Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 40 of 97
Found at i:16432260 original size:10 final size:10
Alignment explanation
Indices: 16432236--16432281 Score: 62
Period size: 9 Copynumber: 4.9 Consensus size: 10
16432226 AAAAATTTAA
*
16432236 AAATA-AAAT
1 AAATATAAAC
16432245 AAATATAAAC
1 AAATATAAAC
16432255 AAATATAAA-
1 AAATATAAAC
16432264 AAATATAAAC
1 AAATATAAAC
16432274 AAAT-TAAA
1 AAATATAAA
16432282 AAAACTGAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
9 18 0.53
10 16 0.47
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (10 bp):
AAATATAAAC
Found at i:16432267 original size:19 final size:19
Alignment explanation
Indices: 16432236--16432284 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
16432226 AAAAATTTAA
16432236 AAATA-AAATAAATATAAAC
1 AAATATAAA-AAATATAAAC
16432255 AAATATAAAAAATATAAAC
1 AAATATAAAAAATATAAAC
16432274 AAAT-TAAAAAA
1 AAATATAAAAAA
16432285 ACTGAGAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.24
19 19 0.66
20 3 0.10
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (19 bp):
AAATATAAAAAATATAAAC
Found at i:16433210 original size:68 final size:68
Alignment explanation
Indices: 16433092--16433225 Score: 225
Period size: 68 Copynumber: 2.0 Consensus size: 68
16433082 TTCTGGGTCA
* * *
16433092 CAATTTCGCTGCAGCGAAAAACTTTCTGTTTTATCTCCTATTTTGTCCAATTGCTGCCCTATTTT
1 CAATCTCGCTGCAGCGAAAAACTTTCTGTTTTATCTCCTATCTTGGCCAATTGCTGCCCTATTTT
16433157 TGT
66 TGT
16433160 CAATCTCGCTGCAGCGAAAAAC-TTCTTGTTTTATCTCCTATCTTGGCCAATTGCTGCCCTATTT
1 CAATCTCGCTGCAGCGAAAAACTTTC-TGTTTTATCTCCTATCTTGGCCAATTGCTGCCCTATTT
16433224 TT
65 TT
16433226 CACTTTTTTG
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
67 3 0.05
68 59 0.95
ACGTcount: A:0.19, C:0.25, G:0.13, T:0.42
Consensus pattern (68 bp):
CAATCTCGCTGCAGCGAAAAACTTTCTGTTTTATCTCCTATCTTGGCCAATTGCTGCCCTATTTT
TGT
Found at i:16434168 original size:15 final size:15
Alignment explanation
Indices: 16434148--16434177 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16434138 TGAAAATTCT
*
16434148 AAATTTAAAGGACTC
1 AAATTTAAAAGACTC
16434163 AAATTTAAAAGACTC
1 AAATTTAAAAGACTC
16434178 TTATTCAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (15 bp):
AAATTTAAAAGACTC
Found at i:16435088 original size:17 final size:16
Alignment explanation
Indices: 16435067--16435108 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
16435057 TTTATTTATA
*
16435067 AATAATTATTAAATAT
1 AATAATTAATAAATAT
*
16435083 ATATAAATAATAAATAT
1 A-ATAATTAATAAATAT
16435100 AATAATTAA
1 AATAATTAA
16435109 AACTCTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATAATTAATAAATAT
Found at i:16435904 original size:30 final size:30
Alignment explanation
Indices: 16435870--16435928 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
16435860 ATATAATGTA
* *
16435870 ATAAATAAATGA-ATACATAAGTACAAAAAT
1 ATAAATAAAT-ACATAAATAAGTAAAAAAAT
16435900 ATAAATAAATACATAAATAAGTAAAAAAA
1 ATAAATAAATACATAAATAAGTAAAAAAA
16435929 ACCATGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (30 bp):
ATAAATAAATACATAAATAAGTAAAAAAAT
Found at i:16440756 original size:2 final size:2
Alignment explanation
Indices: 16440751--16440775 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16440741 AGAGACTCCT
16440751 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
16440776 AGGATAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:16445881 original size:67 final size:67
Alignment explanation
Indices: 16445773--16445910 Score: 269
Period size: 67 Copynumber: 2.1 Consensus size: 67
16445763 GGTGAAGCCT
16445773 ATTCTCGCTCGTCCTTGTAGCATTCAACTCTCTCAAGTCTCAAGCAATATCCCTTATGTTTTGGC
1 ATTCTCGCTCGTCCTTGTAGCATTCAACTCTCTCAAGTCTCAAGCAATATCCCTTATGTTTTGGC
16445838 TC
66 TC
16445840 ATTCTCGCTCGTCCTTGTAGCATTCAACTCTCTCAAGTCTCAAGCAATATCCCTTATGTTTTGGC
1 ATTCTCGCTCGTCCTTGTAGCATTCAACTCTCTCAAGTCTCAAGCAATATCCCTTATGTTTTGGC
16445905 TC
66 TC
16445907 -TTCT
1 ATTCT
16445911 GCCCCTTGCT
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
66 4 0.06
67 67 0.94
ACGTcount: A:0.19, C:0.30, G:0.13, T:0.38
Consensus pattern (67 bp):
ATTCTCGCTCGTCCTTGTAGCATTCAACTCTCTCAAGTCTCAAGCAATATCCCTTATGTTTTGGC
TC
Found at i:16452239 original size:13 final size:13
Alignment explanation
Indices: 16452221--16452248 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
16452211 AATTGCTTCC
16452221 AAATCAATGGGGT
1 AAATCAATGGGGT
16452234 AAATCAATGGGGT
1 AAATCAATGGGGT
16452247 AA
1 AA
16452249 TTCTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.29, T:0.21
Consensus pattern (13 bp):
AAATCAATGGGGT
Found at i:16453863 original size:22 final size:23
Alignment explanation
Indices: 16453833--16453876 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
16453823 ATAGAGGTAT
16453833 TTGGTCTTAATT-TTGATAGTAAA
1 TTGGTCTTAATTCTT-ATAGTAAA
*
16453856 TTGG-CTTAGTTCTTATAGTAA
1 TTGGTCTTAATTCTTATAGTAA
16453877 TGTTAGCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (23 bp):
TTGGTCTTAATTCTTATAGTAAA
Found at i:16457257 original size:19 final size:19
Alignment explanation
Indices: 16457233--16457294 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
16457223 TGCCCGTGTG
16457233 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
**** *
16457252 CACGATG-GCTCTGATTGTG
1 CACGATGTGGGGGGA-TGTA
*
16457271 CACGATGTGGGGGGATGCA
1 CACGATGTGGGGGGATGTA
16457290 CACGA
1 CACGA
16457295 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
18 3 0.10
19 24 0.80
20 3 0.10
ACGTcount: A:0.21, C:0.18, G:0.40, T:0.21
Consensus pattern (19 bp):
CACGATGTGGGGGGATGTA
Found at i:16463353 original size:25 final size:25
Alignment explanation
Indices: 16463325--16463374 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
16463315 TCATAATATG
*
16463325 ATTCATA-ACATCAAATCTCATTTCA
1 ATTCATATAAATC-AATCTCATTTCA
*
16463350 ATTCATATAAATCAATTTCATTTCA
1 ATTCATATAAATCAATCTCATTTCA
16463375 TAAAAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (25 bp):
ATTCATATAAATCAATCTCATTTCA
Found at i:16463367 original size:20 final size:20
Alignment explanation
Indices: 16463344--16463384 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
16463334 ATCAAATCTC
*
16463344 ATTTCAATTCATATAAATCA
1 ATTTCAATTCATAAAAATCA
*
16463364 ATTTCATTTCATAAAAATCA
1 ATTTCAATTCATAAAAATCA
16463384 A
1 A
16463385 CAAGGCTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTTCAATTCATAAAAATCA
Found at i:16480932 original size:32 final size:33
Alignment explanation
Indices: 16480891--16480964 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
16480881 GGGTATTAGT
* * *
16480891 AAAGTCTTTAGTA-AATCTCAATCGGCATTGGG
1 AAAGTCTTTAGTATAAGCACAACCGGCATTGGG
* *
16480923 AAAGTCTTTAGTATAAGCACAACCTGTATTGGG
1 AAAGTCTTTAGTATAAGCACAACCGGCATTGGG
16480956 AAAGTCTTT
1 AAAGTCTTT
16480965 CCTGAAAACC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 13 0.36
33 23 0.64
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (33 bp):
AAAGTCTTTAGTATAAGCACAACCGGCATTGGG
Found at i:16481917 original size:35 final size:35
Alignment explanation
Indices: 16481864--16481930 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
16481854 TCATAACGAC
* *
16481864 TTTTCACAGGATCTACCAACAAC-CCTTACAATTGT
1 TTTTCACAAGATCAACCAA-AACTCCTTACAATTGT
* *
16481899 TTTTCACAAGCTCAACCAAAACTCTTTACAAT
1 TTTTCACAAGATCAACCAAAACTCCTTACAAT
16481931 GCCTTTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 3 0.11
35 24 0.89
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.31
Consensus pattern (35 bp):
TTTTCACAAGATCAACCAAAACTCCTTACAATTGT
Found at i:16484780 original size:18 final size:18
Alignment explanation
Indices: 16484759--16484795 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
16484749 CACATTTAAC
*
16484759 TAACTAAAACTTTCAATT
1 TAACTAAAAATTTCAATT
16484777 TAACTAAAAATTTCAATT
1 TAACTAAAAATTTCAATT
16484795 T
1 T
16484796 CTCCCCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.41
Consensus pattern (18 bp):
TAACTAAAAATTTCAATT
Found at i:16489734 original size:23 final size:23
Alignment explanation
Indices: 16489708--16489761 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
16489698 ACTTGAAATC
16489708 TATTTTCCTTAAGCATTTCTCCT
1 TATTTTCCTTAAGCATTTCTCCT
16489731 TATTTTCCTTAAGCATTTCTCCT
1 TATTTTCCTTAAGCATTTCTCCT
16489754 TATTTTCC
1 TATTTTCC
16489762 ATGGTTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.17, C:0.26, G:0.04, T:0.54
Consensus pattern (23 bp):
TATTTTCCTTAAGCATTTCTCCT
Found at i:16495225 original size:35 final size:34
Alignment explanation
Indices: 16495186--16495253 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
16495176 TTAAACCCTC
16495186 ACAATAGCTTTTCAC-AGGATCAACCAACAACCTTT
1 ACAATAGCTTTTCACTA-GATCAACCAA-AACCTTT
* * *
16495221 ACAATGGTTTTTCACTAGCTCAACCAAAACCTT
1 ACAATAGCTTTTCACTAGATCAACCAAAACCTT
16495254 CAACAATGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 6 0.21
35 22 0.76
36 1 0.03
ACGTcount: A:0.35, C:0.28, G:0.09, T:0.28
Consensus pattern (34 bp):
ACAATAGCTTTTCACTAGATCAACCAAAACCTTT
Found at i:16497433 original size:3 final size:3
Alignment explanation
Indices: 16497425--16497463 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
16497415 AACATGCATA
*
16497425 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16497464 AAAAGATGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:16502512 original size:15 final size:15
Alignment explanation
Indices: 16502492--16502535 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
16502482 CTTACAACGC
*
16502492 AAAGTGTGATAGTAT
1 AAAGTGTTATAGTAT
*
16502507 AAAGTGTTATAATAT
1 AAAGTGTTATAGTAT
*
16502522 AAGGTGTTATAGTA
1 AAAGTGTTATAGTA
16502536 CAACACAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.36
Consensus pattern (15 bp):
AAAGTGTTATAGTAT
Found at i:16505340 original size:20 final size:20
Alignment explanation
Indices: 16505315--16505352 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16505305 ATAAGCCTTG
*
16505315 TTGATTTTTACGAAATGAAA
1 TTGATTTATACGAAATGAAA
*
16505335 TTGATTTATATGAAATGA
1 TTGATTTATACGAAATGA
16505353 GATTTGATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (20 bp):
TTGATTTATACGAAATGAAA
Found at i:16509379 original size:14 final size:15
Alignment explanation
Indices: 16509350--16509381 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
16509340 ACTCAGAGCT
16509350 TCTATCTCTAAATTC
1 TCTATCTCTAAATTC
16509365 TCTATCTCT-AATTC
1 TCTATCTCTAAATTC
16509379 TCT
1 TCT
16509382 TTTACTCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.22, C:0.28, G:0.00, T:0.50
Consensus pattern (15 bp):
TCTATCTCTAAATTC
Found at i:16515755 original size:3 final size:3
Alignment explanation
Indices: 16515747--16515774 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
16515737 ACTATCAAGG
16515747 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
16515775 TATTATCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:16517946 original size:14 final size:14
Alignment explanation
Indices: 16517909--16517954 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
16517899 TATCNTTTTA
*
16517909 ATTTAAAATATTTT
1 ATTTAAAATAATTT
**
16517923 ATTTTTAATAATTT
1 ATTTAAAATAATTT
16517937 ATTTAAAAT-A-TT
1 ATTTAAAATAATTT
16517949 ATTTAA
1 ATTTAA
16517955 TTTTTTAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 8 0.30
13 1 0.04
14 18 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTAAAATAATTT
Found at i:16517957 original size:21 final size:21
Alignment explanation
Indices: 16517931--16517979 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
16517921 TTATTTTTAA
16517931 TAATTTATTTAAAAT-ATTATT
1 TAATTT-TTTAAAATAATTATT
*
16517952 TAATTTTTTAATATAATTATT
1 TAATTTTTTAAAATAATTATT
16517973 T-ATTTTT
1 TAATTTTT
16517980 AATTTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TAATTTTTTAAAATAATTATT
Found at i:16517976 original size:37 final size:37
Alignment explanation
Indices: 16517928--16518013 Score: 102
Period size: 37 Copynumber: 2.3 Consensus size: 37
16517918 ATTTTATTTT
16517928 TAATAATTTATTTAAAATATTATTTAATTTTT-TAATA
1 TAATAATTTATTTAAAAT-TTATTTAATTTTTATAATA
* ** * *
16517965 TAATTATTTATTTTTAATTTATTTTATTTTTATAATGT
1 TAATAATTTATTTAAAATTTATTTAATTTTTATAAT-A
16518003 TAATAATTTAT
1 TAATAATTTAT
16518014 ATTTCATTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 12 0.29
37 19 0.46
38 10 0.24
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (37 bp):
TAATAATTTATTTAAAATTTATTTAATTTTTATAATA
Found at i:16518023 original size:38 final size:36
Alignment explanation
Indices: 16517928--16518023 Score: 95
Period size: 38 Copynumber: 2.6 Consensus size: 36
16517918 ATTTTATTTT
*
16517928 TAATAATTTAT-TTAAAATATTATTTAATTTTTTAATA
1 TAATAATTTATATT-TAAT-TTATTTAATTTTTTAATA
* * * *
16517965 TAATTATTTATTTTTAATTTATTTTATTTTTATAATGT
1 TAATAATTTATATTTAATTTATTTAATTTTT-TAAT-A
*
16518003 TAATAATTTATATTTCATTTA
1 TAATAATTTATATTTAATTTA
16518024 AAATATTAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
36 12 0.24
37 17 0.35
38 20 0.41
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (36 bp):
TAATAATTTATATTTAATTTATTTAATTTTTTAATA
Found at i:16518206 original size:53 final size:52
Alignment explanation
Indices: 16518095--16518218 Score: 189
Period size: 53 Copynumber: 2.4 Consensus size: 52
16518085 AAATCTTAAA
16518095 AATTTATAATTAAAA-TTTAATTTAATTTTTAAATTAAAATATTAATTATTAT
1 AATTTAT-ATTAAAATTTTAATTTAATTTTTAAATTAAAATATTAATTATTAT
* *
16518147 ACTTTATATTAAAATTTTAATTTGATTTTTAAATTTAAAATATTAATT-TTCAT
1 AATTTATATTAAAATTTTAATTTAATTTTTAAA-TTAAAATATTAATTATT-AT
16518200 AATTTATATTAAAATTTTA
1 AATTTATATTAAAATTTTA
16518219 GTGTAATGAC
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
51 7 0.11
52 25 0.38
53 34 0.52
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (52 bp):
AATTTATATTAAAATTTTAATTTAATTTTTAAATTAAAATATTAATTATTAT
Found at i:16529517 original size:21 final size:21
Alignment explanation
Indices: 16529485--16529535 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
16529475 ACTTAGAGAA
* *
16529485 TTGAG-AACCTTGAGCACCTAG
1 TTGAGCAA-CTTGAGAACCAAG
* *
16529506 TTGAGCAACTTGGGAACCAAT
1 TTGAGCAACTTGAGAACCAAG
16529527 TTGAGCAAC
1 TTGAGCAAC
16529536 ACATGACTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.24
Consensus pattern (21 bp):
TTGAGCAACTTGAGAACCAAG
Found at i:16533374 original size:19 final size:19
Alignment explanation
Indices: 16533350--16533387 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
16533340 CCATTTGACT
16533350 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
16533369 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
16533388 GTTGAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:16533491 original size:28 final size:28
Alignment explanation
Indices: 16533436--16533494 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
16533426 TTTGGAGCAT
** *
16533436 AGGGGTAAAATGGTAATTTTATCACACC
1 AGGGGTAAAACAGTAATTTTACCACACC
16533464 AGGGGTAAAACAGTAATTTT-CCACCACC
1 AGGGGTAAAACAGTAATTTTACCA-CACC
16533492 AGG
1 AGG
16533495 ACATTTGTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.24
Consensus pattern (28 bp):
AGGGGTAAAACAGTAATTTTACCACACC
Found at i:16547792 original size:2 final size:2
Alignment explanation
Indices: 16547785--16547870 Score: 82
Period size: 2 Copynumber: 43.0 Consensus size: 2
16547775 AAAGAAAGAA
* ** * *
16547785 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT CC AA AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
** * * *
16547827 AT NG AA AG AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16547869 AT
1 AT
16547871 CTCCAAAAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:16547856 original size:52 final size:51
Alignment explanation
Indices: 16547778--16547880 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 51
16547768 AAGAAAGAAA
16547778 GAAAGAAATATATATATATATATATATATATATATATATATCTCCAAAAAT
1 GAAAGAAATATATATATATATATATATATATATATATATATCTCCAAAAAT
16547829 NGAAAGAAATATATATATATATATATATATATATATATATATCTCCAAAAAT
1 -GAAAGAAATATATATATATATATATATATATATATATATATCTCCAAAAAT
16547881 ATGGATTAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.37
Consensus pattern (51 bp):
GAAAGAAATATATATATATATATATATATATATATATATATCTCCAAAAAT
Found at i:16556110 original size:72 final size:70
Alignment explanation
Indices: 16556029--16556192 Score: 195
Period size: 72 Copynumber: 2.3 Consensus size: 70
16556019 AAAATAGTTT
*
16556029 TTTTTTTAAATAA-AAGAATTTTGAAAAAAAAAGAGCTTCAGGAAAAGCTCCTATGATAAGCTTT
1 TTTTTTTAAA-AACAAGAATTTT--AAAAAAAAGAGCTTCAGGAAAAGCTCCTATGAGAAGCTTT
16556093 TTCTTCTC
63 TTCTTCTC
* * * *
16556101 TTTTTTTAAAAATGCAANAATTTTTAAAAAAAGAGCTTCAGGAAAAGCTCCTGTGAGGAGCTTTT
1 TTTTTTTAAAAA--CAAGAATTTTAAAAAAAAGAGCTTCAGGAAAAGCTCCTATGAGAAGCTTTT
*
16556166 TCTTTTC
64 TCTTCTC
*
16556173 TTCTTTTACAAATACAAGAA
1 TTTTTTTA-AAA-ACAAGAA
16556193 AATTTTTATT
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
71 2 0.03
72 65 0.82
73 3 0.04
74 9 0.11
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (70 bp):
TTTTTTTAAAAACAAGAATTTTAAAAAAAAGAGCTTCAGGAAAAGCTCCTATGAGAAGCTTTTTC
TTCTC
Found at i:16565538 original size:38 final size:38
Alignment explanation
Indices: 16565490--16565567 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
16565480 TTTACCTCAA
* * *
16565490 AAAAATCAAATTTATACTATATATTAAAAGTGTGTCCG
1 AAAAACCAAATCTATACTATATATTAAAAGTGAGTCCG
16565528 AAAAACCAAATCTATACTATATATTAAAAGTGAGTCCG
1 AAAAACCAAATCTATACTATATATTAAAAGTGAGTCCG
16565566 AA
1 AA
16565568 TGATAGTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.29
Consensus pattern (38 bp):
AAAAACCAAATCTATACTATATATTAAAAGTGAGTCCG
Found at i:16566506 original size:13 final size:13
Alignment explanation
Indices: 16566488--16566522 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
16566478 AATAATTTTT
16566488 TTAAAAAACAAAA-
1 TTAAAAAA-AAAAC
16566501 TTAAAAAAAAAAC
1 TTAAAAAAAAAAC
16566514 TTAAAAAAA
1 TTAAAAAAA
16566523 GCTTCAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (13 bp):
TTAAAAAAAAAAC
Found at i:16569251 original size:11 final size:11
Alignment explanation
Indices: 16569231--16569260 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
16569221 CGAAGGATTA
*
16569231 CAAATTATTTC
1 CAAATCATTTC
16569242 CAAATCATTTC
1 CAAATCATTTC
16569253 CAAATCAT
1 CAAATCAT
16569261 AACATAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (11 bp):
CAAATCATTTC
Found at i:16572739 original size:18 final size:18
Alignment explanation
Indices: 16572716--16572757 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
16572706 AAAAATCGTT
*
16572716 AATTATAAGTTATTTATG
1 AATTATAAGTTATTTATA
**
16572734 AATTATGTGTTATTTATA
1 AATTATAAGTTATTTATA
16572752 AATTAT
1 AATTAT
16572758 TTGTGAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (18 bp):
AATTATAAGTTATTTATA
Found at i:16572840 original size:22 final size:22
Alignment explanation
Indices: 16572795--16572840 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
16572785 AATTATAAAC
*
16572795 TTTATATTATACAAAAATGCTT
1 TTTATATTATACAAAAATGATT
*
16572817 TTTATATT-TTCAAAAATGTATT
1 TTTATATTATACAAAAATG-ATT
16572839 TT
1 TT
16572841 AAATAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (22 bp):
TTTATATTATACAAAAATGATT
Found at i:16574235 original size:13 final size:13
Alignment explanation
Indices: 16574217--16574242 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16574207 TTTCAGAAAA
16574217 TTTATAAAATCAT
1 TTTATAAAATCAT
16574230 TTTATAAAATCAT
1 TTTATAAAATCAT
16574243 AATTTCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:16578653 original size:19 final size:19
Alignment explanation
Indices: 16578629--16578666 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
16578619 CTACCAAACC
*
16578629 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
16578648 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
16578667 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:16583278 original size:20 final size:20
Alignment explanation
Indices: 16583253--16583296 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
16583243 TTTTGACCCC
16583253 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
16583273 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
16583293 ATTT
1 ATTT
16583297 AAGGTTTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.05, G:0.20, T:0.48
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:16583374 original size:28 final size:27
Alignment explanation
Indices: 16583343--16583395 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
16583333 TTTGGAGTAT
*
16583343 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
16583371 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
16583396 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:16583401 original size:28 final size:28
Alignment explanation
Indices: 16583343--16583401 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
16583333 TTTGGAGTAT
* *
16583343 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
16583371 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
16583399 AGG
1 AGG
16583402 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:16593528 original size:18 final size:18
Alignment explanation
Indices: 16593505--16593542 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
16593495 TTAACTGAAA
*
16593505 AATTTGACT-AATTAAGTT
1 AATTTGAATAAATT-AGTT
16593523 AATTTGAATAAATTAGTT
1 AATTTGAATAAATTAGTT
16593541 AA
1 AA
16593543 AAAATTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (18 bp):
AATTTGAATAAATTAGTT
Found at i:16593976 original size:16 final size:16
Alignment explanation
Indices: 16593957--16593987 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16593947 ATATAACTTA
16593957 TTATATTAACTTATTT
1 TTATATTAACTTATTT
*
16593973 TTATATTAAGTTATT
1 TTATATTAACTTATT
16593988 AATATAGTAT
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:0.03, G:0.03, T:0.61
Consensus pattern (16 bp):
TTATATTAACTTATTT
Found at i:16594311 original size:18 final size:18
Alignment explanation
Indices: 16594297--16594332 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
16594287 TATTAATAAT
*
16594297 TAACTATATTATAATATC
1 TAACAATATTATAATATC
16594315 TAACAATATTATATATAT
1 TAACAATATTATA-ATAT
16594333 ATATTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (18 bp):
TAACAATATTATAATATC
Found at i:16594331 original size:2 final size:2
Alignment explanation
Indices: 16594320--16594359 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
16594310 ATATCTAACA
16594320 AT AT -T AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
16594360 CGCTATTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 31 0.89
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16594338 original size:13 final size:13
Alignment explanation
Indices: 16594320--16594359 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
16594310 ATATCTAACA
16594320 ATATTATATATAT
1 ATATTATATATAT
16594333 ATATTATATATAT
1 ATATTATATATAT
16594346 ATA-TATATAGTAT
1 ATATTATATA-TAT
16594359 A
1 A
16594360 CGCTATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 6 0.23
13 20 0.77
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
ATATTATATATAT
Found at i:16595264 original size:13 final size:12
Alignment explanation
Indices: 16595246--16595291 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
16595236 TGATGTTTAA
*
16595246 TTTGATTTTGTGT
1 TTTGATTTTAT-T
16595259 TTTGATTTTATT
1 TTTGATTTTATT
*
16595271 TTTTATTTTATTT
1 TTTGATTTTA-TT
16595284 TTTGATTT
1 TTTGATTT
16595292 CATTGAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.13, C:0.00, G:0.11, T:0.76
Consensus pattern (12 bp):
TTTGATTTTATT
Found at i:16595278 original size:12 final size:12
Alignment explanation
Indices: 16595258--16595291 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
16595248 TGATTTTGTG
*
16595258 TTTTGATTTTAT
1 TTTTTATTTTAT
16595270 TTTTTATTTTAT
1 TTTTTATTTTAT
16595282 TTTTTGATTT
1 TTTTT-ATTT
16595292 CATTGAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (12 bp):
TTTTTATTTTAT
Found at i:16600449 original size:19 final size:19
Alignment explanation
Indices: 16600410--16600460 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
16600400 TTAATATTTT
*
16600410 AATATTATTTTATTTATAA
1 AATATTATTTTGTTTATAA
16600429 AATATTATTTTGTTCTA-AA
1 AATATTATTTTGTT-TATAA
* *
16600448 AATTTTATCTTGT
1 AATATTATTTTGT
16600461 CTCTTTGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 26 0.93
20 2 0.07
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (19 bp):
AATATTATTTTGTTTATAA
Found at i:16602306 original size:4 final size:4
Alignment explanation
Indices: 16602297--16602342 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
16602287 TTTGATTTCT
16602297 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
16602343 TAAACTATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:16606710 original size:20 final size:19
Alignment explanation
Indices: 16606685--16606735 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
16606675 ATATATATAT
*
16606685 ATATATTGTTTTACATTAAA
1 ATATATTATTTTA-ATTAAA
*
16606705 ATATATTATTTTAATTAAT
1 ATATATTATTTTAATTAAA
*
16606724 AT-TTTTATTTTA
1 ATATATTATTTTA
16606736 TTTTATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 9 0.32
19 7 0.25
20 12 0.43
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
ATATATTATTTTAATTAAA
Found at i:16611059 original size:21 final size:20
Alignment explanation
Indices: 16611035--16611074 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
16611025 AAAATTCACT
16611035 TTAAATGGATGTTTTAGATAC
1 TTAAATGGAT-TTTTAGATAC
**
16611056 TTAAATTTATTTTTAGATA
1 TTAAATGGATTTTTAGATA
16611075 TGAAATGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (20 bp):
TTAAATGGATTTTTAGATAC
Found at i:16627188 original size:2 final size:2
Alignment explanation
Indices: 16627152--16627179 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16627142 TTTCTATAAC
16627152 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16627180 TTGTATATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16627274 original size:42 final size:42
Alignment explanation
Indices: 16627216--16627305 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
16627206 ATCATCCCAC
*
16627216 CATCATCAGCTCATGTGCCCTCCCACA-AGCACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCCCACACA-CACATAGCTGGGT
* * *
16627258 CATCATCAGCTTATGTGCACTCCTACACACACCTAGCTGGGT
1 CATCATCAGCTCATGTGCACTCCCACACACACATAGCTGGGT
16627300 CATCAT
1 CATCAT
16627306 TATCACATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 42 0.98
43 1 0.02
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.24
Consensus pattern (42 bp):
CATCATCAGCTCATGTGCACTCCCACACACACATAGCTGGGT
Found at i:16629542 original size:17 final size:16
Alignment explanation
Indices: 16629504--16629594 Score: 67
Period size: 17 Copynumber: 5.3 Consensus size: 16
16629494 AGGAAAATGA
16629504 AAAAATACAAAAAAAT
1 AAAAATACAAAAAAAT
16629520 AGAAAATACAAAAAGTAAT
1 A-AAAATACAAAAA--AAT
**
16629539 AAAAATTAC-TGAAAAT
1 AAAAA-TACAAAAAAAT
* *
16629555 AAAAGACACAAAGAAATT
1 AAAA-ATACAAA-AAAAT
*
16629573 AAAAATACAGAAAAAT
1 AAAAATACAAAAAAAT
16629589 GAAAAA
1 -AAAAA
16629595 AAAAAACAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
16 14 0.24
17 23 0.40
18 14 0.24
19 7 0.12
ACGTcount: A:0.71, C:0.07, G:0.08, T:0.14
Consensus pattern (16 bp):
AAAAATACAAAAAAAT
Found at i:16629595 original size:52 final size:53
Alignment explanation
Indices: 16629496--16629597 Score: 118
Period size: 52 Copynumber: 1.9 Consensus size: 53
16629486 AAACGTGCAG
* *
16629496 GAAAATGAAAAAATACAAAAAAATAGAAAATACAAAAAGTAATAAAAATTACT
1 GAAAATGAAAAAACACAAAAAAATAGAAAATACAAAAAATAATAAAAATTACT
* * *
16629549 GAAAAT-AAAAGACACAAAGAAATTA-AAAATACAGAAAAATGAAAAAAAA
1 GAAAATGAAAAAACACAAA-AAAATAGAAAATACA-AAAAAT-AATAAAAA
16629598 AAACAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
52 18 0.44
53 16 0.39
54 7 0.17
ACGTcount: A:0.72, C:0.06, G:0.09, T:0.14
Consensus pattern (53 bp):
GAAAATGAAAAAACACAAAAAAATAGAAAATACAAAAAATAATAAAAATTACT
Found at i:16646780 original size:16 final size:17
Alignment explanation
Indices: 16646745--16646871 Score: 84
Period size: 18 Copynumber: 7.4 Consensus size: 17
16646735 TTTATAATTA
*
16646745 AAAAAATT-AATAATAC
1 AAAAAATTAAAAAATAC
*
16646761 AAAAAA-TAAAAAA-AT
1 AAAAAATTAAAAAATAC
* *
16646776 TAAAAATTAAAAGTATA-
1 AAAAAATTAAAA-AATAC
** *
16646793 GGAAAATGAAAAAACATAC
1 AAAAAAT-TAAAAA-ATAC
16646812 TAAAAAA-TAAAGAAATAC
1 -AAAAAATTAAA-AAATAC
*
16646830 AAAAAATAATAAAAATAC
1 AAAAAATTA-AAAAATAC
*
16646848 AAAAAAATAAAAAATAC
1 AAAAAATTAAAAAATAC
16646865 AAAAAAT
1 AAAAAAT
16646872 ACTATTCTTC
Statistics
Matches: 85, Mismatches: 15, Indels: 21
0.70 0.12 0.17
Matches are distributed among these distances:
15 7 0.08
16 15 0.18
17 26 0.31
18 29 0.34
19 4 0.05
20 4 0.05
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.17
Consensus pattern (17 bp):
AAAAAATTAAAAAATAC
Found at i:16646781 original size:17 final size:18
Alignment explanation
Indices: 16646756--16646871 Score: 84
Period size: 17 Copynumber: 6.7 Consensus size: 18
16646746 AAAAATTAAT
16646756 AATACAAAAAA-TAAAAA
1 AATACAAAAAATTAAAAA
* *
16646773 AAT--TAAAAATTAAAAG
1 AATACAAAAAATTAAAAA
* ** *
16646789 TATA-GGAAAATGAAAAA
1 AATACAAAAAATTAAAAA
*
16646806 ACATACTAAAAAA-TAAAGA
1 A-ATAC-AAAAAATTAAAAA
16646825 AATACAAAAAA-TAATAAA
1 AATACAAAAAATTAA-AAA
*
16646843 AATACAAAAAAAT-AAAA
1 AATACAAAAAATTAAAAA
16646860 AATACAAAAAAT
1 AATACAAAAAAT
16646872 ACTATTCTTC
Statistics
Matches: 78, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
15 5 0.06
16 7 0.09
17 35 0.45
18 21 0.27
19 6 0.08
20 4 0.05
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.16
Consensus pattern (18 bp):
AATACAAAAAATTAAAAA
Found at i:16646829 original size:18 final size:16
Alignment explanation
Indices: 16646802--16646872 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 16
16646792 AGGAAAATGA
16646802 AAAAACATACTAAAAAAT
1 AAAAA-ATAC-AAAAAAT
16646820 AAAGAAATACAAAAAAT
1 AAA-AAATACAAAAAAT
16646837 AATAAAAATACAAAAAAAT
1 -A-AAAAATAC-AAAAAAT
16646856 AAAAAATACAAAAAAT
1 AAAAAATACAAAAAAT
16646872 A
1 A
16646873 CTATTCTTCT
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.16
17 15 0.31
18 15 0.31
19 11 0.22
ACGTcount: A:0.77, C:0.07, G:0.01, T:0.14
Consensus pattern (16 bp):
AAAAAATACAAAAAAT
Found at i:16646843 original size:9 final size:8
Alignment explanation
Indices: 16646743--16646872 Score: 75
Period size: 9 Copynumber: 15.2 Consensus size: 8
16646733 TTTTTATAAT
16646743 TAAAAAAA
1 TAAAAAAA
* *
16646751 T-TAATAA
1 TAAAAAAA
16646758 TACAAAAAA
1 TA-AAAAAA
16646767 TAAAAAAA
1 TAAAAAAA
* *
16646775 TTAAAAAT
1 TAAAAAAA
**
16646783 TAAAAGTA
1 TAAAAAAA
**
16646791 TAGGAAAA
1 TAAAAAAA
16646799 TGAAAAAACA
1 T-AAAAAA-A
16646809 TACTAAAAAA
1 TA--AAAAAA
*
16646819 TAAAGAAA
1 TAAAAAAA
16646827 TACAAAAAA
1 TA-AAAAAA
16646836 TAATAAAAA
1 TAA-AAAAA
16646845 TACAAAAAA
1 TA-AAAAAA
16646854 -ATAAAAAA
1 TA-AAAAAA
16646862 TACAAAAAA
1 TA-AAAAAA
16646871 TA
1 TA
16646873 CTATTCTTCT
Statistics
Matches: 92, Mismatches: 20, Indels: 19
0.70 0.15 0.15
Matches are distributed among these distances:
7 5 0.05
8 37 0.40
9 39 0.42
10 6 0.07
11 5 0.05
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.18
Consensus pattern (8 bp):
TAAAAAAA
Found at i:16646872 original size:16 final size:16
Alignment explanation
Indices: 16646745--16646872 Score: 96
Period size: 16 Copynumber: 7.5 Consensus size: 16
16646735 TTTATAATTA
* *
16646745 AAAAAATTAATAATAC
1 AAAAAATAAAAAATAC
*
16646761 AAAAAATAAAAAA-AT
1 AAAAAATAAAAAATAC
* * * *
16646776 TAAAAATTAAAAGTAT
1 AAAAAATAAAAAATAC
*
16646792 AGGAAAATGAAAAAACATAC
1 A-AAAAAT--AAAAA-ATAC
16646812 TAAAAAATAAAGAAATAC
1 -AAAAAATAAA-AAATAC
16646830 AAAAAATAATAAAAATAC
1 AAAAAAT-A-AAAAATAC
16646848 AAAAAAATAAAAAATAC
1 -AAAAAATAAAAAATAC
16646865 AAAAAATA
1 AAAAAATA
16646873 CTATTCTTCT
Statistics
Matches: 90, Mismatches: 12, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
15 11 0.12
16 21 0.23
17 20 0.22
18 15 0.17
19 15 0.17
20 7 0.08
21 1 0.01
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.17
Consensus pattern (16 bp):
AAAAAATAAAAAATAC
Found at i:16646873 original size:9 final size:9
Alignment explanation
Indices: 16646802--16646873 Score: 78
Period size: 9 Copynumber: 8.0 Consensus size: 9
16646792 AGGAAAATGA
16646802 AAAAACATAC
1 AAAAA-ATAC
16646812 TAAAAAATA-
1 -AAAAAATAC
*
16646821 AAGAAATAC
1 AAAAAATAC
16646830 AAAAAATA-
1 AAAAAATAC
16646838 ATAAAAATAC
1 A-AAAAATAC
*
16646848 AAAAAA-AT
1 AAAAAATAC
16646856 AAAAAATAC
1 AAAAAATAC
16646865 AAAAAATAC
1 AAAAAATAC
16646874 TATTCTTCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
8 15 0.28
9 29 0.55
10 4 0.08
11 5 0.09
ACGTcount: A:0.76, C:0.08, G:0.01, T:0.14
Consensus pattern (9 bp):
AAAAAATAC
Found at i:16650303 original size:19 final size:19
Alignment explanation
Indices: 16650279--16650315 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
16650269 CTTCTAAACT
16650279 TCAAATCATACTCCAATAC
1 TCAAATCATACTCCAATAC
*
16650298 TCAAATCGTACTCCAATA
1 TCAAATCATACTCCAATA
16650316 AGTCAAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.03, T:0.27
Consensus pattern (19 bp):
TCAAATCATACTCCAATAC
Found at i:16658471 original size:28 final size:28
Alignment explanation
Indices: 16658440--16658514 Score: 141
Period size: 28 Copynumber: 2.7 Consensus size: 28
16658430 TAAGTATAGA
*
16658440 GGCAAAACGGTAATTTTGCCATACCGAG
1 GGCAAAATGGTAATTTTGCCATACCGAG
16658468 GGCAAAATGGTAATTTTGCCATACCGAG
1 GGCAAAATGGTAATTTTGCCATACCGAG
16658496 GGCAAAATGGTAATTTTGC
1 GGCAAAATGGTAATTTTGC
16658515 ACCACCAACA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (28 bp):
GGCAAAATGGTAATTTTGCCATACCGAG
Found at i:16659657 original size:13 final size:13
Alignment explanation
Indices: 16659639--16659663 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16659629 GGAGAAATTG
16659639 TGATTTTATAAAA
1 TGATTTTATAAAA
16659652 TGATTTTATAAA
1 TGATTTTATAAA
16659664 TTTTATGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:16661032 original size:21 final size:23
Alignment explanation
Indices: 16660989--16661033 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
16660979 TACCTTAATC
* *
16660989 TTATTCAAACAACTAAATTTAAA
1 TTATTCAAAAAACTAAAATTAAA
16661012 TTATT-AAAAAAC-AAAATTAAA
1 TTATTCAAAAAACTAAAATTAAA
16661033 T
1 T
16661034 CTAACAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 6 0.30
23 5 0.25
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (23 bp):
TTATTCAAAAAACTAAAATTAAA
Found at i:16673431 original size:13 final size:13
Alignment explanation
Indices: 16673413--16673437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16673403 AGAGAAATTG
16673413 TGATTTTATAAAA
1 TGATTTTATAAAA
16673426 TGATTTTATAAA
1 TGATTTTATAAA
16673438 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:16679114 original size:18 final size:19
Alignment explanation
Indices: 16679083--16679118 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
16679073 GTTAGTTTAT
*
16679083 TTATTTATGATTGTTTTCA
1 TTATTTAAGATTGTTTTCA
16679102 TTATTTAAG-TTGTTTTC
1 TTATTTAAGATTGTTTTC
16679119 GTTTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.19, C:0.06, G:0.11, T:0.64
Consensus pattern (19 bp):
TTATTTAAGATTGTTTTCA
Found at i:16683299 original size:20 final size:20
Alignment explanation
Indices: 16683276--16683318 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
16683266 ACTTAAAGAT
16683276 AGAAACAACTTAGTCGACTA
1 AGAAACAACTTAGTCGACTA
** *
16683296 AGAAGGAAGTTAGTCGACTA
1 AGAAACAACTTAGTCGACTA
16683316 AGA
1 AGA
16683319 GCTCACTGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.19
Consensus pattern (20 bp):
AGAAACAACTTAGTCGACTA
Found at i:16689124 original size:20 final size:20
Alignment explanation
Indices: 16689099--16689137 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16689089 TAATGAATGT
* *
16689099 TTGATGATGATTGATAATAC
1 TTGATGATAATTGAGAATAC
16689119 TTGATGATAATTGAGAATA
1 TTGATGATAATTGAGAATA
16689138 GTGCTTGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGATGATAATTGAGAATAC
Found at i:16691694 original size:19 final size:19
Alignment explanation
Indices: 16691670--16691707 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
16691660 CTCCCATGTC
*
16691670 CTTTTT-CTTCTTTTCCTTT
1 CTTTTTACTT-TTATCCTTT
16691689 CTTTTTACTTTTATCCTTT
1 CTTTTTACTTTTATCCTTT
16691708 TTTCTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (19 bp):
CTTTTTACTTTTATCCTTT
Found at i:16693698 original size:13 final size:13
Alignment explanation
Indices: 16693680--16693704 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16693670 TTTCAGAAAA
16693680 TTTATAAAATCAT
1 TTTATAAAATCAT
16693693 TTTATAAAATCA
1 TTTATAAAATCA
16693705 CAATTTCTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:16694969 original size:28 final size:27
Alignment explanation
Indices: 16694921--16694974 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
16694911 AAATGCTCTG
* *
16694921 GGGGTGCAAAATTACCGTTTTGCCCCC
1 GGGGTGCAAAATTACAGTTTTACCCCC
*
16694948 GGGGTGGCAAAATTACATTTTTACCCC
1 GGGGT-GCAAAATTACAGTTTTACCCC
16694975 AAAAACTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (27 bp):
GGGGTGCAAAATTACAGTTTTACCCCC
Found at i:16694974 original size:27 final size:27
Alignment explanation
Indices: 16694921--16694974 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
16694911 AAATGCTCTG
* *
16694921 GGGGTGCAAAATTACCGTTTTGCCCCC
1 GGGGTGCAAAATTACCATTTTGACCCC
*
16694948 GGGGTGGCAAAATTA-CATTTTTACCCC
1 GGGGT-GCAAAATTACCATTTTGACCCC
16694975 AAAAACTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (27 bp):
GGGGTGCAAAATTACCATTTTGACCCC
Found at i:16695524 original size:16 final size:15
Alignment explanation
Indices: 16695483--16695569 Score: 52
Period size: 16 Copynumber: 5.5 Consensus size: 15
16695473 TTTTTATTTT
*
16695483 ATTTTATTATTTTAAA
1 ATTTTATT-TTTTTAA
**
16695499 ATTAAATTTTTTTAA
1 ATTTTATTTTTTTAA
16695514 ATTTTATTTTTATTATA
1 ATTTTATTTTT-TTA-A
* *
16695531 TTATTTGATTATTTT--
1 --ATTTTATTTTTTTAA
16695546 ATTTTATTTTTATTAA
1 ATTTTATTTTT-TTAA
*
16695562 TTTTTATT
1 ATTTTATT
16695570 ATATATTTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
13 9 0.17
14 2 0.04
15 15 0.28
16 16 0.30
17 1 0.02
18 2 0.04
19 9 0.17
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (15 bp):
ATTTTATTTTTTTAA
Found at i:16695555 original size:32 final size:31
Alignment explanation
Indices: 16695514--16695585 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 31
16695504 ATTTTTTTAA
16695514 ATTTTATTTTTATTATATTATTTGATTAT-T-TT
1 ATTTTATTTTTATTA-ATT-TTT-ATTATATATT
16695546 ATTTTATTTTTATTAATTTTTATTATATATT
1 ATTTTATTTTTATTAATTTTTATTATATATT
*
16695577 TTTTTATTT
1 ATTTTATTT
16695586 AGGGAATAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 5 0.14
30 4 0.11
31 13 0.35
32 15 0.41
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (31 bp):
ATTTTATTTTTATTAATTTTTATTATATATT
Found at i:16695585 original size:21 final size:21
Alignment explanation
Indices: 16695515--16695585 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
16695505 TTTTTTTAAA
16695515 TTTTATTTTTATTATATTATTT
1 TTTTATTTTTATTATA-TATTT
**
16695537 GATTA-TTTTATT-T-TATTT
1 TTTTATTTTTATTATATATTT
16695555 TTATTAATTTTTATTATATATTT
1 TT-TT-ATTTTTATTATATATTT
16695578 TTTTATTT
1 TTTTATTT
16695586 AGGGAATAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
18 5 0.12
19 2 0.05
20 2 0.05
21 18 0.45
22 6 0.15
23 7 0.17
ACGTcount: A:0.24, C:0.00, G:0.01, T:0.75
Consensus pattern (21 bp):
TTTTATTTTTATTATATATTT
Found at i:16696048 original size:23 final size:23
Alignment explanation
Indices: 16696017--16696062 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
16696007 TGATGCATAA
* *
16696017 TCTCGTTATTGCTGCTTTTGATT
1 TCTCATTATTGCTGCCTTTGATT
16696040 TCTCATTATTGCTGCCTTTGATT
1 TCTCATTATTGCTGCCTTTGATT
16696063 ACAACTGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.20, G:0.15, T:0.54
Consensus pattern (23 bp):
TCTCATTATTGCTGCCTTTGATT
Found at i:16701129 original size:15 final size:15
Alignment explanation
Indices: 16701089--16701171 Score: 52
Period size: 15 Copynumber: 5.7 Consensus size: 15
16701079 CTTGATTGAG
*
16701089 GATGAAGACGATG-A
1 GATGAAGAAGATGAA
* *
16701103 CATGCAAAAAGATGAA
1 GATG-AAGAAGATGAA
16701119 GATGAAGAAGATGAA
1 GATGAAGAAGATGAA
16701134 -ATGGAATG-AGATGAA
1 GAT-GAA-GAAGATGAA
* *
16701149 AAT--A-AAGATGAC
1 GATGAAGAAGATGAA
16701161 GATGAAGAAGA
1 GATGAAGAAGA
16701172 AGATGAACTT
Statistics
Matches: 53, Mismatches: 7, Indels: 17
0.69 0.09 0.22
Matches are distributed among these distances:
12 8 0.15
13 1 0.02
14 6 0.11
15 31 0.58
16 7 0.13
ACGTcount: A:0.52, C:0.05, G:0.29, T:0.14
Consensus pattern (15 bp):
GATGAAGAAGATGAA
Found at i:16701916 original size:21 final size:20
Alignment explanation
Indices: 16701892--16701949 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
16701882 ATATGTTGTC
*
16701892 TTAAGATATTTCTAATATTTG
1 TTAAGAAATTT-TAATATTTG
16701913 TTAATGAAATTGTT-ATATTTG
1 TTAA-GAAATT-TTAATATTTG
16701934 TTAA-AAATTTTAATAT
1 TTAAGAAATTTTAATAT
16701950 ATAAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 2 0.06
19 9 0.27
21 15 0.45
22 6 0.18
23 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.52
Consensus pattern (20 bp):
TTAAGAAATTTTAATATTTG
Found at i:16703793 original size:45 final size:45
Alignment explanation
Indices: 16703698--16703795 Score: 108
Period size: 45 Copynumber: 2.2 Consensus size: 45
16703688 TTGGAAATGC
** * *
16703698 TTTTCCAACGGAATTGTTTCCAATGGAAAATTCCGTTGGAAACCA
1 TTTTCCAACAAAATTGTTTCCAACGGAAAATTCCGTTCGAAACCA
* ** *
16703743 ATTTCCAACAAAATTGTTTCCAACGGAATTTTCCG-TCGAAACTTA
1 TTTTCCAACAAAATTGTTTCCAACGGAAAATTCCGTTCGAAAC-CA
16703788 TTTTCCAA
1 TTTTCCAA
16703796 TAGAAAATTT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
44 6 0.14
45 37 0.86
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (45 bp):
TTTTCCAACAAAATTGTTTCCAACGGAAAATTCCGTTCGAAACCA
Found at i:16705138 original size:17 final size:19
Alignment explanation
Indices: 16705113--16705166 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 19
16705103 CCATTGTGTA
16705113 AATCAAGAATATGACATG-
1 AATCAAGAATATGACATGT
* *
16705131 AA-CAAGAACATGCATTATGT
1 AATCAAGAATATG-A-CATGT
16705151 AATCAAGAATATGACA
1 AATCAAGAATATGACA
16705167 AACAAACTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
17 9 0.32
18 3 0.11
19 4 0.14
20 3 0.11
21 9 0.32
ACGTcount: A:0.50, C:0.13, G:0.15, T:0.22
Consensus pattern (19 bp):
AATCAAGAATATGACATGT
Found at i:16712641 original size:17 final size:17
Alignment explanation
Indices: 16712619--16712662 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
16712609 AATTAATTAT
16712619 ATTAAAAATATATAAAA
1 ATTAAAAATATATAAAA
*
16712636 ATTAAAAAAATATAAAA
1 ATTAAAAATATATAAAA
*
16712653 ATAAAAAATA
1 ATTAAAAATA
16712663 ATTAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
ATTAAAAATATATAAAA
Found at i:16712665 original size:27 final size:27
Alignment explanation
Indices: 16712621--16712672 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
16712611 TTAATTATAT
*
16712621 TAAAAATATATAAAAATTAAAAAAATA
1 TAAAAATATAAAAAAATTAAAAAAATA
*
16712648 TAAAAATA-AAAAATAATTAATAAAA
1 TAAAAATATAAAAA-AATTAAAAAAA
16712673 CTATTTGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (27 bp):
TAAAAATATAAAAAAATTAAAAAAATA
Found at i:16727494 original size:635 final size:636
Alignment explanation
Indices: 16725811--16727600 Score: 2131
Period size: 630 Copynumber: 2.8 Consensus size: 636
16725801 AGTGTGAAGA
** * * *
16725811 CTAGCTTTTTAGGATCATTGTTTCTGGTTTGCTTTTCTTTGAAAGCTTGACAAGGATGTGATCAG
1 CTAGC-TTTTAGGATTGTTGCTTCTGGTTTGCTTTTCTTTGAAGGCTTGACAAGGATGTGATCAT
* *
16725876 TGGGTTAGGTTGTTGGTGGCTATTGAGTATTAGGTTGACTAGAATTCTAAATCTTATTTAACTAG
65 TGGGTTAGGTTGTT-G-GGCTGTT-AGT-TTAGGTTGACTAGAATTCTAAATCTTATTTGACTAG
*
16725941 GATTCTTATTTGTGTACAACATTGAATAGTTATATGGTTTTAAAGTTCTTGTTCCACATCAAGTC
126 GATTCTTGTTTGTGTACAACATTGAATAGTTATATGGTTTTAAAGTTCTTGTTCCACATCAAGTC
* * **
16726006 ATAATCCCATTCTACTTCAAAGTTTATATTATAAAAGTCGATCTCTAGGCTTTGGAAGAGT-AAG
191 ATAATCCCATTCTATTTGAACTTTTATATTATAAAAGTCGATCTCTAGGCTTTGGAAGAGTGAA-
* * * *
16726070 TAATGCTTTGGGAGCTCTAGAGAAGAATACCTTGTAACTTTGTCTTTTGCTTTAGGTGAAGTTAG
255 TAATGCTTTAGAAGCTCTAGAGAAAAATACCTTGTAACTTTGTCTTTTGCTTTAGGTGAAGCTAG
* ** * *
16726135 AGTGGTTTAGGTGAGTACTCTTGGGAAGTTATTGAGAGAAGGTGTGCAAAGGATCTTGGGTTGGT
320 AGT-GTTTGGGTGAGTGTTCTTGGGAGGTTATTGAGA-AAGGTGTGCAAGGGATCTTGGGTTGGT
* * * * *
16726200 TT-GGAGAACCATAGAGGTCAGTTTATTGCACTTTAATTTCTCAATAATAGAAGAACGGTTTCAC
383 TTGGGA-AACCATAAAGGTCAATTTATTGTACTTTAATTTTTCAATAATAAAAGAACGGTTTCAC
* * *
16726264 TCTTTGGATGTAGGTAAGAGCAAACCACATAAATTCTTGTATTTTTCTATTTGCTTGATTTCTCT
447 TCTGTGGATGTAGGTAAGAG--AACCACATAAATTCTCGTACTTTTCTATTTGCTTGATTTCTCT
* * * * * * **
16726329 AGGTTTTATCTTTGTTGTTTCTTGGGTGATTTTCATAATAAATTGGTATCAGTGTTTCGAGTTCA
510 AGGTTTTATCTTTGTTGTTTCCTAGGTGATTTTCATAACAAACTAGTATAAGAATTTCGAGTTCA
* * *
16726394 ATAAATCAAGATTCATCAAGAATGTTGAAAATTACTAGTTCTACAAATTTTAGGGTTATTGC
575 ATAAATCAAGATTCAACAAGAATGTTGAAAATTACTAGTTATACAAATTTTAGGGTAATTGC
* * *
16726456 CTTTTAGATTAGCTTTTTAGGATTGTTGCTTCTAGTTTGTTTTTCTTTGAAGGTTTGACAAGGAT
1 C--------TAGC-TTTTAGGATTGTTGCTTCTGGTTTGCTTTTCTTTGAAGGCTTGACAAGGAT
* * *
16726521 GTGATCATTGGATTAGGTTGTT--GATG---G-TT--GTTG---AG-----T---T-TTAGGTTG
57 GTGATCATTGGGTTAGGTTGTTGGGCTGTTAGTTTAGGTTGACTAGAATTCTAAATCTTA-TTTG
16726566 ACTAGGATTCTTGTTTGTGTACAA-ATTTGAATAGTTATATGGTTTTAAAGTTCTTGTTCCACAT
121 ACTAGGATTCTTGTTTGTGTACAACA-TTGAATAGTTATATGGTTTTAAAGTTCTTGTTCCACAT
* * *
16726630 TAAGTCTTAATCCCATTCTACTTTGAACTTTTATATTATAAAAGTCGATCTCTAGGCTTTGGAGG
185 CAAGTCATAATCCCATTCTA-TTTGAACTTTTATATTATAAAAGTCGATCTCTAGGCTTTGGAAG
* * * * *
16726695 AGTGAGTAATGCTTGA-AAGCTCTACAGAAAAATACCTTGTAACTCTGTATTTTGCTTTAGGTGA
249 AGTGAATAATGCTTTAGAAGCTCTAGAGAAAAATACCTTGTAACTTTGTCTTTTGCTTTAGGTGA
* * * **
16726759 AGCTAGAGTGATTTGGATAAGTGTTTTTAAGAGGTTATTGAGAAAAGGTGTGCAAGGGATCTTGG
314 AGCTAGAGTG-TTTGGGTGAGTGTTCTTGGGAGGTTATTGAG-AAAGGTGTGCAAGGGATCTTGG
* **
16726824 GTTGGTTTGAGAAACCATAAAATTCAATTTATTGTACTTTAATTTTTCAATAATAAAAGAA-GGA
377 GTTGGTTTGGGAAACCATAAAGGTCAATTTATTGTACTTTAATTTTTCAATAATAAAAGAACGG-
* * * **
16726888 TTTCACT-TAGTGGATGTAGGT-A-AG-A-CACGTGAATTCTCGTGCTTTTCTATTTTTTTGATT
441 TTTCACTCT-GTGGATGTAGGTAAGAGAACCACATAAATTCTCGTACTTTTCTATTTGCTTGATT
* * *
16726948 TCTCTGGGTTTTATCTTTGTTGTTTCCTAGGTGATTTTCATAACAAACTAGTATAAGAATTTTGG
505 TCTCTAGGTTTTATCTTTGTTGTTTCCTAGGTGATTTTCATAACAAACTAGTATAAGAATTTCGA
* * *
16727013 GTTCAGTAAATCAAGATTTAACAAGAATGTTGAAAGTTACTAGTTATACAAATTTTAGGGTAATT
570 GTTCAATAAATCAAGATTCAACAAGAATGTTGAAAATTACTAGTTATACAAATTTTAGGGTAATT
16727078 G-
635 GC
*
16727079 C-A-C-TTTAGGATTGTTGCTTCTGGTTTGCTTTTCTTTGAAGGCTAGACAAGGATGTGATCATT
1 CTAGCTTTTAGGATTGTTGCTTCTGGTTTGCTTTTCTTTGAAGGCTTGACAAGGATGTGATCATT
16727141 GGGTTAGGTTGTTAGCGGCTGTTAAGTTTTAGGTTGACTAGAATTCTAAATCTTATTTGACTAGG
66 GGGTTAGGTTGTT-G-GGCTGTT-AG-TTTAGGTTGACTAGAATTCTAAATCTTATTTGACTAGG
* *
16727206 ACTCTTGTTTGTGTACAACATTGAATAGTTATATGGTTTTAAAGTTCTTGTTCCACATCAAGTCC
127 ATTCTTGTTTGTGTACAACATTGAATAGTTATATGGTTTTAAAGTTCTTGTTCCACATCAAGTCA
* * * *
16727271 TAATCCGATTCTATTTTGGACTTTTATATTATAAAAGTCGATTTATAGGCTTTGGAAGAGTGAAT
192 TAATCCCATTCTA-TTTGAACTTTTATATTATAAAAGTCGATCTCTAGGCTTTGGAAGAGTGAAT
*
16727336 AATGCTTTAGAAGCTCTAGAGAAAAATACCTTGTAACTTTGTCTTTTGCTTTAGGTGAAGCTAAA
256 AATGCTTTAGAAGCTCTAGAGAAAAATACCTTGTAACTTTGTCTTTTGCTTTAGGTGAAGCTAGA
*
16727401 GTAGTTTGGGTGAGTGTTCTTGGGAGGTTATCGA-AAACGAGTGTGCAAGGGATCTTGGGTTGGT
321 GT-GTTTGGGTGAGTGTTCTTGGGAGGTTATTGAGAAA-G-GTGTGCAAGGGATCTTGGGTTGGT
* * *
16727465 TTGGGAAACCATAAAGGTCAATTTATTGTACTTCAATTTTCCAATAATATAAGAACGG-TTCACT
383 TTGGGAAACCATAAAGGTCAATTTATTGTACTTTAATTTTTCAATAATAAAAGAACGGTTTCACT
* ** ** * ** *
16727529 CCGTAAATGTAGGTAAGAGGCCCAACCATGTAAATTCTTGTGTTTTTCTATTTGCTTGATTTCTT
448 CTGTGGATGTAGGTAAGA-G---AACCACATAAATTCTCGTACTTTTCTATTTGCTTGATTTCTC
16727594 TAGGTTT
509 TAGGTTT
16727601 CTTGGGTGAT
Statistics
Matches: 971, Mismatches: 118, Indels: 115
0.81 0.10 0.10
Matches are distributed among these distances:
611 67 0.07
613 1 0.00
614 1 0.00
615 3 0.00
619 1 0.00
621 2 0.00
623 5 0.01
624 142 0.15
625 1 0.00
626 2 0.00
628 2 0.00
629 9 0.01
630 243 0.25
631 54 0.06
632 1 0.00
633 4 0.00
634 153 0.16
635 155 0.16
636 4 0.00
637 1 0.00
638 2 0.00
641 5 0.01
642 38 0.04
643 2 0.00
645 2 0.00
649 2 0.00
653 69 0.07
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.40
Consensus pattern (636 bp):
CTAGCTTTTAGGATTGTTGCTTCTGGTTTGCTTTTCTTTGAAGGCTTGACAAGGATGTGATCATT
GGGTTAGGTTGTTGGGCTGTTAGTTTAGGTTGACTAGAATTCTAAATCTTATTTGACTAGGATTC
TTGTTTGTGTACAACATTGAATAGTTATATGGTTTTAAAGTTCTTGTTCCACATCAAGTCATAAT
CCCATTCTATTTGAACTTTTATATTATAAAAGTCGATCTCTAGGCTTTGGAAGAGTGAATAATGC
TTTAGAAGCTCTAGAGAAAAATACCTTGTAACTTTGTCTTTTGCTTTAGGTGAAGCTAGAGTGTT
TGGGTGAGTGTTCTTGGGAGGTTATTGAGAAAGGTGTGCAAGGGATCTTGGGTTGGTTTGGGAAA
CCATAAAGGTCAATTTATTGTACTTTAATTTTTCAATAATAAAAGAACGGTTTCACTCTGTGGAT
GTAGGTAAGAGAACCACATAAATTCTCGTACTTTTCTATTTGCTTGATTTCTCTAGGTTTTATCT
TTGTTGTTTCCTAGGTGATTTTCATAACAAACTAGTATAAGAATTTCGAGTTCAATAAATCAAGA
TTCAACAAGAATGTTGAAAATTACTAGTTATACAAATTTTAGGGTAATTGC
Found at i:16731747 original size:148 final size:147
Alignment explanation
Indices: 16731479--16731754 Score: 543
Period size: 148 Copynumber: 1.9 Consensus size: 147
16731469 AAGTGAACAT
16731479 TTTGATTAATAATAGTTAGTCAATTGTTAGACATAATAACCTATTTGACCTAAAATAAATGTATA
1 TTTGATTAATAATAGTTAGTCAATTGTTAGACATAATAACCTATTTGACCTAAAATAAATGTATA
16731544 AGAACTTGATTGAAAGTAATAGTATAACAAGATCTTAATTGAATTTTTTTTTGAATAATTCAAAC
66 AGAACTTGATTGAAAGTAATAGTATAACAAGATCTTAATTGAATTTTTTTTTGAATAATTCAAAC
16731609 TTGTATTTNAAGTGACTA
131 TTGTATTT-AAGTGACTA
16731627 TTTGATTAATAATAGTTAGTCAATTGTTAGACATAATAACCTATTTGACCTAAAATAAATGTATA
1 TTTGATTAATAATAGTTAGTCAATTGTTAGACATAATAACCTATTTGACCTAAAATAAATGTATA
16731692 AGAACTTGATTGAAAGTAATAGTATAACAAGATCTTAATTGAATTTTTTTTTGAATAATTCAA
66 AGAACTTGATTGAAAGTAATAGTATAACAAGATCTTAATTGAATTTTTTTTTGAATAATTCAA
16731755 GAATTTTTTA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
148 128 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (147 bp):
TTTGATTAATAATAGTTAGTCAATTGTTAGACATAATAACCTATTTGACCTAAAATAAATGTATA
AGAACTTGATTGAAAGTAATAGTATAACAAGATCTTAATTGAATTTTTTTTTGAATAATTCAAAC
TTGTATTTAAGTGACTA
Found at i:16734174 original size:39 final size:39
Alignment explanation
Indices: 16734092--16734165 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
16734082 TAGGAGACAA
* *
16734092 AAACAGAAGGTTTTTCGCTGCAGCGAAATTGTAACTCGG
1 AAACAGAAGGTTTCTCGCTGCAGCGAAATTGCAACTCGG
* *
16734131 AAACAGAATGTTTCTCGCTGCAGTGAAATT-CAACT
1 AAACAGAAGGTTTCTCGCTGCAGCGAAATTGCAACT
16734166 GATGAAACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 4 0.13
39 27 0.87
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (39 bp):
AAACAGAAGGTTTCTCGCTGCAGCGAAATTGCAACTCGG
Found at i:16734649 original size:38 final size:39
Alignment explanation
Indices: 16734563--16734665 Score: 138
Period size: 38 Copynumber: 2.6 Consensus size: 39
16734553 ACCCGGCTCA
* *
16734563 TGTACATCCCCCCAGATCGTGCACATAGCCGGCACCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCAGG-ACCATCG
* *
16734603 TGTGCATCCCCCCACATCGTGCACA-ATCAGTG-CCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCAG-GACCATCG
16734641 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
16734666 CGGGCACTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
38 30 0.53
39 3 0.05
40 24 0.42
ACGTcount: A:0.22, C:0.41, G:0.17, T:0.19
Consensus pattern (39 bp):
TGTACATCCCCCCACATCGTGCACATAGCAGGACCATCG
Found at i:16734658 original size:19 final size:19
Alignment explanation
Indices: 16734563--16734661 Score: 65
Period size: 19 Copynumber: 5.1 Consensus size: 19
16734553 ACCCGGCTCA
*
16734563 TGTACATCCCCCCAGATCG
1 TGTACATCCCCCCACATCG
* * **
16734582 TGCACATAGCCGGCACCATCG
1 TGTACAT-CCCCCCA-CATCG
*
16734603 TGTGCATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
* ****
16734622 TGCACAATCAGTGC-CATCG
1 TGTAC-ATCCCCCCACATCG
16734641 TGTACATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
16734660 TG
1 TG
16734662 CACACGGGCA
Statistics
Matches: 55, Mismatches: 21, Indels: 8
0.65 0.25 0.10
Matches are distributed among these distances:
18 4 0.07
19 30 0.55
20 12 0.22
21 9 0.16
ACGTcount: A:0.21, C:0.40, G:0.18, T:0.20
Consensus pattern (19 bp):
TGTACATCCCCCCACATCG
Found at i:16735563 original size:19 final size:19
Alignment explanation
Indices: 16735539--16735577 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
16735529 AGAAGAAGAC
*
16735539 AAGCTGTTGGAAATTCAAG
1 AAGCTGCTGGAAATTCAAG
16735558 AAGCTGCTGGAAATTCAAG
1 AAGCTGCTGGAAATTCAAG
16735577 A
1 A
16735578 TATTTATAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (19 bp):
AAGCTGCTGGAAATTCAAG
Found at i:16746836 original size:21 final size:19
Alignment explanation
Indices: 16746800--16746840 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
16746790 ACATGTTGAG
16746800 TAGTTAATTTAAGTTATTT
1 TAGTTAATTTAAGTTATTT
*
16746819 TAGTTAAGTTTTATGTTATTT
1 TAGTTAA--TTTAAGTTATTT
16746840 T
1 T
16746841 GTTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (19 bp):
TAGTTAATTTAAGTTATTT
Found at i:16749986 original size:42 final size:41
Alignment explanation
Indices: 16749846--16749978 Score: 187
Period size: 42 Copynumber: 3.1 Consensus size: 41
16749836 ACCATCCCAC
16749846 CATCATCAACTCATGTGCACTTCCCACTAGCACATAGCTAGGT
1 CATCATCAACTCATGTGCAC-TCCCAC-AGCACATAGCTAGGT
* *
16749889 CATCATCAACTCATGTGCACTCCACACCGCACATAGCTAGAT
1 CATCATCAACTCATGTGCACTCC-CACAGCACATAGCTAGGT
*
16749931 CATCATCAGCTCATGTGCACTCCCACAGGCACATAGCT-GCGT
1 CATCATCAACTCATGTGCACTCCCACA-GCACATAGCTAG-GT
16749973 CATCAT
1 CATCAT
16749979 TATCTCATAA
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
41 4 0.05
42 55 0.67
43 23 0.28
ACGTcount: A:0.28, C:0.35, G:0.14, T:0.23
Consensus pattern (41 bp):
CATCATCAACTCATGTGCACTCCCACAGCACATAGCTAGGT
Found at i:16768856 original size:15 final size:15
Alignment explanation
Indices: 16768836--16768869 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
16768826 TATTAATGTA
*
16768836 AAAATATAAATAAAT
1 AAAATAAAAATAAAT
*
16768851 AAAATAAAAATAACT
1 AAAATAAAAATAAAT
16768866 AAAA
1 AAAA
16768870 AGAGAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATAAAAATAAAT
Found at i:16769271 original size:4 final size:4
Alignment explanation
Indices: 16769262--16769325 Score: 64
Period size: 4 Copynumber: 16.8 Consensus size: 4
16769252 CATTCAATAA
*
16769262 AAAT AAAT AAAT AAAT AAAT AAAT ATAAT -AA- AAAT AAAA AAAT AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT
* *
16769308 AAAT GAA- ACAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAA
16769326 AGTAAAAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
3 8 0.16
4 38 0.78
5 3 0.06
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:16769293 original size:31 final size:32
Alignment explanation
Indices: 16769257--16769341 Score: 104
Period size: 31 Copynumber: 2.7 Consensus size: 32
16769247 ACACCCATTC
* *
16769257 AATAAAAATAAATAAATAAATAAAT-AAATAT-
1 AATAAAAATAAAAAAATAAA-AAATGAAACATA
16769288 AATAAAAATAAAAAAATAAAAAATGAAACATA
1 AATAAAAATAAAAAAATAAAAAATGAAACATA
* *
16769320 AATAAAAGTAAAAATA-AAAAAA
1 AATAAAAATAAAAAAATAAAAAA
16769342 GAAGAGTCTG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.08
31 30 0.62
32 14 0.29
ACGTcount: A:0.78, C:0.01, G:0.02, T:0.19
Consensus pattern (32 bp):
AATAAAAATAAAAAAATAAAAAATGAAACATA
Found at i:16781914 original size:59 final size:59
Alignment explanation
Indices: 16781717--16782402 Score: 627
Period size: 59 Copynumber: 11.7 Consensus size: 59
16781707 CGGTGAATTA
* * * ** * * *
16781717 AATCGAACATATTTTGAGATAGGTCGAGTTTAGATTAAGTCTAAAAATTTCAATTTTTA
1 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAAGAATTTCAATTTTTT
* * * * * * * ** * * * *
16781776 AATCGAACTTGTTTTAAAATAGATCAAACCTAGGTCAAGCCTAGGAATTTTAATTTTTTT
1 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAAGAATTTCAA-TTTTTT
* * * *
16781836 ACATCGAACCTGTTGTGAGATAGATCGAGCTTAGATTAAGTCTAAGAGTTTCAATTTTTT
1 A-ATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAAGAATTTCAATTTTTT
* * * * *
16781896 AATCGAACCTATTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAATTTTTT
1 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAAGAATTTCAATTTTTT
* * * *
16781955 ACATGGAACCTGTTGTGAGATAAGTCGAGCTTAGATTAAGTCTAAGAATTTCAA---TTT
1 A-ATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAAGAATTTCAATTTTTT
* * * * * * *
16782012 --TCGAACCTGTTTTAAGATAGGTCAAGCCTAGATTACA-TCTAAGAATTTTAACTTTTA
1 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTA-AGTCTAAGAATTTCAATTTTTT
* * * * * *
16782069 AATCAAACCTGTTATGAGATAAGTCGAGCCTAAATTAAGTTTAGGAATTTGAATTTTTT
1 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAAGAATTTCAATTTTTT
* * * * * * *
16782128 AAATCGAACTTGTTGTGTGATAGGTCGAGTCTAAATTAAGTTTAGGAATTTGAATTTTTA
1 -AATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAAGAATTTCAATTTTTT
* * *
16782188 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAGGAGTTTCAATTTTTA
1 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAAGAATTTCAATTTTTT
* *
16782247 AATCGAACCTGTTGTGAGATAGGTCGAGCGTAAATTAAGTCT-AGAATTT-AA-ATTTT
1 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAAGAATTTCAATTTTTT
* * * * * * *
16782303 AATTCGAACTTGTCGTGAGATAGTTTGAGCCTAAATTAAGT-TTAGAAATTTGAATTTTTA
1 AA-TCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAAG-AATTTCAATTTTTT
* *
16782363 AATCGAACCTGTTGTGAGATAGGTCAAGCCTAGATTAAGT
1 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGT
16782403 TAGGGATTTT
Statistics
Matches: 514, Mismatches: 97, Indels: 32
0.80 0.15 0.05
Matches are distributed among these distances:
54 42 0.08
55 1 0.00
56 6 0.01
57 42 0.08
58 11 0.02
59 260 0.51
60 113 0.22
61 39 0.08
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (59 bp):
AATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAAGAATTTCAATTTTTT
Found at i:16782000 original size:119 final size:118
Alignment explanation
Indices: 16781714--16782415 Score: 699
Period size: 119 Copynumber: 6.0 Consensus size: 118
16781704 CATCGGTGAA
* * * * ** * *
16781714 TTAAATCGAACATATTTTGAGATAGGTCGAGTTTAGATTAAGTCTAAAAATTTCAATTTTTAAAT
1 TTAAATCGAACCTGTTGTGAGATAAGTCGAGCCTAAATTAAGTCTAAGAATTTCAATTTTTAAAT
* * * * * * ** * *
16781779 CGAACTTGTTTTAAAATAGATCAAACCTAGGTCAAGCCTAGGAATTTTAATTTTT
66 CGAACCTGTTGTGAGATAGGTCAAGCCTAAATTAAGTCTAGGAATTTTAA--TTT
* * * * *
16781834 TTACATCGAACCTGTTGTGAGAT-AGATCGAGCTTAGATTAAGTCTAAGAGTTTCAATTTTTTAA
1 TTAAATCGAACCTGTTGTGAGATAAG-TCGAGCCTAAATTAAGTCTAAGAATTTCAATTTTTAAA
* * * *
16781898 TCGAACCTATTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAATTTT
65 TCGAACCTGTTGTGAGATAGGTCAAGCCTAAATTAAGTCTAGGAATTTTAA-TTT
* * * *
16781953 TTACATGGAACCTGTTGTGAGATAAGTCGAGCTTAGATTAAGTCTAAGAATTTCAA--TTT---T
1 TTAAATCGAACCTGTTGTGAGATAAGTCGAGCCTAAATTAAGTCTAAGAATTTCAATTTTTAAAT
* * * * *
16782013 CGAACCTGTTTTAAGATAGGTCAAGCCTAGATTACA-TCTAAGAATTTTAACTT
66 CGAACCTGTTGTGAGATAGGTCAAGCCTAAATTA-AGTCTAGGAATTTTAATTT
* * * * *
16782066 TTAAATCAAACCTGTTATGAGATAAGTCGAGCCTAAATTAAGTTTAGGAATTTGAATTTTTTAAA
1 TTAAATCGAACCTGTTGTGAGATAAGTCGAGCCTAAATTAAGTCTAAGAATTTCAA-TTTTTAAA
* * * * * *
16782131 TCGAACTTGTTGTGTGATAGGTCGAGTCTAAATTAAGTTTAGGAATTTGAATTT
65 TCGAACCTGTTGTGAGATAGGTCAAGCCTAAATTAAGTCTAGGAATTTTAATTT
* * *
16782185 TTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAGGAGTTTCAATTTTTAAAT
1 TTAAATCGAACCTGTTGTGAGATAAGTCGAGCCTAAATTAAGTCTAAGAATTTCAATTTTTAAAT
* * *
16782250 CGAACCTGTTGTGAGATAGGTCGAGCGTAAATTAAGTCTA-GAA-TTTAAATT
66 CGAACCTGTTGTGAGATAGGTCAAGCCTAAATTAAGTCTAGGAATTTTAATTT
* * * * * *
16782301 TTAATTCGAACTTGTCGTGAGAT-AGTTTGAGCCTAAATTAAGT-TTAGAAATTTGAATTTTTAA
1 TTAAATCGAACCTGTTGTGAGATAAG-TCGAGCCTAAATTAAGTCTAAG-AATTTCAATTTTTAA
* *
16782364 ATCGAACCTGTTGTGAGATAGGTCAAGCCTAGATTAAGT-TAGGGATTTTAAT
64 ATCGAACCTGTTGTGAGATAGGTCAAGCCTAAATTAAGTCTAGGAATTTTAAT
16782416 CGAACCTGTT
Statistics
Matches: 489, Mismatches: 79, Indels: 31
0.82 0.13 0.05
Matches are distributed among these distances:
113 49 0.10
114 42 0.09
115 6 0.01
116 96 0.20
117 11 0.02
118 45 0.09
119 147 0.30
120 93 0.19
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (118 bp):
TTAAATCGAACCTGTTGTGAGATAAGTCGAGCCTAAATTAAGTCTAAGAATTTCAATTTTTAAAT
CGAACCTGTTGTGAGATAGGTCAAGCCTAAATTAAGTCTAGGAATTTTAATTT
Found at i:16782086 original size:173 final size:175
Alignment explanation
Indices: 16781838--16782402 Score: 653
Period size: 173 Copynumber: 3.2 Consensus size: 175
16781828 ATTTTTTTAC
* * *
16781838 ATCGAACCTGTTGTGAGATAGATCGAGCTTAGATTAAGTCTAAGAGTTTCAATTTTTTAATCGAA
1 ATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAGTTTCAATTTTTAAATCGAA
* * * *
16781903 CCTATTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAATTTTTTACATGGAACCTGT
66 CCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTAAATTTTTTAAATCGAACCTGT
*
16781968 TGTGAGATAAGTCGAG-CTTAGATTAAGTCTAAGAATTTCAA-TTT
131 TGTGAGATAAGTCGAGTC-TAAATTAAGTCTAAGAATTTCAATTTT
* * * * * * *
16782012 -TCGAACCTGTTTTAAGATAGGTCAAGCCTAGATTACA-TCTAAGAATTTTAACTTTTAAATCAA
1 ATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTA-AGTCTAAGAGTTTCAATTTTTAAATCGA
* * *
16782075 ACCTGTTATGAGATAAGTCGAGCCTAAATTAAGTTTAGGAATTTGAATTTTTTAAATCGAACTTG
65 ACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTAAATTTTTTAAATCGAACCTG
* * * * *
16782140 TTGTGTGATAGGTCGAGTCTAAATTAAGTTTAGGAATTTGAATTTTT
130 TTGTGAGATAAGTCGAGTCTAAATTAAGTCTAAGAATTTCAA-TTTT
* *
16782187 AAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTCTAGGAGTTTCAATTTTTAAATCG
1 --ATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAGTTTCAATTTTTAAATCG
* * * * *
16782252 AACCTGTTGTGAGATAGGTCGAGCGTAAATTAAGTCTA-GAATTTAAA--TTTTAATTCGAACTT
64 AACCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTAAATTTTTTAAATCGAACCT
* * * * *
16782314 GTCGTGAGAT-AGTTTGAGCCTAAATTAAGT-TTAGAAATTTGAATTTTT
129 GTTGTGAGATAAG-TCGAGTCTAAATTAAGTCTAAG-AATTTCAA-TTTT
*
16782362 AAATCGAACCTGTTGTGAGATAGGTCAAGCCTAGATTAAGT
1 --ATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGT
16782403 TAGGGATTTT
Statistics
Matches: 335, Mismatches: 46, Indels: 19
0.84 0.12 0.05
Matches are distributed among these distances:
173 144 0.43
174 5 0.01
175 92 0.27
177 9 0.03
178 85 0.25
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (175 bp):
ATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAGTTTCAATTTTTAAATCGAA
CCTGTTATGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTAAATTTTTTAAATCGAACCTGT
TGTGAGATAAGTCGAGTCTAAATTAAGTCTAAGAATTTCAATTTT
Found at i:16782439 original size:50 final size:52
Alignment explanation
Indices: 16782358--16782462 Score: 128
Period size: 50 Copynumber: 2.1 Consensus size: 52
16782348 AAATTTGAAT
* *
16782358 TTTTAAATCGAACCTGTTGTGAGATAGGTCAAGCCTAGATTAAGT-TAGGGA
1 TTTTAAATCGAACCTGTTGTGAGATAGGTCAAGCCTAGATCAAGTCTAGGAA
* *
16782409 TTTT-AATCGAACCTGTT-TTA-ATATGAGTCAAGCCTATATCAAGTCTAGGAA
1 TTTTAAATCGAACCTGTTGTGAGATA-G-GTCAAGCCTAGATCAAGTCTAGGAA
16782460 TTT
1 TTT
16782463 CAATTTTGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
48 3 0.06
49 3 0.06
50 29 0.62
51 12 0.26
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.35
Consensus pattern (52 bp):
TTTTAAATCGAACCTGTTGTGAGATAGGTCAAGCCTAGATCAAGTCTAGGAA
Found at i:16782614 original size:6 final size:6
Alignment explanation
Indices: 16782603--16782683 Score: 62
Period size: 6 Copynumber: 13.3 Consensus size: 6
16782593 ACACCCATTC
* *
16782603 AATAAA AATAAA TAA-ATA AATAAA TATAATA AA-AATA AA-AAA AATAAAA
1 AATAAA AATAAA -AATAAA AATAAA AATAA-A AATAA-A AATAAA AAT-AAA
*
16782652 AATGAAA AA-ATA AATAAA AATAAA AATAAA AA
1 AAT-AAA AATAAA AATAAA AATAAA AATAAA AA
16782684 AAGAAGAGTT
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
5 9 0.15
6 38 0.61
7 15 0.24
ACGTcount: A:0.80, C:0.00, G:0.01, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:16782617 original size:4 final size:4
Alignment explanation
Indices: 16782608--16782669 Score: 60
Period size: 4 Copynumber: 15.8 Consensus size: 4
16782598 CATTCAATAA
*
16782608 AAAT AAAT AAAT AAAT AAAT ATAAT -AA- AAAT AAAAA AAAT AAA- AAAT
1 AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT -AAAT AAAT AAAT AAAT
16782655 GAAA- AAAT AAAT AAA
1 -AAAT AAAT AAAT AAA
16782670 AATAAAAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
3 10 0.20
4 30 0.61
5 9 0.18
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:16782647 original size:24 final size:23
Alignment explanation
Indices: 16782603--16782685 Score: 80
Period size: 24 Copynumber: 3.3 Consensus size: 23
16782593 ACACCCATTC
16782603 AATAAAAATAAATAAATAAATAAATAT
1 AATAAAAAT-AA-AAA-AAATAAA-AT
16782630 AATAAAAATAAAAAAAATAAAA-
1 AATAAAAATAAAAAAAATAAAAT
16782652 AATGAAAAAATAAATAAAAATAAAAAT
1 AAT--AAAAATAAA-AAAAAT-AAAAT
16782679 AA-AAAAA
1 AATAAAAA
16782686 GAAGAGTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
22 3 0.06
23 1 0.02
24 21 0.41
25 9 0.18
26 6 0.12
27 11 0.22
ACGTcount: A:0.81, C:0.00, G:0.01, T:0.18
Consensus pattern (23 bp):
AATAAAAATAAAAAAAATAAAAT
Found at i:16782663 original size:43 final size:40
Alignment explanation
Indices: 16782606--16782685 Score: 117
Period size: 40 Copynumber: 1.9 Consensus size: 40
16782596 CCCATTCAAT
16782606 AAAAATAAATAAATAAATAAATATAATAAAAATAAAAAAAATA
1 AAAAATAAATAAATAAAT-AA-A-AATAAAAATAAAAAAAATA
16782649 AAAAATGAAA-AAATAAATAAAAATAAAAATAAAAAAA
1 AAAAAT-AAATAAATAAATAAAAATAAAAATAAAAAAA
16782686 GAAGAGTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
40 16 0.44
41 1 0.03
42 2 0.06
43 14 0.39
44 3 0.08
ACGTcount: A:0.81, C:0.00, G:0.01, T:0.17
Consensus pattern (40 bp):
AAAAATAAATAAATAAATAAAAATAAAAATAAAAAAAATA
Found at i:16785695 original size:20 final size:20
Alignment explanation
Indices: 16785666--16785709 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
16785656 ATTAGGTTAC
16785666 TTTTAAGTTAGTTATTTTAA
1 TTTTAAGTTAGTTATTTTAA
* * *
16785686 TTTTATGTTATTTCTTTTAA
1 TTTTAAGTTAGTTATTTTAA
16785706 TTTT
1 TTTT
16785710 TTTATTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (20 bp):
TTTTAAGTTAGTTATTTTAA
Found at i:16785717 original size:21 final size:20
Alignment explanation
Indices: 16785680--16785719 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
16785670 AAGTTAGTTA
*
16785680 TTTTAATTTTATGTTATTTC
1 TTTTAATTTTATATTATTTC
*
16785700 TTTTAATTTTTTTATTATTT
1 TTTTAA-TTTTATATTATTT
16785720 ATTAGTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.75
Consensus pattern (20 bp):
TTTTAATTTTATATTATTTC
Found at i:16786838 original size:14 final size:14
Alignment explanation
Indices: 16786803--16786838 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
16786793 CTTGTTAGTT
16786803 TTAATTTTAGTTAA
1 TTAATTTTAGTTAA
* *
16786817 TCAGTTTTAGTTAA
1 TTAATTTTAGTTAA
16786831 TTAATTTT
1 TTAATTTT
16786839 GATTATTTGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (14 bp):
TTAATTTTAGTTAA
Found at i:16797273 original size:30 final size:31
Alignment explanation
Indices: 16797206--16797273 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
16797196 AATCATTAAT
* *
16797206 TATAAGGATTTATTTGACTCAAAATAAAAAA
1 TATAAGAATTTATTTAACTCAAAATAAAAAA
*
16797237 TATAAGAATTTATTTAACTCAAAAT-AAAAG
1 TATAAGAATTTATTTAACTCAAAATAAAAAA
16797267 TATAAGA
1 TATAAGA
16797274 GCTTGATTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 11 0.32
31 23 0.68
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (31 bp):
TATAAGAATTTATTTAACTCAAAATAAAAAA
Found at i:16797904 original size:29 final size:31
Alignment explanation
Indices: 16797837--16797910 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 31
16797827 CACTTGTCAA
*
16797837 TTTAACCCTTAATTATAAGGAATCAAAAACG
1 TTTAACCCTTAATTATAAGCAATCAAAAACG
* * *
16797868 TTTGACCCTTAATTATTA-CAAT-TAAAACG
1 TTTAACCCTTAATTATAAGCAATCAAAAACG
16797897 TTTAACCCTTAATT
1 TTTAACCCTTAATT
16797911 GAAAAAGTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 19 0.50
30 3 0.08
31 16 0.42
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (31 bp):
TTTAACCCTTAATTATAAGCAATCAAAAACG
Found at i:16810815 original size:40 final size:40
Alignment explanation
Indices: 16810760--16810838 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
16810750 TTGGCTATTT
*
16810760 TTCACCTTAGTGGGGTTTTCAACCTTGCCAAGATTGGTGA
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
*
16810800 TTCACCTTAGTGGGGTTTTCAACCTCGCCACGATTGGTG
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTG
16810839 TCTTTCACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (40 bp):
TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
Found at i:16815742 original size:40 final size:40
Alignment explanation
Indices: 16815683--16815761 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
16815673 TTGACTATTT
*
16815683 TTCACCTTAGTGGGATTTTCAACCTTGCAAAGATTGGTGA
1 TTCACCTTAGTGGGATTTTCAACCTCGCAAAGATTGGTGA
* *
16815723 TTCACCTTAGT-GGAGTTTTCAACCTCGCTACGATTGGTG
1 TTCACCTTAGTGGGA-TTTTCAACCTCGCAAAGATTGGTG
16815762 TCTTTCACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 3 0.09
40 32 0.91
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (40 bp):
TTCACCTTAGTGGGATTTTCAACCTCGCAAAGATTGGTGA
Found at i:16815792 original size:19 final size:20
Alignment explanation
Indices: 16815758--16815802 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
16815748 CGCTACGATT
*
16815758 GGTGTCTTTCACAACGTCCA
1 GGTGTCTTTCACAACGCCCA
*
16815778 GGTGTCTTT-ACAACGCCCC
1 GGTGTCTTTCACAACGCCCA
16815797 GGTGTC
1 GGTGTC
16815803 ACTTTTACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.16, C:0.31, G:0.24, T:0.29
Consensus pattern (20 bp):
GGTGTCTTTCACAACGCCCA
Found at i:16815995 original size:19 final size:20
Alignment explanation
Indices: 16815952--16815996 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
16815942 CGCTACGATT
16815952 GGTGTCTTTCACAACGCCCA
1 GGTGTCTTTCACAACGCCCA
* * *
16815972 AGTGTCTTT-ACAATGCCCC
1 GGTGTCTTTCACAACGCCCA
16815991 GGTGTC
1 GGTGTC
16815997 ACTTTTACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.18, C:0.31, G:0.22, T:0.29
Consensus pattern (20 bp):
GGTGTCTTTCACAACGCCCA
Found at i:16816010 original size:194 final size:194
Alignment explanation
Indices: 16815681--16816070 Score: 735
Period size: 194 Copynumber: 2.0 Consensus size: 194
16815671 TTTTGACTAT
* *
16815681 TTTTCACCTTAGTGGGATTTTCAACCTTGCAAAGATTGGTGATTCACCTTAGTGGAGTTTTCAAC
1 TTTTCACCTTAGTAGGATTTTCAACCTTGCAAAAATTGGTGATTCACCTTAGTGGAGTTTTCAAC
* *
16815746 CTCGCTACGATTGGTGTCTTTCACAACGTCCAGGTGTCTTTACAACGCCCCGGTGTCACTTTTAC
66 CTCGCTACGATTGGTGTCTTTCACAACGCCCAAGTGTCTTTACAACGCCCCGGTGTCACTTTTAC
16815811 TTGTTTGAACACTTTTAAGAGTTGATCCTTATACTTTAGGTTGGGGATAAAGTCCTCTATCCAG
131 TTGTTTGAACACTTTTAAGAGTTGATCCTTATACTTTAGGTTGGGGATAAAGTCCTCTATCCAG
16815875 TTTTCACCTTAGTAGGATTTTCAACCTTGCAAAAATTGGTGATTCACCTTAGTGGAGTTTTCAAC
1 TTTTCACCTTAGTAGGATTTTCAACCTTGCAAAAATTGGTGATTCACCTTAGTGGAGTTTTCAAC
*
16815940 CTCGCTACGATTGGTGTCTTTCACAACGCCCAAGTGTCTTTACAATGCCCCGGTGTCACTTTTAC
66 CTCGCTACGATTGGTGTCTTTCACAACGCCCAAGTGTCTTTACAACGCCCCGGTGTCACTTTTAC
16816005 TTGTTTGAACACTTTTAAGAGTTGATCCTTATACTTTAGGTTGGGGATAAAGTCCTCTATCCAG
131 TTGTTTGAACACTTTTAAGAGTTGATCCTTATACTTTAGGTTGGGGATAAAGTCCTCTATCCAG
16816069 TT
1 TT
16816071 CACCAAGTAA
Statistics
Matches: 191, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
194 191 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (194 bp):
TTTTCACCTTAGTAGGATTTTCAACCTTGCAAAAATTGGTGATTCACCTTAGTGGAGTTTTCAAC
CTCGCTACGATTGGTGTCTTTCACAACGCCCAAGTGTCTTTACAACGCCCCGGTGTCACTTTTAC
TTGTTTGAACACTTTTAAGAGTTGATCCTTATACTTTAGGTTGGGGATAAAGTCCTCTATCCAG
Found at i:16820573 original size:20 final size:19
Alignment explanation
Indices: 16820548--16820585 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
16820538 ATTTTGCCTA
16820548 AGTGATCCTTGAATAGCTTG
1 AGTGATCCTTGAAT-GCTTG
16820568 AGTGATCCTTGAATGCTT
1 AGTGATCCTTGAATGCTT
16820586 TTAATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (19 bp):
AGTGATCCTTGAATGCTTG
Found at i:16820858 original size:22 final size:22
Alignment explanation
Indices: 16820788--16820860 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
16820778 TCTTGAAGCT
* *
16820788 AAAAGAACTAA-TATCTAGAGA
1 AAAAGAACTAATTATCAAGACA
* *
16820809 GGAAAGAACTAATTCTCAAGACA
1 -AAAAGAACTAATTATCAAGACA
16820832 AAAAGAACTAATTTATCAAGA-A
1 AAAAGAACTAA-TTATCAAGACA
*
16820854 TAAAGAA
1 AAAAGAA
16820861 TCGATTCTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
22 27 0.64
23 15 0.36
ACGTcount: A:0.56, C:0.11, G:0.14, T:0.19
Consensus pattern (22 bp):
AAAAGAACTAATTATCAAGACA
Found at i:16821443 original size:29 final size:29
Alignment explanation
Indices: 16821348--16821437 Score: 137
Period size: 29 Copynumber: 3.1 Consensus size: 29
16821338 TAGTGTTGTA
*
16821348 AAGAGGTTACGCCTGATCCTTGAAAAGGC
1 AAGAGGTTACGCCTGATCCTTGAAAAGGT
*
16821377 AAGAGGCTACG-CTGGATCCTTGAAAAGGT
1 AAGAGGTTACGCCT-GATCCTTGAAAAGGT
*
16821406 AAGAGGTTACGCCTGATCCTTGAAAAAGT
1 AAGAGGTTACGCCTGATCCTTGAAAAGGT
16821435 AAG
1 AAG
16821438 GAGTTATGCT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
28 2 0.04
29 51 0.93
30 2 0.04
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (29 bp):
AAGAGGTTACGCCTGATCCTTGAAAAGGT
Found at i:16826671 original size:15 final size:15
Alignment explanation
Indices: 16826651--16826679 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16826641 TGCGTGTTTG
16826651 GTTGCAATTTTTGGT
1 GTTGCAATTTTTGGT
16826666 GTTGCAATTTTTGG
1 GTTGCAATTTTTGG
16826680 ATTTTATTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.28, T:0.52
Consensus pattern (15 bp):
GTTGCAATTTTTGGT
Done.