * * *
46575198 TTAAGTTGAGTTATGCATCCAGCAAACAATTTTAAAGCAAAAGCTTGAAGATGAGATGATTGAAA
126 TGAAGTTGA-CTATGCATCCAGTAAACAATTTCAAAGCAAAAGATTGAACATGAGATAACTGAAA
*
46575263 AATAAAAGAATTATCCACTCACT
190 AATAAAAGAATAATCCACTCACT
**
46575286 CAGCGGCTTTGCATTCCTTATTTTTCTTACTAGTCTTCTCTCCTTTATTTAGGGTTGAATCAAAA
1 CAGCGGCTTTGCATTCCTGGTTTTTCTTACTAGTCTTCTCTCCTTTATTTAGGGTTGAATCAAAA
* *
46575351 TCAAAATCACCCAACCTGCAACAGATACAATATACAGGCTAACAAAT-AAAAAATGAATGTGAAG
66 TCAAAATCATCCAACCTGCAACAGATACAATGTACAGGCTAACAAATAAAAAAATGAATGTGAAG
46575415 TTGACT-TGCACGTCCAGTAAACAATTTCAAAGCAAAAGATTGAACATGAGATAACTGAAAAATA
131 TTGACTATGCA--TCCAGTAAACAATTTCAAAGCAAAAGATTGAACATGAGATAACTGAAAAATA
46575479 AAAGAATAATCCACTCACT
194 AAAGAATAATCCACTCACT
* * * *
46575498 CAGCGTCTTTGCTTTCCTGGTTTTTCTTACTAGTCTTCTCTCCTTTATTCAGGGCTGAATCAAAA
1 CAGCGGCTTTGCATTCCTGGTTTTTCTTACTAGTCTTCTCTCCTTTATTTAGGGTTGAATCAAAA
* * * *
46575563 TCAAAATCATCCAACCTGCAACAAATCCAATGTACAGGCTAACAAATAAAAAAATTACTGTGAAG
66 TCAAAATCATCCAACCTGCAACAGATACAATGTACAGGCTAACAAATAAAAAAATGAATGTGAAG
* *
46575628 TGGACTCATGCATCCAATAAACAATTT
131 TTGACT-ATGCATCCAGTAAACAATTT
46575655 TAAAACATGA
Statistics
Matches: 331, Mismatches: 33, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
210 4 0.01
211 1 0.00
212 186 0.56
213 34 0.10
215 4 0.01
216 1 0.00
218 101 0.31
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.29
Consensus pattern (212 bp):
CAGCGGCTTTGCATTCCTGGTTTTTCTTACTAGTCTTCTCTCCTTTATTTAGGGTTGAATCAAAA
TCAAAATCATCCAACCTGCAACAGATACAATGTACAGGCTAACAAATAAAAAAATGAATGTGAAG
TTGACTATGCATCCAGTAAACAATTTCAAAGCAAAAGATTGAACATGAGATAACTGAAAAATAAA
AGAATAATCCACTCACT
Found at i:46590824 original size:18 final size:18
Alignment explanation
Indices: 46590801--46590860 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
46590791 TTAAAACAAG
46590801 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
*** * *
46590819 TTACATAAGAAAATT-G-T
1 TTACAT-TCTATATTAGAA
46590836 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
46590854 TTACATT
1 TTACATT
46590861 AGAATTACAT
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 4 0.14
17 7 0.24
18 14 0.48
19 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (18 bp):
TTACATTCTATATTAGAA
Found at i:46596802 original size:65 final size:65
Alignment explanation
Indices: 46596722--46596851 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
46596712 GCTCACATTA
*
46596722 CACGTTTGATGCATGTGGTTCGGCTTTTTATGGTGCAACAAAGTCAATAATTCAGCAACCCATCT
1 CACGTTTGATGCATGTGGTTCGGCTTTTTATGGTGCAACAAAGTCAATAACTCAGCAACCCATCT
46596787 CACGTTTGATGCATGTGGTTCGGCTTTTTATGGTGCAACAAAGTCAATAACTCAGCAACCCATCT
1 CACGTTTGATGCATGTGGTTCGGCTTTTTATGGTGCAACAAAGTCAATAACTCAGCAACCCATCT
46596852 TTAATATAAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (65 bp):
CACGTTTGATGCATGTGGTTCGGCTTTTTATGGTGCAACAAAGTCAATAACTCAGCAACCCATCT
Found at i:46598699 original size:21 final size:21
Alignment explanation
Indices: 46598647--46598699 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
46598637 ATTTTTATTT
46598647 AATTTTAATTATAAAATATATA
1 AATTTTAA-TATAAAATATATA
* *
46598669 AATATCAATATAAAATGATAT-
1 AATTTTAATATAAAAT-ATATA
*
46598690 ATTTTTAATA
1 AATTTTAATA
46598700 ATTTATTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
AATTTTAATATAAAATATATA
Found at i:46613887 original size:43 final size:43
Alignment explanation
Indices: 46613822--46613937 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
46613812 ATTTAGTGGC
* *
46613822 TTAGCAGCGTTTGTGGGAAAAGCGCCACTAAATGT-CATATTCT
1 TTAGCGGCGTTTGTAGGAAAAGCGCCACTAAA-GTCCATATTCT
* * * * *
46613865 TTAGCGGTGTTTTTAGTAAAAGCGCCGCTAAAGTCCATGTTCT
1 TTAGCGGCGTTTGTAGGAAAAGCGCCACTAAAGTCCATATTCT
* *
46613908 TTAGTGGCGTTTGTGGGAAAA-CGCCACTAA
1 TTAGCGGCGTTTGTAGGAAAAGCGCCACTAA
46613938 TTTAGCAGAT
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
42 10 0.17
43 49 0.83
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
TTAGCGGCGTTTGTAGGAAAAGCGCCACTAAAGTCCATATTCT
Found at i:46623371 original size:5 final size:5
Alignment explanation
Indices: 46623358--46623429 Score: 62
Period size: 5 Copynumber: 14.4 Consensus size: 5
46623348 TTGTTTTATG
46623358 TATATA TATAA TATAA TATAA TAT-A T-TAA TGATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
46623406 CATAA TCATTAC TATAA TATAA TA
1 TATAA T-A-TAA TATAA TATAA TA
46623430 ATATTTTTAC
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 34 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (5 bp):
TATAA
Found at i:46623383 original size:19 final size:19
Alignment explanation
Indices: 46623359--46623401 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
46623349 TGTTTTATGT
46623359 ATATATATAAT-ATAATATA
1 ATATAT-TAATGATAATATA
46623378 ATATATTAATGATAATATA
1 ATATATTAATGATAATATA
46623397 ATATA
1 ATATA
46623402 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATATATTAATGATAATATA
Found at i:46623411 original size:24 final size:24
Alignment explanation
Indices: 46623365--46623430 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
46623355 ATGTATATAT
* * *
46623365 ATAATATAATATAATATATTAATG
1 ATAATATAATATAATAAAATAATC
46623389 ATAATATAATATAA-AAACATAATC
1 ATAATATAATATAATAAA-ATAATC
*
46623413 ATTACTATAATATAATAA
1 A-TAATATAATATAATAA
46623431 TATTTTTACA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.06
24 19 0.54
25 12 0.34
26 2 0.06
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (24 bp):
ATAATATAATATAATAAAATAATC
Found at i:46623848 original size:21 final size:21
Alignment explanation
Indices: 46623823--46623866 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
46623813 ATTGGGCTGT
* *
46623823 TACACTCCACCTGTTTTGGAG
1 TACACTCCACCTGCTGTGGAG
46623844 TACACTCCACCTGCTGTGGAG
1 TACACTCCACCTGCTGTGGAG
46623865 TA
1 TA
46623867 TTGTTCGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (21 bp):
TACACTCCACCTGCTGTGGAG
Found at i:46627711 original size:47 final size:48
Alignment explanation
Indices: 46627606--46627732 Score: 204
Period size: 47 Copynumber: 2.6 Consensus size: 48
46627596 TGAATATTTT
* *
46627606 TTTCAAGCAACGAAAAGACCGAGAAAGAAAAGGGACATAGGATTTTGGG
1 TTTCAAGCAAAGAAAAGACTGAGAAAGAAAAGGGA-ATAGGATTTTGGG
46627655 TTTCAAGCAAAGAAAAGTA-TGAGAAAGAAAAGGG-ATAGGATTTTGGG
1 TTTCAAGCAAAGAAAAG-ACTGAGAAAGAAAAGGGAATAGGATTTTGGG
46627702 TTTCAAGCAAAGAAAAGACTGAGAAAGAAAA
1 TTTCAAGCAAAGAAAAGACTGAGAAAGAAAA
46627733 TAAATTGTGC
Statistics
Matches: 74, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
46 1 0.01
47 42 0.57
49 30 0.41
50 1 0.01
ACGTcount: A:0.47, C:0.09, G:0.27, T:0.17
Consensus pattern (48 bp):
TTTCAAGCAAAGAAAAGACTGAGAAAGAAAAGGGAATAGGATTTTGGG
Found at i:46628585 original size:23 final size:23
Alignment explanation
Indices: 46628555--46628598 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
46628545 TATGAAAAGT
46628555 TATGAAGAGTGAAGAGACTTGAA
1 TATGAAGAGTGAAGAGACTTGAA
46628578 TATGAAGAGTGAAGAGACTTG
1 TATGAAGAGTGAAGAGACTTG
46628599 TAGATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.32, T:0.23
Consensus pattern (23 bp):
TATGAAGAGTGAAGAGACTTGAA
Found at i:46629217 original size:69 final size:69
Alignment explanation
Indices: 46629142--46629285 Score: 270
Period size: 69 Copynumber: 2.1 Consensus size: 69
46629132 ATGTGTGGGA
*
46629142 GCTTTTCTAGGAGGTGAGTCCTCATTCGACTTGATTCCCTTGCGCTTACTGCTGCCAACAGACTC
1 GCTTTTCTAGGAGGTGAGTCCTCATTCGACTCGATTCCCTTGCGCTTACTGCTGCCAACAGACTC
46629207 CTTC
66 CTTC
46629211 GCTTTTCTAGGAGGTGAGTCCTCATTCGACTCGATTCCCTTGCGCTTACTGCTGCCAACAGACTC
1 GCTTTTCTAGGAGGTGAGTCCTCATTCGACTCGATTCCCTTGCGCTTACTGCTGCCAACAGACTC
46629276 CTTC
66 CTTC
*
46629280 ACTTTT
1 GCTTTT
46629286 TGCCTAGGCT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.16, C:0.31, G:0.19, T:0.34
Consensus pattern (69 bp):
GCTTTTCTAGGAGGTGAGTCCTCATTCGACTCGATTCCCTTGCGCTTACTGCTGCCAACAGACTC
CTTC
Found at i:46629368 original size:6 final size:6
Alignment explanation
Indices: 46629357--46629383 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
46629347 CTTCATAGCG
46629357 CTCTTC CTCTTC CTCTTC CTCTTC CTC
1 CTCTTC CTCTTC CTCTTC CTCTTC CTC
46629384 CGATTCTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CTCTTC
Found at i:46630971 original size:23 final size:23
Alignment explanation
Indices: 46630941--46630986 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
46630931 TATGAAAAGT
46630941 TATGAAGAGTGAAGAGACTTGAA
1 TATGAAGAGTGAAGAGACTTGAA
46630964 TATGAAGAGTGAAGAGACTTGAA
1 TATGAAGAGTGAAGAGACTTGAA
46630987 GATAAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.30, T:0.22
Consensus pattern (23 bp):
TATGAAGAGTGAAGAGACTTGAA
Found at i:46631205 original size:20 final size:21
Alignment explanation
Indices: 46631180--46631230 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
46631170 TACATAAAAA
46631180 ATTATTTCTC-TTTTCATTAT
1 ATTATTTCTCATTTTCATTAT
* * *
46631200 ATTATTTATCATTTTCTTTGT
1 ATTATTTCTCATTTTCATTAT
*
46631221 TTTATTTCTC
1 ATTATTTCTC
46631231 CAAATATTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.18, C:0.14, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTATTTCTCATTTTCATTAT
Found at i:46646334 original size:66 final size:66
Alignment explanation
Indices: 46646222--46646355 Score: 173
Period size: 66 Copynumber: 2.0 Consensus size: 66
46646212 GCAAATTGCT
*
46646222 CAACTTAAAGTAGAGGCGGCATCAAGAGAAGCAGAGGCTAAAAGAAAATATGAAAAACTCCAGCT
1 CAACTTAAAGTAGAGGCAGCATCAAGAGAAGCAGAGGCTAAAAGAAAATATGAAAAACTCCAGCT
46646287 A
66 A
* * * * **
46646288 CAACTTAAAGTGGAGGCAGCA-GAGAGGGAAGCAGAGGC-AAGTAGAAAATATGAGGAACTCCAG
1 CAACTTAAAGTAGAGGCAGCATCA-AGAGAAGCAGAGGCTAA-AAGAAAATATGAAAAACTCCAG
46646351 CTA
64 CTA
46646354 CA
1 CA
46646356 TCTTTAGAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 3 0.05
66 56 0.95
ACGTcount: A:0.44, C:0.16, G:0.27, T:0.13
Consensus pattern (66 bp):
CAACTTAAAGTAGAGGCAGCATCAAGAGAAGCAGAGGCTAAAAGAAAATATGAAAAACTCCAGCT
A
Found at i:46646820 original size:43 final size:43
Alignment explanation
Indices: 46646730--46646823 Score: 136
Period size: 43 Copynumber: 2.2 Consensus size: 43
46646720 CATTAAATGT
* *
46646730 CATGTTCTTTAGCGGCATTTGTGGGAAAAGCGTCGCTAAAGGT
1 CATGTTCTTTAGCGGCATTTGTGGGAAAAGCCTCGCTAAAGGC
* *
46646773 CATGTTCTTTAGCGGCGTTTGTGGGAAAAGCACT-GCTACAGGC
1 CATGTTCTTTAGCGGCATTTGTGGGAAAAGC-CTCGCTAAAGGC
46646816 CATGTTCT
1 CATGTTCT
46646824 ATAGTGGCCT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 45 0.98
44 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (43 bp):
CATGTTCTTTAGCGGCATTTGTGGGAAAAGCCTCGCTAAAGGC
Found at i:46647076 original size:20 final size:19
Alignment explanation
Indices: 46647053--46647095 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
46647043 CAAAGTGTCC
*
46647053 ATACTCTACTCAAGATATTG
1 ATACTCTAC-AAAGATATTG
* *
46647073 ATACTTTACAAAGGTATTG
1 ATACTCTACAAAGATATTG
46647092 ATAC
1 ATAC
46647096 ATTATTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (19 bp):
ATACTCTACAAAGATATTG
Found at i:46648643 original size:43 final size:42
Alignment explanation
Indices: 46648556--46648702 Score: 152
Period size: 43 Copynumber: 3.4 Consensus size: 42
46648546 ACCGAGATGA
* * * *
46648556 GATTACGTGTAAAACCATGTCT-GAGAAATTGGCATTGTACTAT
1 GATTACATGTAAGACCATGTCTAG-GACATTGGCATCGTA-TAT
46648599 GATTACATGTAAGACCATGTCTAGGACATTGGCATCGTTATAT
1 GATTACATGTAAGACCATGTCTAGGACATTGGCATCG-TATAT
* * * * * *
46648642 GATTTCGTATAAGACCCTGTCTAGGACAGTGGCATCGATATGT
1 GATTACATGTAAGACCATGTCTAGGACATTGGCATCG-TATAT
*
46648685 GATAACATGTAAGACCAT
1 GATTACATGTAAGACCAT
46648703 ATACGGGATA
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
43 83 0.97
44 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (42 bp):
GATTACATGTAAGACCATGTCTAGGACATTGGCATCGTATAT
Found at i:46657410 original size:15 final size:14
Alignment explanation
Indices: 46657366--46657443 Score: 70
Period size: 15 Copynumber: 5.4 Consensus size: 14
46657356 GATAAGAAGA
46657366 AAACC-GAATAAAG
1 AAACCAGAATAAAG
*
46657379 AAATCCA-AGATAGAG
1 AAA-CCAGA-ATAAAG
46657394 AAACCTAGAATAAAG
1 AAACC-AGAATAAAG
46657409 AAATCCAGAATAAAG
1 AAA-CCAGAATAAAG
* *
46657424 AGATCCAGGATAAAG
1 A-AACCAGAATAAAG
46657439 AAACC
1 AAACC
46657444 CAATATACGA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
13 3 0.06
14 8 0.15
15 38 0.72
16 4 0.08
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (14 bp):
AAACCAGAATAAAG
Found at i:46657437 original size:30 final size:30
Alignment explanation
Indices: 46657371--46657446 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
46657361 GAAGAAAACC
*
46657371 GAATAAAGAAATCCAAGATAGAGAAACCTA
1 GAATAAAGAAATCCAAGATAAAGAAACCTA
*
46657401 GAATAAAGAAATCC-AGAATAAAGAGATCC-A
1 GAATAAAGAAATCCAAG-ATAAAGA-AACCTA
* *
46657431 GGATAAAGAAACCCAA
1 GAATAAAGAAATCCAA
46657447 TATACGATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 2 0.05
30 33 0.85
31 4 0.10
ACGTcount: A:0.57, C:0.14, G:0.17, T:0.12
Consensus pattern (30 bp):
GAATAAAGAAATCCAAGATAAAGAAACCTA
Found at i:46665752 original size:3 final size:3
Alignment explanation
Indices: 46665729--46665776 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
46665719 ATTCCTTTAC
* *
46665729 ATT ATT -TT AATT ATT -TT ATT ATT ACT ATT GTT ATT ATT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
46665773 ATT A
1 ATT A
46665777 CTCTTATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 4 0.11
3 32 0.84
4 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:46680136 original size:15 final size:15
Alignment explanation
Indices: 46680116--46680145 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
46680106 GTTACAACTC
46680116 AATACCCATGTTTGT
1 AATACCCATGTTTGT
46680131 AATACCCATGTTTGT
1 AATACCCATGTTTGT
46680146 TGCATTCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (15 bp):
AATACCCATGTTTGT
Found at i:46682825 original size:14 final size:14
Alignment explanation
Indices: 46682801--46682833 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
46682791 TCAAAGACCT
46682801 ATAATATGGAATGCA
1 ATAATATGGAAT-CA
46682816 ATAA-ATGGAATCA
1 ATAATATGGAATCA
46682829 ATAAT
1 ATAAT
46682834 TATCGGGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.35
14 7 0.41
15 4 0.24
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (14 bp):
ATAATATGGAATCA
Found at i:46684405 original size:13 final size:13
Alignment explanation
Indices: 46684387--46684416 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
46684377 GACCATAACT
46684387 TAAAAAATAAAAA
1 TAAAAAATAAAAA
46684400 TAAAAAATAAAAA
1 TAAAAAATAAAAA
46684413 -AAAA
1 TAAAA
46684417 TGAAAACAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:46686272 original size:3 final size:3
Alignment explanation
Indices: 46686260--46686297 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
46686250 CAAAACAAAA
46686260 CTC C-C CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
46686298 TCTGTTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:46690947 original size:41 final size:41
Alignment explanation
Indices: 46690856--46691064 Score: 224
Period size: 41 Copynumber: 5.0 Consensus size: 41
46690846 CACCAAAACA
* * * * * *
46690856 AAGCCTGCCAAGCTC-GAGGCTTGATACAATTACACCGGCACA
1 AAGCCTGCTAAGCACAGA-GCTTGATATAAAT-CACTGGCACG
* *
46690898 AAGCCTGCTAGGCACAGAGCTTGATATAAATCACTAGCACG
1 AAGCCTGCTAAGCACAGAGCTTGATATAAATCACTGGCACG
* * *
46690939 GAGCCTGCTAAGCACAAAGCTTGACATAAATCACTGGCACG
1 AAGCCTGCTAAGCACAGAGCTTGATATAAATCACTGGCACG
* * *
46690980 AAGCCTGCTAGGCACAGAGCCTGATATAAATCACCGGCACG
1 AAGCCTGCTAAGCACAGAGCTTGATATAAATCACTGGCACG
* *
46691021 AAGCCTGCTAAGCACA-ACGCTTGATATGAACTCACCGGCACG
1 AAGCCTGCTAAGCACAGA-GCTTGATAT-AAATCACTGGCACG
46691063 AA
1 AA
46691065 ACTTGCTAGA
Statistics
Matches: 142, Mismatches: 22, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
40 1 0.01
41 101 0.71
42 38 0.27
43 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.17
Consensus pattern (41 bp):
AAGCCTGCTAAGCACAGAGCTTGATATAAATCACTGGCACG
Found at i:46690993 original size:82 final size:83
Alignment explanation
Indices: 46690888--46691073 Score: 266
Period size: 82 Copynumber: 2.3 Consensus size: 83
46690878 GATACAATTA
* * * *
46690888 CACCGGCACAAAGCCTGCTAGGCACAGAGCTTGATATAAATCACTAGCACGGAGCCTGCTAAGCA
1 CACCGGCACGAAGCCTGCTAGGCACAGAGCCTGATATAAATCACCAGCACGAAGCCTGCTAAGCA
46690953 CAAAGCTTGACAT-AAAT
66 CAAAGCTTGACATGAAAT
* *
46690970 CACTGGCACGAAGCCTGCTAGGCACAGAGCCTGATATAAATCACCGGCACGAAGCCTGCTAAGCA
1 CACCGGCACGAAGCCTGCTAGGCACAGAGCCTGATATAAATCACCAGCACGAAGCCTGCTAAGCA
* * *
46691035 CAACGCTTGATATGAACT
66 CAAAGCTTGACATGAAAT
* *
46691053 CACCGGCACGAAACTTGCTAG
1 CACCGGCACGAAGCCTGCTAG
46691074 ACTCAAGGTT
Statistics
Matches: 91, Mismatches: 12, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
82 70 0.77
83 21 0.23
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.17
Consensus pattern (83 bp):
CACCGGCACGAAGCCTGCTAGGCACAGAGCCTGATATAAATCACCAGCACGAAGCCTGCTAAGCA
CAAAGCTTGACATGAAAT
Found at i:46691344 original size:19 final size:19
Alignment explanation
Indices: 46691320--46691359 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
46691310 TTAATAAATT
46691320 GAATGGAATTATTAATTTA
1 GAATGGAATTATTAATTTA
46691339 GAATGGAATTATTAATTTA
1 GAATGGAATTATTAATTTA
46691358 GA
1 GA
46691360 TAGTAAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.40
Consensus pattern (19 bp):
GAATGGAATTATTAATTTA
Found at i:46696569 original size:16 final size:16
Alignment explanation
Indices: 46696544--46696574 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46696534 ATGATATAGA
46696544 AATATGACATGAAATG
1 AATATGACATGAAATG
*
46696560 AATATTACATGAAAT
1 AATATGACATGAAAT
46696575 ACAAGAAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (16 bp):
AATATGACATGAAATG
Found at i:46700163 original size:13 final size:13
Alignment explanation
Indices: 46700145--46700173 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
46700135 TTTCAAAATT
46700145 ATTATTTTTTAAA
1 ATTATTTTTTAAA
46700158 ATTATTTTTTAAA
1 ATTATTTTTTAAA
46700171 ATT
1 ATT
46700174 TTTATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATTTTTTAAA
Found at i:46700178 original size:16 final size:15
Alignment explanation
Indices: 46700139--46700175 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
46700129 TTTAGATTTC
46700139 AAAATTATTATTTTTT
1 AAAATT-TTATTTTTT
46700155 AAAA--TTATTTTTT
1 AAAATTTTATTTTTT
46700168 AAAATTTT
1 AAAATTTT
46700176 TATATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
13 13 0.68
15 2 0.11
16 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AAAATTTTATTTTTT
Found at i:46700216 original size:17 final size:18
Alignment explanation
Indices: 46700162--46700218 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
46700152 TTTAAAATTA
* *
46700162 TTTTTTAAAATTTTTATAT
1 TTTTTTAAAATATATA-AT
* * *
46700181 ATTTTTGAAATTTATAAT
1 TTTTTTAAAATATATAAT
46700199 TTTTTTAAAATATA-AAT
1 TTTTTTAAAATATATAAT
46700216 TTT
1 TTT
46700219 AGAATTTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
17 6 0.19
18 13 0.41
19 13 0.41
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTTTTAAAATATATAAT
Found at i:46700253 original size:53 final size:50
Alignment explanation
Indices: 46700149--46700253 Score: 113
Period size: 53 Copynumber: 2.0 Consensus size: 50
46700139 AAAATTATTA
** * *
46700149 TTTTTTAAAATTATTTTTTAAAATTTTTATATATTTTTGAAATTTATAAT
1 TTTTTTAAAATTAAATTTTAAAATTTTTAAATATTTTTGAAATTTAAAAT
* *
46700199 TTTTTTAAAATATAAATTTTAGAATTTTTGTAAATATTTTT-AATTTTCAAAAT
1 TTTTTTAAAAT-TAAATTTTA-AAATTTT-TAAATATTTTTGAAATTT-AAAAT
46700252 TT
1 TT
46700254 AAAAATTACT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
50 11 0.24
51 7 0.16
52 11 0.24
53 16 0.36
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (50 bp):
TTTTTTAAAATTAAATTTTAAAATTTTTAAATATTTTTGAAATTTAAAAT
Found at i:46705010 original size:30 final size:31
Alignment explanation
Indices: 46704966--46705049 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
46704956 TTTAAGCCCT
46704966 TAAATTTTTT-AAAATTTTAATTAAA-CCTC
1 TAAATTTTTTGAAAATTTTAATTAAATCCTC
* *
46704995 -AAATTTTTTTGAAAATTCTCATTAAATCCTC
1 TAAA-TTTTTTGAAAATTTTAATTAAATCCTC
* *
46705026 TAGATTTTTTGAAAATTTAAATTA
1 TAAATTTTTTGAAAATTTTAATTA
46705050 GGCCCCCTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
28 3 0.07
29 6 0.13
30 13 0.29
31 21 0.47
32 2 0.04
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.48
Consensus pattern (31 bp):
TAAATTTTTTGAAAATTTTAATTAAATCCTC
Found at i:46707594 original size:12 final size:12
Alignment explanation
Indices: 46707579--46707624 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
46707569 ACTTTTTCCC
46707579 CCTTTTTTTATT
1 CCTTTTTTTATT
*
46707591 CCTTTTTCTTCTT
1 CCTTTTT-TTATT
**
46707604 TTTTTTTTTATT
1 CCTTTTTTTATT
46707616 CCTTTTTTT
1 CCTTTTTTT
46707625 TAAATAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
12 18 0.67
13 9 0.33
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.78
Consensus pattern (12 bp):
CCTTTTTTTATT
Found at i:46709752 original size:7 final size:7
Alignment explanation
Indices: 46709740--46709774 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
46709730 TTTTTAGGAA
46709740 TTAAATT
1 TTAAATT
46709747 TTAAATT
1 TTAAATT
46709754 TTAAATT
1 TTAAATT
46709761 TTAAATT
1 TTAAATT
46709768 TTAAATT
1 TTAAATT
46709775 AAATTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTAAATT
Found at i:46709785 original size:21 final size:22
Alignment explanation
Indices: 46709738--46709790 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
46709728 GATTTTTAGG
46709738 AATTAAATTTTAAATTTTAAATT
1 AATTAAATTTTAAA-TTTAAATT
46709761 --TTAAATTTTAAA-TTAAATT
1 AATTAAATTTTAAATTTAAATT
46709780 AATTAATATTT
1 AATTAA-ATTT
46709791 ATATTTTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 7 0.26
21 16 0.59
22 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTAAATTTTAAATTTAAATT
Found at i:46710624 original size:28 final size:27
Alignment explanation
Indices: 46710593--46710691 Score: 82
Period size: 27 Copynumber: 3.7 Consensus size: 27
46710583 TTATAAAAAA
* *
46710593 TAATAATAAT-TAGAAAAATATTAAATTT
1 TAATAAAAATATA-AAAAA-ATAAAATTT
46710621 TAATAAAAATATAAAAAAATAAAATTT
1 TAATAAAAATATAAAAAAATAAAATTT
**
46710648 T--TAAAAA-ATAAAATATTGTAAAATTT
1 TAATAAAAATATAAAA-A-AATAAAATTT
46710674 T-ATAAAAATCATAAAAAA
1 TAATAAAAAT-ATAAAAAA
46710692 TTAACAACCC
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
24 6 0.10
25 7 0.12
26 9 0.15
27 15 0.25
28 15 0.25
29 8 0.13
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (27 bp):
TAATAAAAATATAAAAAAATAAAATTT
Found at i:46710643 original size:16 final size:16
Alignment explanation
Indices: 46710622--46710660 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
46710612 ATTAAATTTT
46710622 AATAAAAATATAAAAA
1 AATAAAAATATAAAAA
* * *
46710638 AATAAAATTTTTAAAA
1 AATAAAAATATAAAAA
46710654 AATAAAA
1 AATAAAA
46710661 TATTGTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAAAATATAAAAA
Found at i:46710643 original size:26 final size:26
Alignment explanation
Indices: 46710606--46710691 Score: 86
Period size: 27 Copynumber: 3.2 Consensus size: 26
46710596 TAATAATTAG
* *
46710606 AAAAATATTAAATTTTAATAAAAATAT
1 AAAAAAATAAAATTTT-ATAAAAATAT
46710633 AAAAAAATAAAATTTT-TAAAAA-AT
1 AAAAAAATAAAATTTTATAAAAATAT
**
46710657 AAAATATTGTAAAATTTTATAAAAATCAT
1 AAAA-A-AATAAAATTTTATAAAAAT-AT
46710686 AAAAAA
1 AAAAAA
46710692 TTAACAACCC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
24 6 0.12
25 7 0.14
26 9 0.18
27 20 0.41
28 1 0.02
29 6 0.12
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (26 bp):
AAAAAAATAAAATTTTATAAAAATAT
Found at i:46710670 original size:16 final size:16
Alignment explanation
Indices: 46710634--46710670 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
46710624 TAAAAATATA
*
46710634 AAAAAATAAAATTTTT
1 AAAAAATAAAATTTGT
46710650 AAAAAATAAAATATTGT
1 AAAAAATAAAAT-TTGT
46710667 AAAA
1 AAAA
46710671 TTTTATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAAAATAAAATTTGT
Found at i:46710973 original size:12 final size:12
Alignment explanation
Indices: 46710956--46710984 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
46710946 AAAAAAATAT
46710956 ATTTTTTTTATG
1 ATTTTTTTTATG
46710968 ATTTTTTTTATG
1 ATTTTTTTTATG
46710980 -TTTTT
1 ATTTTT
46710985 CTAATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
ATTTTTTTTATG
Found at i:46711292 original size:175 final size:167
Alignment explanation
Indices: 46711101--46711437 Score: 408
Period size: 175 Copynumber: 2.0 Consensus size: 167
46711091 GCTTTGTTAC
* *
46711101 TTTTTTTGAAAAAGTTTAAGG-GTCTTTTTTATACATTTTGAAAGTTCAAGT-GTCCAATTGAAT
1 TTTTTTTGAAAAAGTTT--GGAGTCTTTTTGATACATTTTGAAAGTTCAAGTACT-CAATTGAAT
*
46711164 GCAAAAAAAAAAAAAGTAGAGGCTTAATTATTTTCTTTAAAAGATTTGAGAGCATTTTTTTATAT
63 GC----AAAAAAAAAGTAGAGGCTTAATTATTTT-TTTAAAA-ATTTGAGAGCA-TTTTTTATAC
* *
46711229 ATTTTGAAAGTTCAAGTACCCAAATGAGTGCAAAAAAAAAACAAGGG
121 ATCTTGAAAGTTCAAGTACCCAAATGAATGCAAAAAAAAAACAAGGG
** * *
46711276 TTTTTTTTTAAAAGTTTGGAAGTCTTTTTGATGCATTTTGAAAGTTCAAGTACTCAATTGAGTGC
1 TTTTTTTGAAAAAGTTTGG-AGTCTTTTTGATACATTTTGAAAGTTCAAGTACTCAATTGAATGC
* * * * * * *
46711341 AAAAAAATAGTAGGGGCTTAATTGTTTTTTTGAAAATTTGGGAGTATTTTTTATGCATCTTGAAA
65 AAAAAAAAAGTAGAGGCTTAATTATTTTTTTAAAAATTTGAGAGCATTTTTTATACATCTTGAAA
*
46711406 GTTCAAGTACCTAAATGAATGCAAAAAAAAAA
130 GTTCAAGTACCCAAATGAATGCAAAAAAAAAA
46711438 AAACAGCTTA
Statistics
Matches: 142, Mismatches: 17, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
168 46 0.32
169 9 0.06
170 6 0.04
171 25 0.18
173 2 0.01
175 53 0.37
176 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (167 bp):
TTTTTTTGAAAAAGTTTGGAGTCTTTTTGATACATTTTGAAAGTTCAAGTACTCAATTGAATGCA
AAAAAAAAGTAGAGGCTTAATTATTTTTTTAAAAATTTGAGAGCATTTTTTATACATCTTGAAAG
TTCAAGTACCCAAATGAATGCAAAAAAAAAACAAGGG
Found at i:46711447 original size:87 final size:86
Alignment explanation
Indices: 46711125--46711462 Score: 278
Period size: 87 Copynumber: 3.9 Consensus size: 86
46711115 TTTAAGGGTC
* *
46711125 TTTTTTATACATTTTGAAAGTTCAAGTGTCC-AATTGAATGCAAAAAAAAAAAAAGTAGAGGCTT
1 TTTTTTATACATTTTGAAAGTTCAAGT-ACCTAAATGAATGC-AAAAAAAAAAAA--AGA-GCTT
* *
46711189 AATTATTTTCTTTAAAAGATTTGAGAGCA
61 AATTATTTT-TTT-AAA-ATTTGGGAGTA
* * * * *
46711218 TTTTTTTATATATTTTGAAAGTTCAAGTACCCAAATGAGTGCAAAAAAAAAACAAG-G----GTT
1 -TTTTTTATACATTTTGAAAGTTCAAGTACCTAAATGAATGCAAAAAAAAAAAAAGAGCTTAATT
* *
46711278 -TTTTTTTAAAAGTTTGGAAGTC
65 ATTTTTTTAAAA-TTTGGGAGTA
* * * * * ** * *
46711300 TTTTTGATGCATTTTGAAAGTTCAAGTA-CTCAATTGAGTGCAAAAAAATAGTAGGGGCTTAATT
1 TTTTTTATACATTTTGAAAGTTCAAGTACCT-AAATGAATGCAAAAAAAAAAAAAGAGCTTAATT
*
46711364 GTTTTTTTGAAAATTTGGGAGTA
65 ATTTTTTT-AAAATTTGGGAGTA
* * * *
46711387 TTTTTTATGCATCTTGAAAGTTCAAGTACCTAAATGAATGCAAAAAAAAAAAAACAGCTTAAATA
1 TTTTTTATACATTTTGAAAGTTCAAGTACCTAAATGAATGCAAAAAAAAAAAAAGAGCTTAATTA
*
46711452 TTTTTTAAAAA
66 TTTTTTTAAAA
46711463 AAGTTTGAGG
Statistics
Matches: 198, Mismatches: 35, Indels: 30
0.75 0.13 0.11
Matches are distributed among these distances:
80 1 0.01
81 45 0.23
82 10 0.05
83 3 0.02
84 4 0.02
85 2 0.01
86 6 0.03
87 71 0.36
88 6 0.03
89 1 0.01
91 2 0.01
93 13 0.07
94 34 0.17
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (86 bp):
TTTTTTATACATTTTGAAAGTTCAAGTACCTAAATGAATGCAAAAAAAAAAAAAGAGCTTAATTA
TTTTTTTAAAATTTGGGAGTA
Found at i:46712864 original size:18 final size:19
Alignment explanation
Indices: 46712841--46712880 Score: 64
Period size: 18 Copynumber: 2.1 Consensus size: 19
46712831 TTTTGGAAAC
46712841 TTAATTAAAAAT-ATTATT
1 TTAATTAAAAATCATTATT
46712859 TTAATTAAAAATGCATTATT
1 TTAATTAAAAAT-CATTATT
46712879 TT
1 TT
46712881 TACTAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 12 0.60
20 8 0.40
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (19 bp):
TTAATTAAAAATCATTATT
Found at i:46718633 original size:43 final size:43
Alignment explanation
Indices: 46718585--46718735 Score: 178
Period size: 43 Copynumber: 3.5 Consensus size: 43
46718575 CGTTATAGAA
* * *
46718585 CATGTTCTTTAGCGGCGTTTTTAGTAAAAGCACCGTTAAAGAT
1 CATGTTCTTTAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGAT
* * * * ** * *
46718628 GATGTTCTATAACGGCGTTTGTAGTAAAAGTGCTACAAAAAAT
1 CATGTTCTTTAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGAT
*
46718671 CATGTTCTTTAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGAC
1 CATGTTCTTTAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGAT
46718714 CATGTT-TTATAGCGGCGTTTGT
1 CATGTTCTT-TAGCGGCGTTTGT
46718736 GAGAAAATGC
Statistics
Matches: 87, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 2 0.02
43 85 0.98
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (43 bp):
CATGTTCTTTAGCGGCGTTTGTAGTAAAAGCGCCGCTAAAGAT
Found at i:46719470 original size:13 final size:14
Alignment explanation
Indices: 46719444--46719472 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
46719434 ACAAACGATG
46719444 AATTAAACCATTAT
1 AATTAAACCATTAT
46719458 AATTAAA-CATTAT
1 AATTAAACCATTAT
46719471 AA
1 AA
46719473 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:46722235 original size:18 final size:18
Alignment explanation
Indices: 46722212--46722246 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
46722202 CAAGTCCGCA
46722212 TCATTAGGA-TCATCCTCT
1 TCATTA-GATTCATCCTCT
46722230 TCATTAGATTCATCCTC
1 TCATTAGATTCATCCTC
46722247 ACTCTGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.23, C:0.29, G:0.09, T:0.40
Consensus pattern (18 bp):
TCATTAGATTCATCCTCT
Found at i:46725360 original size:25 final size:25
Alignment explanation
Indices: 46725332--46725388 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
46725322 TAAGCTCTTC
46725332 TGAGCTGAATAACGAGAAAA-TCATG
1 TGAGCTGAATAAC-AGAAAACTCATG
*
46725357 TGAGCTAAATAACAGAAAACTCATG
1 TGAGCTGAATAACAGAAAACTCATG
*
46725382 CGAGCTG
1 TGAGCTG
46725389 TGGTGTGTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 6 0.21
25 22 0.79
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (25 bp):
TGAGCTGAATAACAGAAAACTCATG
Found at i:46734056 original size:25 final size:25
Alignment explanation
Indices: 46733971--46734063 Score: 116
Period size: 25 Copynumber: 3.8 Consensus size: 25
46733961 GATACAGCAA
* *
46733971 AGGACTATCGATAGCGATGCGGTAG
1 AGGACTATTGATGGCGATGCGGTAG
*
46733996 A-GACTGTTGATGGCGATGCGGTAG
1 AGGACTATTGATGGCGATGCGGTAG
* **
46734020 AAGACTGCTGATGGCGATGCGGTAG
1 AGGACTATTGATGGCGATGCGGTAG
*
46734045 AGGACTATTGATGGTGATG
1 AGGACTATTGATGGCGATG
46734064 TAGCAGACAT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
24 21 0.36
25 38 0.64
ACGTcount: A:0.25, C:0.13, G:0.39, T:0.24
Consensus pattern (25 bp):
AGGACTATTGATGGCGATGCGGTAG
Found at i:46734149 original size:35 final size:35
Alignment explanation
Indices: 46734076--46734192 Score: 130
Period size: 35 Copynumber: 3.4 Consensus size: 35
46734066 GCAGACATTG
* * * *
46734076 GGGAAAAAATTAAGGGA-TTGGGGAAAATGATTTG
1 GGGAAAAAACTAAGGGATTTCGGGAAAATGAATTA
*
46734110 GGGAAAAGACTAAGGGATTTCGGGAAAATGAATTA
1 GGGAAAAAACTAAGGGATTTCGGGAAAATGAATTA
* * * *
46734145 GGGAAAAAAGTAAGGGATTTCAGAGAAACTG-ATTT
1 GGGAAAAAACTAAGGGATTTC-GGGAAAATGAATTA
46734180 GGGAAAAAACTAA
1 GGGAAAAAACTAA
46734193 AGCTATCAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 15 0.21
35 48 0.69
36 7 0.10
ACGTcount: A:0.44, C:0.04, G:0.31, T:0.21
Consensus pattern (35 bp):
GGGAAAAAACTAAGGGATTTCGGGAAAATGAATTA
Found at i:46748195 original size:6 final size:6
Alignment explanation
Indices: 46748184--46748263 Score: 124
Period size: 6 Copynumber: 13.3 Consensus size: 6
46748174 ATATAAAGAC
* *
46748184 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAGATA AAGATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* *
46748232 AAAATA AAAATA AAAATA AACATA AAGATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AA
46748264 TGGACTCAGT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:46749949 original size:11 final size:11
Alignment explanation
Indices: 46749929--46749958 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
46749919 CACACACAAT
46749929 AATAATAAAGA
1 AATAATAAAGA
*
46749940 AATGATAAAGA
1 AATAATAAAGA
46749951 AATAATAA
1 AATAATAA
46749959 TAATATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (11 bp):
AATAATAAAGA
Found at i:46749959 original size:3 final size:3
Alignment explanation
Indices: 46749951--46750024 Score: 80
Period size: 3 Copynumber: 24.7 Consensus size: 3
46749941 ATGATAAAGA
* * **
46749951 AAT AAT AAT AAT -AT AAT AAT AAT GAT GAT AAT AAT AAT -AT GGACC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT --AAT
46749996 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
46750025 AGAAAAATAA
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
2 4 0.07
3 57 0.93
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:46750034 original size:34 final size:34
Alignment explanation
Indices: 46749963--46750039 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
46749953 TAATAATAAT
* * ** **
46749963 ATAATAATAATGATGATAATAATAATATGGACCA
1 ATAATAATAATAATAATAATAATAATAAAGAAAA
46749997 ATAATAATAATAATAATAATAATAATAAAGAAAA
1 ATAATAATAATAATAATAATAATAATAAAGAAAA
46750031 ATAA-AATAA
1 ATAATAATAA
46750040 ATAACTAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 5 0.14
34 32 0.86
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (34 bp):
ATAATAATAATAATAATAATAATAATAAAGAAAA
Found at i:46757036 original size:22 final size:20
Alignment explanation
Indices: 46757003--46757042 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
46756993 CTTTGAATCA
*
46757003 GCCCGTTTTGTTCTTTTTTG
1 GCCCGTTTTGTTCCTTTTTG
46757023 GCCCGTTTTATGTTCCTTTT
1 GCCCG-TTT-TGTTCCTTTT
46757043 GTTTCCCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 3 0.18
22 9 0.53
ACGTcount: A:0.03, C:0.23, G:0.17, T:0.57
Consensus pattern (20 bp):
GCCCGTTTTGTTCCTTTTTG
Found at i:46766160 original size:40 final size:40
Alignment explanation
Indices: 46766078--46766165 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
46766068 CAATGTGCGA
*
46766078 CACTAAGTGTGCGGTTCGAAATAGCTTCGACTACAAATGG
1 CACTAAGTGTGCGGTTCGAAATAGCTTCGACCACAAATGG
* * *
46766118 CACTAAGTGTGCGAGTT-GGAATAGCTTCGGCCATAAGA-GG
1 CACTAAGTGTGCG-GTTCGAAATAGCTTCGACCACAA-ATGG
46766158 CACTAAGT
1 CACTAAGT
46766166 ATGTAATACT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 38 0.90
41 4 0.10
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (40 bp):
CACTAAGTGTGCGGTTCGAAATAGCTTCGACCACAAATGG
Found at i:46767101 original size:37 final size:37
Alignment explanation
Indices: 46767048--46767120 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
46767038 CCCACACGGT
*
46767048 TGAGCATAAAGACGTGTGTCTCGACCTTGTGGCCGTG
1 TGAGCACAAAGACGTGTGTCTCGACCTTGTGGCCGTG
*
46767085 TGAGCACAAAGGCGTGTGTCTCGACCTTGTGGCCGT
1 TGAGCACAAAGACGTGTGTCTCGACCTTGTGGCCGT
46767121 ATGGTGAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.18, C:0.23, G:0.33, T:0.26
Consensus pattern (37 bp):
TGAGCACAAAGACGTGTGTCTCGACCTTGTGGCCGTG
Found at i:46769319 original size:17 final size:18
Alignment explanation
Indices: 46769276--46769336 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 18
46769266 TATATAAACT
*
46769276 AAAAATGATATATAATTATAT
1 AAAAAT-ATA-ATAATT-TAA
46769297 AAAAATA-AATAATTTAA
1 AAAAATATAATAATTTAA
*
46769314 AAAAATATAA-ATTTTAA
1 AAAAATATAATAATTTAA
46769331 AAAAAT
1 AAAAAT
46769337 CCAAATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
17 21 0.57
18 8 0.22
19 1 0.03
20 1 0.03
21 6 0.16
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAAATATAATAATTTAA
Found at i:46769342 original size:17 final size:17
Alignment explanation
Indices: 46769309--46769343 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
46769299 AAATAAATAA
*
46769309 TTTAAAAAAATATAAAT
1 TTTAAAAAAATACAAAT
*
46769326 TTTAAAAAAATCCAAAT
1 TTTAAAAAAATACAAAT
46769343 T
1 T
46769344 AAAAGTTGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (17 bp):
TTTAAAAAAATACAAAT
Found at i:46770411 original size:24 final size:26
Alignment explanation
Indices: 46770356--46770411 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 26
46770346 AAAATTTATC
*
46770356 ATTTAATATAATAAATAATTTAAAAT
1 ATTTATTATAATAAATAATTTAAAAT
* * *
46770382 AATTATTA-AATAAATCA-TTAAAGT
1 ATTTATTATAATAAATAATTTAAAAT
46770406 ATTTAT
1 ATTTAT
46770412 ATGAATTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 11 0.44
25 8 0.32
26 6 0.24
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTTATTATAATAAATAATTTAAAAT
Found at i:46773660 original size:131 final size:130
Alignment explanation
Indices: 46773531--46773837 Score: 353
Period size: 131 Copynumber: 2.3 Consensus size: 130
46773521 ACATGATTCT
* * * * *
46773531 CGAATTGTCAAACGCCAAATATTGCCTTCGTTTTAAATAATTTTTAGAAGATATGAATGAAATTT
1 CGAATTG-CAAACACCAAATATCGCCTTCGTTTTAAAGAA-TTTTAAAAGACATGAATGAAATTT
* * *
46773596 TGAAGGGATACTCGATTATTTTGAGCAAACGCGAAATTGTAACCCAACACATTAGGGCACGATTC
64 TGAAGGGATACTCGATTATTTCGAGCAAACGCGAAATGGCAACCCAACACATTAGGGCACGATTC
46773661 CG
129 CG
* * * * * * * * *
46773663 CGGATTGCTAAATATCGAATCTCGTCTTCGTTTTGAAGAATTTTAAAAGGCATGAGTGAAATTTT
1 CGAATTGC-AAACACCAAATATCGCCTTCGTTTTAAAGAATTTTAAAAGACATGAATGAAATTTT
* * *
46773728 GAAGTGATATTCGATTATTTCGAGCAAACGCGAAATGGCAACCCAACACGTTAGGGCACGATTCC
65 GAAGGGATACTCGATTATTTCGAGCAAACGCGAAATGGCAACCCAACACATTAGGGCACGATTCC
46773793 G
130 G
* * * * *
46773794 CGAATTGCCAAATATCGAATCTCGCCTTCGTTTTGAAGAATTTT
1 CGAATTG-CAAACACCAAATATCGCCTTCGTTTTAAAGAATTTT
46773838 TGAATGAATA
Statistics
Matches: 151, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
131 122 0.81
132 29 0.19
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (130 bp):
CGAATTGCAAACACCAAATATCGCCTTCGTTTTAAAGAATTTTAAAAGACATGAATGAAATTTTG
AAGGGATACTCGATTATTTCGAGCAAACGCGAAATGGCAACCCAACACATTAGGGCACGATTCCG
Found at i:46776923 original size:46 final size:46
Alignment explanation
Indices: 46776870--46777025 Score: 118
Period size: 46 Copynumber: 3.2 Consensus size: 46
46776860 TGAATTATAC
46776870 TCTAGTGACTGTATTGCTCTTTTGATGTAAATGGCATGTACCTAAG
1 TCTAGTGACTGTATTGCTCTTTTGATGTAAATGGCATGTACCTAAG
* * * *** * *
46776916 TCTAGTGAACTTCATGAGTTTGGTTAGTTGGTTGAT-TAAACCCCATTGTA-TTATAC
1 TCTAGTG-AC-T-GT-A--TT-GCT-CTT--TTGATGTAAATGGCA-TGTACCTA-AG
46776972 TCTAGTGACTGTATTGCTCTTTTGATGTAAATGGCATGTACCTAAG
1 TCTAGTGACTGTATTGCTCTTTTGATGTAAATGGCATGTACCTAAG
46777018 TCTAGTGA
1 TCTAGTGA
46777026 ACTTCATGAG
Statistics
Matches: 80, Mismatches: 16, Indels: 28
0.65 0.13 0.23
Matches are distributed among these distances:
46 25 0.31
47 10 0.12
48 3 0.04
49 3 0.04
50 3 0.04
52 3 0.04
53 3 0.04
54 3 0.04
55 10 0.12
56 17 0.21
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (46 bp):
TCTAGTGACTGTATTGCTCTTTTGATGTAAATGGCATGTACCTAAG
Found at i:46776969 original size:102 final size:102
Alignment explanation
Indices: 46776740--46777055 Score: 533
Period size: 102 Copynumber: 3.0 Consensus size: 102
46776730 ACATACCATA
*
46776740 AAACCCCATTGTATTATACTCTAGTGATTGTATTGCTCTTTTGAATTTTGAGATGTAAATGGCAT
1 AAACCCCATTGTATTATACTCTAGTGACTGTATTGCTC-------TTTT--GATGTAAATGGCAT
46776805 GTACCTAAGTCTAGTGAACTTCATGAGTTTGGTTAGTTGGTTGATT
57 GTACCTAAGTCTAGTGAACTTCATGAGTTTGGTTAGTTGGTTGATT
*
46776851 AAACCCCATTGAATTATACTCTAGTGACTGTATTGCTCTTTTGATGTAAATGGCATGTACCTAAG
1 AAACCCCATTGTATTATACTCTAGTGACTGTATTGCTCTTTTGATGTAAATGGCATGTACCTAAG
46776916 TCTAGTGAACTTCATGAGTTTGGTTAGTTGGTTGATT
66 TCTAGTGAACTTCATGAGTTTGGTTAGTTGGTTGATT
46776953 AAACCCCATTGTATTATACTCTAGTGACTGTATTGCTCTTTTGATGTAAATGGCATGTACCTAAG
1 AAACCCCATTGTATTATACTCTAGTGACTGTATTGCTCTTTTGATGTAAATGGCATGTACCTAAG
46777018 TCTAGTGAACTTCATGAGTTTGGTTAGTTGGTTGATT
66 TCTAGTGAACTTCATGAGTTTGGTTAGTTGGTTGATT
46777055 A
1 A
46777056 TGGTTATGTA
Statistics
Matches: 202, Mismatches: 3, Indels: 9
0.94 0.01 0.04
Matches are distributed among these distances:
102 162 0.80
104 4 0.02
111 36 0.18
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (102 bp):
AAACCCCATTGTATTATACTCTAGTGACTGTATTGCTCTTTTGATGTAAATGGCATGTACCTAAG
TCTAGTGAACTTCATGAGTTTGGTTAGTTGGTTGATT
Found at i:46779944 original size:29 final size:30
Alignment explanation
Indices: 46779895--46779970 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
46779885 ATTTGAACCA
*
46779895 TAAAGTTTCATGTGTATAATTACACA-AAAT
1 TAAAG-TTCATGTATATAATTACACATAAAT
* *
46779925 TAAAGTTCATGTATCA-AATTCCACATTGAAT
1 TAAAGTTCATGTAT-ATAATTACACA-TAAAT
*
46779956 TAAAGTTTATGTATA
1 TAAAGTTCATGTATA
46779971 ATTTTGAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 16 0.41
30 7 0.18
31 16 0.41
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (30 bp):
TAAAGTTCATGTATATAATTACACATAAAT
Found at i:46780567 original size:14 final size:15
Alignment explanation
Indices: 46780539--46780577 Score: 62
Period size: 14 Copynumber: 2.6 Consensus size: 15
46780529 TTTTAATTTT
46780539 TTTTAAAAAATAATAA
1 TTTT-AAAAATAATAA
46780555 TTTTAAAAA-AATAA
1 TTTTAAAAATAATAA
46780569 TTTTAAAAA
1 TTTTAAAAA
46780578 GCACTTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.61
15 5 0.22
16 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTTAAAAATAATAA
Found at i:46785522 original size:19 final size:19
Alignment explanation
Indices: 46785477--46785528 Score: 88
Period size: 18 Copynumber: 2.8 Consensus size: 19
46785467 ATCTTCAATT
*
46785477 ATATGTAATCTTAGATATG
1 ATATGCAATCTTAGATATG
46785496 AT-TGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
46785514 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
46785529 AGATATGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 17 0.55
19 14 0.45
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:46785554 original size:22 final size:22
Alignment explanation
Indices: 46785489--46785537 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 22
46785479 ATGTAATCTT
46785489 AGATATGAT-TGCAATCTT---
1 AGATATGATATGCAATCTTAGA
46785507 AGATATGATATGCAATCTTAGA
1 AGATATGATATGCAATCTTAGA
46785529 AGATATGAT
1 AGATATGAT
46785538 TTTGTAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.33
19 9 0.33
22 9 0.33
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (22 bp):
AGATATGATATGCAATCTTAGA
Found at i:46785842 original size:18 final size:17
Alignment explanation
Indices: 46785819--46785852 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
46785809 GTTCCCTGAT
*
46785819 TTTTTTTATATATTTTAA
1 TTTTTTAATA-ATTTTAA
46785837 TTTTTTAATAATTTTA
1 TTTTTTAATAATTTTA
46785853 GTATCATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTAATAATTTTAA
Found at i:46794657 original size:78 final size:78
Alignment explanation
Indices: 46794544--46794836 Score: 417
Period size: 78 Copynumber: 3.8 Consensus size: 78
46794534 AAGAAACAGG
** * * * *
46794544 TTTGGCATCTCCATATTCGACGAAGAGCAGATCGAAGACATCGCAGATCTGACCTTCATTGAAGC
1 TTTGGCATCTCTGTATTAGACGAGGAACAGATCGAAGACATAGCAGATCTGACCTTCATTGAAGC
46794609 AGATCCAAGATGA
66 AGATCCAAGATGA
* * *
46794622 TTTGGCATCTCTGTATTAGACGGGGAACAGATCGAAGACACAGCAGATCTGACTTTCATTGAAGC
1 TTTGGCATCTCTGTATTAGACGAGGAACAGATCGAAGACATAGCAGATCTGACCTTCATTGAAGC
46794687 AGATCCAAGATGA
66 AGATCCAAGATGA
* * * * * *
46794700 TTTGGCATTTCTGTATTAGACGGGGAGCAGATCAAAGACATAACAGAT-TGGACCTTCCTTGAAG
1 TTTGGCATCTCTGTATTAGACGAGGAACAGATCGAAGACATAGCAGATCT-GACCTTCATTGAAG
*
46794764 TAGATCCAAGATGA
65 CAGATCCAAGATGA
*
46794778 TTTGGCATCTCTGTATTAGACAAGGAACAGATCGAAGACATAGCAGATCTGACCTTCAT
1 TTTGGCATCTCTGTATTAGACGAGGAACAGATCGAAGACATAGCAGATCTGACCTTCAT
46794837 GTGTTTACAT
Statistics
Matches: 189, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
77 1 0.01
78 187 0.99
79 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (78 bp):
TTTGGCATCTCTGTATTAGACGAGGAACAGATCGAAGACATAGCAGATCTGACCTTCATTGAAGC
AGATCCAAGATGA
Found at i:46794929 original size:45 final size:45
Alignment explanation
Indices: 46794865--46795049 Score: 259
Period size: 45 Copynumber: 4.1 Consensus size: 45
46794855 ATCCAAAATG
*
46794865 ACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATA-AGAGATA
1 ACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATAGA-AGATA
* * *
46794910 ACAGATTTGACATCTCTGTATTAGATGGGGAGCAGATTGAAGA-A
1 ACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATAGAAGATA
* * * *
46794954 GCAGATTTGGCGTCTCTGTATTAAACGGGGAGCAGATCGAAGATA
1 ACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATAGAAGATA
46794999 ACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCA-AAGATA
1 ACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGAT-AGAAGATA
46795044 ACAGAT
1 ACAGAT
46795050 GTCGCATTCC
Statistics
Matches: 123, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
44 38 0.31
45 84 0.68
46 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.25
Consensus pattern (45 bp):
ACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATAGAAGATA
Found at i:46794982 original size:89 final size:89
Alignment explanation
Indices: 46794866--46795035 Score: 270
Period size: 89 Copynumber: 1.9 Consensus size: 89
46794856 TCCAAAATGA
*
46794866 CAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATA-AGAGATAACAGATTTGACATCTCTGTA
1 CAGATTTGGCATCTCTGTATTAAACGGGGAGCAAATAGA-AGATAACAGATTTGACATCTCTGTA
*
46794930 TTAGATGGGGAGCAGATTGAAGAAG
65 TTAGACGGGGAGCAGATTGAAGAAG
* * * *
46794955 CAGATTTGGCGTCTCTGTATTAAACGGGGAGCAGATCGAAGATAACAGATTTGGCATCTCTGTAT
1 CAGATTTGGCATCTCTGTATTAAACGGGGAGCAAATAGAAGATAACAGATTTGACATCTCTGTAT
46795020 TAGACGGGGAGCAGAT
66 TAGACGGGGAGCAGAT
46795036 CAAAGATAAC
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
89 73 0.99
90 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (89 bp):
CAGATTTGGCATCTCTGTATTAAACGGGGAGCAAATAGAAGATAACAGATTTGACATCTCTGTAT
TAGACGGGGAGCAGATTGAAGAAG
Found at i:46795079 original size:89 final size:89
Alignment explanation
Indices: 46794877--46795054 Score: 223
Period size: 89 Copynumber: 2.0 Consensus size: 89
46794867 AGATTTGGCA
* * * * *
46794877 TCTCTGTATTAGACGGGGAGCAAAT-AAGAGATAACAGATTTGACATCTCTGTATTAGATGGGGA
1 TCTCTGTATTAAACGGGAAGCAGATCGA-AGATAACAGATTTGACATCTCTGTATTAGACGGGGA
** * * *
46794941 GCAGATTGAAGAAGCAGATTTGGCG
65 GCAGATCAAAGAAACAGATGTCGCG
* *
46794966 TCTCTGTATTAAACGGGGAGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAG
1 TCTCTGTATTAAACGGGAAGCAGATCGAAGATAACAGATTTGACATCTCTGTATTAGACGGGGAG
46795031 CAGATCAAAGATAACAGATGTCGC
66 CAGATCAAAGA-AACAGATGTCGC
46795055 ATTCCTGAGT
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
89 67 0.87
90 10 0.13
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.25
Consensus pattern (89 bp):
TCTCTGTATTAAACGGGAAGCAGATCGAAGATAACAGATTTGACATCTCTGTATTAGACGGGGAG
CAGATCAAAGAAACAGATGTCGCG
Found at i:46798311 original size:40 final size:40
Alignment explanation
Indices: 46798252--46798404 Score: 252
Period size: 40 Copynumber: 3.8 Consensus size: 40
46798242 GAACATTGGA
* *
46798252 ATATATCCGGGTTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
46798292 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
46798332 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
46798372 ATATGTCCGGGTTAAGACCCGAAGGCAAATATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATG
46798405 TTTGCGGCTG
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 107 1.00
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:46806164 original size:40 final size:39
Alignment explanation
Indices: 46806133--46806342 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
46806123 GGACTAAGAT
* *
46806133 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
46806173 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
46806213 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
46806253 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
46806293 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
46806332 CCGAAGGCATT
1 CCGAAGGCATT
46806343 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:46806296 original size:120 final size:120
Alignment explanation
Indices: 46806080--46806342 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
46806070 TTGAATGCTG
* *
46806080 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
46806144 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
46806200 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
46806263 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
46806319 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
46806343 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:46806362 original size:79 final size:80
Alignment explanation
Indices: 46806081--46806377 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
46806071 TGAATGCTGT
* ** * * * **
46806081 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
46806144 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
46806161 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
46806225 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
46806241 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
46806305 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
46806320 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
46806378 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:46819154 original size:2 final size:2
Alignment explanation
Indices: 46819149--46819179 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46819139 GTGTGTGTGT
46819149 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
46819180 GTGGGCATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:46823844 original size:21 final size:21
Alignment explanation
Indices: 46823819--46823862 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
46823809 ATTGGGCTGT
* *
46823819 TACACTCCACCTGTTTTGGAG
1 TACACTCCACCTGCTGTGGAG
46823840 TACACTCCACCTGCTGTGGAG
1 TACACTCCACCTGCTGTGGAG
46823861 TA
1 TA
46823863 TTGCTCGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (21 bp):
TACACTCCACCTGCTGTGGAG
Found at i:46827753 original size:23 final size:23
Alignment explanation
Indices: 46827727--46827775 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
46827717 AATTAAAAAG
46827727 ATGAAAGCATATTAGCTATCATT
1 ATGAAAGCATATTAGCTATCATT
46827750 ATGAAAGCATATTAGCTATCATT
1 ATGAAAGCATATTAGCTATCATT
46827773 ATG
1 ATG
46827776 TTGTTTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (23 bp):
ATGAAAGCATATTAGCTATCATT
Found at i:46828223 original size:14 final size:15
Alignment explanation
Indices: 46828188--46828216 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46828178 ACAAAAATAA
46828188 GAAAAGAAAATGAGG
1 GAAAAGAAAATGAGG
46828203 GAAAAGAAAA-GAGG
1 GAAAAGAAAATGAGG
46828217 TACAAGAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.03
Consensus pattern (15 bp):
GAAAAGAAAATGAGG
Found at i:46831515 original size:23 final size:23
Alignment explanation
Indices: 46831489--46831537 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
46831479 AATTAAAAAG
46831489 ATGAAAGCATATTAGCTATCATT
1 ATGAAAGCATATTAGCTATCATT
46831512 ATGAAAGCATATTAGCTATCATT
1 ATGAAAGCATATTAGCTATCATT
46831535 ATG
1 ATG
46831538 TTGTTTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (23 bp):
ATGAAAGCATATTAGCTATCATT
Found at i:46831627 original size:9 final size:9
Alignment explanation
Indices: 46831615--46831646 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
46831605 ACAAATATTA
46831615 AAAATAAAC
1 AAAATAAAC
46831624 AAAATAAAC
1 AAAATAAAC
46831633 AAAATAAAC
1 AAAATAAAC
46831642 AAAAT
1 AAAAT
46831647 GCACCAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAATAAAC
Found at i:46841264 original size:29 final size:28
Alignment explanation
Indices: 46841208--46841271 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
46841198 TATATATAAC
46841208 TATATTAATTATATTAATGATGAGTAAA
1 TATATTAATTATATTAATGATGAGTAAA
*
46841236 TTATATTAATTA-ATTATTGTAT-AGTTAAA
1 -TATATTAATTATATTAATG-ATGAG-TAAA
46841265 TATATTA
1 TATATTA
46841272 CGTGTGGGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 15 0.47
29 17 0.53
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (28 bp):
TATATTAATTATATTAATGATGAGTAAA
Found at i:46848328 original size:21 final size:22
Alignment explanation
Indices: 46848285--46848342 Score: 84
Period size: 21 Copynumber: 2.7 Consensus size: 22
46848275 GTGGGGGTCA
46848285 ACACGGCCGTGTGAGAGGAGGC
1 ACACGGCCGTGTGAGAGGAGGC
46848307 ACACGGCCGTGTG-GTA-GAGGC
1 ACACGGCCGTGTGAG-AGGAGGC
*
46848328 ACACGCCCGTGTGAG
1 ACACGGCCGTGTGAG
46848343 CCAAGGATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.21, C:0.26, G:0.41, T:0.12
Consensus pattern (22 bp):
ACACGGCCGTGTGAGAGGAGGC
Found at i:46856157 original size:12 final size:12
Alignment explanation
Indices: 46856138--46856168 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
46856128 TCAATAGCTG
46856138 GATGGAGGTGGA
1 GATGGAGGTGGA
*
46856150 GGTGGAGGTGGA
1 GATGGAGGTGGA
46856162 GATGGAG
1 GATGGAG
46856169 ACATGAAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.61, T:0.16
Consensus pattern (12 bp):
GATGGAGGTGGA
Found at i:46856315 original size:24 final size:24
Alignment explanation
Indices: 46856275--46856353 Score: 95
Period size: 24 Copynumber: 3.3 Consensus size: 24
46856265 TTCAAGGCAG
* *
46856275 TGTTGGTACCTCAGTTGGTGGATC
1 TGTTGGTTCCTCGGTTGGTGGATC
*
46856299 TGTTGGTTTCTCGGTTGGTGGATC
1 TGTTGGTTCCTCGGTTGGTGGATC
* * * *
46856323 TATTGGTTCCTCGATTGGTGTACC
1 TGTTGGTTCCTCGGTTGGTGGATC
46856347 TGTTGGT
1 TGTTGGT
46856354 GTCAATGTTA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.09, C:0.15, G:0.33, T:0.43
Consensus pattern (24 bp):
TGTTGGTTCCTCGGTTGGTGGATC
Found at i:46856369 original size:15 final size:15
Alignment explanation
Indices: 46856349--46856399 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
46856339 GGTGTACCTG
*
46856349 TTGGTGTCAATGTTA
1 TTGGTGACAATGTTA
* *
46856364 TTGGTGCCAATGTCA
1 TTGGTGACAATGTTA
46856379 TTGGTGACAATGTTA
1 TTGGTGACAATGTTA
46856394 TTGGTG
1 TTGGTG
46856400 GTATTGGTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.20, C:0.10, G:0.29, T:0.41
Consensus pattern (15 bp):
TTGGTGACAATGTTA
Found at i:46856461 original size:33 final size:34
Alignment explanation
Indices: 46856384--46856465 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 34
46856374 TGTCATTGGT
* *
46856384 GACAATGTTATTGGTGGTATTGGTGGCAAGAACG
1 GACAATGTTATTGGTGGCAATGGTGGCAAGAACG
* * * *
46856418 GA-GATCTTATTGGTGGCAATGGTGGGAATAAC-
1 GACAATGTTATTGGTGGCAATGGTGGCAAGAACG
46856450 GACAATGTTATTGGTG
1 GACAATGTTATTGGTG
46856466 ACACTTCAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
32 2 0.05
33 35 0.90
34 2 0.05
ACGTcount: A:0.27, C:0.09, G:0.34, T:0.30
Consensus pattern (34 bp):
GACAATGTTATTGGTGGCAATGGTGGCAAGAACG
Found at i:46860897 original size:92 final size:92
Alignment explanation
Indices: 46860743--46860950 Score: 204
Period size: 92 Copynumber: 2.3 Consensus size: 92
46860733 CTGCGTATAT
* * * * * * *
46860743 TTATCTGATCTGGCAGTTAAACTGCAATATACCGGTATAGCGGTTTACCGCATCGAATTGTACCG
1 TTATCTGATCTGGCAGTTAAACTGAAATATACCGGTATAACGATTTACCACATCAAACTGTACCA
*
46860808 TATGTACGTTAGCTATGCTACGTACCA
66 CATGTACGTTAGCTATGCTACGTACCA
* * ** *
46860835 TTATCTGATCTGGCAGTTTAATTGTAAAT-TACCGGTATAACGATTTTTCACATTAAACTGTACC
1 TTATCTGATCTGGCAGTTAAACTG-AAATATACCGGTATAACGATTTACCACATCAAACTGTACC
* ** *
46860899 ACATGTACGTTGGCTATATTACGTA-TA
65 ACATGTACGTTAGCTATGCTACGTACCA
* * *
46860926 TATATTTGATTTGGCAGTTCAACTG
1 T-TATCTGATCTGGCAGTTAAACTG
46860951 TATTTTGATA
Statistics
Matches: 93, Mismatches: 21, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
91 2 0.02
92 88 0.95
93 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (92 bp):
TTATCTGATCTGGCAGTTAAACTGAAATATACCGGTATAACGATTTACCACATCAAACTGTACCA
CATGTACGTTAGCTATGCTACGTACCA
Found at i:46867437 original size:24 final size:24
Alignment explanation
Indices: 46867387--46867440 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
46867377 TATTTATTTA
* * *
46867387 ATATTTATTATTTATGAGTATAAT
1 ATATTTAATATTTATGAGCACAAT
* *
46867411 ATATTTAATATTTATTAGCACAGT
1 ATATTTAATATTTATGAGCACAAT
46867435 ATATTT
1 ATATTT
46867441 GACTATAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (24 bp):
ATATTTAATATTTATGAGCACAAT
Found at i:46871676 original size:43 final size:43
Alignment explanation
Indices: 46871615--46871729 Score: 151
Period size: 43 Copynumber: 2.7 Consensus size: 43
46871605 TATCGAGATA
* *
46871615 TGATTACCTGTAAGACCATGTCTGGGGCATTGGCATTGTATTG
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTG
*
46871658 TGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTTAAT-
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATTG-TATTG
* * * *
46871701 CGATTTCGTGTAAGACCCTGTCTGGGACA
1 TGATTACATGTAAGACCATGTCTGGGACA
46871730 AAGGCATCAA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
43 61 0.95
44 3 0.05
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (43 bp):
TGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTG
Found at i:46872488 original size:16 final size:16
Alignment explanation
Indices: 46872467--46872500 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
46872457 ATTGGTTTGT
46872467 TGATGATGAAATGGTA
1 TGATGATGAAATGGTA
46872483 TGATGATGAAATGGTA
1 TGATGATGAAATGGTA
46872499 TG
1 TG
46872501 TTTAAAGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (16 bp):
TGATGATGAAATGGTA
Found at i:46875255 original size:53 final size:53
Alignment explanation
Indices: 46875174--46875381 Score: 323
Period size: 53 Copynumber: 3.9 Consensus size: 53
46875164 GACGAAAAAT
*
46875174 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCA
46875226 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCA
**
46875279 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCA
* * *
46875332 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGT
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGT
46875382 ATGATATGTG
Statistics
Matches: 147, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
51 4 0.03
52 11 0.07
53 132 0.90
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCA
Found at i:46877345 original size:13 final size:13
Alignment explanation
Indices: 46877327--46877356 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
46877317 TGCTCCAGAA
*
46877327 TTTTATTTTTATT
1 TTTTATATTTATT
46877340 TTTTATATTTATT
1 TTTTATATTTATT
46877353 TTTT
1 TTTT
46877357 TGTGTGAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTATATTTATT
Found at i:46878495 original size:22 final size:21
Alignment explanation
Indices: 46878424--46878503 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
46878414 GAAGTAGTAT
46878424 ACGACACATAAAGTGCCTGAA
1 ACGACACATAAAGTGCCTGAA
* ** * *
46878445 ACGACATACGAGGTGCCTAAA
1 ACGACACATAAAGTGCCTGAA
46878466 ACGACACATAAAGTGCCTGAA
1 ACGACACATAAAGTGCCTGAA
* *
46878487 TATGACACATGAAGTGC
1 -ACGACACATAAAGTGC
46878504 GTGATCGGTA
Statistics
Matches: 46, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 32 0.70
22 14 0.30
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (21 bp):
ACGACACATAAAGTGCCTGAA
Found at i:46878656 original size:10 final size:10
Alignment explanation
Indices: 46878641--46878680 Score: 80
Period size: 10 Copynumber: 4.0 Consensus size: 10
46878631 AATCCCACTT
46878641 CACATATTCA
1 CACATATTCA
46878651 CACATATTCA
1 CACATATTCA
46878661 CACATATTCA
1 CACATATTCA
46878671 CACATATTCA
1 CACATATTCA
46878681 TAATTTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (10 bp):
CACATATTCA
Found at i:46878706 original size:13 final size:13
Alignment explanation
Indices: 46878684--46878722 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
46878674 ATATTCATAA
46878684 TTTAATTCATTTT
1 TTTAATTCATTTT
* *
46878697 TTTTATTCATCTT
1 TTTAATTCATTTT
46878710 TTTAATTCATTTT
1 TTTAATTCATTTT
46878723 CCAATCAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTAATTCATTTT
Found at i:46882795 original size:49 final size:50
Alignment explanation
Indices: 46882655--46882800 Score: 197
Period size: 50 Copynumber: 2.9 Consensus size: 50
46882645 AACTATTGTG
* * **
46882655 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTATATCAGATGGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
46882705 AGGTCACGTGTGTAGTACTTAGTGCAGCCTACTACGTGTACC-GAATAATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG-ATAATT
* *
46882755 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
46882801 GCTTCGGCTA
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
49 41 0.49
50 43 0.51
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (50 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:46891140 original size:21 final size:21
Alignment explanation
Indices: 46891116--46891156 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
46891106 TATCAATAAT
46891116 AATAATAATAAT-AATATCTAC
1 AATAAT-ATAATAAATATCTAC
*
46891137 AATAATTTAATAAATATCTA
1 AATAATATAATAAATATCTA
46891157 TTAAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (21 bp):
AATAATATAATAAATATCTAC
Found at i:46891299 original size:32 final size:30
Alignment explanation
Indices: 46891262--46891343 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 30
46891252 ATTATTTAAT
*
46891262 TAATAAATATCT-TTTAACTTAATAATAATAAG
1 TAATAAATATCTATTT-ACTT-A-AATAAAAAG
46891294 TAATAAATATCTATTTACTTAAATAAAAAG
1 TAATAAATATCTATTTACTTAAATAAAAAG
*
46891324 TAATTAAATATTTATGTTAC
1 TAA-TAAATATCTAT-TTAC
46891344 AATTGTATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
30 11 0.24
31 11 0.24
32 20 0.44
33 3 0.07
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (30 bp):
TAATAAATATCTATTTACTTAAATAAAAAG
Found at i:46892433 original size:40 final size:40
Alignment explanation
Indices: 46892389--46892464 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
46892379 ACACATCATG
46892389 TGGGGATAAAATCGACCCACCCAGCCCTACACACCACGTA
1 TGGGGATAAAATCGACCCACCCAGCCCTACACACCACGTA
* *
46892429 TGGGGATAAAATCGACCGATCCAGCCCTACACACCA
1 TGGGGATAAAATCGACCCACCCAGCCCTACACACCA
46892465 AGTGGTACTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.33, C:0.36, G:0.18, T:0.13
Consensus pattern (40 bp):
TGGGGATAAAATCGACCCACCCAGCCCTACACACCACGTA
Found at i:46898470 original size:258 final size:258
Alignment explanation
Indices: 46898010--46898530 Score: 916
Period size: 258 Copynumber: 2.0 Consensus size: 258
46898000 ATTCGGCCTC
* * * *
46898010 ATACTCAGCCACTTAACGGTCTCCTTTAGTAAGATTCAAAAGCTCACGTTGCCTGGTGTCAGTGT
1 ATACTCAGCCACTAAACGGTCTCCCTTAGTAAGATTCAAAAGCTCACGTTGCCTAGCGTCAGTGT
*
46898075 AGCTAGCTCCCATATACTTACTCAGATAGGTGGTCTTAAACAAATCCCAAGTCAACCTATCAGGC
66 AGCTAGCTCCCACATACTTACTCAGATAGGTGGTCTTAAACAAATCCCAAGTCAACCTATCAGGC
* *
46898140 TGAGTATCCTCCTTAATGGTCAACCACCACTGGTATGCCTCATTGCGAAGCAGAGACACAGCCCC
131 TGAGTACCCTCCTTAATGGTCAACCACCACTGGTATGCCTCATCGCGAAGCAGAGACACAGCCCC
* *
46898205 TTTGAGCTTCTGTTCATCAGTAAAATCCAAGTCATCCATTATGCACTCTATGGCCTTCATCCA
196 CTTGAGCTTCTGCTCATCAGTAAAATCCAAGTCATCCATTATGCACTCTATGGCCTTCATCCA
*
46898268 ATACTCAGCCACTAAACGGTCTCCCTTAGTAAGATTCAGAAGCTCACGTTGCCTAGCGTCAGTGT
1 ATACTCAGCCACTAAACGGTCTCCCTTAGTAAGATTCAAAAGCTCACGTTGCCTAGCGTCAGTGT
*
46898333 AGCTAGCTCCCACATACTTACTTAGATAGGTGGTCTTAAACAAATCCCAAGTCAACCTATCAGGC
66 AGCTAGCTCCCACATACTTACTCAGATAGGTGGTCTTAAACAAATCCCAAGTCAACCTATCAGGC
46898398 TGAGTACCCTCCTTAATGGTCAACCACCACTGGTATGCCTCATCGCGAAGCAGAGACACAGCCCC
131 TGAGTACCCTCCTTAATGGTCAACCACCACTGGTATGCCTCATCGCGAAGCAGAGACACAGCCCC
* * *
46898463 CTTGAGCTTCTGCTCATTAGTAAAATCCAAGTCATCCATTATGCGCTCTATGGCCTTTATCCA
196 CTTGAGCTTCTGCTCATCAGTAAAATCCAAGTCATCCATTATGCACTCTATGGCCTTCATCCA
46898526 ATACT
1 ATACT
46898531 TGGCCACACT
Statistics
Matches: 249, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
258 249 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (258 bp):
ATACTCAGCCACTAAACGGTCTCCCTTAGTAAGATTCAAAAGCTCACGTTGCCTAGCGTCAGTGT
AGCTAGCTCCCACATACTTACTCAGATAGGTGGTCTTAAACAAATCCCAAGTCAACCTATCAGGC
TGAGTACCCTCCTTAATGGTCAACCACCACTGGTATGCCTCATCGCGAAGCAGAGACACAGCCCC
CTTGAGCTTCTGCTCATCAGTAAAATCCAAGTCATCCATTATGCACTCTATGGCCTTCATCCA
Found at i:46899863 original size:38 final size:38
Alignment explanation
Indices: 46899821--46899911 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 38
46899811 GTCCAACCCA
46899821 ACACACCATGTGGGGATAAAATCGACCT-ACCCAGCCCT
1 ACACACCATGTGGGGATAAAATCGA-CTGACCCAGCCCT
* * *
46899859 ACACACCAAGTATGGGGATAAAATTGACTGATCCAGCCCT
1 ACACACC-A-TGTGGGGATAAAATCGACTGACCCAGCCCT
* *
46899899 ATACACCAAGTGG
1 ACACACCATGTGG
46899912 TACTGTAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
38 10 0.23
39 4 0.09
40 30 0.68
ACGTcount: A:0.34, C:0.29, G:0.20, T:0.18
Consensus pattern (38 bp):
ACACACCATGTGGGGATAAAATCGACTGACCCAGCCCT
Found at i:46899878 original size:40 final size:40
Alignment explanation
Indices: 46899831--46899909 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
46899821 ACACACCATG
46899831 TGGGGATAAAATCGACCT-ACCCAGCCCTACACACCAAGTA
1 TGGGGATAAAATCGA-CTGACCCAGCCCTACACACCAAGTA
* * *
46899871 TGGGGATAAAATTGACTGATCCAGCCCTATACACCAAGT
1 TGGGGATAAAATCGACTGACCCAGCCCTACACACCAAGT
46899910 GGTACTGTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 2 0.06
40 33 0.94
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (40 bp):
TGGGGATAAAATCGACTGACCCAGCCCTACACACCAAGTA
Found at i:46900458 original size:101 final size:100
Alignment explanation
Indices: 46900276--46900461 Score: 257
Period size: 101 Copynumber: 1.8 Consensus size: 100
46900266 TGCCCGTATA
*
46900276 GATCACACAGCCTAGCCCAAGACCCATACGCCCATGTGGTTCACCCGTGTGACCCACACGCCCGT
1 GATCACACAGCCTAGCCCAAGACCCACACGCCCATGTGGTTCACCCGTGTGACCCACACGCCCGT
* *
46900341 GAGGCCCAAACGGCCCAAATTAGCATTATTCATGTC
66 GAGACACAAAC-GCCCAAATTAGCATTATTCATGTC
* * * * *
46900377 GATCACATAGCCTATCCCAAGACCCACATGCCCGTGTGGTTCCCCCGTGTGACCCACACGCCCGT
1 GATCACACAGCCTAGCCCAAGACCCACACGCCCATGTGGTTCACCCGTGTGACCCACACGCCCGT
*
46900442 GCGACTTACAAA-GCCCAAAT
66 GAGAC--ACAAACGCCCAAAT
46900462 GGTCCAGCTT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
101 70 0.95
103 4 0.05
ACGTcount: A:0.25, C:0.38, G:0.19, T:0.18
Consensus pattern (100 bp):
GATCACACAGCCTAGCCCAAGACCCACACGCCCATGTGGTTCACCCGTGTGACCCACACGCCCGT
GAGACACAAACGCCCAAATTAGCATTATTCATGTC
Done.