Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 186 of 770
Found at i:55713987 original size:40 final size:40
Alignment explanation
Indices: 55713821--55713988 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
55713811 TCTTCAGAAT
* * * *
55713821 TTAG-CCGGATATAACCTCAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* * ** * *
55713860 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
** * *
55713900 TTAGCCCAAATATAA-CAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAATC-ACTAGCACAAATGCCTTCGGGTC
* *
55713940 TTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
55713980 TTAGCCCGG
1 TTAGCCCGG
55713989 GTATCATTCA
Statistics
Matches: 101, Mismatches: 25, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
39 3 0.03
40 97 0.96
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
Found at i:55715996 original size:14 final size:14
Alignment explanation
Indices: 55715974--55716008 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
55715964 TGCCGAGGTA
*
55715974 TTTTCAATTTCTGG
1 TTTTCAATTTCTGC
*
55715988 TTTTTAATTTCTGC
1 TTTTCAATTTCTGC
55716002 TTTTCAA
1 TTTTCAA
55716009 AAAAATCAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGC
Found at i:55716067 original size:91 final size:89
Alignment explanation
Indices: 55715900--55716167 Score: 314
Period size: 87 Copynumber: 3.0 Consensus size: 89
55715890 TATCCTGATA
* *
55715900 TTTTT-ATTTCTGTTTTTC--AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTTGGGCCA
1 TTTTTAATTTCTG-TTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCA
*
55715962 CATGCCGAGGTATTTTCAATTTCTGG
65 CATGCTGAGGTATTTTCAATTTCT-G
* *
55715988 TTTTTAATTTCTGCTTTTCAAAAAAATCAACTCATATTATGAGAGGTGAGTTGAGCCTCAGGTCA
1 TTTTTAATTTCTG-TTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCA
* * *
55716053 TATGCTGAGATATTTTCATTTTCTG
65 CATGCTGAGGTATTTTCAATTTCTG
* * * * * *
55716078 TTTTCAA-TT-T-ATATGAAAAAAGATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGTCA
1 TTTTTAATTTCTGTTTTCAAAAAA-ATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCA
* *
55716140 CATGCTGAGGTATTTTCAGTTTATG
65 CATGCTGAGGTATTTTCAATTTCTG
55716165 TTT
1 TTT
55716168 CAAAAAAATT
Statistics
Matches: 155, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
86 8 0.05
87 60 0.39
88 6 0.04
89 14 0.09
90 7 0.05
91 60 0.39
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.38
Consensus pattern (89 bp):
TTTTTAATTTCTGTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCAC
ATGCTGAGGTATTTTCAATTTCTG
Found at i:55716275 original size:77 final size:77
Alignment explanation
Indices: 55715988--55716472 Score: 564
Period size: 77 Copynumber: 6.1 Consensus size: 77
55715978 CAATTTCTGG
* ** **
55715988 TTTTTAATTTCTGCTTTTCAAAAAAATCAACTCATATTATGAGAGGTGAGTTGAGCCTC-AGGTC
1 TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGA-GTC
* * *
55716052 ATATGCTGAGATA
65 ACACGCTGAGGTA
* * *
55716065 TTTTCATTTTCTGTTTTCAATTTATATGAAAAAAGATCAACTCATATTGCGAGAGGTGAGCTGAG
1 TTTTCAATTTC-----T--ATTT-T-TCAAAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAG
* *
55716130 CCTCGGGTCACATGCTGAGGTA
56 CCTCGAGTCACACGCTGAGGTA
* * *
55716152 TTTTC-AGTT-TATGTTTCAAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCA
1 TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCA
*
55716215 CACGGTGAGGTA
66 CACGCTGAGGTA
*
55716227 TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCA
*
55716292 CACGCCGAGGTA
66 CACGCTGAGGTA
* * * *
55716304 TTTTTCAATTTCTATCTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGGCTCGGGTC
1 -TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTC
55716369 ACACGCTGAGGTA
65 ACACGCTGAGGTA
* *
55716382 TTTTCAATTTCCATTTTTCAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTC-A
1 TTTTCAATTTCTATTTTTC----AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGA
55716446 GGTCACACGCTGAGGTA
62 -GTCACACGCTGAGGTA
55716463 TTTTCAATTT
1 TTTTCAATTT
55716473 TTTTCTTTTT
Statistics
Matches: 353, Mismatches: 36, Indels: 34
0.83 0.09 0.08
Matches are distributed among these distances:
75 52 0.15
76 10 0.03
77 88 0.25
78 76 0.22
80 1 0.00
81 63 0.18
82 1 0.00
84 2 0.01
85 1 0.00
86 9 0.03
87 50 0.14
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (77 bp):
TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCA
CACGCTGAGGTA
Found at i:55716379 original size:155 final size:153
Alignment explanation
Indices: 55716003--55716549 Score: 621
Period size: 155 Copynumber: 3.5 Consensus size: 153
55715993 AATTTCTGCT
* * * * *
55716003 TTTCAAAAAAATCAACTCATATTATGAGAGGTGAGTTGAGCCTCAGGTCATATGCTGAGATATTT
1 TTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTT
* * *
55716068 TCATTTTCTGTTTTCAATTTATATGAAAAAAGATCAACTCATATTGCGAGAGGTGAGCTGAGCCT
66 TCAATTTC-----T--ATTT-T-TCAAAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* * *
55716133 CGGGTCACATGCTGAGGTATTTTC-AGTTTATG
121 CGGGTCACACGCTGAGGTATTTTCAATTTTATC
* * * *
55716165 TTTCAAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACACGGTGAGGTATTT
1 TTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTT
55716230 TCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACAC
66 TCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACAC
*
55716295 GCCGAGGTATTTTTCAATTTCTATC
131 GCTGAGGTA-TTTTCAATTT-TATC
*
55716320 TTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGGCTCGGGTCACACGCTGAGGTATTT
1 TTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTT
* * *
55716385 TCAATTTCCATTTTTCAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTC
66 TCAATTTCTATTTTTC----AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
*
55716450 ACACGCTGAGGTATTTTCAATTTTTTTC
127 ACACGCTGAGGTATTTTCAA-TTTTATC
*** * * * * * * * * *
55716478 TTTTTCAAAGATCAACTCATAATCCAATAGGTGAGTTGAACTTCGGGTCACATC-TTGAGCTATT
1 TTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACA-CGCTGAGGTATT
55716542 TTCAATTT
65 TTCAATTT
55716550 TTTTGTTTTT
Statistics
Matches: 337, Mismatches: 39, Indels: 22
0.85 0.10 0.06
Matches are distributed among these distances:
152 49 0.15
153 12 0.04
154 4 0.01
155 82 0.24
157 1 0.00
158 67 0.20
159 59 0.18
162 63 0.19
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (153 bp):
TTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTT
TCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACAC
GCTGAGGTATTTTCAATTTTATC
Found at i:55716465 original size:236 final size:234
Alignment explanation
Indices: 55715988--55716529 Score: 614
Period size: 236 Copynumber: 2.3 Consensus size: 234
55715978 CAATTTCTGG
* ** * *
55715988 TTTTTAATTTCTGCTTTTCAAAAAAATCAACTCATATTATGAGAGGTGAGTTGAGCCTCAGGTCA
1 TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCA
* * * * * * *
55716053 TATGCTGAGATATTTTCATTTTCTGTTTTCAATTTATATGAAAAAAGATCAACTCATATTGCGAG
66 CACGCCGAGATATTTTCAATTTC----TT-AATCTATATCAAAAAAGATCAACTCATATTACGAG
* * *
55716118 AGGTGAGCTGAGCCTCGGGTCACATGCTGAGGTATTTTCAGTTTATGTTTCAAAAAAATTAACTC
126 AGGTGAGCTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATTTATGTTTCAAAAAAATCAACTC
* *
55716183 ATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACACGGTGAGGTA
191 ATATTGCGAGAGGTGAGTTAAGCCTCGAGTCACACGCTGAGGTA
*
55716227 TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCA
*
55716292 CACGCCGAGGTATTTTTCAATTTC-T-ATCT-T-TCAAAAAA-ATCAACTCATATTACGAGAGGT
66 CACGCCGAGATA-TTTTCAATTTCTTAATCTATATCAAAAAAGATCAACTCATATTACGAGAGGT
* * *
55716352 GAGTTGAGGCTCGGGTCACACGCTGAGGTATTTTCAATTTCCATTTTTCAAAAAAAAAAATCAAC
130 GAGCTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATTT--ATGTTTC----AAAAAAATCAAC
55716417 TCATATTGCGAGAGGTGAGTTAAGCCTC-AGGTCACACGCTGAGGTA
189 TCATATTGCGAGAGGTGAGTTAAGCCTCGA-GTCACACGCTGAGGTA
* * * * * * * * *
55716463 TTTTCAATTTTTTTCTTTTTC--AAAGATCAACTCATAATCCAATAGGTGAGTTGAACTTCGGGT
1 TTTTCAA--TTTCTATTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGT
55716526 CACA
64 CACA
55716530 TCTTGAGCTA
Statistics
Matches: 262, Mismatches: 31, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
230 57 0.22
231 7 0.03
232 7 0.03
233 3 0.01
235 2 0.01
236 99 0.38
238 10 0.04
239 67 0.26
240 10 0.04
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (234 bp):
TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCA
CACGCCGAGATATTTTCAATTTCTTAATCTATATCAAAAAAGATCAACTCATATTACGAGAGGTG
AGCTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATTTATGTTTCAAAAAAATCAACTCATATT
GCGAGAGGTGAGTTAAGCCTCGAGTCACACGCTGAGGTA
Found at i:55716527 original size:77 final size:77
Alignment explanation
Indices: 55716171--55716562 Score: 412
Period size: 77 Copynumber: 5.0 Consensus size: 77
55716161 TATGTTTCAA
* * *
55716171 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACACGGTGAGGTATTTTCAA--
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATT
* *
55716234 TTTCTATTTTTC
66 TTTTTCTTTTTC
*
55716246 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCA
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA-TTTTCA
* * ***
55716311 ATTTCTATCTTTCAA
63 ATTTTTTTCTTTTTC
* *
55716326 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGGCTCGGGTCACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAA-T
******
55716391 TCCATTTTTCAAAAAA
65 T---TTTTTCTTTTTC
* *
55716407 AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATT
55716472 TTTTTCTTTTTC
66 TTTTTCTTTTTC
* * * * * * * * *
55716484 AAAGATCAACTCATAATCCAATAGGTGAGTTGAACTTCGGGTCACATC-TTGAGCTATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA-CGCTGAGGTATTTTCAAT
*
55716548 TTTTTTGTTTTTC
65 TTTTTTCTTTTTC
55716561 AA
1 AA
55716563 TAAAGAATAA
Statistics
Matches: 266, Mismatches: 41, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
77 130 0.49
78 63 0.24
80 8 0.03
81 65 0.24
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (77 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAATT
TTTTTCTTTTTC
Found at i:55716786 original size:30 final size:30
Alignment explanation
Indices: 55716752--55716856 Score: 124
Period size: 30 Copynumber: 3.5 Consensus size: 30
55716742 AAAAAATAAA
*
55716752 AAATTCCATTTTGACCCCTAAACTTTTCCT
1 AAATTTCATTTTGACCCCTAAACTTTTCCT
* * *
55716782 AAATTTCATTTTAACCCCCAAACTTTT-TT
1 AAATTTCATTTTGACCCCTAAACTTTTCCT
* *
55716811 AAATTTCACTTCGACCCCTAAAC-TTTCCTT
1 AAATTTCATTTTGACCCCTAAACTTTTCC-T
*
55716841 AAATTGCATTTTGACC
1 AAATTTCATTTTGACC
55716857 TTCAATTTTC
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
28 3 0.05
29 20 0.33
30 38 0.62
ACGTcount: A:0.29, C:0.28, G:0.04, T:0.40
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTTCCT
Found at i:55716827 original size:29 final size:29
Alignment explanation
Indices: 55716764--55716845 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
55716754 ATTCCATTTT
* * *
55716764 GACCCCTAAACTTTTCCTAAATTTCATTTT
1 GACCCCTAAACTTTT-TTAAATTTCACTTC
* *
55716794 AACCCCCAAACTTTTTTAAATTTCACTTC
1 GACCCCTAAACTTTTTTAAATTTCACTTC
*
55716823 GACCCCTAAACTTTCCTTAAATT
1 GACCCCTAAACTTT-TTTAAATT
55716846 GCATTTTGAC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 23 0.53
30 20 0.47
ACGTcount: A:0.29, C:0.29, G:0.02, T:0.39
Consensus pattern (29 bp):
GACCCCTAAACTTTTTTAAATTTCACTTC
Found at i:55716874 original size:59 final size:60
Alignment explanation
Indices: 55716750--55716880 Score: 135
Period size: 59 Copynumber: 2.2 Consensus size: 60
55716740 TTAAAAAATA
* * * *
55716750 AAAAATTCCATTTTGACCCCTAAACTTTTCCTAAATTTCATTTTAACCCCCAAACTTTTT
1 AAAAATTACACTTCGACCCCTAAACTTTTCCTAAATTGCATTTTAACCCCCAAACTTTTT
* * * **
55716810 -TAAATTTCACTTCGACCCCTAAAC-TTTCCTTAAATTGCATTTTGACCTTC-AA-TTTTCT
1 AAAAATTACACTTCGACCCCTAAACTTTTCC-TAAATTGCATTTTAACCCCCAAACTTTT-T
55716868 AAAAATTACACTT
1 AAAAATTACACTT
55716881 TGGTCCCAGA
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
57 4 0.07
58 8 0.14
59 46 0.79
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.40
Consensus pattern (60 bp):
AAAAATTACACTTCGACCCCTAAACTTTTCCTAAATTGCATTTTAACCCCCAAACTTTTT
Found at i:55718375 original size:17 final size:17
Alignment explanation
Indices: 55718355--55718479 Score: 54
Period size: 18 Copynumber: 7.1 Consensus size: 17
55718345 TATAAAAAAA
55718355 TTCGGGTTTCAAAAATT
1 TTCGGGTTTCAAAAATT
** *
55718372 TTCGTATTTTAAAAAATT
1 TTCG-GGTTTCAAAAATT
*** ***
55718390 TTCATCTTTTTTAAATT
1 TTCGGGTTTCAAAAATT
*
55718407 TATCGGGTTTCAAAGATT
1 T-TCGGGTTTCAAAAATT
* * *
55718425 CTCAGGTTTTCAAGAATT
1 TTC-GGGTTTCAAAAATT
* *
55718443 TTTGTGTTTTC-AAAATCT
1 TTCG-GGTTTCAAAAAT-T
*
55718461 CTCGGGTTTCAAAAATT
1 TTCGGGTTTCAAAAATT
55718478 TT
1 TT
55718480 TTTTCGAGTT
Statistics
Matches: 75, Mismatches: 27, Indels: 12
0.66 0.24 0.11
Matches are distributed among these distances:
17 27 0.36
18 48 0.64
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (17 bp):
TTCGGGTTTCAAAAATT
Found at i:55723469 original size:43 final size:43
Alignment explanation
Indices: 55723357--55723512 Score: 161
Period size: 43 Copynumber: 3.6 Consensus size: 43
55723347 CAATGCCCTA
* * * * * *
55723357 TCCCAGATATGGTCTTACATGTCATCCTATATCGATGCCACTG
1 TCCCAGACATGGTCTTACACGTAATCATATAACGATGCCAATG
* * * **
55723400 TGCTAGACAGGGTCTTACACAAAATCATATAACGATGCCAATG
1 TCCCAGACATGGTCTTACACGTAATCATATAACGATGCCAATG
* * *
55723443 TCCCATACATGGTCTTACACGTAATCACA-ATACAATGCCAATG
1 TCCCAGACATGGTCTTACACGTAATCATATA-ACGATGCCAATG
*
55723486 TCCCAGACATGGTCTTACATGTAATCA
1 TCCCAGACATGGTCTTACACGTAATCA
55723513 CATCTCGGTA
Statistics
Matches: 91, Mismatches: 21, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 1 0.01
43 90 0.99
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGTAATCATATAACGATGCCAATG
Found at i:55727894 original size:46 final size:46
Alignment explanation
Indices: 55727844--55728019 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
55727834 ATGGTTGGCA
55727844 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
55727890 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
55727937 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
55727983 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
55728020 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:55727999 original size:93 final size:93
Alignment explanation
Indices: 55727840--55728011 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
55727830 TAGGATGGTT
* *
55727840 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
55727905 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
55727933 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
55727998 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
55728012 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:55730497 original size:15 final size:15
Alignment explanation
Indices: 55730458--55730536 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
55730448 GTATCTTGGG
*
55730458 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
55730473 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
55730488 TTTCTTTATTC-GGG
1 TTTCTTTATTCTGGA
*
55730502 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
55730517 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
55730531 TTTCTT
1 TTTCTT
55730537 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.04
14 17 0.32
15 32 0.60
16 2 0.04
ACGTcount: A:0.10, C:0.18, G:0.14, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:55730521 original size:29 final size:29
Alignment explanation
Indices: 55730449--55730535 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
55730439 CATAGTATCG
* * * *
55730449 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTC-GGATTTCTC
*
55730479 TAT-TCTGGATTTCTTTATTCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCGGATTTCTC
*
55730508 TATCTTGGATTTCTTTATTCGGTTTTCT
1 TATCTTGGATTTCTTTATTCGGATTTCT
55730536 TGTTATCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 32 0.65
30 17 0.35
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.56
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCGGATTTCTC
Found at i:55732967 original size:46 final size:46
Alignment explanation
Indices: 55732912--55733092 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
55732902 TAGGATGGTT
55732912 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
55732958 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
55733004 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
55733051 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
55733093 GCGGGTTACA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 71 0.61
47 33 0.28
48 2 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:55733073 original size:93 final size:93
Alignment explanation
Indices: 55732914--55733084 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
55732904 GGATGGTTGA
* *
55732914 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
55732979 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
55733007 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
55733072 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
55733085 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:55735958 original size:9 final size:9
Alignment explanation
Indices: 55735925--55735990 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
55735915 TGTAAATTTT
55735925 TTATAAAAA
1 TTATAAAAA
55735934 -TATAAAAA
1 TTATAAAAA
*
55735942 -TAT--TAA
1 TTATAAAAA
55735948 TTATAAAAA
1 TTATAAAAA
55735957 TTATAATAAA
1 TTATAA-AAA
* *
55735967 TGAAAAATAA
1 TTATAAA-AA
*
55735977 TTGTAAAAA
1 TTATAAAAA
55735986 TTATA
1 TTATA
55735991 TAGAGAATTG
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
6 2 0.05
7 3 0.07
8 11 0.25
9 15 0.34
10 13 0.30
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:55736077 original size:30 final size:30
Alignment explanation
Indices: 55736015--55736078 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
55736005 GAAAATATTT
** *
55736015 AAAAATATCTAAAATAGTATAAAATAAGAA
1 AAAAATATCTAAAATAACATAAAATAACAA
*
55736045 AAAAATAT-TAAAATAACATATAAATTACAA
1 AAAAATATCTAAAATAACATA-AAATAACAA
55736075 AAAA
1 AAAA
55736079 TATAACAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (30 bp):
AAAAATATCTAAAATAACATAAAATAACAA
Found at i:55736110 original size:10 final size:9
Alignment explanation
Indices: 55736066--55736131 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 9
55736056 AATAACATAT
*
55736066 AAATTACAA
1 AAATTATAA
*
55736075 AAAATATAA
1 AAATTATAA
*
55736084 CAAATTGTAA
1 -AAATTATAA
55736094 AAATTATAA
1 AAATTATAA
55736103 AAATTTATTTAA
1 AAA-TTA--TAA
*
55736115 AAACTATAAA
1 AAATTAT-AA
55736125 AAATTAT
1 AAATTAT
55736132 TAAACATATT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
9 19 0.42
10 18 0.40
11 2 0.04
12 6 0.13
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (9 bp):
AAATTATAA
Found at i:55736117 original size:21 final size:19
Alignment explanation
Indices: 55736074--55736155 Score: 78
Period size: 19 Copynumber: 4.2 Consensus size: 19
55736064 ATAAATTACA
55736074 AAAAATATAACAAATTGTA--
1 AAAAATATAA-AAATT-TATT
*
55736093 AAAATTATAAAAATTTATTT
1 AAAAATATAAAAATTTA-TT
*
55736113 AAAAACTATAAAAAATTATT
1 AAAAA-TATAAAAATTTATT
* *
55736133 AAACATATTAAAATTTATT
1 AAAAATATAAAAATTTATT
55736152 AAAA
1 AAAA
55736156 TTTACAATGT
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
17 2 0.04
18 5 0.10
19 24 0.46
20 10 0.19
21 11 0.21
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (19 bp):
AAAAATATAAAAATTTATT
Found at i:55736117 original size:40 final size:39
Alignment explanation
Indices: 55736073--55736155 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 39
55736063 TATAAATTAC
*
55736073 AAAAAATATAACAAATT-GTAAAAATTATAAAAATTTATTT
1 AAAAAATATAAAAAATTAGTAAAAA-TATAAAAATTTA-TT
* * * *
55736113 AAAAACTATAAAAAATTATTAAACATATTAAAATTTATT
1 AAAAAATATAAAAAATTAGTAAAAATATAAAAATTTATT
55736152 AAAA
1 AAAA
55736156 TTTACAATGT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 6 0.16
40 26 0.70
41 5 0.14
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (39 bp):
AAAAAATATAAAAAATTAGTAAAAATATAAAAATTTATT
Found at i:55736150 original size:19 final size:20
Alignment explanation
Indices: 55736091--55736155 Score: 78
Period size: 21 Copynumber: 3.2 Consensus size: 20
55736081 TAACAAATTG
*
55736091 TAAAAATTATAAAAATTTATT
1 TAAAAACTATAAAAATTTA-T
*
55736112 TAAAAACTATAAAAAATTAT
1 TAAAAACTATAAAAATTTAT
* *
55736132 TAAACA-TATTAAAATTTAT
1 TAAAAACTATAAAAATTTAT
55736151 TAAAA
1 TAAAA
55736156 TTTACAATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.39
20 6 0.16
21 17 0.45
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAACTATAAAAATTTAT
Found at i:55736159 original size:10 final size:10
Alignment explanation
Indices: 55736091--55736155 Score: 62
Period size: 10 Copynumber: 6.5 Consensus size: 10
55736081 TAACAAATTG
55736091 TAAAAATTA-
1 TAAAAATTAT
55736100 TAAAAATTTATT
1 TAAAAA-TTA-T
*
55736112 TAAAAACTAT
1 TAAAAATTAT
*
55736122 AAAAAATTAT
1 TAAAAATTAT
*
55736132 TAAACA-TAT
1 TAAAAATTAT
*
55736141 TAAAATTTAT
1 TAAAAATTAT
55736151 TAAAA
1 TAAAA
55736156 TTTACAATGT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
9 13 0.29
10 24 0.53
11 2 0.04
12 6 0.13
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:55740098 original size:51 final size:51
Alignment explanation
Indices: 55740035--55740134 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 51
55740025 CTACCACATA
* *
55740035 ACATGTAACACATCC-CTAATGAACTCGGACCTCTCAACGAGTTCGGATGTT
1 ACATGTAACACATCCAC-AATGAACTCAGACCTCTCAACGAGCTCGGATGTT
* *
55740086 ACATG-AATCACATCCACCATGAACTTAGACCTCTCAACGAGCTCGGATG
1 ACATGTAA-CACATCCACAATGAACTCAGACCTCTCAACGAGCTCGGATG
55740135 CTTGCATCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
50 2 0.05
51 40 0.93
52 1 0.02
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (51 bp):
ACATGTAACACATCCACAATGAACTCAGACCTCTCAACGAGCTCGGATGTT
Found at i:55740402 original size:25 final size:22
Alignment explanation
Indices: 55740374--55740427 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 22
55740364 AACAATCAAT
55740374 AAGCATATAATTCATAATTATAATA
1 AAGCAT-TAA-TCAT-ATTATAATA
* *
55740399 AAGCATTTATCATATTATATTA
1 AAGCATTAATCATATTATAATA
55740421 AAGCATT
1 AAGCATT
55740428 TAAAACATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 15 0.56
23 4 0.15
24 2 0.07
25 6 0.22
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (22 bp):
AAGCATTAATCATATTATAATA
Found at i:55740417 original size:22 final size:23
Alignment explanation
Indices: 55740385--55740429 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
55740375 AGCATATAAT
55740385 TCATAATTATAATAAAGCATTTA
1 TCATAATTATAATAAAGCATTTA
*
55740408 TCAT-ATTATATTAAAGCATTTA
1 TCATAATTATAATAAAGCATTTA
55740430 AAACATACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (23 bp):
TCATAATTATAATAAAGCATTTA
Found at i:55756054 original size:17 final size:18
Alignment explanation
Indices: 55756027--55756060 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55756017 AATTAAATAT
55756027 ATGCATATTAAATTATTA
1 ATGCATATTAAATTATTA
*
55756045 ATGC-TATTAATTTATT
1 ATGCATATTAAATTATT
55756061 TAAAACAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
ATGCATATTAAATTATTA
Found at i:55766369 original size:21 final size:21
Alignment explanation
Indices: 55766345--55766386 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
55766335 TCTTTGACGT
55766345 ATTCATCAAGATTTCTTATTG
1 ATTCATCAAGATTTCTTATTG
55766366 ATTCATCAAGATTTCTTATTG
1 ATTCATCAAGATTTCTTATTG
55766387 TACTTCTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.48
Consensus pattern (21 bp):
ATTCATCAAGATTTCTTATTG
Found at i:55772631 original size:14 final size:16
Alignment explanation
Indices: 55772597--55772636 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
55772587 TTAAACATAT
55772597 ATATATCATCTATTTC
1 ATATATCATCTATTTC
*
55772613 CTATATCA-CT-TTTC
1 ATATATCATCTATTTC
55772627 ATATATCATC
1 ATATATCATC
55772637 GTTTTCTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 11 0.52
15 3 0.14
16 7 0.33
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATATCATCTATTTC
Found at i:55774860 original size:15 final size:15
Alignment explanation
Indices: 55774835--55774905 Score: 79
Period size: 15 Copynumber: 4.7 Consensus size: 15
55774825 GAAATGACAT
*
55774835 GAAAACCAAGACAAA
1 GAAATCCAAGACAAA
*
55774850 GAAGTCCAAGACAAA
1 GAAATCCAAGACAAA
* *
55774865 GAAATCCTAGATAAA
1 GAAATCCAAGACAAA
* *
55774880 GAAATCCAAGATACA
1 GAAATCCAAGACAAA
*
55774895 GAAATCTAAGA
1 GAAATCCAAGA
55774906 TAAAATATCA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 48 1.00
ACGTcount: A:0.56, C:0.17, G:0.15, T:0.11
Consensus pattern (15 bp):
GAAATCCAAGACAAA
Found at i:55776173 original size:29 final size:27
Alignment explanation
Indices: 55776102--55776181 Score: 67
Period size: 29 Copynumber: 2.9 Consensus size: 27
55776092 TGGATTATGT
* *
55776102 AGAAAGAATAAAGAAATGAAAAAAAAA
1 AGAAAAAAGAAAGAAATGAAAAAAAAA
*
55776129 AGAAAAAAAGAGAGAATATGAAGAAAAACAA
1 AG-AAAAAAGAAAGAA-ATGAA-AAAAA-AA
*
55776160 AG-AAAAGGAAAGAAA--AAAAAAA
1 AGAAAAAAGAAAGAAATGAAAAAAA
55776182 GTGTTCATTC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
25 5 0.11
26 2 0.05
27 2 0.05
28 11 0.25
29 15 0.34
30 5 0.11
31 4 0.09
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.05
Consensus pattern (27 bp):
AGAAAAAAGAAAGAAATGAAAAAAAAA
Found at i:55777373 original size:29 final size:29
Alignment explanation
Indices: 55777340--55777471 Score: 138
Period size: 29 Copynumber: 4.6 Consensus size: 29
55777330 GTGACGAGAT
55777340 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* *
55777369 TGGCACTAAGTGTGCATGCTGAAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * *
55777398 TGGCACTAACTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* ** * * ***
55777427 CGGCACTGGGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
55777456 TGGCACTATGTGTGCG
1 TGGCACTAAGTGTGCG
55777472 GGCTTAAATT
Statistics
Matches: 85, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 85 1.00
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:55782237 original size:40 final size:40
Alignment explanation
Indices: 55782171--55782321 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
55782161 AAATTGAATG
* *
55782171 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
* * ****
55782210 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
* *
55782250 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GAAATT
* *
55782290 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
55782322 ACGTGGTTAT
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
39 16 0.18
40 72 0.80
41 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
Found at i:55782335 original size:40 final size:40
Alignment explanation
Indices: 55782208--55782337 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
55782198 ATGCTGGAAA
* * *
55782208 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * ***
55782248 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGACA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
55782288 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
55782328 TTATATCCGG
1 TTATATCCGG
55782338 TTATATTCCG
Statistics
Matches: 72, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 1 0.01
40 71 0.99
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:55782336 original size:80 final size:79
Alignment explanation
Indices: 55782171--55782337 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
55782161 AAATTGAATG
*
55782171 ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCAA
1 ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAA
55782236 TTGTGCTAGTGGCT
66 TTGTGCTAGTGGCT
* * * * *
55782250 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATTCTATCCGGGCTAAGACCCGAAGG
1 ATATCCGGGCTAAG-CCCGAAGACAATT-ATGCTG-GAAATTATATCCGGGCTAAGACCCGAAGG
* *
55782313 CATTTGTGC-ACGTGGTT
63 CAATTGTGCTA-GTGGCT
55782330 ATATCCGG
1 ATATCCGG
55782338 TTATATTCCG
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
79 18 0.24
80 57 0.76
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (79 bp):
ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCTAGTGGCT
Found at i:55789734 original size:40 final size:40
Alignment explanation
Indices: 55789679--55789894 Score: 316
Period size: 40 Copynumber: 5.5 Consensus size: 40
55789669 TGGATGATAA
* *
55789679 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
55789719 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
55789759 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
55789798 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
55789838 CCGGGCTATGTCCCGAAGGCATTCGAGC-AG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
55789877 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
55789895 TACTTGGCTT
Statistics
Matches: 165, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
38 15 0.09
39 50 0.30
40 100 0.61
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:55789811 original size:79 final size:79
Alignment explanation
Indices: 55789679--55789894 Score: 314
Period size: 79 Copynumber: 2.7 Consensus size: 79
55789669 TGGATGATAA
*
55789679 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAGT-TCCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AGTTACTA-TATCCGGGCTAAGTCCCGAAGGCATTT
55789743 GTGCGAGTTACTATAT
64 GTGCGAGTTACTATAT
55789759 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
55789823 TGCGAGTTACTATAT
65 TGCGAGTTACTATAT
* * * * *
55789838 CCGGGCTATGTCCCGAAGGCATTCGAGCAG-TAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAGTTA-CTATATCCGGGCTAAGTCCCGAAGG
55789895 TACTTGGCTT
Statistics
Matches: 126, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
78 17 0.13
79 84 0.67
80 25 0.20
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
GCGAGTTACTATAT
Found at i:55797929 original size:40 final size:40
Alignment explanation
Indices: 55797872--55798089 Score: 289
Period size: 40 Copynumber: 5.5 Consensus size: 40
55797862 TGGATGATAA
* * *
55797872 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
* *
55797912 CTGGGCTCAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
55797952 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
55797992 CCGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
55798032 CCGGGCTATGTCCCGAAGGCATTCGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
55798072 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
55798090 TACTTGGCTT
Statistics
Matches: 160, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 16 0.10
40 144 0.90
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:55806375 original size:24 final size:24
Alignment explanation
Indices: 55806347--55806422 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
55806337 GAACATGAGT
55806347 ATGTGTGATAAGGCCAAATGGCCA
1 ATGTGTGATAAGGCCAAATGGCCA
* **
55806371 ATGTGATGA-ATGTG--AACAT-GCGT
1 ATGTG-TGATAAG-GCCAA-ATGGCCA
*
55806394 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCAAATGGCCA
55806418 ATGTG
1 ATGTG
55806423 ATGGATGTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 14
0.64 0.12 0.24
Matches are distributed among these distances:
22 4 0.11
23 13 0.34
24 17 0.45
25 4 0.11
ACGTcount: A:0.30, C:0.13, G:0.32, T:0.25
Consensus pattern (24 bp):
ATGTGTGATAAGGCCAAATGGCCA
Found at i:55806375 original size:47 final size:47
Alignment explanation
Indices: 55806324--55806804 Score: 651
Period size: 47 Copynumber: 10.1 Consensus size: 47
55806314 TTAGGATTTT
* * *
55806324 ATGTGTTGGATGTGAACATGAGTATGTGTGATAAGGCCAAATGGCCA
1 ATGTGATGAATGTGAACATGAGTATGTGTGATAAGGCCGAATGGCCA
*
55806371 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGAGTATGTGTGATAAGGCCGAATGGCCA
* *
55806418 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGAGTATGTGTGATAAGGCCGAATGGCCA
* *
55806465 ATGTGATGAATGTGAACCCGTAT-ATATATGTGTGATAAGGCCAAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGA-GTATGTGTGATAAGGCCGAATGGCCA
* *
55806516 ATGTGATGAATGTGAACATGCGTATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGAGTATGTGTGATAAGGCCGAATGGCCA
* * * *
55806563 ATGCGATGAATGTGAACCTGTATATATATGCGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATG---A-GTATGTGTGATAAGGCCGAATGGCCA
*
55806614 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGAGTATGTGTGATAAGGCCGAATGGCCA
*
55806661 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGAGTATGTGTGATAAGGCCGAATGGCCA
* * *
55806708 ATGTGATGAATGTGAACATGCA-TATATGAGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATG-AGTATGTGTGATAAGGCCGAATGGCCA
* * * *
55806755 ATGTGATGAATGTGAACATGAATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGAGTATGTGTGATAAGGCCGAATGGCCA
55806802 ATG
1 ATG
55806805 CGAAACGTGT
Statistics
Matches: 390, Mismatches: 32, Indels: 24
0.87 0.07 0.05
Matches are distributed among these distances:
46 1 0.00
47 304 0.78
49 2 0.01
51 83 0.21
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGAGTATGTGTGATAAGGCCGAATGGCCA
Found at i:55806503 original size:145 final size:143
Alignment explanation
Indices: 55806346--55806804 Score: 667
Period size: 145 Copynumber: 3.2 Consensus size: 143
55806336 TGAACATGAG
55806346 TATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA
1 TATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA
* *
55806411 ATGGCCAATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAAT
66 ATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAT
55806476 GTGAACCCGTATATA
131 GTGAA-CCG-ATATA
*
55806491 TATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAACATGCGTATATGTGATAAGGCCGA
1 TATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA
* ** *
55806556 ATGGCCAATGCGATGAATGTGAACCTGTATATATATGCGTGATAAGGCCGAATGGCCAATGTGAT
66 ATGGCCAATGTGATGAATGTGAA-C---ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGAT
***
55806621 GAATGTGAA-C-ATGCG
127 GAATGTGAACCGATATA
*
55806636 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA
1 TATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA
* * *
55806701 ATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCTGAATGGCCAATGTGATGAAT
66 ATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAT
*
55806766 GTGAACATGA-ATA
131 GTGAAC-CGATATA
* *
55806779 TATGTG-G-TAAGGCCGAATGGCTAATG
1 TATGTGTGATAAGGCCAAATGGCCAATG
55806805 CGAAACGTGT
Statistics
Matches: 283, Mismatches: 24, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
141 58 0.20
142 1 0.00
143 6 0.02
144 2 0.01
145 172 0.61
146 1 0.00
147 1 0.00
149 42 0.15
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.26
Consensus pattern (143 bp):
TATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGA
ATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAT
GTGAACCGATATA
Found at i:55806534 original size:98 final size:96
Alignment explanation
Indices: 55806324--55806804 Score: 679
Period size: 98 Copynumber: 5.0 Consensus size: 96
55806314 TTAGGATTTT
* * * *
55806324 ATGTGTTGGATGTGAACATGAGTATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAA-C
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
***
55806388 -ATGCGTATGTGTGATAAGGCCGAATGGCCA
66 GATATATATGTGTGATAAGGCCGAATGGCCA
*
55806418 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-C
*
55806483 CGTATATATATGTGTGATAAGGCCAAATGGCCA
65 CG-ATATATATGTGTGATAAGGCCGAATGGCCA
* *
55806516 ATGTGATGAATGTGAACATGCGTATATGTGATAAGGCCGAATGGCCAATGCGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
*
55806581 TGTATATATATGCGTGATAAGGCCGAATGGCCA
66 -G-ATATATATGTGTGATAAGGCCGAATGGCCA
55806614 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-C
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
***
55806678 -ATGCGTATGTGTGATAAGGCCGAATGGCCA
66 GATATATATGTGTGATAAGGCCGAATGGCCA
* * * *
55806708 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCTGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC-
* *
55806773 TGA-ATATATGTG-G-TAAGGCCGAATGGCTA
65 CGATATATATGTGTGATAAGGCCGAATGGCCA
55806802 ATG
1 ATG
55806805 CGAAACGTGT
Statistics
Matches: 352, Mismatches: 27, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
94 163 0.46
95 1 0.00
96 7 0.02
97 4 0.01
98 177 0.50
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.26
Consensus pattern (96 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
GATATATATGTGTGATAAGGCCGAATGGCCA
Found at i:55806641 original size:23 final size:23
Alignment explanation
Indices: 55806614--55806688 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
55806604 CGAATGGCCA
55806614 ATGTGATGAATGTGAACATGCGT
1 ATGTGATGAATGTGAACATGCGT
* * **
55806637 ATGTG-TGATAAG-G-CCGAATGGCCA
1 ATGTGATGA-ATGTGAAC--AT-GCGT
55806661 ATGTGATGAATGTGAACATGCGT
1 ATGTGATGAATGTGAACATGCGT
55806684 ATGTG
1 ATGTG
55806689 TGATAAGGCC
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
21 1 0.03
22 4 0.11
23 16 0.43
24 11 0.30
25 4 0.11
26 1 0.03
ACGTcount: A:0.29, C:0.11, G:0.32, T:0.28
Consensus pattern (23 bp):
ATGTGATGAATGTGAACATGCGT
Found at i:55806862 original size:46 final size:46
Alignment explanation
Indices: 55806778--55806868 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
55806768 GAACATGAAT
* * *
55806778 ATATGTGGTAAGGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
* ** *
55806824 ATATGTGGTAAAGCCAAATGGCTAATGTGGGATATGTATGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATG
55806869 TGTATATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.32, C:0.09, G:0.33, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
Found at i:55806875 original size:141 final size:140
Alignment explanation
Indices: 55806324--55806860 Score: 537
Period size: 145 Copynumber: 3.8 Consensus size: 140
55806314 TTAGGATTTT
* * * * * * *
55806324 ATGTGTTGGATGTGAACATGAGTATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGAATATATGTGATAAGGCCGAATGGCCAATGCGA-GAACGTGAACA
* * * * *
55806389 TGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGG-ATGTGAACATGCGTATGTGTGATAAG
65 TGCGTATGTGTGATAAAGCCAAATGGCCAATGTGA-GGAATGTGAACATGCATATATGAGATAAG
55806453 GCCGAATGGCCA
129 GCCGAATGGCCA
** * * *
55806465 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTG
1 ATGTGATGAATGTGAACATG-A-ATATA--TGTGATAAGGCCGAATGGCCAATGCGA-GAACGTG
* * * * * * *
55806530 AACATGCGTATATGTGATAAGGCCGAATGGCCAATGCGATGAATGTGAACCTGTATATATATGCG
61 AACATGCGTATGTGTGATAAAGCCAAATGGCCAATGTGAGGAATGTGAACATG--CATATAT--G
*
55806595 TGATAAGGCCGAATGGCCA
122 AGATAAGGCCGAATGGCCA
** * * *
55806614 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGAATATATGTGATAAGGCCGAATGGCCAATGCGA-GAACGTGAACA
* * *
55806679 TGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGG
65 TGCGTATGTGTGATAAAGCCAAATGGCCAATGTGAGGAATGTGAACATGCATATATGAGATAAGG
*
55806744 CTGAATGGCCA
130 CCGAATGGCCA
* *
55806755 ATGTGATGAATGTGAACATGAATATATGTGGTAAGGCCGAATGGCTAATGCGA-AACGTGTATGA
1 ATGTGATGAATGTGAACATGAATATATGTGATAAGGCCGAATGGCCAATGCGAGAACGTG-A--A
* *
55806819 GATG-GATATGTG-G-TAAAGCCAAATGGCTAATGTG-GGATATGT
63 CATGCG-TATGTGTGATAAAGCCAAATGGCCAATGTGAGGA-ATGT
55806861 ATGAGATGTG
Statistics
Matches: 345, Mismatches: 37, Indels: 29
0.84 0.09 0.07
Matches are distributed among these distances:
139 7 0.02
140 23 0.07
141 83 0.24
142 11 0.03
143 9 0.03
144 1 0.00
145 166 0.48
147 7 0.02
149 38 0.11
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.26
Consensus pattern (140 bp):
ATGTGATGAATGTGAACATGAATATATGTGATAAGGCCGAATGGCCAATGCGAGAACGTGAACAT
GCGTATGTGTGATAAAGCCAAATGGCCAATGTGAGGAATGTGAACATGCATATATGAGATAAGGC
CGAATGGCCA
Found at i:55807064 original size:37 final size:37
Alignment explanation
Indices: 55807014--55807121 Score: 171
Period size: 37 Copynumber: 2.9 Consensus size: 37
55807004 GGAAATATAT
55807014 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
55807051 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * * *
55807088 TCTGGGTAAGACCCGATAACTTCATGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
55807122 TCGTCTGAGC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:55809709 original size:20 final size:19
Alignment explanation
Indices: 55809684--55809721 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
55809674 ATACAGAAAC
55809684 CATGCAATAAAATGTAAAAT
1 CATGCAA-AAAATGTAAAAT
*
55809704 CATGCAAGAAATGTAAAA
1 CATGCAAAAAATGTAAAA
55809722 GTAAGAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.55, C:0.11, G:0.13, T:0.21
Consensus pattern (19 bp):
CATGCAAAAAATGTAAAAT
Found at i:55816630 original size:48 final size:46
Alignment explanation
Indices: 55816541--55816760 Score: 178
Period size: 46 Copynumber: 4.7 Consensus size: 46
55816531 TTTATGGGCT
* * * *
55816541 AGTGTAAGACGTGTCTGGTACATGCATCAGCCA-C-ATTATGAGAGAC
1 AGTGTAAGACATGTCTGGGACATGCATC-GGCATCGA-GATGAGAGAC
* * *
55816587 AGTGTAAGACCATGTGTGGGACATGGCATCGGCATCGAGATGAGTGAT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGATGAGAGAC
* * *
55816635 AGTGTAAGACATGTCTGGGACATGCATCGACATCGAGACGTA-AGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGATG-AGAGAC
* * * * * *
55816681 AGTGTAAGACATGTTTGGGATATGCATCGGC-TACGGGTTGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCAT-CGAGATGAGAGAC
* *
55816727 AGGGTACGACCATGTCTGGGACATGGCATCGGCA
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA
55816761 CCTTAATGAA
Statistics
Matches: 141, Mismatches: 23, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
45 2 0.01
46 68 0.48
47 40 0.28
48 30 0.21
49 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGATGAGAGAC
Found at i:55820641 original size:29 final size:29
Alignment explanation
Indices: 55820607--55820711 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 29
55820597 TACTCGATTT
* * *
55820607 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATACCATTCAAGCC
** * * *
55820636 CGCACACACAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * *
55820665 CGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
*
55820694 TGCACACTTAGTGCCATA
1 CGCACACTTAGTGCCATA
55820712 TATTTCCAGC
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACCATTCAAGCC
Found at i:55820699 original size:58 final size:59
Alignment explanation
Indices: 55820645--55820767 Score: 178
Period size: 58 Copynumber: 2.1 Consensus size: 59
55820635 CCGCACACAC
* *
55820645 AGTGCCATACCCTTCGAGC-TCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
1 AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
* * * *
55820703 AGTGCCATATATTTCCAGCAT-GCACACTCAGTGCCATATTTTTCCAGCATGCACACTT
1 AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
55820761 AGTGCCA
1 AGTGCCA
55820768 ATCTCGTCAC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 57 0.98
59 1 0.02
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.28
Consensus pattern (59 bp):
AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
Found at i:55820712 original size:29 final size:29
Alignment explanation
Indices: 55820666--55820767 Score: 186
Period size: 29 Copynumber: 3.5 Consensus size: 29
55820656 CTTCGAGCTC
55820666 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
55820695 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
* *
55820724 GCACACTCAGTGCCATATTTTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
55820753 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
55820768 ATCTCGTCAC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:55828606 original size:29 final size:29
Alignment explanation
Indices: 55828572--55828676 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 29
55828562 TACTCGATTT
* * *
55828572 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATACCATTCAAGCC
** * * *
55828601 CGCACACACAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * *
55828630 CGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
*
55828659 TGCACACTTAGTGCCATA
1 CGCACACTTAGTGCCATA
55828677 TATTTCCAGC
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACCATTCAAGCC
Found at i:55828664 original size:58 final size:59
Alignment explanation
Indices: 55828610--55828731 Score: 169
Period size: 58 Copynumber: 2.1 Consensus size: 59
55828600 CCGCACACAC
* *
55828610 AGTGCCATACCCTTCGAGC-TCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
1 AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
* * * *
55828668 AGTGCCATATATTTCCAGCAT-GCACACTCAGTGCCATATTTTTCC-GCATGCACACTT
1 AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
55828725 AGTGCCA
1 AGTGCCA
55828732 ATCTCGTCAC
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 19 0.33
58 37 0.65
59 1 0.02
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.29
Consensus pattern (59 bp):
AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
Found at i:55828677 original size:29 final size:29
Alignment explanation
Indices: 55828631--55828731 Score: 177
Period size: 29 Copynumber: 3.5 Consensus size: 29
55828621 CTTCGAGCTC
55828631 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
55828660 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
* *
55828689 GCACACTCAGTGCCATATTTTTCC-GCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
55828717 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
55828732 ATCTCGTCAC
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
28 18 0.26
29 51 0.74
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.30
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:55830572 original size:30 final size:30
Alignment explanation
Indices: 55830531--55830589 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
55830521 TCCGAGCCTT
*
55830531 GGGGAAAAAGTGTAAATATGTAAAAGTTTA
1 GGGGAAAAAGTGTAAATATGCAAAAGTTTA
* * *
55830561 GGGGTAAAAGTGTAATTTTGCAAAAGTTT
1 GGGGAAAAAGTGTAAATATGCAAAAGTTT
55830590 GAGTCAAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.27, T:0.31
Consensus pattern (30 bp):
GGGGAAAAAGTGTAAATATGCAAAAGTTTA
Found at i:55831013 original size:55 final size:53
Alignment explanation
Indices: 55830926--55831180 Score: 245
Period size: 55 Copynumber: 4.8 Consensus size: 53
55830916 ATTAGGGTTT
*
55830926 AAGGATACCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAA-GTTTCTAAGGC
* * * *
55830981 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTT--TCTAAGGC
* * * * *
55831036 AAAGG-TTCCATGTAAGACCATGCCAAGCCAAGGCATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTTTC-TAAGGC
* *
55831089 AAGGATACCATGTAAGACCATGTCGAGACATGGCAA-TGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAAGTTTCTAAGGC
* ** * *
55831138 AAGGATACCACGTAAGACCATGAAAAGTCATGGAAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAG
55831181 GTACCGTGTA
Statistics
Matches: 168, Mismatches: 24, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
48 2 0.01
49 35 0.21
52 7 0.04
53 38 0.23
54 12 0.07
55 70 0.42
56 4 0.02
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTTTCTAAGGC
Found at i:55831132 original size:108 final size:110
Alignment explanation
Indices: 55830933--55831133 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 110
55830923 TTTAAGGATA
* *
55830933 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGATACCATGTAAGA
1 CCATGTAAGACCATGCCAAGCCAAGGAAATTGGTAAGGTTTCTAAGGCAAGGATACCATGTAAGA
*
55830998 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTT
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTT
* *
55831043 CCATGTAAGACCATGCCAAGCCAAGG-CATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGCCAAGGAAATTGGTAAGGTTTC-TAAGGCAAGGATACCATGTAAG
* *
55831105 ACCATGTCGAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
55831134 TCAAAAGGAT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
107 3 0.04
108 49 0.59
109 7 0.08
110 24 0.29
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.22
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGCCAAGGAAATTGGTAAGGTTTCTAAGGCAAGGATACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTT
Found at i:55831277 original size:23 final size:24
Alignment explanation
Indices: 55831251--55831295 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
55831241 GTAAGGTAAG
*
55831251 GTAAGACGAGTT-ATACTAAAAAA
1 GTAAGACAAGTTCATACTAAAAAA
55831274 GTAAGACAAGTTCATACTAAAA
1 GTAAGACAAGTTCATACTAAAA
55831296 GAGAAAAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22
Consensus pattern (24 bp):
GTAAGACAAGTTCATACTAAAAAA
Found at i:55838355 original size:29 final size:29
Alignment explanation
Indices: 55838318--55838449 Score: 203
Period size: 29 Copynumber: 4.6 Consensus size: 29
55838308 GTTGAGAGAT
*
55838318 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATGCA
*
55838347 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATGCA
55838376 TGGCACTAAGTGTGCGAGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATGCA
* **
55838405 TGGCACTAAGTGTGCGAG-TTTAAAGTATA
1 TGGCACTAAGTGTGCGAGCTTGAAA-TGCA
55838434 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
55838450 CGGCTGATTA
Statistics
Matches: 98, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
28 5 0.05
29 93 0.95
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATGCA
Found at i:55851453 original size:29 final size:28
Alignment explanation
Indices: 55851415--55851517 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 28
55851405 GTGACGAGAT
* *
55851415 TGGCACTAAGTGTGCAAGCTTGAAATGTA
1 TGGCACTAAGTGTGCGAGCTT-AAATATA
55851444 TGGCACTAAGTGTGCGAGCTTAAATTATA
1 TGGCACTAAGTGTGCGAGCTTAAA-TATA
* *
55851473 TGGCACTATGTGTGCGAGCTTAAATCACA
1 TGGCACTAAGTGTGCGAGCTTAAAT-ATA
55851502 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
55851518 TGATCGATTA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
28 4 0.06
29 63 0.94
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTAAATATA
Found at i:55852927 original size:13 final size:13
Alignment explanation
Indices: 55852909--55852933 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55852899 CCTAGAGCAG
55852909 AAAAAAAATATAA
1 AAAAAAAATATAA
55852922 AAAAAAAATATA
1 AAAAAAAATATA
55852934 TATAAAGGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAAAAATATAA
Found at i:55856113 original size:40 final size:39
Alignment explanation
Indices: 55856069--55856250 Score: 238
Period size: 39 Copynumber: 4.6 Consensus size: 39
55856059 GTTCAAAACA
* * ** * *
55856069 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
55856109 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
55856149 CCTTCGGGCTTAGCCCGGGTATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
55856188 CCTTCGGGCTTAGCCCGGATATCATAGCTTGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
55856227 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
55856251 CTCGAACATT
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 88 0.69
40 40 0.31
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:55856180 original size:39 final size:39
Alignment explanation
Indices: 55856099--55856250 Score: 241
Period size: 39 Copynumber: 3.9 Consensus size: 39
55856089 TATGGTAACC
* * * *
55856099 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCATAGCT
*
55856139 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
55856178 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
*
55856217 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
55856251 CTCGAACATT
Statistics
Matches: 105, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 88 0.84
40 17 0.16
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
Found at i:55862504 original size:37 final size:37
Alignment explanation
Indices: 55862445--55862553 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
55862435 AGCTCAGACG
* *
55862445 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
55862482 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
55862519 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
55862554 ATATATTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:55862669 original size:48 final size:48
Alignment explanation
Indices: 55862598--55863142 Score: 721
Period size: 48 Copynumber: 11.0 Consensus size: 48
55862588 TGTTACAACA
* * *
55862598 TTCACATTAGCCATTCGGCTTTACCACATATTCATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACACATAT
* *
55862646 TTCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACACATAT
55862694 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACAC----ACATAT
** *
55862746 CACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCAC----A-TT---A---GCCATTCGGCTTTACCACATATACATATCACACACATAT
* *
55862805 TTCATATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACACATAT
** *
55862853 TTCACATTAGCCGCTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACACATAT
* *
55862901 TTCATATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACACATAT
* *
55862949 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACACATAT
* * *
55862997 TTCACATTGGCCCTTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACACATAT
** *
55863045 TTCACATTAGCCGCTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACACATAT
* * *
55863093 TTCATATTAGCCATTCGGCTTTACCACATATACATATCACGCATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACACATAT
55863141 TT
1 TT
55863143 ATTTATCTTG
Statistics
Matches: 447, Mismatches: 35, Indels: 30
0.87 0.07 0.06
Matches are distributed among these distances:
48 391 0.87
51 1 0.00
52 8 0.02
54 2 0.00
55 1 0.00
56 1 0.00
57 2 0.00
59 7 0.02
60 1 0.00
63 33 0.07
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.34
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACACATAT
Found at i:55862741 original size:63 final size:63
Alignment explanation
Indices: 55862670--55862803 Score: 268
Period size: 63 Copynumber: 2.1 Consensus size: 63
55862660 TCGGCTTTAC
55862670 CACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCA
1 CACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCA
55862733 CACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCA
1 CACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCA
55862796 CACATATA
1 CACATATA
55862804 TTTCATATTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.31
Consensus pattern (63 bp):
CACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCA
Found at i:55862756 original size:17 final size:15
Alignment explanation
Indices: 55862718--55862755 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
55862708 TCGGCTTTAC
55862718 CACATATACATATCA
1 CACATATACATATCA
55862733 CACATATACATATCA
1 CACATATACATATCA
55862748 CACATATA
1 CACATATA
55862756 TTTCACATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (15 bp):
CACATATACATATCA
Found at i:55866366 original size:40 final size:40
Alignment explanation
Indices: 55866317--55866628 Score: 507
Period size: 40 Copynumber: 7.8 Consensus size: 40
55866307 CCAGCATGAT
*
55866317 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
55866357 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
55866397 TGCTCTTTGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
55866437 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
55866477 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
55866517 TGCTCTTCGGGATTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
55866557 TGCTCTTCGGGATTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
55866597 TGCTCTTCGGGATTTAACCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
55866629 CTCAATTCTC
Statistics
Matches: 264, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 264 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:55868657 original size:37 final size:37
Alignment explanation
Indices: 55868594--55868702 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
55868584 AGCTCAGACG
* * *
55868594 AAATCTCCACACGAAGTTATCAGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
55868631 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
55868668 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
55868703 ATATATTTCC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:55868818 original size:48 final size:47
Alignment explanation
Indices: 55868747--55869324 Score: 852
Period size: 48 Copynumber: 12.0 Consensus size: 47
55868737 TGTTACAACA
*
55868747 TTCACATTAGCCATTCGGCTTTACCACATATTCATATCTACTAC-ATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATC-AC-ACAATAT
*
55868795 TTCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACA-ATAT
55868843 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACA-ATAT
* ** *
55868891 TTCATATTAGCCGCTCGGCTTTACCACATACACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACA-ATAT
*
55868939 TTCACATTAGTCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACA-ATAT
** *
55868987 TTCACATTAGCCGCTCGGCTTTACCACACATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACA-ATAT
*
55869035 TTCATATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACA-ATAT
* *
55869083 TTCATATTAGCCATTCGGCTTTACCACATATGCATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACA-ATAT
* *
55869131 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACA-ATAT
* *
55869179 TTCACATTGGCCCTTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACA-ATAT
**
55869227 TTCACATTAGCCGCTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACA-ATAT
*
55869275 TTCATATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACA-ATAT
55869323 TT
1 TT
55869325 ATTTATCTTG
Statistics
Matches: 491, Mismatches: 37, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
46 2 0.00
47 2 0.00
48 487 0.99
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.34
Consensus pattern (47 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACAATAT
Found at i:55872358 original size:20 final size:20
Alignment explanation
Indices: 55872333--55872370 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55872323 TTTCCAGTGA
*
55872333 TGGTATTCTGGTTGATCCCG
1 TGGTATTCGGGTTGATCCCG
55872353 TGGTATTCGGGTTGATCC
1 TGGTATTCGGGTTGATCC
55872371 TAGTAAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.18, G:0.32, T:0.39
Consensus pattern (20 bp):
TGGTATTCGGGTTGATCCCG
Found at i:55873406 original size:29 final size:29
Alignment explanation
Indices: 55873364--55873422 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
55873354 ATAGTCGATA
55873364 GATTGACTAAATCGACCCATTTTATACTG
1 GATTGACTAAATCGACCCATTTTATACTG
55873393 GATTGACTAAATCGACCCATTTTATACTG
1 GATTGACTAAATCGACCCATTTTATACTG
55873422 G
1 G
55873423 TACGCACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (29 bp):
GATTGACTAAATCGACCCATTTTATACTG
Found at i:55878761 original size:26 final size:26
Alignment explanation
Indices: 55878701--55878762 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
55878691 AAAAAATAAT
*
55878701 AAAAATAAAACTAAATAACTATTTTT
1 AAAAATAAAACTAAATAACTATTTTA
**
55878727 AAACTTAAAAC-AAATATACTA-TTTA
1 AAAAATAAAACTAAATA-ACTATTTTA
55878752 ACAAAATAAAA
1 A-AAAATAAAA
55878763 ATATTTCTCC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
25 9 0.31
26 20 0.69
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (26 bp):
AAAAATAAAACTAAATAACTATTTTA
Found at i:55882352 original size:24 final size:24
Alignment explanation
Indices: 55882325--55882374 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
55882315 TTATAAGGTA
55882325 AATATAAACCTATACCAATGCCAC
1 AATATAAACCTATACCAATGCCAC
55882349 AATATAAACCTATACCAATGCCAC
1 AATATAAACCTATACCAATGCCAC
55882373 AA
1 AA
55882375 AGTTTATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.28, G:0.04, T:0.20
Consensus pattern (24 bp):
AATATAAACCTATACCAATGCCAC
Found at i:55890003 original size:31 final size:32
Alignment explanation
Indices: 55889965--55890036 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 32
55889955 GGGTAAATAT
*
55889965 ATTAGGCCCAG-AAAATAGACTTAGATAAAAA
1 ATTAGGCCCAGAAAAATAGACTTAGACAAAAA
*
55889996 ATTAGGCCC-GAAAAATAGACTTGGACAAAAA
1 ATTAGGCCCAGAAAAATAGACTTAGACAAAAA
*
55890027 ATTAAGCCCA
1 ATTAGGCCCA
55890037 TTTAAAATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.18
Consensus pattern (32 bp):
ATTAGGCCCAGAAAAATAGACTTAGACAAAAA
Found at i:55896054 original size:13 final size:13
Alignment explanation
Indices: 55896038--55896071 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
55896028 TAAATTATAA
*
55896038 ATTATTATTAACT
1 ATTATTATTAAAT
55896051 ATTATTATTAAAT
1 ATTATTATTAAAT
*
55896064 AATATTAT
1 ATTATTAT
55896072 ATATATATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTATTATTAAAT
Found at i:55896123 original size:17 final size:17
Alignment explanation
Indices: 55896101--55896135 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
55896091 AAATGAAGAA
*
55896101 AAAGAATAAAAAGAAAC
1 AAAGAAGAAAAAGAAAC
*
55896118 AAAGAAGAATAAGAAAC
1 AAAGAAGAAAAAGAAAC
55896135 A
1 A
55896136 GAGAGCATTC
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:0.74, C:0.06, G:0.14, T:0.06
Consensus pattern (17 bp):
AAAGAAGAAAAAGAAAC
Found at i:55896615 original size:13 final size:13
Alignment explanation
Indices: 55896575--55896608 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
55896565 ACATATATAT
* *
55896575 ATAATATTATTTA
1 ATAATAATAGTTA
55896588 ATAATAATAGTTA
1 ATAATAATAGTTA
55896601 ATAATAAT
1 ATAATAAT
55896609 TTATAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (13 bp):
ATAATAATAGTTA
Found at i:55901914 original size:49 final size:48
Alignment explanation
Indices: 55901859--55902112 Score: 361
Period size: 47 Copynumber: 5.3 Consensus size: 48
55901849 TTATGAGATA
*
55901859 TATATATGTGATAAGGCATAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG-GTG
*
55901908 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG-GTG
55901957 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG-AAGGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGGTG
* *
55902004 TATATATGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAAA-GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGGTG
* * * * * * *
55902051 TATATATGTGATAGGGCCGAGTGGCCAACGTGATGGATGTGGAA-GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGGTG
*
55902098 TATAAATGTGATAAG
1 TATATATGTGATAAG
55902113 TCCGAAGGGC
Statistics
Matches: 191, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
47 98 0.51
48 5 0.03
49 88 0.46
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (48 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGGTG
Found at i:55907197 original size:20 final size:20
Alignment explanation
Indices: 55907172--55907210 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
55907162 AAATTTTCAA
55907172 TTATTTCAC-ACATTTACAAC
1 TTATTTCACAAC-TTTACAAC
*
55907192 TTATTTTACAACTTTACAA
1 TTATTTCACAACTTTACAA
55907211 AATAACCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATTTCACAACTTTACAAC
Found at i:55908509 original size:24 final size:25
Alignment explanation
Indices: 55908482--55908533 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
55908472 GCCTAGCCTC
*
55908482 TTTTAAT-AACTGGGGTAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
*
55908506 TTTTGATAAACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
55908531 TTT
1 TTT
55908534 CGGCAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (25 bp):
TTTTAATAAACTGGGGCAAAGCCCT
Found at i:55908541 original size:25 final size:25
Alignment explanation
Indices: 55908489--55908558 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
55908479 CTCTTTTAAT
* * *
55908489 AACTGGGGTAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGACA
*
55908514 AACTGGGGCAAAGCCCTTTTCGGCA
1 AACTGGGGCAAAGCCCTTTTCGACA
* *
55908539 AACTAGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
55908559 AGCACTTCCT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGACA
Found at i:55909430 original size:27 final size:27
Alignment explanation
Indices: 55909368--55909432 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
55909358 GGGCATATTC
55909368 GTCATTTTACCATACAGGAGTATTACG
1 GTCATTTTACCATACAGGAGTATTACG
* * *
55909395 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTACCATACAGGAG-TATTACG
*
55909422 GTCTTTTTACC
1 GTCATTTTACC
55909433 TATTAGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAGGAGTATTACG
Found at i:55909493 original size:27 final size:27
Alignment explanation
Indices: 55909463--55909672 Score: 167
Period size: 27 Copynumber: 7.7 Consensus size: 27
55909453 TTTCATCCTA
* *
55909463 CAAGGGTGTTTTGGTAAATTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
** ** *
55909490 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
55909517 CAATGGTATTTCT-ATAATTTTTAGAAAGT
1 CAAGGGTATTT-TGGTAA-TTTTACAAA-T
*
55909546 CAAGGGTATTTCT-GTAATTTTATAAAT
1 CAAGGGTATTT-TGGTAATTTTACAAAT
* *
55909573 TAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
55909600 TAAGGGTATTTCGGTAATTTCACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
55909626 CAAGTGGTATTTTTGTAATTTTACAAA-
1 CAAG-GGTATTTTGGTAATTTTACAAAT
* *
55909653 CTAGGGGTATTTTGCTAATT
1 C-AAGGGTATTTTGGTAATT
55909673 CTACCCTATA
Statistics
Matches: 148, Mismatches: 29, Indels: 12
0.78 0.15 0.06
Matches are distributed among these distances:
26 4 0.03
27 112 0.76
28 17 0.11
29 15 0.10
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:55909664 original size:54 final size:54
Alignment explanation
Indices: 55909462--55909652 Score: 199
Period size: 54 Copynumber: 3.5 Consensus size: 54
55909452 ATTTCATCCT
* * *
55909462 ACAAG-GGTGTTTTGGTAAATTTACAAATCAAGGGTATTTCAGTAATTTTGTAA
1 ACAAGTGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTATAA
* * *
55909515 ACCAA-TGGTATTTCT-ATAATTTTTAGAAAGTCAAGGGTATTTCTGTAATTTTATAA
1 A-CAAGTGGTATTT-TGGTAA-TTTTACAAA-TCAAGGGTATTTCAGTAATTTTATAA
** * * * * *
55909571 ATTAGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAA
1 ACAAGTGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTATAA
*
55909625 ACAAGTGGTATTTTTGTAATTTTACAAA
1 ACAAGTGGTATTTTGGTAATTTTACAAA
55909653 CTAGGGGTAT
Statistics
Matches: 112, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
53 1 0.01
54 58 0.52
55 18 0.16
56 35 0.31
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.41
Consensus pattern (54 bp):
ACAAGTGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTATAA
Found at i:55909688 original size:81 final size:80
Alignment explanation
Indices: 55909546--55909714 Score: 205
Period size: 81 Copynumber: 2.1 Consensus size: 80
55909536 TTTAGAAAGT
* * * *
55909546 CAAGGGTATTTCTGTAATTTTATAAATTAGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTT
1 CAAGGGTATTTCTGTAATTTTACAAACTAGGGGTATTTTGCTAATTCTACAAATTAAGGGTATTT
*
55909611 CGGTAATTTCACAAA
66 CAGTAATTTCACAAA
* ** *
55909626 CAAGTGGTATTTTTGTAATTTTACAAACTAGGGGTATTTTGCTAATTCTAC-CCTATAGGGGTAT
1 CAAG-GGTATTTCTGTAATTTTACAAACTAGGGGTATTTTGCTAATTCTACAAAT-TAAGGGTAT
* *
55909690 TTTAGTAATTTCACAAT
64 TTCAGTAATTTCACAAA
*
55909707 CGAGGGTA
1 CAAGGGTA
55909715 AAACGGTAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
80 9 0.12
81 66 0.88
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (80 bp):
CAAGGGTATTTCTGTAATTTTACAAACTAGGGGTATTTTGCTAATTCTACAAATTAAGGGTATTT
CAGTAATTTCACAAA
Found at i:55909689 original size:54 final size:54
Alignment explanation
Indices: 55909521--55909705 Score: 139
Period size: 54 Copynumber: 3.4 Consensus size: 54
55909511 GTAAACCAAT
* * * *
55909521 GGTATTTCTA-TAATTTTTAGAAAGTCAAGGGTATTTCTG-TAATTTTATAA-ATTAGG
1 GGTATTT-TAGTAA-TTTTACAAACT-AAGGGTATTTC-GCTAATTTCACAACA-TAGG
* * * *
55909577 GGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACA-AGT
1 GGTATTTTAGTAATTTTACAAACTAAGGGTATTTCGCTAATTTCAC-AACATAGG
* * * *
55909631 GGTATTTTTGTAATTTTACAAACTAGGGGTATTTTGCTAA-TTCTAC-CCTATAGG
1 GGTATTTTAGTAATTTTACAAACTAAGGGTATTTCGCTAATTTC-ACAAC-ATAGG
*
55909685 GGTATTTTAGTAATTTCACAA
1 GGTATTTTAGTAATTTTACAA
55909706 TCGAGGGTAA
Statistics
Matches: 107, Mismatches: 15, Indels: 16
0.78 0.11 0.12
Matches are distributed among these distances:
52 1 0.01
53 5 0.05
54 78 0.73
55 12 0.11
56 11 0.10
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (54 bp):
GGTATTTTAGTAATTTTACAAACTAAGGGTATTTCGCTAATTTCACAACATAGG
Found at i:55909712 original size:27 final size:27
Alignment explanation
Indices: 55909573--55909712 Score: 113
Period size: 27 Copynumber: 5.2 Consensus size: 27
55909563 TTTTATAAAT
*
55909573 TAGGGGTATTTTGGTAATTTTACAAAT-
1 TAGGGGTATTTTGGTAATTTCAC-AATC
* * *
55909600 TAAGGGTATTTCGGTAATTTCACAAAC
1 TAGGGGTATTTTGGTAATTTCACAATC
* * * * *
55909627 AAGTGGTATTTTTGTAATTTTACAAAC
1 TAGGGGTATTTTGGTAATTTCACAATC
* ** *
55909654 TAGGGGTATTTTGCTAA-TTCTACCCTA
1 TAGGGGTATTTTGGTAATTTC-ACAATC
*
55909681 TAGGGGTATTTTAGTAATTTCACAATC
1 TAGGGGTATTTTGGTAATTTCACAATC
*
55909708 GAGGG
1 TAGGG
55909713 TAAAACGGTA
Statistics
Matches: 85, Mismatches: 25, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
26 4 0.05
27 78 0.92
28 3 0.04
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (27 bp):
TAGGGGTATTTTGGTAATTTCACAATC
Found at i:55909723 original size:26 final size:26
Alignment explanation
Indices: 55909693--55909795 Score: 100
Period size: 27 Copynumber: 3.8 Consensus size: 26
55909683 GGGGTATTTT
55909693 AGTAATTT-CACAATCGAGGGTAAAAC
1 AGTAATTTGCA-AATCGAGGGTAAAAC
* *
55909719 GGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAA-TTTGCAAATCGAGGGTAAAAC
* * *
55909746 AGTAATTCTGTAAATCAAGAGTAAAAC
1 AGTAATT-TGCAAATCGAGGGTAAAAC
**
55909773 AGTAATTCTATAAATCGAGGGTA
1 AGTAATT-TGCAAATCGAGGGTA
55909796 CGTTGGTAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.09
27 59 0.89
28 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (26 bp):
AGTAATTTGCAAATCGAGGGTAAAAC
Found at i:55909734 original size:27 final size:27
Alignment explanation
Indices: 55909704--55909795 Score: 139
Period size: 27 Copynumber: 3.4 Consensus size: 27
55909694 GTAATTTCAC
* *
55909704 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
55909731 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
* * *
55909758 AATCAAGAGTAAAACAGTAATTCTATA
1 AATCGAGGGTAAAACAGTAATTCTGTA
55909785 AATCGAGGGTA
1 AATCGAGGGTA
55909796 CGTTGGTAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.26
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGTAATTCTGTA
Found at i:55911822 original size:25 final size:25
Alignment explanation
Indices: 55911794--55911863 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
55911784 CTCTTTTAAT
*
55911794 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
55911819 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
55911844 AACTAGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
55911864 AGCACTTCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:55912708 original size:27 final size:26
Alignment explanation
Indices: 55912673--55912750 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 26
55912663 GGGCATATTC
55912673 GTCATTTTACCATATAGGGGTATTACG
1 GTCATTTTACC-TATAGGGGTATTACG
* *
55912700 GTCAGTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTA-CCTATAGGGG-TATTACG
*
55912727 GTCTTTTTACCTATTAGGGGTATT
1 GTCATTTTACCTA-TAGGGGTATT
55912751 TTAGTCATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
26 5 0.12
27 34 0.81
28 3 0.07
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (26 bp):
GTCATTTTACCTATAGGGGTATTACG
Found at i:55912821 original size:27 final size:27
Alignment explanation
Indices: 55912791--55912969 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
55912781 GTAAATCTAC
*
55912791 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
55912818 AAACCAATGGTATTTCTA-TAATTTTTAG
1 AAACCAAGGGTATTTC-AGTAA-TTTTAT
* * *
55912846 AAAGTCAAGGGGATTTCAGTAATTTTGT
1 AAA-CCAAGGGTATTTCAGTAATTTTAT
* * ** *
55912874 AAATCAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
*** * *
55912901 AAATTGAGGGTATTTCGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
** *
55912928 AAACC-AGTGGTATTTTGGTAATTTTAC
1 AAACCAAG-GGTATTTCAGTAATTTTAT
* *
55912955 AAACTAGGGGTATTT
1 AAACCAAGGGTATTT
55912970 TGGTAATTCT
Statistics
Matches: 123, Mismatches: 23, Indels: 12
0.78 0.15 0.08
Matches are distributed among these distances:
26 2 0.02
27 91 0.74
28 17 0.14
29 13 0.11
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTAT
Found at i:55912970 original size:27 final size:26
Alignment explanation
Indices: 55912864--55913010 Score: 150
Period size: 27 Copynumber: 5.5 Consensus size: 26
55912854 GGGGATTTCA
**
55912864 GTAATTTTGTAAATCAGGGGTATTTTG
1 GTAATTTTACAAAT-AGGGGTATTTTG
* *
55912891 GTAATTTTACAAATTGAGGGTATTTCG
1 GTAATTTTACAAATAG-GGGTATTTTG
* *
55912918 GTAATTTTACAAACCAGTGGTATTTTG
1 GTAATTTTACAAA-TAGGGGTATTTTG
55912945 GTAATTTTACAAACTAGGGGTATTTTG
1 GTAATTTTACAAA-TAGGGGTATTTTG
* ** *
55912972 GTAATTCTATCCTATAGGGGTATTTTA
1 GTAATTTTA-CAAATAGGGGTATTTTG
*
55912999 GTAATTTCACAA
1 GTAATTTTACAA
55913011 TTGAGGGTAA
Statistics
Matches: 99, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
26 2 0.02
27 94 0.95
28 3 0.03
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.41
Consensus pattern (26 bp):
GTAATTTTACAAATAGGGGTATTTTG
Found at i:55912977 original size:54 final size:54
Alignment explanation
Indices: 55912776--55912969 Score: 196
Period size: 54 Copynumber: 3.6 Consensus size: 54
55912766 TACAAGGGTG
* * * * *
55912776 TTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAATGGTA
1 TTTTGGTAATTTTACAAACTAGGGGTATTTCAGTAATTTTGTAAACCAGTGGTA
* * * * *
55912830 TTTCT-ATAATTTTTAGAAAGTCAAGGGG-ATTTCAGTAATTTTGTAAATCAGGGGTA
1 TTT-TGGTAA-TTTTACAAA--CTAGGGGTATTTCAGTAATTTTGTAAACCAGTGGTA
* * **
55912886 TTTTGGTAATTTTACAAA-TTGAGGGTATTTCGGTAATTTTACAAACCAGTGGTA
1 TTTTGGTAATTTTACAAACTAG-GGGTATTTCAGTAATTTTGTAAACCAGTGGTA
55912940 TTTTGGTAATTTTACAAACTAGGGGTATTT
1 TTTTGGTAATTTTACAAACTAGGGGTATTT
55912970 TGGTAATTCT
Statistics
Matches: 113, Mismatches: 19, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
52 1 0.01
53 3 0.03
54 55 0.49
55 18 0.16
56 31 0.27
57 5 0.04
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (54 bp):
TTTTGGTAATTTTACAAACTAGGGGTATTTCAGTAATTTTGTAAACCAGTGGTA
Found at i:55913028 original size:26 final size:26
Alignment explanation
Indices: 55912998--55913073 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
55912988 GGGGTATTTT
*
55912998 AGTAATTT-CACAATTGAGGGTAAAAC
1 AGTAATTTGCA-AATCGAGGGTAAAAC
* *
55913024 GGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAA-TTTGCAAATCGAGGGTAAAAC
**
55913051 AGTAATTCTATAAATCGAGGGTA
1 AGTAATT-TGCAAATCGAGGGTA
55913074 CTTTAGTAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
26 6 0.14
27 35 0.83
28 1 0.02
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.29
Consensus pattern (26 bp):
AGTAATTTGCAAATCGAGGGTAAAAC
Found at i:55913043 original size:27 final size:27
Alignment explanation
Indices: 55913013--55913073 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
55913003 TTTCACAATT
* * *
55913013 GAGGGTAAAACGGTAATTTTGTAAATC
1 GAGGGTAAAACAGTAATTCTATAAATC
55913040 GAGGGTAAAACAGTAATTCTATAAATC
1 GAGGGTAAAACAGTAATTCTATAAATC
55913067 GAGGGTA
1 GAGGGTA
55913074 CTTTAGTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.26
Consensus pattern (27 bp):
GAGGGTAAAACAGTAATTCTATAAATC
Found at i:55914747 original size:138 final size:137
Alignment explanation
Indices: 55914463--55914737 Score: 489
Period size: 138 Copynumber: 2.0 Consensus size: 137
55914453 AATCATGCCT
*
55914463 AATTAAACATTTAAATAATTATTAGAAATAGAATTCTATGAGAAGTATGGACATTTTGAAAATTT
1 AATTAAACATTTAAATAATTATTAGAAATAGAATTCTATGAGAAGTAAGGACATTTTGAAAATTT
*
55914528 TTGAAATCCGGCATGAGTATCAATACTCTTACTGAGAATGCTAAAAATTCACAAGTTGAAACATT
66 TTGAAATCCAGCATGAGTATCAATACTCTTACTGAGAATGCTAAAAATTCACAAGTTGAAACATT
55914593 TTTCATG
131 TTTCATG
*
55914600 AATTAAACATTTAAATAATTATTAGAAATAGAATTCT-TCGATAAGTAAGGACCATTTTGAAAAT
1 AATTAAACATTTAAATAATTATTAGAAATAGAATTCTAT-GAGAAGTAAGGA-CATTTTGAAAAT
*
55914664 TTTTGAAATCCAGCATGAGTATCGATACTCTTACTGAGAATGCTAAAAATTCACAAGTTGAAACA
64 TTTTGAAATCCAGCATGAGTATCAATACTCTTACTGAGAATGCTAAAAATTCACAAGTTGAAACA
55914729 TTTTTCATG
129 TTTTTCATG
55914738 CTTAAAACAT
Statistics
Matches: 132, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
136 1 0.01
137 47 0.36
138 84 0.64
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (137 bp):
AATTAAACATTTAAATAATTATTAGAAATAGAATTCTATGAGAAGTAAGGACATTTTGAAAATTT
TTGAAATCCAGCATGAGTATCAATACTCTTACTGAGAATGCTAAAAATTCACAAGTTGAAACATT
TTTCATG
Found at i:55925846 original size:21 final size:22
Alignment explanation
Indices: 55925820--55925866 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
55925810 GGTAATTATG
* *
55925820 TTTAGTTTAATT-AATTCATAT
1 TTTAGTATAATTGAATTCAGAT
*
55925841 TTTAGTATATTTGAATTCAGAT
1 TTTAGTATAATTGAATTCAGAT
55925863 TTTA
1 TTTA
55925867 ATATCTGCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.55
Consensus pattern (22 bp):
TTTAGTATAATTGAATTCAGAT
Found at i:55929096 original size:16 final size:16
Alignment explanation
Indices: 55929061--55929094 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
55929051 TCGTGGAAAG
55929061 AAATATTTTATGTTAA
1 AAATATTTTATGTTAA
55929077 AAATATTTTAT-TTAA
1 AAATATTTTATGTTAA
55929092 AAA
1 AAA
55929095 ATTATTGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
AAATATTTTATGTTAA
Found at i:55930700 original size:11 final size:10
Alignment explanation
Indices: 55930662--55930701 Score: 53
Period size: 11 Copynumber: 3.7 Consensus size: 10
55930652 CACAATAGTC
55930662 CTCTCACAATT
1 CTCTCA-AATT
55930673 CTCTCCAAATT
1 CTCT-CAAATT
55930684 CTCTCAAATTT
1 CTCTCAAA-TT
55930695 CTCTCAA
1 CTCTCAA
55930702 TTTTTGTCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.15
11 21 0.78
12 2 0.07
ACGTcount: A:0.28, C:0.35, G:0.00, T:0.38
Consensus pattern (10 bp):
CTCTCAAATT
Found at i:55932434 original size:30 final size:30
Alignment explanation
Indices: 55932398--55932463 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
55932388 TGACGACGCG
* *
55932398 GGCCCATCAACAGTACCCACACAGTCATCA
1 GGCCCATCAACAGCACCCACACAATCATCA
* *
55932428 GGCCCATCAACAGCGCCCACACAATCATCG
1 GGCCCATCAACAGCACCCACACAATCATCA
55932458 GGCCCA
1 GGCCCA
55932464 ACACTTCAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.30, C:0.42, G:0.17, T:0.11
Consensus pattern (30 bp):
GGCCCATCAACAGCACCCACACAATCATCA
Found at i:55933021 original size:68 final size:68
Alignment explanation
Indices: 55932940--55933079 Score: 262
Period size: 68 Copynumber: 2.1 Consensus size: 68
55932930 GTGAGTGAAA
* *
55932940 TTATTAAATAGGACTTGTGTGAAATTTTTTGAAAATGTGATATGTTAATTTTGTAGTGGCCAAAT
1 TTATTAAATAGGACTTGTGTGAAAATTTTTGAAAATGTGATAGGTTAATTTTGTAGTGGCCAAAT
55933005 AAT
66 AAT
55933008 TTATTAAATAGGACTTGTGTGAAAATTTTTGAAAATGTGATAGGTTAATTTTGTAGTGGCCAAAT
1 TTATTAAATAGGACTTGTGTGAAAATTTTTGAAAATGTGATAGGTTAATTTTGTAGTGGCCAAAT
55933073 AAT
66 AAT
55933076 TTAT
1 TTAT
55933080 GGTGTTAAAT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.34, C:0.04, G:0.19, T:0.42
Consensus pattern (68 bp):
TTATTAAATAGGACTTGTGTGAAAATTTTTGAAAATGTGATAGGTTAATTTTGTAGTGGCCAAAT
AAT
Found at i:55933779 original size:25 final size:25
Alignment explanation
Indices: 55933746--55933800 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
55933736 TAAGCTTGTT
55933746 AATTTGTTCTTAATAATTCCGGTTA
1 AATTTGTTCTTAATAATTCCGGTTA
55933771 AATTTGTTCTTAATAATTCCGGTTA
1 AATTTGTTCTTAATAATTCCGGTTA
55933796 AATTT
1 AATTT
55933801 TCCCTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (25 bp):
AATTTGTTCTTAATAATTCCGGTTA
Found at i:55934712 original size:45 final size:45
Alignment explanation
Indices: 55934644--55934850 Score: 278
Period size: 45 Copynumber: 4.6 Consensus size: 45
55934634 TATCGTACAG
* * * *
55934644 TACTATTCGGGCCTTTGATCCTAGCAAGCTATAATGCCAGTGATA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATACCAGTGAGA
* *
55934689 TACTATTCAGGCCTTTGAGCCTAGCAGGCTATAATACCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATACCAGTGAGA
55934734 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATACC-GATGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATACCAG-TGAGA
* * *
55934779 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCAGTGAAA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATACCAGTGAGA
*
55934824 TGA-TATT-GGG-CTTTGAGCTTAGCAGGC
1 T-ACTATTCGGGCCTTTGAGCCTAGCAGGC
55934851 GAAATGTCGG
Statistics
Matches: 147, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
43 15 0.10
44 4 0.03
45 126 0.86
46 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.28
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATACCAGTGAGA
Found at i:55939218 original size:126 final size:126
Alignment explanation
Indices: 55938993--55939259 Score: 417
Period size: 126 Copynumber: 2.1 Consensus size: 126
55938983 CCAAATAGTA
* * *
55938993 ACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCCGTAATTTTGTTGATAGTGCATCCT
1 ACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCCGTAAATTTGTTGACAGTGCATCCA
* * *
55939058 GCTTGAAGCGTTTTGGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAAAT
66 ACTTGAAGCGTTTTGGACACTATTTGTTCAGAAACGTCTTCTCAAAATTAGTTTCTCAAAT
* *
55939119 ACTACTGTAGTAAAAGAGTGTCCACGTGGGAGCTTTTTTCCGTAAATTTGTTGACAGTGCATCCA
1 ACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCCGTAAATTTGTTGACAGTGCATCCA
* * *
55939184 ACTTGAAGCGTTTTTGACACTATTTGTTTAGAAACGTCTTCTCAAAATTAGTTTCTCTAAT
66 ACTTGAAGCGTTTTGGACACTATTTGTTCAGAAACGTCTTCTCAAAATTAGTTTCTCAAAT
* *
55939245 ACTATTGCAGCAAAA
1 ACTACTGTAGCAAAA
55939260 ATAAAATAAA
Statistics
Matches: 127, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
126 127 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (126 bp):
ACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCCGTAAATTTGTTGACAGTGCATCCA
ACTTGAAGCGTTTTGGACACTATTTGTTCAGAAACGTCTTCTCAAAATTAGTTTCTCAAAT
Found at i:55939393 original size:56 final size:56
Alignment explanation
Indices: 55939333--55939482 Score: 158
Period size: 65 Copynumber: 2.5 Consensus size: 56
55939323 CTAATAACCC
*
55939333 TAAACCCTAAACCCTAATTTAATTGATTCTTTT-AAATTAATAGTTAATTTAATTAA
1 TAAACCCTAAACCCTAATTTAATTGATT-TTTTAAAATTAATAGTTAACTTAATTAA
55939389 TAAACCTTAAAAGTCCTAAACCCTAATTTAATTGATTTTTTAAAATTAATAGTTAACTTAATTAA
1 TAAA-C--------CCTAAACCCTAATTTAATTGATTTTTTAAAATTAATAGTTAACTTAATTAA
* * * *
55939454 TTAACCCTCAACCCTAAGTTAATTAATTT
1 TAAACCCTAAACCCTAATTTAATTGATTT
55939483 GTCCCTTAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
56 25 0.32
57 1 0.01
64 5 0.06
65 48 0.61
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.41
Consensus pattern (56 bp):
TAAACCCTAAACCCTAATTTAATTGATTTTTTAAAATTAATAGTTAACTTAATTAA
Found at i:55939415 original size:65 final size:65
Alignment explanation
Indices: 55939338--55939459 Score: 210
Period size: 65 Copynumber: 1.9 Consensus size: 65
55939328 AACCCTAAAC
*
55939338 CCTAAACCCTAATTTAATTGATTCTTTT-AAATTAATAGTTAATTTAATTAATAAACCTTAAAAG
1 CCTAAACCCTAATTTAATTGATT-TTTTAAAATTAATAGTTAACTTAATTAATAAACCTTAAAAG
55939402 T
65 T
*
55939403 CCTAAACCCTAATTTAATTGATTTTTTAAAATTAATAGTTAACTTAATTAATTAACC
1 CCTAAACCCTAATTTAATTGATTTTTTAAAATTAATAGTTAACTTAATTAATAAACC
55939460 CTCAACCCTA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
64 4 0.07
65 50 0.93
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.42
Consensus pattern (65 bp):
CCTAAACCCTAATTTAATTGATTTTTTAAAATTAATAGTTAACTTAATTAATAAACCTTAAAAGT
Found at i:55939482 original size:65 final size:65
Alignment explanation
Indices: 55939324--55939461 Score: 185
Period size: 65 Copynumber: 2.2 Consensus size: 65
55939314 TAATTAACTC
* *
55939324 TAAT-AACCCT-AAA-CCCTAAACCCTAATTTAATTGATTCTTTTAAATTAATAGTTAATTTAAT
1 TAATAAACCCTAAAAGCCCTAAACACTAATTTAATTGATTCTTTTAAATTAATAGTTAACTTAAT
* * *
55939386 TAATAAACCTTAAAAGTCCTAAACCCTAATTTAATTGATT-TTTTAAAATTAATAGTTAACTTAA
1 TAATAAACCCTAAAAGCCCTAAACACTAATTTAATTGATTCTTTT-AAATTAATAGTTAACTTAA
55939450 T
65 T
*
55939451 TAATTAACCCT
1 TAATAAACCCT
55939462 CAACCCTAAG
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
62 4 0.06
63 5 0.07
64 7 0.10
65 51 0.76
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.40
Consensus pattern (65 bp):
TAATAAACCCTAAAAGCCCTAAACACTAATTTAATTGATTCTTTTAAATTAATAGTTAACTTAAT
Found at i:55939535 original size:13 final size:13
Alignment explanation
Indices: 55939517--55939547 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
55939507 TAAACTCTTA
55939517 AAACCCTAAACCT
1 AAACCCTAAACCT
*
55939530 AAACCCTAACCCT
1 AAACCCTAAACCT
55939543 AAACC
1 AAACC
55939548 AATAAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.42, G:0.00, T:0.13
Consensus pattern (13 bp):
AAACCCTAAACCT
Found at i:55940185 original size:20 final size:21
Alignment explanation
Indices: 55940120--55940185 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 21
55940110 AAAAATAAAC
55940120 AAAAGA-ATCTAAATA-TTATA
1 AAAAGATAT-TAAATATTTATA
* *
55940140 AAAAGTATATTAAAAATTCA-A
1 AAAAG-ATATTAAATATTTATA
55940161 GAAAAG-TATTAAATATTTATA
1 -AAAAGATATTAAATATTTATA
55940182 AAAA
1 AAAA
55940186 TTCATAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
20 20 0.54
21 8 0.22
22 9 0.24
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (21 bp):
AAAAGATATTAAATATTTATA
Found at i:55940197 original size:42 final size:42
Alignment explanation
Indices: 55940100--55940200 Score: 104
Period size: 42 Copynumber: 2.5 Consensus size: 42
55940090 CATGTCAACA
55940100 AAAAATTC-T-AAAAAA-TAAACAAAAGAATCTAAATATTAT
1 AAAAATTCATAAAAAAATTAAACAAAAGAATCTAAATATTAT
* * * * *
55940139 AAAAAGT-ATATTAAAAATTCAAGAAAAGTAT-TAAATATTTAT
1 AAAAATTCATA-AAAAAATTAAACAAAAGAATCTAAATA-TTAT
55940181 AAAAATTCATAAAAAAATTA
1 AAAAATTCATAAAAAAATTA
55940201 TCAGGTTTTC
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
39 7 0.15
41 11 0.23
42 27 0.56
43 3 0.06
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.29
Consensus pattern (42 bp):
AAAAATTCATAAAAAAATTAAACAAAAGAATCTAAATATTAT
Found at i:55942756 original size:93 final size:93
Alignment explanation
Indices: 55942597--55942767 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
55942587 GCCCATAAGT
* *
55942597 GAACTCGGACTCAACTCAACGAGCTTGGGCATTCGCATCCATGAGTGAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
55942662 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
55942690 GAACTCGGACTCAACTCAACGAG-TTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTT-GGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
55942754 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
55942768 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:55942764 original size:46 final size:46
Alignment explanation
Indices: 55942589--55942764 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
55942579 TGTAACCCGC
* *
55942589 CCATAAGTGAACTCGGACTCAACTCAACGAGCTT-GGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTTGCAT
* * * *
55942635 CCATGAGTGAACTCGAACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
* *
55942685 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
55942728 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
55942765 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 4 0.04
46 60 0.55
47 28 0.26
48 2 0.02
49 2 0.02
50 5 0.05
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:55942934 original size:18 final size:18
Alignment explanation
Indices: 55942913--55942950 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
55942903 ATGTATATCA
55942913 CATAATTTGACATATTAT
1 CATAATTTGACATATTAT
55942931 CATAATTTGACATATTAT
1 CATAATTTGACATATTAT
55942949 CA
1 CA
55942951 AACAATTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.42
Consensus pattern (18 bp):
CATAATTTGACATATTAT
Found at i:55950044 original size:43 final size:42
Alignment explanation
Indices: 55949949--55950051 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 42
55949939 GGTTACTGAT
* *
55949949 ATTACGTGTAAGACCATATCTAGGATATGGCATCGATATGAG
1 ATTACGTGTAAGACCATAGCTAGGATATGGCATCGATACGAG
* * * *
55949991 ACTT-TGTGTAAAACCATAGCTGGGCTATTGGCATCGATACGAG
1 A-TTACGTGTAAGACCATAGCTAGGATA-TGGCATCGATACGAG
*
55950034 ATTACATGTAAGACCATA
1 ATTACGTGTAAGACCATA
55950052 TTTGGGATAT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
42 21 0.43
43 28 0.57
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (42 bp):
ATTACGTGTAAGACCATAGCTAGGATATGGCATCGATACGAG
Found at i:55953793 original size:16 final size:16
Alignment explanation
Indices: 55953772--55953804 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55953762 AAATAGGGTT
55953772 TAGATAAGACTTACTC
1 TAGATAAGACTTACTC
55953788 TAGATAAGACTTACTC
1 TAGATAAGACTTACTC
55953804 T
1 T
55953805 TGGAACTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (16 bp):
TAGATAAGACTTACTC
Found at i:55957802 original size:40 final size:39
Alignment explanation
Indices: 55957730--55958053 Score: 409
Period size: 40 Copynumber: 8.1 Consensus size: 39
55957720 CAGGATTTAA
* *
55957730 CCGGATATAGCT-ACTCGCTCAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAATGCCTTCGGGACTTAGC
*
55957769 CCGGGTATAGTAACTCGCACAATTGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAA-TGCCTTCGGGACTTAGC
*
55957809 CCGGATATAGTAACTCGTACAGATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACA-ATGCCTTCGGGACTTAGC
*
55957849 CCGGATATAGTAACTCGTACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCAC-AATGCCTTCGGGACTTAGC
* * * *
55957889 CCGGATGTAATAACTCGTACAAATTCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCAC-AATGCCTTCGGGACTTAGC
55957929 CCGGATATAGTAACTCGCACAGATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACA-ATGCCTTCGGGACTTAGC
* * * *
55957969 CTGGATGTAATAACTCGCGCAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCAC-AATGCCTTCGGGACTTAGC
* *
55958009 CCGGA-ACTAGTCACTAGCGCAAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTAACT--CGCACAATGCCTTCGGGACTTAGC
55958050 CCGG
1 CCGG
55958054 TTATCATCCA
Statistics
Matches: 254, Mismatches: 22, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
38 1 0.00
39 19 0.07
40 205 0.81
41 26 0.10
42 3 0.01
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (39 bp):
CCGGATATAGTAACTCGCACAATGCCTTCGGGACTTAGC
Done.