Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010105.1 Kokia drynarioides strain JFW-HI SEQ_124891, whole genome shotgun sequence
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: 523673
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 37 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:332889 original size:14 final size:15
Alignment explanation
Indices: 332870--332904 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
332860 AGCATGAATG
*
332870 AATAAATAT-AGGAA
1 AATAAATATAAGAAA
332884 AATAAATATAAGAAA
1 AATAAATATAAGAAA
332899 AATAAA
1 AATAAA
332905 ATACAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (15 bp):
AATAAATATAAGAAA
Found at i:333166 original size:29 final size:28
Alignment explanation
Indices: 333103--333312 Score: 174
Period size: 29 Copynumber: 7.2 Consensus size: 28
333093 AGGGTTTGAA
* * *
333103 GTAAAAATATGATTTTTGAGAAGTCCAA-G
1 GTAAAAATGTAATTTTTG-GAAGT-TAAGG
* * * *
333132 GCAAAAGTGTGATTTTTGGAAGTCTGAGG
1 GTAAAAATGTAATTTTTGGAAGT-TAAGG
*
333161 GTAAAAATGTAATTTTTAGAA-TATAAGGG
1 GTAAAAATGTAATTTTTGGAAGT-TAA-GG
* **
333190 GTAAAAATGTGATTTTTGGAAGTTCGGGG
1 GTAAAAATGTAATTTTTGGAAGTT-AAGG
*
333219 GTAAAAATGTAATTTTTGGAAGTTTAAGT
1 GTAAAAATGTAATTTTTGGAAG-TTAAGG
* *
333248 GTAAAAATATAA-TTTTGAGAAGTTTAGGG
1 GTAAAAATGTAATTTTTG-GAAG-TTAAGG
*
333277 GTAAAAATGTAATTTTTGGAAGTTTAGG
1 GTAAAAATGTAATTTTTGGAAGTTAAGG
333305 TGTAAAAA
1 -GTAAAAA
333313 ATATTATTTT
Statistics
Matches: 148, Mismatches: 25, Indels: 16
0.78 0.13 0.08
Matches are distributed among these distances:
28 19 0.13
29 121 0.82
30 8 0.05
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (28 bp):
GTAAAAATGTAATTTTTGGAAGTTAAGG
Found at i:333201 original size:58 final size:57
Alignment explanation
Indices: 333103--333312 Score: 194
Period size: 58 Copynumber: 3.6 Consensus size: 57
333093 AGGGTTTGAA
* * ** * *
333103 GTAAAAATATGATTTTTGAGAAGTCCAA-GGCAAAAGTGTGATTTTTGGAAGTCTGAGG
1 GTAAAAATGTAATTTTT-AGAAGTATAAGGGTAAAAATGTGATTTTTGGAAGT-TGAGG
*
333161 GTAAAAATGTAATTTTTAGAA-TATAAGGGGTAAAAATGTGATTTTTGGAAGTTCGGGG
1 GTAAAAATGTAATTTTTAGAAGTATAA-GGGTAAAAATGTGATTTTTGGAAGTT-GAGG
* * * * * *
333219 GTAAAAATGTAATTTTTGGAAGTTTAAGTGTAAAAATAT-AATTTTGAGAAGTTTAGGG
1 GTAAAAATGTAATTTTTAGAAGTATAAGGGTAAAAATGTGATTTTTG-GAAGTTGA-GG
* *
333277 GTAAAAATGTAATTTTTGGAAGT-TTAGGTGTAAAAA
1 GTAAAAATGTAATTTTTAGAAGTATAAGG-GTAAAAA
333313 ATATTATTTT
Statistics
Matches: 129, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
56 3 0.02
57 14 0.11
58 108 0.84
59 4 0.03
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (57 bp):
GTAAAAATGTAATTTTTAGAAGTATAAGGGTAAAAATGTGATTTTTGGAAGTTGAGG
Found at i:333300 original size:87 final size:86
Alignment explanation
Indices: 333103--333385 Score: 250
Period size: 87 Copynumber: 3.2 Consensus size: 86
333093 AGGGTTTGAA
* * * * * * * * *
333103 GTAAAAATATGATTTTTGAGAAGTCCA-AGGCAAAAGTGTGATTTTTGGAAGTCTGAGGGTAAAA
1 GTAAAAATGTAATTTTTG-GAAGTTCAGGGGTAAAAATGTAATTTTTGGAAGTTTAAGGGTAAAA
* * *
333167 ATGTAATTTTTAGAATATAAGGG
65 ATATAATTTTGAGAAT-TTAGGG
* * *
333190 GTAAAAATGTGATTTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTAAGTGTAAAAA
1 GTAAAAATGTAATTTTTGGAAGTTCAGGGGTAAAAATGTAATTTTTGGAAGTTTAAGGGTAAAAA
333255 TATAATTTTGAGAAGTTTAGGG
66 TATAATTTTGAGAA-TTTAGGG
* * * * * *
333277 GTAAAAATGTAATTTTTGGAAGTTTAGGTGTAAAAA-ATATTATTTTGGAAAAGTTTAGGGGTTA
1 GTAAAAATGTAATTTTTGGAAGTTCAGGGGTAAAAATGTAAT-TTTTGG--AAGTTTAAGGGTAA
* *
333341 AAATA-AATTTTAGAAAAATTTAAGG
63 AAATATAATTTT-G-AGAATTTAGGG
*
333366 GTCAAAATGTAA-TTTTGGAA
1 GTAAAAATGTAATTTTTGGAA
333386 AAGTTTAGGG
Statistics
Matches: 164, Mismatches: 25, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
86 9 0.05
87 103 0.63
88 15 0.09
89 34 0.21
90 3 0.02
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (86 bp):
GTAAAAATGTAATTTTTGGAAGTTCAGGGGTAAAAATGTAATTTTTGGAAGTTTAAGGGTAAAAA
TATAATTTTGAGAATTTAGGG
Found at i:333322 original size:29 final size:28
Alignment explanation
Indices: 333145--333351 Score: 150
Period size: 29 Copynumber: 7.1 Consensus size: 28
333135 AAAGTGTGAT
* *
333145 TTTTGGAAGTCTGAGG-GTAAAAATGTAA
1 TTTTGGAAGT-TTAGGTGTAAAAATATAA
* * * * *
333173 TTTTTAGAA-TATAAGGGGTAAAAATGTGAT
1 -TTTTGGAAGT-TTAGGTGTAAAAATAT-AA
** * *
333203 TTTTGGAAGTTCGGGGGTAAAAATGTAA
1 TTTTGGAAGTTTAGGTGTAAAAATATAA
*
333231 TTTTTGGAAGTTTAAGTGTAAAAATATAA
1 -TTTTGGAAGTTTAGGTGTAAAAATATAA
* *
333260 TTTTGAGAAGTTTAGGGGTAAAAATGTAA
1 TTTTG-GAAGTTTAGGTGTAAAAATATAA
*
333289 TTTTTGGAAGTTTAGGTGTAAAAAATATTA
1 -TTTTGGAAGTTTAGGTGT-AAAAATATAA
* *
333319 TTTTGGAAAAGTTTAGGGGTTAAAATA-AA
1 TTTTGG--AAGTTTAGGTGTAAAAATATAA
333348 TTTT
1 TTTT
333352 AGAAAAATTT
Statistics
Matches: 147, Mismatches: 22, Indels: 18
0.79 0.12 0.10
Matches are distributed among these distances:
28 11 0.07
29 104 0.71
30 21 0.14
31 11 0.07
ACGTcount: A:0.37, C:0.01, G:0.24, T:0.38
Consensus pattern (28 bp):
TTTTGGAAGTTTAGGTGTAAAAATATAA
Found at i:333344 original size:30 final size:30
Alignment explanation
Indices: 333186--333395 Score: 175
Period size: 29 Copynumber: 7.1 Consensus size: 30
333176 TTAGAATATA
* * *
333186 AGGGGTAAAAATGTGATTTTTGG--AAGTTC
1 AGGGGTAAAAATAT-AATTTTGGAAAAGTTT
* *
333215 GGGGGTAAAAATGTAATTTTTGG--AAGTTT
1 AGGGGTAAAAATATAA-TTTTGGAAAAGTTT
* * *
333244 AAGTGTAAAAATATAATTTT-GAGAAGTTT
1 AGGGGTAAAAATATAATTTTGGAAAAGTTT
*
333273 AGGGGTAAAAATGTAATTTTTGG--AAGTTT
1 AGGGGTAAAAATATAA-TTTTGGAAAAGTTT
* *
333302 AGGTGTAAAAAATATTATTTTGGAAAAGTTT
1 AGGGGT-AAAAATATAATTTTGGAAAAGTTT
* * *
333333 AGGGGTTAAAATA-AATTTTAGAAAAATTT
1 AGGGGTAAAAATATAATTTTGGAAAAGTTT
* * *
333362 AAGGGTCAAAATGTAATTTTGGAAAAGTTT
1 AGGGGTAAAAATATAATTTTGGAAAAGTTT
333392 AGGG
1 AGGG
333396 ACCTTTTTGG
Statistics
Matches: 148, Mismatches: 24, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
27 1 0.01
28 5 0.03
29 95 0.64
30 35 0.24
31 12 0.08
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.36
Consensus pattern (30 bp):
AGGGGTAAAAATATAATTTTGGAAAAGTTT
Found at i:333350 original size:59 final size:59
Alignment explanation
Indices: 333159--333395 Score: 216
Period size: 58 Copynumber: 4.0 Consensus size: 59
333149 GGAAGTCTGA
* * * * * * **
333159 GGGTAAAAATGTAATTTTTAGAA-TATAAGGGGTAAAAATGTGATTTTTGG--AAGTTCGG
1 GGGTAAAAATGAAATTTTTGGAAGT-TTAGGTGTAAAAATAT-AATTTTGGAAAAGTTTAG
* * *
333217 GGGTAAAAATGTAATTTTTGGAAGTTTAAGTGTAAAAATATAATTTT-GAGAAGTTTAG
1 GGGTAAAAATGAAATTTTTGGAAGTTTAGGTGTAAAAATATAATTTTGGAAAAGTTTAG
* *
333275 GGGTAAAAATGTAATTTTTGGAAGTTTAGGTGTAAAAAATATTATTTTGGAAAAGTTTAG
1 GGGTAAAAATGAAATTTTTGGAAGTTTAGGTGT-AAAAATATAATTTTGGAAAAGTTTAG
* * * * * *
333335 GGGTTAAAAT-AAATTTTAGAAAAATTTAAGG-GTCAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTAAAAATGAAATTTTTG-GAAGTTT-AGGTGTAAAAATATAATTTTGGAAAAGTTTAG
333394 GG
1 GG
333396 ACCTTTTTGG
Statistics
Matches: 153, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
56 1 0.01
57 5 0.03
58 72 0.47
59 46 0.30
60 26 0.17
61 3 0.02
ACGTcount: A:0.39, C:0.01, G:0.24, T:0.36
Consensus pattern (59 bp):
GGGTAAAAATGAAATTTTTGGAAGTTTAGGTGTAAAAATATAATTTTGGAAAAGTTTAG
Found at i:334459 original size:12 final size:13
Alignment explanation
Indices: 334428--334469 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
334418 TATTCATTTC
334428 TTATTATT--TAT
1 TTATTATTAATAT
334439 TTATTATTAATAT
1 TTATTATTAATAT
334452 TT-TTATTAATAT
1 TTATTATTAATAT
334464 TATATT
1 T-TATT
334470 TAATATGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 8 0.30
12 11 0.41
13 6 0.22
14 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATTATTAATAT
Found at i:335071 original size:6 final size:6
Alignment explanation
Indices: 335060--335144 Score: 54
Period size: 6 Copynumber: 14.3 Consensus size: 6
335050 GGACATTATT
* ** *
335060 AATTTA AATTTA GAA--TA ATTTTA AATTTA AAAATA AATTTA AACTTA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
335107 AA-TTA AATTTTA AATTTTTA AA--TA AATTTA AACTTA AA
1 AATTTA AA-TTTA AA--TTTA AATTTA AATTTA AATTTA AA
335145 ATAAAATTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
4 5 0.08
5 7 0.11
6 37 0.59
7 7 0.11
8 7 0.11
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:335098 original size:12 final size:12
Alignment explanation
Indices: 335080--335174 Score: 72
Period size: 12 Copynumber: 8.1 Consensus size: 12
335070 TAGAATAATT
335080 TTAAATTTAAAA
1 TTAAATTTAAAA
* *
335092 ATAAATTTAAAC
1 TTAAATTTAAAA
*
335104 TTAAA-TTAAATT
1 TTAAATTTAAA-A
*
335116 TTAAATTTTTAAA
1 TTAAA-TTTAAAA
*
335129 -TAAATTTAAAC
1 TTAAATTTAAAA
*
335140 TTAAA-ATAAAA
1 TTAAATTTAAAA
**
335151 TTAACCTTAAAA
1 TTAAATTTAAAA
335163 -TAAATTTAAAA
1 TTAAATTTAAAA
335174 T
1 T
335175 GAATGGATTT
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
11 27 0.43
12 32 0.51
14 4 0.06
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
TTAAATTTAAAA
Found at i:335120 original size:36 final size:34
Alignment explanation
Indices: 335060--335172 Score: 122
Period size: 36 Copynumber: 3.2 Consensus size: 34
335050 GGACATTATT
*
335060 AATTTAAATTTAGAAT-AATTTTAAATTTAAAAATA
1 AATTTAAACTTA-AATAAATTTTAAATTT-AAAATA
*
335095 AATTTAAACTTAAATTAAATTTTAAATTTTTAAATA
1 AATTTAAACTTAAA-TAAATTTTAAA-TTTAAAATA
* **
335131 AATTTAAACTTAAAATAAA-ATTAACCTTAAAATA
1 AATTTAAACTT-AAATAAATTTTAAATTTAAAATA
335165 AATTTAAA
1 AATTTAAA
335173 ATGAATGGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
34 17 0.25
35 16 0.24
36 29 0.43
37 6 0.09
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.41
Consensus pattern (34 bp):
AATTTAAACTTAAATAAATTTTAAATTTAAAATA
Found at i:335148 original size:17 final size:17
Alignment explanation
Indices: 335060--335172 Score: 118
Period size: 17 Copynumber: 6.5 Consensus size: 17
335050 GGACATTATT
* *
335060 AATTTAAATTTAGAATA
1 AATTTAAACTTAAAATA
* *
335077 ATTTTAAATTTAAAAATA
1 AATTTAAACTT-AAAATA
*
335095 AATTTAAACTTAAATTA
1 AATTTAAACTTAAAATA
* *
335112 AATTTTAAATTTTTAAATA
1 AA-TTTAAA-CTTAAAATA
335131 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAATA
* *
335148 AAATTAACCTTAAAATA
1 AATTTAAACTTAAAATA
335165 AATTTAAA
1 AATTTAAA
335173 ATGAATGGAT
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
17 45 0.57
18 26 0.33
19 8 0.10
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.41
Consensus pattern (17 bp):
AATTTAAACTTAAAATA
Found at i:335762 original size:39 final size:39
Alignment explanation
Indices: 335609--336079 Score: 268
Period size: 39 Copynumber: 12.1 Consensus size: 39
335599 TGATCAGGGT
* * * *
335609 GAGATTTGTTGATGATGATCTGCCCGAAGCTCGGGGTAA
1 GAGATTTGCTGATGGTGATCTGCCCCAGGCTCGGGGTAA
* * * * * * * * *
335648 GAGA-TCGAATGGTTGTAATCTGTCTCATGATCGGGGTAA
1 GAGATTTG-CTGATGGTGATCTGCCCCAGGCTCGGGGTAA
** * * * *
335687 GAGATTTTTTTATGGTGATTTGCCCCTGGTTCGGGGTAA
1 GAGATTTGCTGATGGTGATCTGCCCCAGGCTCGGGGTAA
* * * *
335726 GAGATTTGTTGATGGTGATCTACCTCAGGCTTGGGGTAA
1 GAGATTTGCTGATGGTGATCTGCCCCAGGCTCGGGGTAA
* **** * ** * * *
335765 AAGATCAAATGGTGGCAATCTGCCCCATGATCAGGGTAA
1 GAGATTTGCTGATGGTGATCTGCCCCAGGCTCGGGGTAA
* * *
335804 AAGATTTGCTGA---TGATTTACCCCAGGCTCGGGGTAA
1 GAGATTTGCTGATGGTGATCTGCCCCAGGCTCGGGGTAA
* * *
335840 GAGA--T-C-GAATTGGTTGCACTTTGCCCCAGGCTCGAGATAA
1 GAGATTTGCTG-A-TGG-TG-A-TCTGCCCCAGGCTCGGGGTAA
* ** * *
335880 GAGATTTGTTGATGGTGGGCTACCCCAAGG-TGGGGGTAA
1 GAGATTTGCTGATGGTGATCTGCCCC-AGGCTCGGGGTAA
* *
335919 GAGATTTGCTAATGGTGATCTGCCCCAGGCTCAGGGTAA
1 GAGATTTGCTGATGGTGATCTGCCCCAGGCTCGGGGTAA
* *
335958 GAGA--T-C-GAATGGCTGCAATCTGCCCCAGGATC-GAGTAAA
1 GAGATTTGCTG-ATGG-TG--ATCTGCCCCAGGCTCGGGGT-AA
* *
335997 GAGATTTGCTGATGGTGATCTACCTCAGGCTCGGGGTAA
1 GAGATTTGCTGATGGTGATCTGCCCCAGGCTCGGGGTAA
*
336036 GAGATTTGCTGATGGTGATCTGCCTCAGGCTCGGGGTAA
1 GAGATTTGCTGATGGTGATCTGCCCCAGGCTCGGGGTAA
336075 GAGAT
1 GAGAT
336080 CGAATGACTG
Statistics
Matches: 321, Mismatches: 85, Indels: 52
0.70 0.19 0.11
Matches are distributed among these distances:
32 1 0.00
33 2 0.01
34 1 0.00
36 25 0.08
37 3 0.01
38 10 0.03
39 233 0.73
40 29 0.09
41 5 0.02
42 9 0.03
43 2 0.01
44 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.28
Consensus pattern (39 bp):
GAGATTTGCTGATGGTGATCTGCCCCAGGCTCGGGGTAA
Found at i:336020 original size:117 final size:117
Alignment explanation
Indices: 335823--336134 Score: 412
Period size: 117 Copynumber: 2.7 Consensus size: 117
335813 TGATGATTTA
* * * *
335823 CCCCAGGCTCGGGGTAAGAGATCGAATTGGTTGCACTTTGCCCCAGGCTCGAG-ATAAGAGATTT
1 CCCCAGGCTCGGGGTAAGAGATCGAA-TGGCTGCAATCTGCCCCAGGATCGAGTA-AAGAGATTT
* ** *
335887 GTTGATGGTGGGCTACCCCAAGG-TGGGGGTAAGAGATTTGCTAATGGTGATCTG
64 GCTGATGGTGATCTACCCC-AGGCTCGGGGTAAGAGATTTGCTAATGGTGATCTG
*
335941 CCCCAGGCTCAGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGATCGAGTAAAGAGATTTGC
1 CCCCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGATCGAGTAAAGAGATTTGC
* *
336006 TGATGGTGATCTACCTCAGGCTCGGGGTAAGAGATTTGCTGATGGTGATCTG
66 TGATGGTGATCTACCCCAGGCTCGGGGTAAGAGATTTGCTAATGGTGATCTG
* * * * * **
336058 CCTCAGGCTCGGGGTAAGAGATCGAATGACTGCAATCTACCCCAGGATCGGGTTAAGAGATTAAC
1 CCCCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGATCGAGTAAAGAGATTTGC
*
336123 TGATAGTGATCT
66 TGATGGTGATCT
336135 GCCTCAGGTT
Statistics
Matches: 172, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
116 3 0.02
117 143 0.83
118 26 0.15
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (117 bp):
CCCCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTGCCCCAGGATCGAGTAAAGAGATTTGC
TGATGGTGATCTACCCCAGGCTCGGGGTAAGAGATTTGCTAATGGTGATCTG
Found at i:336096 original size:78 final size:77
Alignment explanation
Indices: 335707--336134 Score: 281
Period size: 78 Copynumber: 5.5 Consensus size: 77
335697 TATGGTGATT
* * * * * * *
335707 TGCCCCTGGTTCGGGGTAAGAGATTTGTTGATGGTGATCTACCTCAGGCTTGGGGTAAAAGATCA
1 TGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGGTGATCTACCCCAGGCTCGGGGTAAGAGATCG
335772 AATGGTGGCAATC
66 AATGGT-GCAATC
* * * * *
335785 TGCCCCATGATCAGGGTAAAAGATTTGCTGA---TGATTTACCCCAGGCTCGGGGTAAGAGATCG
1 TGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGGTGATCTACCCCAGGCTCGGGGTAAGAGATCG
* *
335847 AATTGGTTGCACTT
66 AA-TGG-TGCAATC
* * * ** *
335861 TGCCCCAGGCTCGAGATAAGAGATTTGTTGATGGTGGGCTACCCCAAGG-TGGGGGTAAGAGATT
1 TGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGGTGATCTACCCC-AGGCTCGGGGTAAGAGA--
*
335925 TGCTAATGGTG--ATC
63 T-CGAATGGTGCAATC
* * * *
335939 TGCCCCAGGCTCAGGGTAAGAGA--T-C-GAATGGCTGCAATCTGCCCCAGGATC-GAGTAAAGA
1 TGCCCCAGGCTCGGGGTAAGAGATTTGCTG-ATGG-TG--ATCTACCCCAGGCTCGGGGT-AAGA
335999 GATTTGCTG-ATGGTG--ATC
61 GA--T-C-GAATGGTGCAATC
* * * *
336017 TACCTCAGGCTCGGGGTAAGAGATTTGCTGATGGTGATCTGCCTCAGGCTCGGGGTAAGAGATCG
1 TGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGGTGATCTACCCCAGGCTCGGGGTAAGAGATCG
*
336082 AATGACTGCAATC
66 AATG-GTGCAATC
* * * ** *
336095 TACCCCAGGATCGGGTTAAGAGATTAACTGATAGTGATCT
1 TGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGGTGATCT
336135 GCCTCAGGTT
Statistics
Matches: 275, Mismatches: 50, Indels: 50
0.73 0.13 0.13
Matches are distributed among these distances:
74 2 0.01
75 36 0.13
76 37 0.13
77 7 0.03
78 149 0.54
79 23 0.08
80 8 0.03
81 9 0.03
82 4 0.01
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.26
Consensus pattern (77 bp):
TGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGGTGATCTACCCCAGGCTCGGGGTAAGAGATCG
AATGGTGCAATC
Found at i:336151 original size:78 final size:78
Alignment explanation
Indices: 336014--336158 Score: 200
Period size: 78 Copynumber: 1.9 Consensus size: 78
336004 GCTGATGGTG
* * ** * * *
336014 ATCTACCTCAGGCTCGGGGTAAGAGATTTGCTGATGGTGATCTGCCTCAGGCTCGGGGTAAGAGA
1 ATCTACCCCAGGATCGGGGTAAGAGATTAACTGATAGTGATCTGCCTCAGGCTCAGGGTAAAAGA
336079 TCGAATGACTGCA
66 TCGAATGACTGCA
* * *
336092 ATCTACCCCAGGATCGGGTTAAGAGATTAACTGATAGTGATCTGCCTCAGGTTTAGGGTAAAAGA
1 ATCTACCCCAGGATCGGGGTAAGAGATTAACTGATAGTGATCTGCCTCAGGCTCAGGGTAAAAGA
336157 TC
66 TC
336159 AGATCTTCAA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
78 57 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (78 bp):
ATCTACCCCAGGATCGGGGTAAGAGATTAACTGATAGTGATCTGCCTCAGGCTCAGGGTAAAAGA
TCGAATGACTGCA
Found at i:346941 original size:17 final size:17
Alignment explanation
Indices: 346899--346933 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
346889 CCCACATGTT
*
346899 TGCACAAAAGTGAAAAC
1 TGCACGAAAGTGAAAAC
346916 TGCACGAAAGTGAAAAC
1 TGCACGAAAGTGAAAAC
346933 T
1 T
346934 TTACGAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.17, G:0.20, T:0.14
Consensus pattern (17 bp):
TGCACGAAAGTGAAAAC
Found at i:347851 original size:97 final size:97
Alignment explanation
Indices: 347680--347860 Score: 308
Period size: 97 Copynumber: 1.9 Consensus size: 97
347670 TTGAAAAAGG
* *
347680 GTATTCGATTATCCCGGTTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGCACAAATTTCCAAAAC
1 GTATTCGAATATCCCAGTTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGCACAAATTTCCAAAAC
*
347745 CCGATATAAAGGAATATTGACTTGATTTAAGT
66 CCGAGATAAAGGAATATTGACTTGATTTAAGT
* * *
347777 GTATTCGAATATCCCAGTTTGAAGAAAAATCGTGTCTAGTAAGTTAAGGCACAAATTTTCAAAAT
1 GTATTCGAATATCCCAGTTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGCACAAATTTCCAAAAC
347842 CCGAGATAAAGGAATATTG
66 CCGAGATAAAGGAATATTG
347861 CCTCAATTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 78 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (97 bp):
GTATTCGAATATCCCAGTTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGCACAAATTTCCAAAAC
CCGAGATAAAGGAATATTGACTTGATTTAAGT
Found at i:348020 original size:14 final size:15
Alignment explanation
Indices: 348001--348039 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
347991 AGCACGAATG
348001 AATAAATATACG-AA
1 AATAAATATACGAAA
*
348015 AATAAATATAAGAAA
1 AATAAATATACGAAA
348030 AATAAA-ATAC
1 AATAAATATAC
348040 AAATTATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (15 bp):
AATAAATATACGAAA
Found at i:348273 original size:29 final size:30
Alignment explanation
Indices: 348239--348542 Score: 224
Period size: 29 Copynumber: 10.5 Consensus size: 30
348229 AGAGTTCGGA
*
348239 GTAAAAATATGATTTTTGAGAAGTCCG-GG
1 GTAAAAATGTGATTTTTGAGAAGTCCGAGG
* * **
348268 GCAAAAGTGTGATTTTTG-GAAGTTTG-GAG
1 GTAAAAATGTGATTTTTGAGAAGTCCGAG-G
* * * *
348297 GCAAAAATGTAATTTTT-AGAAG-CTTGAGA
1 GTAAAAATGTGATTTTTGAGAAGTC-CGAGG
*
348326 GTAAAAATGTGATTTTT-AGAAGTTCGAGG
1 GTAAAAATGTGATTTTTGAGAAGTCCGAGG
*
348355 GTAAAAATGTGATTTTTG-GAAGTTCAGAGG
1 GTAAAAATGTGATTTTTGAGAAG-TCCGAGG
* ** *
348385 GT-AAAATAT-ATTTTTG-GAAGTTTGGGG
1 GTAAAAATGTGATTTTTGAGAAGTCCGAGG
* * *
348412 GTAAAAATTTAATTTTTGAGAAGTTCGAGG
1 GTAAAAATGTGATTTTTGAGAAGTCCGAGG
**
348442 GT-AAAATGT-A-TTTTG-GAAGTTTGAGG
1 GTAAAAATGTGATTTTTGAGAAGTCCGAGG
* * * * *
348468 GTAAAATTGTAATTTTTGAGATGTTCGTGG
1 GTAAAAATGTGATTTTTGAGAAGTCCGAGG
* * *
348498 GTAAAAATGTAAATTTTG-GAAGTTCGAGG
1 GTAAAAATGTGATTTTTGAGAAGTCCGAGG
348527 GTAAAAATGTGATTTT
1 GTAAAAATGTGATTTT
348543 GGAAAAGTTG
Statistics
Matches: 226, Mismatches: 35, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
26 12 0.05
27 17 0.08
28 26 0.12
29 128 0.57
30 43 0.19
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (30 bp):
GTAAAAATGTGATTTTTGAGAAGTCCGAGG
Found at i:348305 original size:87 final size:85
Alignment explanation
Indices: 348236--348546 Score: 287
Period size: 86 Copynumber: 3.6 Consensus size: 85
348226 GGGAGAGTTC
* *
348236 GGAGTAAAAATATGATTTTTGAGAAGTCCG-GGGCAAAAGTGTGATTTTTGGAAGTTTGGAGGCA
1 GGAGTAAAAATATGATTTTTGAGAAGTTCGAGGGTAAAA-TGTGATTTTTGGAAGTTTGGAGGCA
*
348300 AAAATGTAATTTTTAGAAGCTT
65 AAAATGT-ATTTTTGGAAGCTT
* ** *
348322 GAGAGTAAAAATGTGATTTTT-AGAAGTTCGAGGGTAAAAATGTGATTTTTGGAAGTTCAGAGGG
1 G-GAGTAAAAATATGATTTTTGAGAAGTTCGAGGGT-AAAATGTGATTTTTGGAAGTTTGGAGGC
* * *
348386 TAAAATATATTTTTGGAAGTTT
64 AAAAATGTATTTTTGGAAGCTT
* * * *
348408 GGGGGTAAAAATTTAATTTTTGAGAAGTTCGAGGGTAAAATGT-A-TTTTGGAAGTTT-GAGGGT
1 -GGAGTAAAAATATGATTTTTGAGAAGTTCGAGGGTAAAATGTGATTTTTGGAAGTTTGGA-GGC
* *
348470 AAAATTGTAATTTTTGAGATG-TT
64 AAAAATGT-ATTTTTG-GAAGCTT
* * * *
348493 CGTGGGTAAAAATGTAAATTTTG-GAAGTTCGAGGGTAAAAATGTGA-TTTTGGAA
1 -G-GAGTAAAAATATGATTTTTGAGAAGTTCGAGGGT-AAAATGTGATTTTTGGAA
348547 AAGTTGGAGG
Statistics
Matches: 192, Mismatches: 22, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
83 2 0.01
84 18 0.09
85 24 0.12
86 72 0.38
87 72 0.38
88 4 0.02
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (85 bp):
GGAGTAAAAATATGATTTTTGAGAAGTTCGAGGGTAAAATGTGATTTTTGGAAGTTTGGAGGCAA
AAATGTATTTTTGGAAGCTT
Found at i:348416 original size:57 final size:58
Alignment explanation
Indices: 348239--348564 Score: 335
Period size: 58 Copynumber: 5.6 Consensus size: 58
348229 AGAGTTCGGA
* * * *
348239 GTAAAAATATGATTTTTGAGAAGTCCG-GGGCAAAAGTGTGATTTTTGGAAGTTTG-GAG
1 GTAAAAATGTAATTTTTGAGAAGTTCGAGGGTAAAA-TGTGATTTTTGGAAGTTTGAG-G
* * * *
348297 GCAAAAATGTAATTTTT-AGAAGCTT-GAGAGTAAAAATGTGATTTTTAGAAGTTCGAGG
1 GTAAAAATGTAATTTTTGAGAAG-TTCGAGGGT-AAAATGTGATTTTTGGAAGTTTGAGG
* * *
348355 GTAAAAATGTGATTTTTG-GAAGTTCAGAGGGTAAAATAT-ATTTTTGGAAGTTTGGGG
1 GTAAAAATGTAATTTTTGAGAAGTTC-GAGGGTAAAATGTGATTTTTGGAAGTTTGAGG
*
348412 GTAAAAATTTAATTTTTGAGAAGTTCGAGGGTAAAATGT-A-TTTTGGAAGTTTGAGG
1 GTAAAAATGTAATTTTTGAGAAGTTCGAGGGTAAAATGTGATTTTTGGAAGTTTGAGG
* * * * * *
348468 GTAAAATTGTAATTTTTGAGATGTTCGTGGGTAAAAATGTAAATTTTGGAAGTTCGAGG
1 GTAAAAATGTAATTTTTGAGAAGTTCGAGGGT-AAAATGTGATTTTTGGAAGTTTGAGG
* * * *
348527 GTAAAAATGTGATTTTGGAAAAGTTGGAGGGTTAAAAT
1 GTAAAAATGTAATTTTTGAGAAGTTCGAGGG-TAAAAT
348565 AAAATTTTAG
Statistics
Matches: 225, Mismatches: 31, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
56 43 0.19
57 59 0.26
58 68 0.30
59 54 0.24
60 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (58 bp):
GTAAAAATGTAATTTTTGAGAAGTTCGAGGGTAAAATGTGATTTTTGGAAGTTTGAGG
Found at i:348557 original size:30 final size:29
Alignment explanation
Indices: 348299--348607 Score: 217
Period size: 30 Copynumber: 10.7 Consensus size: 29
348289 GTTTGGAGGC
* *
348299 AAAAATGTAATTTT-TAGAAGCTT-GAGAGT
1 AAAAATGTAATTTTGGA-AAG-TTCGAGGGT
* *
348328 AAAAATGTGATTTT-TAGAAGTTCGAGGGT
1 AAAAATGTAATTTTGGA-AAGTTCGAGGGT
*
348357 AAAAATGTGATTTTTGG-AAGTTCAGAGGGT
1 AAAAATGT-AATTTTGGAAAGTTC-GAGGGT
* * * *
348387 -AAAATATATTTTTGG-AAGTTTGGGGGT
1 AAAAATGTAATTTTGGAAAGTTCGAGGGT
* *
348414 AAAAATTTAATTTTTGAGAAGTTCGAGGGT
1 AAAAATGTAATTTTGGA-AAGTTCGAGGGT
*
348444 -AAAATGT-ATTTTGG-AAGTTTGAGGGT
1 AAAAATGTAATTTTGGAAAGTTCGAGGGT
* * * *
348470 AAAATTGTAATTTTTGAGATGTTCGTGGGT
1 AAAAATGTAATTTTGGA-AAGTTCGAGGGT
348500 AAAAATGTAAATTTTGG-AAGTTCGAGGGT
1 AAAAATGT-AATTTTGGAAAGTTCGAGGGT
* *
348529 AAAAATGTGATTTTGGAAAAGTTGGAGGGT
1 AAAAATGTAATTTTGG-AAAGTTCGAGGGT
* ** * * *
348559 TAAAATAAAATTTTAGAAAAATT-TAGGGGT
1 AAAAATGTAATTTT-GGAAAGTTCGA-GGGT
*
348589 CAAAATGTAATTTTGGAAA
1 AAAAATGTAATTTTGGAAA
348608 AGTTTAGGGA
Statistics
Matches: 226, Mismatches: 38, Indels: 32
0.76 0.13 0.11
Matches are distributed among these distances:
26 11 0.05
27 11 0.05
28 46 0.20
29 73 0.32
30 77 0.34
31 8 0.04
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (29 bp):
AAAAATGTAATTTTGGAAAGTTCGAGGGT
Found at i:350310 original size:17 final size:17
Alignment explanation
Indices: 350288--350412 Score: 151
Period size: 17 Copynumber: 7.2 Consensus size: 17
350278 ATTATTAATA
* *
350288 TAAATTTAGAATAATTT
1 TAAATTTAAAATAAATT
350305 TAAATTTAAAAATAAATT
1 TAAATTT-AAAATAAATT
* *
350323 TAAACTTAAATTAAATT
1 TAAATTTAAAATAAATT
* *
350340 TAAATTTTTAAACAAATT
1 TAAA-TTTAAAATAAATT
*
350358 TAAACTTAAAATAAATT
1 TAAATTTAAAATAAATT
350375 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATT
**
350392 TAACCTTAAAATAAATT
1 TAAATTTAAAATAAATT
350409 TAAA
1 TAAA
350413 ATAAATGAGT
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
17 64 0.70
18 27 0.30
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:350314 original size:6 final size:6
Alignment explanation
Indices: 350303--350412 Score: 70
Period size: 6 Copynumber: 19.0 Consensus size: 6
350293 TTAGAATAAT
** *
350303 TTTAAA TTTAAA AATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA --TTTAAA
* * * * *
350352 --CAAA TTTAAA CTTAAA -ATAAA TTTAAA TTTAAA -ATAAA TTTAAC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
350396 CTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
350413 ATAAATGAGT
Statistics
Matches: 79, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
4 3 0.04
5 17 0.22
6 53 0.67
8 6 0.08
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:350357 original size:35 final size:35
Alignment explanation
Indices: 350288--350412 Score: 171
Period size: 35 Copynumber: 3.6 Consensus size: 35
350278 ATTATTAATA
* * * *
350288 TAAATTTAGAATAATTTTAAATTTAAAAATAAATT
1 TAAACTTAAAATAAATTTAAATTTTAAAATAAATT
* * *
350323 TAAACTTAAATTAAATTTAAATTTTTAAACAAATT
1 TAAACTTAAAATAAATTTAAATTTTAAAATAAATT
350358 TAAACTTAAAATAAATTTAAA-TTTAAAATAAATT
1 TAAACTTAAAATAAATTTAAATTTTAAAATAAATT
*
350392 TAACCTTAAAATAAATTTAAA
1 TAAACTTAAAATAAATTTAAA
350413 ATAAATGAGT
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
34 31 0.39
35 48 0.61
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (35 bp):
TAAACTTAAAATAAATTTAAATTTTAAAATAAATT
Found at i:356778 original size:12 final size:13
Alignment explanation
Indices: 356757--356866 Score: 54
Period size: 12 Copynumber: 8.7 Consensus size: 13
356747 TATGGGTAAC
356757 AAAT-AAATAAA-
1 AAATAAAATAAAT
356768 AAATAAAATAAAT
1 AAATAAAATAAAT
*
356781 AATTAAAAT-AAT
1 AAATAAAATAAAT
*
356793 GCAAATTAAATAAAT
1 --AAATAAAATAAAT
* *
356808 AAA-AAAGTAAGT
1 AAATAAAATAAAT
* *
356820 AATTAAAAT-CAT
1 AAATAAAATAAAT
*
356832 GCAAATTAAATAAAT
1 --AAATAAAATAAAT
*
356847 -AA-AAAATAAGT
1 AAATAAAATAAAT
*
356858 AATTAAAAT
1 AAATAAAAT
356867 TATGCAAATT
Statistics
Matches: 72, Mismatches: 16, Indels: 20
0.67 0.15 0.19
Matches are distributed among these distances:
11 11 0.15
12 22 0.31
13 20 0.28
14 14 0.19
15 5 0.07
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:356803 original size:39 final size:38
Alignment explanation
Indices: 356756--356888 Score: 196
Period size: 38 Copynumber: 3.5 Consensus size: 38
356746 ATATGGGTAA
*
356756 CAAA-TAAATAAAAAATAAAATAAATAATTAAAATAATG
1 CAAATTAAATAAAAAA-AAAATAAGTAATTAAAATAATG
* *
356794 CAAATTAAATAAATAAAAAAGTAAGTAATTAAAATCATG
1 CAAATTAAATAAA-AAAAAAATAAGTAATTAAAATAATG
* *
356833 CAAATTAAATAAATAAAAAATAAGTAATTAAAATTATG
1 CAAATTAAATAAAAAAAAAATAAGTAATTAAAATAATG
356871 CAAATTAAATAAAAAAAA
1 CAAATTAAATAAAAAAAA
356889 TAAGGAGGAC
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
38 43 0.50
39 40 0.47
40 3 0.03
ACGTcount: A:0.67, C:0.04, G:0.05, T:0.25
Consensus pattern (38 bp):
CAAATTAAATAAAAAAAAAATAAGTAATTAAAATAATG
Found at i:360972 original size:3 final size:3
Alignment explanation
Indices: 360964--361012 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
360954 ATAAACTATG
* *
360964 TAT TAT TAT TAT TAT TAT TCT TAT TAT TCT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
361012 T
1 T
361013 CTTTTGTGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:361232 original size:72 final size:73
Alignment explanation
Indices: 361104--361277 Score: 165
Period size: 72 Copynumber: 2.4 Consensus size: 73
361094 TTCTTAACTT
* * **
361104 TTATATATATATAGTATGTATATATTGACCACATACATTCTCCTTCCTTAATTTATA-CATATAT
1 TTATTTATATATAGTATGAATATATTGACCACATACACACTCCTTCCTTAATTTATAGCATATAT
* *
361168 ATGGTTTA
66 ATAGCTTA
* ** * *
361176 TTATTTATATATAGTATGAATATATT-AGCCATATACACACTGTTTTCTCTAA-TTATATGTATA
1 TTATTTATATATAGTATGAATATATTGA-CCACATACACACTCCTTCCT-TAATTTATA-GCATA
361239 TATATAGCTTA
63 TATATAGCTTA
* *
361250 TTGTTTATATATAGAATGTAAATATATT
1 TTATTTATATATAGTATG--AATATATT
361278 TTATTCTGTA
Statistics
Matches: 83, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
71 1 0.01
72 43 0.52
73 3 0.04
74 28 0.34
76 8 0.10
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (73 bp):
TTATTTATATATAGTATGAATATATTGACCACATACACACTCCTTCCTTAATTTATAGCATATAT
ATAGCTTA
Found at i:372818 original size:50 final size:50
Alignment explanation
Indices: 372747--372874 Score: 186
Period size: 50 Copynumber: 2.6 Consensus size: 50
372737 ATCTTTTACC
* * * *
372747 CCTAAAGCTATGGAGGTGCAGATTGAAGCCGCAATGGTAAATCTCA-TACA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATGGCAAATCTCACT-CA
*
372797 CCTAAAGCTGTAGAGGGGCAGAATGAAGCCGCAATGGCAAATCTCACTCA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATGGCAAATCTCACTCA
*
372847 CCTAAAGCTGTAGAGGGGCATATTGAAG
1 CCTAAAGCTGTAGAGGGGCAGATTGAAG
372875 TCACAAGGAT
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 69 0.99
51 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.20
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCAATGGCAAATCTCACTCA
Found at i:373021 original size:40 final size:40
Alignment explanation
Indices: 372951--373157 Score: 153
Period size: 40 Copynumber: 5.3 Consensus size: 40
372941 CTCAACCATG
* * *
372951 GGGCAAATTGAAGTAATTCA-AGTCTTTTACCCTAACCAGA
1 GGGCAGATTGAAGCAATCCAGA-TCTTTTACCCTAACCAGA
* * * **
372991 GGGCAGATTGAAGTAATCTAGATCTCTTACCCCGACCATG-
1 GGGCAGATTGAAGCAATCCAGATCTTTTACCCTAACCA-GA
* * *
373031 GGGCAGATT-AAGCCAT-TAGATCTTTTACCCTAACTAGA
1 GGGCAGATTGAAGCAATCCAGATCTTTTACCCTAACCAGA
* * * *
373069 GGGCAGATTGAAGACCA-CCAGATCTCTTA-TCTCGACCATG-
1 GGGCAGATTGAAG-CAATCCAGATCTTTTACCCT-AACCA-GA
*
373109 GGGTAGATTGAAGCAATCCA-A-CTTTTACCCTAACCAGA
1 GGGCAGATTGAAGCAATCCAGATCTTTTACCCTAACCAGA
*
373147 AGGCAGATTGA
1 GGGCAGATTGA
373158 GACAATCTAA
Statistics
Matches: 132, Mismatches: 24, Indels: 24
0.73 0.13 0.13
Matches are distributed among these distances:
37 2 0.02
38 43 0.33
39 15 0.11
40 69 0.52
41 3 0.02
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (40 bp):
GGGCAGATTGAAGCAATCCAGATCTTTTACCCTAACCAGA
Found at i:373062 original size:78 final size:78
Alignment explanation
Indices: 372945--373161 Score: 255
Period size: 78 Copynumber: 2.8 Consensus size: 78
372935 TTTTAGCTCA
* * *
372945 ACCATGGGGCAAATTGAAGTAATTCAAGTCTTTTACCCTAACCAGAGGGCAGATTGAAGTA-ATC
1 ACCATGGGGCAGATTGAAGCAATCCAA-TCTTTTACCCTAACCAGAGGGCAGATTGAAG-ACA-C
*
373009 TAGATCTCTTACCCCG
63 CAGATCTCTTACCCCG
* * *
373025 ACCATGGGGCAGATT-AAGCCAT-TAGATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCACC
1 ACCATGGGGCAGATTGAAGCAATCCA-ATCTTTTACCCTAACCAGAGGGCAGATTGAAGA-CACC
* *
373088 AGATCTCTTATCTCG
64 AGATCTCTTACCCCG
* *
373103 ACCATGGGGTAGATTGAAGCAATCCAA-CTTTTACCCTAACCAGAAGGCAGATTG-AGACA
1 ACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACA
373162 ATCTAATTTT
Statistics
Matches: 119, Mismatches: 13, Indels: 14
0.82 0.09 0.10
Matches are distributed among these distances:
76 2 0.02
77 4 0.03
78 84 0.71
79 14 0.12
80 15 0.13
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (78 bp):
ACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACACCAG
ATCTCTTACCCCG
Found at i:373923 original size:3 final size:3
Alignment explanation
Indices: 373915--373945 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
373905 TGCCGTCACT
*
373915 GTC GTC GTC GTC GTC GTC GTC GTC ATC GTC G
1 GTC GTC GTC GTC GTC GTC GTC GTC GTC GTC G
373946 ATTTCGTCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.32, G:0.32, T:0.32
Consensus pattern (3 bp):
GTC
Found at i:375038 original size:3 final size:3
Alignment explanation
Indices: 375030--375069 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
375020 ATAAACTATG
375030 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
375070 TTGTGTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:375245 original size:72 final size:70
Alignment explanation
Indices: 375098--375247 Score: 167
Period size: 72 Copynumber: 2.1 Consensus size: 70
375088 TTCCTAACTT
* * * *
375098 ATATATATGGTTTTTTTTATATATAGTATGTATATATTCACCACATACATTCTGCTTCCTTAATT
1 ATATATATGGTTTTTTTTAAATATAGTATGAATATATTCACCACATACATACTGCTTCCTTAAAT
*
375163 TTTAC
66 TATAC
* * * *
375168 ATATATATGGTTTATTATTTAAATATAGTATGAATATATT-AGTCATATACATAGTGTTTCCTTA
1 ATATATATGGTTT-TT-TTTAAATATAGTATGAATATATTCA-CCACATACATACTGCTTCCTTA
*
375232 AATTATAT
63 AATTATAC
*
375240 GTATATAT
1 ATATATAT
375248 ATAGTTAATT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
70 13 0.20
71 3 0.05
72 50 0.76
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (70 bp):
ATATATATGGTTTTTTTTAAATATAGTATGAATATATTCACCACATACATACTGCTTCCTTAAAT
TATAC
Found at i:376484 original size:36 final size:36
Alignment explanation
Indices: 376391--376490 Score: 146
Period size: 36 Copynumber: 2.8 Consensus size: 36
376381 CGTTATTCGA
* * *
376391 TTTACTCCTTGTTGATCCAAAAGTCATGATACTCAT
1 TTTACTCCCTGTTGACCCAAAGGTCATGATACTCAT
* *
376427 TTTACTCCCTATTGACCCAAAGGTCATGATAGTCAT
1 TTTACTCCCTGTTGACCCAAAGGTCATGATACTCAT
*
376463 TTTACTCCCTGTTGACCCAAAGATCATG
1 TTTACTCCCTGTTGACCCAAAGGTCATG
376491 CTTGTTACCA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (36 bp):
TTTACTCCCTGTTGACCCAAAGGTCATGATACTCAT
Found at i:388702 original size:20 final size:20
Alignment explanation
Indices: 388666--388703 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
388656 AAAAAGGTAA
*
388666 AAATAACAAGAATTTAAACC
1 AAATAACAAGAAGTTAAACC
388686 AAATAACAATG-AGTTAAA
1 AAATAACAA-GAAGTTAAA
388704 AAACATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.61, C:0.11, G:0.08, T:0.21
Consensus pattern (20 bp):
AAATAACAAGAAGTTAAACC
Found at i:402248 original size:20 final size:20
Alignment explanation
Indices: 402212--402249 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
402202 AAAAAGGTAA
*
402212 AAATAACAAGAATTTAAACC
1 AAATAACAAGAAGTTAAACC
402232 AAATAACAATG-AGTTAAA
1 AAATAACAA-GAAGTTAAA
402250 AAACATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.61, C:0.11, G:0.08, T:0.21
Consensus pattern (20 bp):
AAATAACAAGAAGTTAAACC
Found at i:413426 original size:21 final size:21
Alignment explanation
Indices: 413402--413450 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
413392 ACTATGACAG
* *
413402 TTCTACCGATACAAGTAAAGC
1 TTCTACCGAAACAAATAAAGC
* *
413423 TTCTACCGAAACAAATCATGC
1 TTCTACCGAAACAAATAAAGC
413444 TTCTACC
1 TTCTACC
413451 AGTACTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.29, G:0.10, T:0.27
Consensus pattern (21 bp):
TTCTACCGAAACAAATAAAGC
Found at i:414629 original size:193 final size:192
Alignment explanation
Indices: 414203--414641 Score: 494
Period size: 193 Copynumber: 2.3 Consensus size: 192
414193 TACCAGTACT
* * * * *
414203 CGATGCTGCTCACACGAGTTGTCGAGGACTCGCAACGTATGCGGTACCCCAGCCACCGATATGGT
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCACCGAGATGAT
* * * *
414268 GCCTGTCTGTACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAGTATGCATA
66 -CCTG-CTGCACTATAAACAGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATACATA
* *
414333 AAGCATAGTCCTAACCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTTCGAGTCA
129 AAGCATAATCCTAACCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTTCGACTCA
* * * *
414397 TGATGCTGCTCACACGAGCTGTCGAGGACTTGCAACATATGCGGTACCTTAGCCATCGACGAT-A
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCACCGA-GATGA
* * *
414461 T-CTG-TGCA-TATAAA-AGTTCCCTAATGATGCTGCTCACATGAGCTGTCGAGAATATACACTT
65 TCCTGCTGCACTATAAACAGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATACA-TA
* * * * * * * *
414522 ATGCATAAAT-ATCAGCCATCGTAGGGCCTGTAATCCATTCTTGGATTCTTTTCTCATTTCTCGA
129 AAGCAT-AATCCT-AACCATCGTAGGGCCTATAATCCATT-TAGGATCCATATCTC-TTT-TCGA
414586 CTCA
189 CTCA
* * *
414590 CGATGCTGGTCACACGAGCTGTCGAGGACTCGTAACATATGAGGTACCTCAG
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAG
414642 TCATTGCGTC
Statistics
Matches: 206, Mismatches: 32, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
188 39 0.19
189 13 0.06
190 29 0.14
191 11 0.05
192 6 0.03
193 53 0.26
194 53 0.26
195 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (192 bp):
CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCACCGAGATGAT
CCTGCTGCACTATAAACAGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATACATAAA
GCATAATCCTAACCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTTCGACTCA
Found at i:419179 original size:195 final size:194
Alignment explanation
Indices: 418786--419231 Score: 472
Period size: 195 Copynumber: 2.3 Consensus size: 194
418776 TACCAGTAGT
* * * * *
418786 CGATGCTACTCACACGAACTATCGAGGACTCGCAACGTATACGGTACCCCAGCCATCGATACGGT
1 CGATGCTACTCACACGAGCTGTCGAGGACTCGCAACATATACGGTACCTCAGCCATCGATACGAT
* * ** * * *
418851 GCCTGTCTGTACTATAAACTGTTCCCTAACGATGCTGGTCACATGAGTTGTCTAGAGTATGCGTA
66 ACCTG-CTGCACTATAAACAATTCCCTAACGATGCTGCTCACATGAGTTGTCGAGAATATGCGTA
* * * * * *
418916 AAGCATACTCCCAGCCATCGTAGGGTCTATAATCCATTTAGGATCCATATCTCTTTCCCGAGTCA
130 AAGCATAATCCCAACCATCGTAAGGCCTATAATCCATTTAGGATCCATATCTCTTTCCCAACTCA
* **
418981 CGATGCTACTAACACGAGCTGTCGAGGACTCATAACATATACGGTACCTCAGCCATCGATACGAT
1 CGATGCTACTCACACGAGCTGTCGAGGACTCGCAACATATACGGTACCTCAGCCATCGATACGAT
* *
419046 ATCTG-TGCA-TAT-AACAATTCCCTAACGATGCTGCTCAGATGAGTTGTCGAGAATATGAAC-T
66 ACCTGCTGCACTATAAACAATTCCCTAACGATGCTGCTCACATGAGTTGTCGAGAATATG--CGT
* * * * * * * * *
419107 TATGCATAAATCTCAACTATCGTAAGGCCTATAATCCATTCTTA-GATTCTTTTTTCATTTCCTA
129 AAAGCAT-AATCCCAACCATCGTAAGGCCTATAATCCA-T-TTAGGATCCATATCTC-TTTCCCA
419171 ACTCA
190 ACTCA
* *
419176 CGATGCTGA-TCACATGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAGCCAT
1 CGATGCT-ACTCACACGAGCTGTCGAGGACTCGCAACATATACGGTACCTCAGCCAT
419232 TGCGTCAGTT
Statistics
Matches: 207, Mismatches: 37, Indels: 14
0.80 0.14 0.05
Matches are distributed among these distances:
191 39 0.19
192 9 0.04
193 28 0.14
194 9 0.04
195 121 0.58
196 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (194 bp):
CGATGCTACTCACACGAGCTGTCGAGGACTCGCAACATATACGGTACCTCAGCCATCGATACGAT
ACCTGCTGCACTATAAACAATTCCCTAACGATGCTGCTCACATGAGTTGTCGAGAATATGCGTAA
AGCATAATCCCAACCATCGTAAGGCCTATAATCCATTTAGGATCCATATCTCTTTCCCAACTCA
Found at i:419730 original size:16 final size:16
Alignment explanation
Indices: 419706--419737 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
419696 TCCTTACAAA
*
419706 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
419722 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
419738 AAAAATCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:427166 original size:27 final size:27
Alignment explanation
Indices: 427136--427295 Score: 126
Period size: 27 Copynumber: 5.9 Consensus size: 27
427126 TTGGTAACCT
* *
427136 GACCCGTTGACCCAAGTTGATCGACCA
1 GACCCATTGACCCGAGTTGATCGACCA
* *
427163 GACCCATTGACCCGAGTTGACCGACCC
1 GACCCATTGACCCGAGTTGATCGACCA
* ** *
427190 GACCTATTGACCAAAGTTGATCTACCCA
1 GACCCATTGACCCGAGTTGATCGA-CCA
* * *
427218 -ACCCGTTAAACCGAGTTGATCGACTC-
1 GACCCATTGACCCGAGTTGATCGAC-CA
* * *
427244 GACCCATTGAACCGAGTTGATCGATCT
1 GACCCATTGACCCGAGTTGATCGACCA
* * * *
427271 GTCCCGTTAACCCGAGTTAATCGAC
1 GACCCATTGACCCGAGTTGATCGAC
427296 ACAACCTGTT
Statistics
Matches: 103, Mismatches: 26, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
26 2 0.02
27 99 0.96
28 2 0.02
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (27 bp):
GACCCATTGACCCGAGTTGATCGACCA
Found at i:427200 original size:54 final size:54
Alignment explanation
Indices: 427136--427267 Score: 149
Period size: 54 Copynumber: 2.4 Consensus size: 54
427126 TTGGTAACCT
* * *
427136 GACCCGTTGACCCAAGTTGATCGA-CCAGACCCATTGACCCGAGTTGACCGACCC
1 GACCCATTGACCCAAGTTGATCGACCCA-ACCCATTAAACCGAGTTGACCGACCC
* * * * * *
427190 GACCTATTGACCAAAGTTGATCTACCCAACCCGTTAAACCGAGTTGATCGACTC
1 GACCCATTGACCCAAGTTGATCGACCCAACCCATTAAACCGAGTTGACCGACCC
* *
427244 GACCCATTGAACCGAGTTGATCGA
1 GACCCATTGACCCAAGTTGATCGA
427268 TCTGTCCCGT
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
54 60 0.95
55 3 0.05
ACGTcount: A:0.27, C:0.32, G:0.20, T:0.20
Consensus pattern (54 bp):
GACCCATTGACCCAAGTTGATCGACCCAACCCATTAAACCGAGTTGACCGACCC
Found at i:427366 original size:27 final size:27
Alignment explanation
Indices: 427310--427376 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
427300 CCTGTTGATC
* * *
427310 GACCCGACCTAATGACTTGAGTTGACT
1 GACCCGACCTATTGACTCGAGTTAACT
** *
427337 GACTTGACCTATTGACTCGAGTTAATT
1 GACCCGACCTATTGACTCGAGTTAACT
427364 GACCCGACCTATT
1 GACCCGACCTATT
427377 AACTTTGACC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (27 bp):
GACCCGACCTATTGACTCGAGTTAACT
Found at i:427434 original size:26 final size:26
Alignment explanation
Indices: 427389--427456 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
427379 CTTTGACCAG
* *
427389 TTGACC-TGACCCATTGACTTTAACT
1 TTGACCTTGATCCGTTGACTTTAACT
*
427414 TTGACCTTGATCCGTTGACTTTGACT
1 TTGACCTTGATCCGTTGACTTTAACT
427440 TTGACCTTGAT-CGTTGA
1 TTGACCTTGATCCGTTGA
427457 TGTAATAGCC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
25 12 0.31
26 27 0.69
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (26 bp):
TTGACCTTGATCCGTTGACTTTAACT
Found at i:437698 original size:21 final size:21
Alignment explanation
Indices: 437674--437724 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
437664 GTCTTGTTTT
* * *
437674 GGTAGAAGTTTCACTTGTATC
1 GGTAGAACTATCACTGGTATC
*
437695 GGTATAACTATCACTGGTATC
1 GGTAGAACTATCACTGGTATC
437716 GGTAGAACT
1 GGTAGAACT
437725 CTACACTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (21 bp):
GGTAGAACTATCACTGGTATC
Found at i:439599 original size:3 final size:3
Alignment explanation
Indices: 439591--439631 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
439581 GGCCCAAATT
439591 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
439632 TATTATTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:449074 original size:20 final size:20
Alignment explanation
Indices: 449045--449084 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
449035 CTCTATAGAA
*
449045 GATTGGTTGGATCTGCAATC
1 GATTGCTTGGATCTGCAATC
449065 GATTGCTTGGATCTGCAATC
1 GATTGCTTGGATCTGCAATC
449085 TGCCCAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (20 bp):
GATTGCTTGGATCTGCAATC
Found at i:449869 original size:16 final size:15
Alignment explanation
Indices: 449830--449874 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
449820 AGCTTGAGAG
*
449830 AGAATTGAAAGAAAA
1 AGAATTGAGAGAAAA
*
449845 AGAAATGAGAGAAAA
1 AGAATTGAGAGAAAA
449860 AGAAGTTGAGA-AAAA
1 AGAA-TTGAGAGAAAA
449875 GAACGTAAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 21 0.81
16 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.11
Consensus pattern (15 bp):
AGAATTGAGAGAAAA
Found at i:449870 original size:14 final size:15
Alignment explanation
Indices: 449839--449877 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
449829 GAGAATTGAA
449839 AGAAAAAGAAATGAG
1 AGAAAAAGAAATGAG
* *
449854 AGAAAAAGAAGT-TG
1 AGAAAAAGAAATGAG
449868 AGAAAAAGAA
1 AGAAAAAGAA
449878 CGTAAGCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.67, C:0.00, G:0.26, T:0.08
Consensus pattern (15 bp):
AGAAAAAGAAATGAG
Found at i:453573 original size:22 final size:21
Alignment explanation
Indices: 453528--453585 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
453518 GAAGGTGCCG
* *
453528 ATACTTTTTGAAACGATATCA
1 ATACTTTTTGAAAAGATATAA
*
453549 ATACTTTTTGTAAAAGGTATAA
1 ATACTTTTTG-AAAAGATATAA
*
453571 ATACTTTTTAAAAAG
1 ATACTTTTTGAAAAG
453586 TATCGATAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (21 bp):
ATACTTTTTGAAAAGATATAA
Found at i:456346 original size:21 final size:21
Alignment explanation
Indices: 456265--456346 Score: 85
Period size: 21 Copynumber: 3.9 Consensus size: 21
456255 TATGTGGTAC
456265 AAGGTATCGATACTTTTTGAA
1 AAGGTATCGATACTTTTTGAA
*
456286 ACA-ATATCGATACTTTTTGTAA
1 A-AGGTATCGATACTTTTTG-AA
** *
456308 AAGGTATAAATACATTTTGAA
1 AAGGTATCGATACTTTTTGAA
* *
456329 AAGGTATCTATAGTTTTT
1 AAGGTATCGATACTTTTT
456347 TGTCATTGTT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
21 33 0.67
22 16 0.33
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.40
Consensus pattern (21 bp):
AAGGTATCGATACTTTTTGAA
Found at i:459248 original size:22 final size:22
Alignment explanation
Indices: 459223--459265 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
459213 AAAATATTTC
*
459223 ATTA-ATAATTTGGGTTTAATTA
1 ATTATATAAATTGGG-TTAATTA
*
459245 ATTATTTAAATTGGGTTAATT
1 ATTATATAAATTGGGTTAATT
459266 TTCTTTGGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
ATTATATAAATTGGGTTAATTA
Found at i:478459 original size:18 final size:17
Alignment explanation
Indices: 478436--478469 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
478426 CTGGGCCCAA
478436 TAAAATTAAAATTTATTT
1 TAAAATT-AAATTTATTT
*
478454 TAAAATTGAATTTATT
1 TAAAATTAAATTTATT
478470 ACAAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TAAAATTAAATTTATTT
Found at i:478494 original size:17 final size:16
Alignment explanation
Indices: 478472--478514 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
478462 AATTTATTAC
478472 AAATTTAAATGAAATTT
1 AAATTTAAAT-AAATTT
*
478489 AAATTTATCATAAATTT
1 AAATTTA-AATAAATTT
*
478506 AACTTTAAA
1 AAATTTAAA
478515 ATTTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 19 0.86
18 2 0.09
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (16 bp):
AAATTTAAATAAATTT
Found at i:478578 original size:30 final size:30
Alignment explanation
Indices: 478539--478631 Score: 134
Period size: 30 Copynumber: 3.1 Consensus size: 30
478529 AAAGTCCATT
*
478539 TACAAATCAAATGGCCCAAATCGGCCCAAA
1 TACATATCAAATGGCCCAAATCGGCCCAAA
478569 TACATATCAAATGGCCCAAATCGGCCCAAA
1 TACATATCAAATGGCCCAAATCGGCCCAAA
* * *
478599 TACATA-CTAAATGGCCGAAGTCAGCCCAAA
1 TACATATC-AAATGGCCCAAATCGGCCCAAA
478629 TAC
1 TAC
478632 CCTAAGCCTA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 1 0.02
30 57 0.98
ACGTcount: A:0.41, C:0.29, G:0.14, T:0.16
Consensus pattern (30 bp):
TACATATCAAATGGCCCAAATCGGCCCAAA
Found at i:479260 original size:7 final size:7
Alignment explanation
Indices: 479228--479269 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
479218 GTCTTTTAAG
*
479228 TTAATAT
1 TTAATAA
*
479235 TTATTAA
1 TTAATAA
479242 TTAATTAA
1 TTAA-TAA
479250 -TAATAA
1 TTAATAA
479256 TTAATAA
1 TTAATAA
479263 TTAATAA
1 TTAATAA
479270 ATAAATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 3 0.10
7 24 0.80
8 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
TTAATAA
Found at i:479263 original size:21 final size:21
Alignment explanation
Indices: 479229--479273 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
479219 TCTTTTAAGT
* * *
479229 TAATATTTATTAATTAATTAA
1 TAATAATTAATAATTAATAAA
479250 TAATAATTAATAATTAATAAA
1 TAATAATTAATAATTAATAAA
479271 TAA
1 TAA
479274 ATAAAAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATAATTAATAATTAATAAA
Found at i:480338 original size:30 final size:29
Alignment explanation
Indices: 480280--480449 Score: 198
Period size: 29 Copynumber: 5.8 Consensus size: 29
480270 GAAGGTCCCT
*
480280 AAACTATCAAAAAATTCCATTTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCCC
* *
480310 GAACTTCCAAAAA-TCTCATTTTTAACCCCA
1 AAACTTCCAAAAATTC-CATTTTT-ACCCCC
*
480340 AAACTTCCAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * ***
480369 GAACTTCCAAAAATCCCATTTTTGACCTAA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
*
480399 AAACTTCCAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
*
480428 AAACTTCCCAAAATTCCATTTT
1 AAACTTCCAAAAATTCCATTTT
480450 AACCTCGAAT
Statistics
Matches: 119, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.02
29 63 0.53
30 52 0.44
31 2 0.02
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:480373 original size:59 final size:59
Alignment explanation
Indices: 480280--480453 Score: 244
Period size: 59 Copynumber: 2.9 Consensus size: 59
480270 GAAGGTCCCT
* * *
480280 AAACTATCAAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCCCA
1 AAACT-TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTAACCCAA
* * *
480340 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTAA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTAACCCAA
* *
480399 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCCAAAAT-TCCA-TTTTAACC
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCT-CATTTTTAACC
480454 TCGAATTTCC
Statistics
Matches: 103, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
58 7 0.07
59 91 0.88
60 5 0.05
ACGTcount: A:0.37, C:0.30, G:0.02, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTAACCCAA
Found at i:480466 original size:29 final size:29
Alignment explanation
Indices: 480290--480471 Score: 170
Period size: 29 Copynumber: 6.2 Consensus size: 29
480280 AAACTATCAA
* * *
480290 AAAATTCCATTTTTACCCCCGAACTT-CC
1 AAAATTCCATTTTTAACCTCAAACTTCCC
* * *
480318 AAAAATCTCATTTTTAACCCCAAAACTTCCA
1 AAAATTC-CATTTTTAACCTC-AAACTTCCC
* * *
480349 AAAATTCCATTTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTTAACCTCAAACTTCCC
* * * *
480378 AAAATCCCATTTTTGACCTAAAAACTTCCA
1 AAAATTCCATTTTTAACCT-CAAACTTCCC
*
480408 AAAATTCCATTTTTACCCTCAAACTTCCC
1 AAAATTCCATTTTTAACCTCAAACTTCCC
* *
480437 AAAATTCCA-TTTTAACCTCGAATTTCCCC
1 AAAATTCCATTTTTAACCTCAAACTT-CCC
480466 AAAATT
1 AAAATT
480472 ACAATTTCAC
Statistics
Matches: 128, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
28 19 0.15
29 62 0.48
30 40 0.31
31 7 0.05
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAATTCCATTTTTAACCTCAAACTTCCC
Found at i:480468 original size:59 final size:58
Alignment explanation
Indices: 480280--480487 Score: 222
Period size: 59 Copynumber: 3.5 Consensus size: 58
480270 GAAGGTCCCT
* * * *
480280 AAACTATCAAAAAATTCCATTTTTACCCCCGAACTT-CCAAAAATCTCATTTTTAACCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCTCGAACTTCCCAAAATTC-CATTTTTAACCTC
* * * *
480339 AAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTAA
1 -AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCCAAAATTCCATTTTTAACCT-C
*
480399 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCCAAAATTCCA-TTTTAACCTC
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCCAAAATTCCATTTTTAACCTC
* * * * * *
480456 GAATTTCCCCAAAATTACAATTTCACCCTCGA
1 AAACTT-CCAAAAATTCCATTTTTACCCTCGA
480488 GAATCCAAAA
Statistics
Matches: 125, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
57 4 0.03
58 28 0.22
59 82 0.66
60 11 0.09
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.31
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCCAAAATTCCATTTTTAACCTC
Found at i:480500 original size:28 final size:28
Alignment explanation
Indices: 480464--480526 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
480454 TCGAATTTCC
480464 CCAAAATTACAATTTCACCCTCGAGAAT
1 CCAAAATTACAATTTCACCCTCGAGAAT
* ** *
480492 CCAAAATTACCATTTTGCCCTCGAGTAT
1 CCAAAATTACAATTTCACCCTCGAGAAT
480520 CCGAAAA
1 CC-AAAA
480527 GTCTCATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.37, C:0.29, G:0.10, T:0.25
Consensus pattern (28 bp):
CCAAAATTACAATTTCACCCTCGAGAAT
Found at i:480536 original size:29 final size:28
Alignment explanation
Indices: 480481--480537 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
480471 TACAATTTCA
*
480481 CCCTCGAGAATCCAAAATTACCATTTTG
1 CCCTCGAGAATCCAAAAGTACCATTTTG
*
480509 CCCTCGAGTATCCGAAAAGT-CTCATTTTG
1 CCCTCGAGAATCC-AAAAGTAC-CATTTTG
480538 AACTCCGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (28 bp):
CCCTCGAGAATCCAAAAGTACCATTTTG
Found at i:482276 original size:12 final size:12
Alignment explanation
Indices: 482244--482290 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
482234 GAGAAAGATC
482244 AAGAAGAAGCAG-
1 AAGAAGAAG-AGA
482256 AAGAAGAAGAAGGA
1 AAGAAGAAG-A-GA
482270 AAGGAAGAAGAGA
1 AA-GAAGAAGAGA
482283 AAGAAGAA
1 AAGAAGAA
482291 AACGAACCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 16 0.52
13 5 0.16
14 3 0.10
15 7 0.23
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (12 bp):
AAGAAGAAGAGA
Found at i:486528 original size:16 final size:16
Alignment explanation
Indices: 486503--486533 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
486493 TTGCTTACTT
486503 AGGATAATTTGCATTA
1 AGGATAATTTGCATTA
*
486519 AGGATCATTTGCATT
1 AGGATAATTTGCATT
486534 TAGCTTAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (16 bp):
AGGATAATTTGCATTA
Found at i:488738 original size:24 final size:24
Alignment explanation
Indices: 488683--488739 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
488673 TAGACTAATA
* *
488683 AGAGTTTAACTGAAACAAATAAAC
1 AGAGTTTAACTAAAACAAAAAAAC
* *
488707 AAAATTTAACTAAAACAAAAAAAC
1 AGAGTTTAACTAAAACAAAAAAAC
488731 AGAGTTTAA
1 AGAGTTTAA
488740 TTGGAAGATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.60, C:0.11, G:0.09, T:0.21
Consensus pattern (24 bp):
AGAGTTTAACTAAAACAAAAAAAC
Found at i:490689 original size:24 final size:24
Alignment explanation
Indices: 490632--490691 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
490622 TAGACTAATA
* * * *
490632 AGAGTTTGACTGAAATAAATAAAT
1 AGAGTTTAATTGAAACAAATAAAC
*
490656 AGAGTTTAATTGAAACAAGTAAAC
1 AGAGTTTAATTGAAACAAATAAAC
490680 AGAGTTTAATTG
1 AGAGTTTAATTG
490692 GAAGATTATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.30
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAATAAAC
Found at i:493007 original size:43 final size:43
Alignment explanation
Indices: 492956--493043 Score: 151
Period size: 43 Copynumber: 2.0 Consensus size: 43
492946 TCGATACCTG
*
492956 GTAAAAGGTATC-GATACTTTTTGAAACGGTATTGATACTTTTT
1 GTAAAAGGTA-CAGATACTTTTTGAAAAGGTATTGATACTTTTT
492999 GTAAAAGGTACAGATACTTTTTGAAAAGGTATTGATACTTTTT
1 GTAAAAGGTACAGATACTTTTTGAAAAGGTATTGATACTTTTT
493042 GT
1 GT
493044 CATTATTTGA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
42 1 0.02
43 42 0.98
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (43 bp):
GTAAAAGGTACAGATACTTTTTGAAAAGGTATTGATACTTTTT
Found at i:493008 original size:22 final size:22
Alignment explanation
Indices: 492956--493043 Score: 126
Period size: 21 Copynumber: 4.1 Consensus size: 22
492946 TCGATACCTG
*
492956 GTAAAAGGTATCGATACTTTTT
1 GTAAAAGGTATTGATACTTTTT
*
492978 G-AAACGGTATTGATACTTTTT
1 GTAAAAGGTATTGATACTTTTT
**
492999 GTAAAAGGTACAGATACTTTTT
1 GTAAAAGGTATTGATACTTTTT
493021 G-AAAAGGTATTGATACTTTTT
1 GTAAAAGGTATTGATACTTTTT
493042 GT
1 GT
493044 CATTATTTGA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
21 38 0.67
22 19 0.33
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (22 bp):
GTAAAAGGTATTGATACTTTTT
Found at i:493760 original size:18 final size:18
Alignment explanation
Indices: 493739--493773 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
493729 TTCGAAAAAC
*
493739 TTGAATAATTCAAATAAT
1 TTGAATAACTCAAATAAT
*
493757 TTGAATAGCTCAAATAA
1 TTGAATAACTCAAATAA
493774 AATATTGGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (18 bp):
TTGAATAACTCAAATAAT
Found at i:494185 original size:21 final size:23
Alignment explanation
Indices: 494152--494193 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
494142 AACAATTTTA
494152 TTTAATTCGACTC-AACTCGAAT
1 TTTAATTCGACTCAAACTCGAAT
*
494174 TTTATTTC-ACTCAAACTCGA
1 TTTAATTCGACTCAAACTCGA
494194 TTTGAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (23 bp):
TTTAATTCGACTCAAACTCGAAT
Found at i:503719 original size:23 final size:24
Alignment explanation
Indices: 503693--503739 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
503683 AAAGAGACAT
*
503693 AAGAATAAT-AAAAATAGAAACAA
1 AAGAAAAATGAAAAATAGAAACAA
* *
503716 AAGAAAAATGAAACATATAAACAA
1 AAGAAAAATGAAAAATAGAAACAA
503740 GTAGATAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.72, C:0.06, G:0.09, T:0.13
Consensus pattern (24 bp):
AAGAAAAATGAAAAATAGAAACAA
Found at i:514736 original size:36 final size:36
Alignment explanation
Indices: 514696--514855 Score: 257
Period size: 36 Copynumber: 4.4 Consensus size: 36
514686 GACTTTTAGG
*
514696 TCAACAGGGAGTAAAATGAGCATAATGACCTTTGGA
1 TCAACAGGGAGTAAAATGAGCATAATGAACTTTGGA
514732 TCAACAGGGAGTAAAATGAGCATAATGAACTTTGGA
1 TCAACAGGGAGTAAAATGAGCATAATGAACTTTGGA
*
514768 TCAACAGGGAGTAAAATGAGCATAATGAACTTTGGG
1 TCAACAGGGAGTAAAATGAGCATAATGAACTTTGGA
* * * * *
514804 TTAACAGAGAGTAAAATGAGCATCATGACCTTTGGG
1 TCAACAGGGAGTAAAATGAGCATAATGAACTTTGGA
514840 TCAACAGGGAGTAAAA
1 TCAACAGGGAGTAAAA
514856 CGAATAACAA
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 116 1.00
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (36 bp):
TCAACAGGGAGTAAAATGAGCATAATGAACTTTGGA
Found at i:517103 original size:21 final size:21
Alignment explanation
Indices: 517057--517110 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
517047 AGAACTAGGT
* *
517057 CTTCTACCGATACAACTCTAG
1 CTTCTATCGATACAACTCTAA
*
517078 GTTCTATCGATACAAC-CATAA
1 CTTCTATCGATACAACTC-TAA
517099 CTTCTATCGATA
1 CTTCTATCGATA
517111 GAACAGACTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.31
Consensus pattern (21 bp):
CTTCTATCGATACAACTCTAA
Found at i:519597 original size:78 final size:78
Alignment explanation
Indices: 519466--519609 Score: 234
Period size: 78 Copynumber: 1.8 Consensus size: 78
519456 ATTTTGATCC
* *
519466 TAACTTACTTTCTTTTTATGCACTTGTCGTGCTCGCCCCACTTCTATTGCCACCGCCAGTACAAA
1 TAACTTACTTTCTTTTTATGCACTTGTCGTGCTCGCCCCACTTCCATTACCACCGCCAGTACAAA
519531 ACAAACATGATAG
66 ACAAACATGATAG
* ** *
519544 TAACTTACTTTCTTTTTATGCACTTGTCGTGCTTGCCCTGCTTCCATTACCACCGTCAGTACAAA
1 TAACTTACTTTCTTTTTATGCACTTGTCGTGCTCGCCCCACTTCCATTACCACCGCCAGTACAAA
519609 A
66 A
519610 AGACCAGGAT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 60 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (78 bp):
TAACTTACTTTCTTTTTATGCACTTGTCGTGCTCGCCCCACTTCCATTACCACCGCCAGTACAAA
ACAAACATGATAG
Found at i:521992 original size:38 final size:38
Alignment explanation
Indices: 521950--522027 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
521940 AAACAGAGCG
521950 TTCTTCTCAAACTCTTTGAGATCAGATAGAAAATCGCT
1 TTCTTCTCAAACTCTTTGAGATCAGATAGAAAATCGCT
521988 TTCTTCTCAAACTCTTTGAGATCAGATAGAAAATCGCT
1 TTCTTCTCAAACTCTTTGAGATCAGATAGAAAATCGCT
522026 TT
1 TT
522028 GTTCCCTGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (38 bp):
TTCTTCTCAAACTCTTTGAGATCAGATAGAAAATCGCT
Found at i:522618 original size:29 final size:29
Alignment explanation
Indices: 522560--522618 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
522550 ATTATAAAAA
*
522560 AAATTATTAATGATCAAAATGATATTTTT
1 AAATTATTAATGATCAAAATGATATGTTT
* *
522589 AAATTATTATTTATCAAAAT-AGTATGTTT
1 AAATTATTAATGATCAAAATGA-TATGTTT
522618 A
1 A
522619 GTTAAGTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (29 bp):
AAATTATTAATGATCAAAATGATATGTTT
Found at i:523060 original size:12 final size:12
Alignment explanation
Indices: 523045--523084 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
523035 AAAATTGAAG
*
523045 GAAAAAAAAAAA
1 GAAAAAAAGAAA
523057 GAAAAAAGAGAAA
1 GAAAAAA-AGAAA
*
523070 GAAAGAAAGAAA
1 GAAAAAAAGAAA
523082 GAA
1 GAA
523085 GAAGGAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
GAAAAAAAGAAA
Found at i:523078 original size:21 final size:21
Alignment explanation
Indices: 523045--523086 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
523035 AAAATTGAAG
523045 GAAAAAAAAAAAGAAAAAAGA
1 GAAAAAAAAAAAGAAAAAAGA
* * *
523066 GAAAGAAAGAAAGAAAGAAGA
1 GAAAAAAAAAAAGAAAAAAGA
523087 AGGAAGAAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (21 bp):
GAAAAAAAAAAAGAAAAAAGA
Found at i:523101 original size:16 final size:15
Alignment explanation
Indices: 523082--523111 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
523072 AAGAAAGAAA
523082 GAAGAAGGAAGAAGGG
1 GAAGAAGG-AGAAGGG
523098 GAAGAAGGAGAAGG
1 GAAGAAGGAGAAGG
523112 AAAAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (15 bp):
GAAGAAGGAGAAGGG
Found at i:523327 original size:13 final size:14
Alignment explanation
Indices: 523311--523344 Score: 54
Period size: 12 Copynumber: 2.6 Consensus size: 14
523301 AATTTTTAAA
523311 TATTTTAATTTG-T
1 TATTTTAATTTGAT
523324 TA-TTTAATTTGAT
1 TATTTTAATTTGAT
523337 TATTTTAA
1 TATTTTAA
523345 GTTTTTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.47
13 5 0.26
14 5 0.26
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (14 bp):
TATTTTAATTTGAT
Found at i:523495 original size:21 final size:20
Alignment explanation
Indices: 523469--523508 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
523459 CAATTTACTT
523469 TAATTTAATTTTGTTAGTTAG
1 TAATTTAATTTTGTT-GTTAG
*
523490 TAATTTTATTTTGTTGTTA
1 TAATTTAATTTTGTTGTTA
523509 ATAGTAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (20 bp):
TAATTTAATTTTGTTGTTAG
Done.