Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 22 of 318
Found at i:5814886 original size:2 final size:2
Alignment explanation
Indices: 5814881--5814927 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
5814871 TCTCTCTCTC
5814881 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5814923 TA TA T
1 TA TA T
5814928 TAGTTTCATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5820112 original size:15 final size:15
Alignment explanation
Indices: 5820087--5820123 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
5820077 ATCTATGTGC
*
5820087 AAATTAATTATTTAA
1 AAATAAATTATTTAA
*
5820102 AAGTAAATTATTTAA
1 AAATAAATTATTTAA
5820117 AAATAAA
1 AAATAAA
5820124 AAAACTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AAATAAATTATTTAA
Found at i:5825023 original size:3 final size:3
Alignment explanation
Indices: 5825015--5825074 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
5825005 TTCACTCACA
*
5825015 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5825063 TAT TAT TAT TAT
1 TAT TAT TAT TAT
5825075 CTCGTCTTAG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:5827046 original size:21 final size:20
Alignment explanation
Indices: 5827022--5827069 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
5827012 TTTTGCTCTG
5827022 CTCTGCTGCCATCGCT-GCTGC
1 CTCTGCT-CCATCGCTCG-TGC
*
5827043 CTCTGCCTCCTTCGCTCGTGC
1 CTCTG-CTCCATCGCTCGTGC
5827064 CTCTGC
1 CTCTGC
5827070 ATCCCTTGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 20 0.83
22 3 0.12
ACGTcount: A:0.02, C:0.46, G:0.21, T:0.31
Consensus pattern (20 bp):
CTCTGCTCCATCGCTCGTGC
Found at i:5827109 original size:21 final size:21
Alignment explanation
Indices: 5827033--5827127 Score: 95
Period size: 21 Copynumber: 4.5 Consensus size: 21
5827023 TCTGCTGCCA
*
5827033 TCGCTGCTGCCTCTGCCTCCT
1 TCGCTGCTGCCGCTGCCTCCT
* *
5827054 TCGCT-CGTGCCTCTGCATCCCT
1 TCGCTGC-TGCCGCTGCCT-CCT
*
5827076 T-GCTGCTGTCGCTGCCTCCT
1 TCGCTGCTGCCGCTGCCTCCT
*
5827096 TCGCTGCTACCGCTGCCTCCT
1 TCGCTGCTGCCGCTGCCTCCT
**
5827117 TCTTTGCTGCC
1 TCGCTGCTGCC
5827128 TCGGCTTTGA
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
20 5 0.08
21 51 0.84
22 5 0.08
ACGTcount: A:0.02, C:0.44, G:0.20, T:0.34
Consensus pattern (21 bp):
TCGCTGCTGCCGCTGCCTCCT
Found at i:5827569 original size:13 final size:14
Alignment explanation
Indices: 5827544--5827572 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5827534 TGATGAATTG
5827544 AATTAAACAATTAT
1 AATTAAACAATTAT
5827558 AATTAAAC-ATTAT
1 AATTAAACAATTAT
5827571 AA
1 AA
5827573 ATATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:5827756 original size:18 final size:18
Alignment explanation
Indices: 5827721--5827761 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
5827711 TCCTACAATA
5827721 TAATAGTAAAAATATTATT
1 TAATAGTAAAAATATTA-T
*
5827740 TAATAGTAAAAA-GTTAT
1 TAATAGTAAAAATATTAT
5827757 TAATA
1 TAATA
5827762 TTTGAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 3 0.14
19 12 0.57
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (18 bp):
TAATAGTAAAAATATTAT
Found at i:5832783 original size:52 final size:53
Alignment explanation
Indices: 5832716--5832889 Score: 140
Period size: 53 Copynumber: 3.3 Consensus size: 53
5832706 TTCGTAAGCT
* * * *
5832716 AGTTATGTAAATTATGATATCAAATATATTTAAGT-A-TTATGTAAGTTATGTA
1 AGTTATGTAAGTTATGATATCAAACATATTTAAGTAAGTTATAT-AGTTATCTA
* * * *
5832768 AGTTATGTAAGTTATGATATGATACATATTTATGTAAGTTATATATTTATCTA
1 AGTTATGTAAGTTATGATATCAAACATATTTAAGTAAGTTATATAGTTATCTA
* * *** * * *
5832821 AGTTATATAAGTTATG-TAAGTTATGTA-AGTTATGTAAGTTATATATTTATCTA
1 AGTTATGTAAGTTATGAT-A-TCAAACATATTTAAGTAAGTTATATAGTTATCTA
*
5832874 AGTTATATAAGTTATG
1 AGTTATGTAAGTTATG
5832890 TAAGTTATGT
Statistics
Matches: 105, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
52 31 0.30
53 65 0.62
54 9 0.09
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.46
Consensus pattern (53 bp):
AGTTATGTAAGTTATGATATCAAACATATTTAAGTAAGTTATATAGTTATCTA
Found at i:5832835 original size:53 final size:50
Alignment explanation
Indices: 5832761--5833074 Score: 266
Period size: 53 Copynumber: 6.1 Consensus size: 50
5832751 ATTATGTAAG
* * * *
5832761 TTATGTAAGTTATGTAAGTTATGATATGATACATATTTATGTAAGTTATATAT
1 TTATCTAAGTTATATAAGTTAT--TATGTTA-ATAGTTATGTAAGTTATATAT
* *
5832814 TTATCTAAGTTATATAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATATAT
1 TTATCTAAGTTATATAAGTTAT-TATGTTA-AT-AGTTATGTAAGTTATATAT
5832867 TTATCTAAGTTATATAAG---TTATG-T-A-AGTTATGTAAGTTATATAT
1 TTATCTAAGTTATATAAGTTATTATGTTAATAGTTATGTAAGTTATATAT
* * * * * *
5832911 TTATCTAAGTTATATAAGTTATCTAAGTTATGTAAGTTATAT-ATTTATCTAAG
1 TTATCTAAGTTATATAAGTTAT-TATGTTA-AT-AGTTATGTAAGTTATAT-AT
* * *
5832964 TTATCTAAGTTATAT-ATTTATCTAAGTTATGTAAGTTATGTAAGTTATATAT
1 TTATCTAAGTTATATAAGTTAT-TATGTTA-AT-AGTTATGTAAGTTATATAT
* * *
5833016 TTATCTAAGTTATATAAGTTATATAAGTTATGTAAGTTATATAAGTTATATAT
1 TTATCTAAGTTATATAAGTTAT-TATGTTA-AT-AGTTATGTAAGTTATATAT
5833069 TTATCT
1 TTATCT
5833075 GTTATAAAAA
Statistics
Matches: 224, Mismatches: 24, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
44 37 0.17
47 1 0.00
48 4 0.02
49 4 0.02
50 1 0.00
52 52 0.23
53 125 0.56
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.48
Consensus pattern (50 bp):
TTATCTAAGTTATATAAGTTATTATGTTAATAGTTATGTAAGTTATATAT
Found at i:5832845 original size:44 final size:44
Alignment explanation
Indices: 5832823--5833064 Score: 317
Period size: 44 Copynumber: 5.5 Consensus size: 44
5832813 TTTATCTAAG
* * *
5832823 TTATATAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATATAT
1 TTATCTAAGTTATATAAGTTATCTAAGTTATGTAAGTTATATAT
*
5832867 TTATCTAAGTTATATAAGTTATGTAAGTTATGTAAGTTATATAT
1 TTATCTAAGTTATATAAGTTATCTAAGTTATGTAAGTTATATAT
5832911 TTATCTAAGTTATATAAGTTATCTAAGTTATGTAAGTTATATAT
1 TTATCTAAGTTATATAAGTTATCTAAGTTATGTAAGTTATATAT
* * * * * *
5832955 TTATCTAAGTTATCTAAGTTATAT-ATTTATCTAAGTTATGTAAG
1 TTATCTAAGTTATATAAGTTATCTAAGTTATGTAAGTTATAT-AT
* * * *
5832999 TTATGTAAGTTATAT-ATTTATCTAAGTTATATAAGTTATATAAG
1 TTATCTAAGTTATATAAGTTATCTAAGTTATGTAAGTTATAT-AT
*
5833043 TTATGTAAGTTATATAAGTTAT
1 TTATCTAAGTTATATAAGTTAT
5833065 ATATTTATCT
Statistics
Matches: 178, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
43 20 0.11
44 153 0.86
45 5 0.03
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.48
Consensus pattern (44 bp):
TTATCTAAGTTATATAAGTTATCTAAGTTATGTAAGTTATATAT
Found at i:5833065 original size:9 final size:9
Alignment explanation
Indices: 5832752--5833067 Score: 295
Period size: 9 Copynumber: 35.8 Consensus size: 9
5832742 TATTTAAGTA
*
5832752 TTATGTAAG
1 TTATATAAG
*
5832761 TTATGTAAG
1 TTATATAAG
*
5832770 TTATGTAAG
1 TTATATAAG
*
5832779 TTATGATATG
1 TTAT-ATAAG
* * *
5832789 ATACAT-AT
1 TTATATAAG
*
5832797 TTATGTAAG
1 TTATATAAG
*
5832806 TTATAT-AT
1 TTATATAAG
*
5832814 TTATCTAAG
1 TTATATAAG
5832823 TTATATAAG
1 TTATATAAG
*
5832832 TTATGTAAG
1 TTATATAAG
*
5832841 TTATGTAAG
1 TTATATAAG
*
5832850 TTATGTAAG
1 TTATATAAG
*
5832859 TTATAT-AT
1 TTATATAAG
*
5832867 TTATCTAAG
1 TTATATAAG
5832876 TTATATAAG
1 TTATATAAG
*
5832885 TTATGTAAG
1 TTATATAAG
*
5832894 TTATGTAAG
1 TTATATAAG
*
5832903 TTATAT-AT
1 TTATATAAG
*
5832911 TTATCTAAG
1 TTATATAAG
5832920 TTATATAAG
1 TTATATAAG
*
5832929 TTATCTAAG
1 TTATATAAG
*
5832938 TTATGTAAG
1 TTATATAAG
*
5832947 TTATAT-AT
1 TTATATAAG
*
5832955 TTATCTAAG
1 TTATATAAG
*
5832964 TTATCTAAG
1 TTATATAAG
*
5832973 TTATAT-AT
1 TTATATAAG
*
5832981 TTATCTAAG
1 TTATATAAG
*
5832990 TTATGTAAG
1 TTATATAAG
*
5832999 TTATGTAAG
1 TTATATAAG
*
5833008 TTATAT-AT
1 TTATATAAG
*
5833016 TTATCTAAG
1 TTATATAAG
5833025 TTATATAAG
1 TTATATAAG
5833034 TTATATAAG
1 TTATATAAG
*
5833043 TTATGTAAG
1 TTATATAAG
5833052 TTATATAAG
1 TTATATAAG
5833061 TTATATA
1 TTATATA
5833068 TTTATCTGTT
Statistics
Matches: 254, Mismatches: 45, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
8 39 0.15
9 210 0.83
10 5 0.02
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.47
Consensus pattern (9 bp):
TTATATAAG
Found at i:5833145 original size:6 final size:7
Alignment explanation
Indices: 5833126--5833151 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5833116 ACTTATAAAC
5833126 GCAAAAA
1 GCAAAAA
5833133 GCAAAAA
1 GCAAAAA
5833140 GCAAAAA
1 GCAAAAA
5833147 GCAAA
1 GCAAA
5833152 TCTATAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.15, G:0.15, T:0.00
Consensus pattern (7 bp):
GCAAAAA
Found at i:5834979 original size:19 final size:19
Alignment explanation
Indices: 5834955--5834992 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5834945 GGTCGTCCAC
5834955 TCGGAGTCTTCAACGGCAG
1 TCGGAGTCTTCAACGGCAG
5834974 TCGGAGTCTTCAACGGCAG
1 TCGGAGTCTTCAACGGCAG
5834993 AAGGATATTT
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:0.21, C:0.26, G:0.32, T:0.21
Consensus pattern (19 bp):
TCGGAGTCTTCAACGGCAG
Found at i:5835049 original size:19 final size:20
Alignment explanation
Indices: 5835015--5835061 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
5835005 ATTTTGATTC
*
5835015 GGGGAAATATTTAGGGACTA
1 GGGGAAATAGTTAGGGACTA
* *
5835035 GGGGAAA-AGTTAGGGATTT
1 GGGGAAATAGTTAGGGACTA
5835054 GGGGAAAT
1 GGGGAAAT
5835062 TTGGGTGGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.34, C:0.02, G:0.40, T:0.23
Consensus pattern (20 bp):
GGGGAAATAGTTAGGGACTA
Found at i:5836299 original size:29 final size:29
Alignment explanation
Indices: 5836260--5836317 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
5836250 TTAGGGTTTA
5836260 GATCATGGGTTATGATTTAGGGGTTAGGC
1 GATCATGGGTTATGATTTAGGGGTTAGGC
5836289 GATCATGGGTTATGATTTAGGGGTTAGGC
1 GATCATGGGTTATGATTTAGGGGTTAGGC
5836318 TTCATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.07, G:0.38, T:0.34
Consensus pattern (29 bp):
GATCATGGGTTATGATTTAGGGGTTAGGC
Found at i:5857898 original size:58 final size:58
Alignment explanation
Indices: 5857830--5857945 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
5857820 GTTAATACAA
*
5857830 CAATAGGGGTTTTAATTAGAAAGAGATTTCAATTAATCAACTTAGAGTCAGTTGTTCT
1 CAATAGGGGTTTTAATTAGAAAGAGATTTCAATTAATCAACCTAGAGTCAGTTGTTCT
5857888 CAATAGGGGTTTTAATTAGAAAGAGATTTCAATTAATCAACCTAGAGTCAGTTGTTCT
1 CAATAGGGGTTTTAATTAGAAAGAGATTTCAATTAATCAACCTAGAGTCAGTTGTTCT
5857946 TACTCTCGAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.35
Consensus pattern (58 bp):
CAATAGGGGTTTTAATTAGAAAGAGATTTCAATTAATCAACCTAGAGTCAGTTGTTCT
Found at i:5858050 original size:11 final size:11
Alignment explanation
Indices: 5858034--5858061 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5858024 TTCAGAATAA
5858034 TAGGTGAAGTC
1 TAGGTGAAGTC
5858045 TAGGTGAAGTC
1 TAGGTGAAGTC
5858056 TAGGTG
1 TAGGTG
5858062 GATTCTTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.07, G:0.39, T:0.29
Consensus pattern (11 bp):
TAGGTGAAGTC
Found at i:5865379 original size:15 final size:15
Alignment explanation
Indices: 5865355--5865391 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
5865345 AGGAAAAGGA
*
5865355 CGAAGAGGTAAAACC
1 CGAAGTGGTAAAACC
5865370 CGAAGTGGTAAAACC
1 CGAAGTGGTAAAACC
5865385 CGAAGTG
1 CGAAGTG
5865392 AGTGTAACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.41, C:0.19, G:0.30, T:0.11
Consensus pattern (15 bp):
CGAAGTGGTAAAACC
Found at i:5866915 original size:35 final size:35
Alignment explanation
Indices: 5866868--5866935 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
5866858 AGAATGAGAC
5866868 AGAGATGAAAGTTGGAAAATACTTTTGGAAAACTA
1 AGAGATGAAAGTTGGAAAATACTTTTGGAAAACTA
*
5866903 AGAGATGGAAGTTGGAAAATACTTTTGGAAAAC
1 AGAGATGAAAGTTGGAAAATACTTTTGGAAAAC
5866936 CAATGGAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (35 bp):
AGAGATGAAAGTTGGAAAATACTTTTGGAAAACTA
Found at i:5869626 original size:39 final size:39
Alignment explanation
Indices: 5869566--5869702 Score: 166
Period size: 39 Copynumber: 3.5 Consensus size: 39
5869556 ATCGTGATCT
* * * * * *
5869566 GAAGCCCGAAGTCTAGCTGAAGCATATAACTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACA
* *
5869605 GAAGCCCGAAGGCTAATTGAAGCACACAAGTGTTAAACA
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACA
* * *
5869644 AAAGCCCAAAGGCTAACTGAAACACACAAGTGCTAAACA
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACA
*
5869683 GAAGCCCGAAGACTAACTGA
1 GAAGCCCGAAGGCTAACTGA
5869703 TGCTCATCAG
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACA
Found at i:5878304 original size:2 final size:2
Alignment explanation
Indices: 5878297--5878329 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5878287 GCCATTTAAA
5878297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5878330 GAATAATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5884582 original size:21 final size:21
Alignment explanation
Indices: 5884556--5884599 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
5884546 ATATTTATAT
5884556 TTATTTTTATTTTTATCTTTA
1 TTATTTTTATTTTTATCTTTA
*
5884577 TTATTTTTATTTTTATGTTTA
1 TTATTTTTATTTTTATCTTTA
5884598 TT
1 TT
5884600 TTGTCTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (21 bp):
TTATTTTTATTTTTATCTTTA
Found at i:5884589 original size:6 final size:6
Alignment explanation
Indices: 5884549--5884601 Score: 61
Period size: 6 Copynumber: 8.3 Consensus size: 6
5884539 TCCATCTATA
* *
5884549 TTTATA TTTATT TTTATT TTTATCTT TATTATT TTTATT TTTATG TTTATT
1 TTTATT TTTATT TTTATT TTTA--TT T-TTATT TTTATT TTTATT TTTATT
5884600 TT
1 TT
5884602 GTCTTTATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
6 32 0.78
7 3 0.07
8 3 0.07
9 3 0.07
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:5886911 original size:33 final size:33
Alignment explanation
Indices: 5886869--5886935 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
5886859 AATTAAGCGG
*
5886869 AGTTGATTGCAATCCTAGAAATAGGACGACATA
1 AGTTGATTGCAATCCTAGAAATAGGACAACATA
*
5886902 AGTTGATTGCAATCTTAGAAATAGGACAACATA
1 AGTTGATTGCAATCCTAGAAATAGGACAACATA
5886935 A
1 A
5886936 AGCTACCGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.25
Consensus pattern (33 bp):
AGTTGATTGCAATCCTAGAAATAGGACAACATA
Found at i:5889430 original size:46 final size:46
Alignment explanation
Indices: 5889377--5889552 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
5889367 TATTTGGGCA
*
5889377 TCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
5889423 TCCGAGCTCGTTGAGTTGAGTTCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* **
5889468 CATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACA
1 --TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
5889516 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5889553 GTGGGTTACA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.58
47 27 0.25
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:5889532 original size:93 final size:93
Alignment explanation
Indices: 5889373--5889545 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
5889363 AGGATATTTG
* ***
5889373 GGCATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAGCTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAG
*
5889438 TTGAGTTCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
5889466 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAG
5889531 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
5889546 CTTATGGGTG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:5892285 original size:30 final size:30
Alignment explanation
Indices: 5892228--5892285 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
5892218 ATAGTATCGT
*
5892228 ATCTTGGATTTCTTTATTCTGGGTTTCTCA
1 ATCTTGGATTTCTTTATTCTAGGTTTCTCA
* *
5892258 ATCTTGGATTTTTTTTATTC-AGTTTTCT
1 ATCTTGGA-TTTCTTTATTCTAGGTTTCT
5892286 TGTTATCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (30 bp):
ATCTTGGATTTCTTTATTCTAGGTTTCTCA
Found at i:5895375 original size:6 final size:6
Alignment explanation
Indices: 5895364--5895525 Score: 324
Period size: 6 Copynumber: 27.0 Consensus size: 6
5895354 TAGTTGAATA
5895364 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
5895412 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
5895460 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
5895508 TATATT TATATT TATATT
1 TATATT TATATT TATATT
5895526 GTATTGCTAG
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 156 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:5900245 original size:44 final size:46
Alignment explanation
Indices: 5900193--5900287 Score: 149
Period size: 44 Copynumber: 2.1 Consensus size: 46
5900183 TTTTAATTAC
5900193 TTTTTTTAACTTTTATCCTATTCTTTCTGCTTC-T-TTTTTTACTT
1 TTTTTTTAACTTTTATCCTATTCTTTCTGCTTCTTCTTTTTTACTT
* *
5900237 TTTTTTTAACTTTTGTCCTATTCTTTCTTCTTCTTCTTTTTTACTT
1 TTTTTTTAACTTTTATCCTATTCTTTCTGCTTCTTCTTTTTTACTT
*
5900283 CTTTT
1 TTTTT
5900288 ATGTTTTATC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 31 0.67
45 1 0.02
46 14 0.30
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.69
Consensus pattern (46 bp):
TTTTTTTAACTTTTATCCTATTCTTTCTGCTTCTTCTTTTTTACTT
Found at i:5900288 original size:44 final size:42
Alignment explanation
Indices: 5900189--5900297 Score: 137
Period size: 44 Copynumber: 2.5 Consensus size: 42
5900179 TTTTTTTTAA
5900189 TTACTTTTTTTAACTTTTATCCTATTCTTTCTGCTTCTTTTT
1 TTACTTTTTTTAACTTTTATCCTATTCTTTCTGCTTCTTTTT
* *
5900231 TTACTTTTTTTTTAACTTTTGTCCTATTCTTTCTTCTTCTTCTTTT
1 TTAC--TTTTTTTAACTTTTATCCTATTCTTTCTGCTTC-T-TTTT
* **
5900277 TTACTTCTTTTATGTTTTATC
1 TTACTTTTTTTAACTTTTATC
5900298 TTTGTCCTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
42 4 0.07
44 44 0.77
45 1 0.02
46 8 0.14
ACGTcount: A:0.11, C:0.18, G:0.03, T:0.68
Consensus pattern (42 bp):
TTACTTTTTTTAACTTTTATCCTATTCTTTCTGCTTCTTTTT
Found at i:5900319 original size:9 final size:9
Alignment explanation
Indices: 5900305--5900332 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
5900295 ATCTTTGTCC
5900305 TTATTTATT
1 TTATTTATT
5900314 TTATTTATT
1 TTATTTATT
5900323 TTATTTATT
1 TTATTTATT
5900332 T
1 T
5900333 ATTATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTATTTATT
Found at i:5900323 original size:13 final size:14
Alignment explanation
Indices: 5900308--5900345 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 14
5900298 TTTGTCCTTA
5900308 TTTATTTTATTTAT
1 TTTATTTTATTTAT
5900322 TTTA-TTTATTTAT
1 TTTATTTTATTTAT
5900335 TATTAATTTTA
1 T-TT-ATTTTA
5900346 AAAAATTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 10 0.48
14 6 0.29
15 1 0.05
16 4 0.19
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:5900449 original size:21 final size:22
Alignment explanation
Indices: 5900418--5900494 Score: 124
Period size: 21 Copynumber: 3.6 Consensus size: 22
5900408 TATTTCTGAA
5900418 ATTATTTTTTAAAATTTTAAAT
1 ATTATTTTTTAAAATTTTAAAT
*
5900440 ATTA-TTTTTAAAATTTTACAT
1 ATTATTTTTTAAAATTTTAAAT
5900461 ATTA-TTTTTAAAATTTTAAAT
1 ATTATTTTTTAAAATTTTAAAT
5900482 A-TATTTTTTAAAA
1 ATTATTTTTTAAAA
5900495 ATATAAAACA
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
20 2 0.04
21 46 0.88
22 4 0.08
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTATTTTTTAAAATTTTAAAT
Found at i:5900564 original size:9 final size:9
Alignment explanation
Indices: 5900547--5900603 Score: 69
Period size: 9 Copynumber: 5.9 Consensus size: 9
5900537 TTATTATTAG
5900547 TTTTATAATA
1 TTTT-TAATA
5900557 TTTTTAATA
1 TTTTTAATA
*
5900566 TTTTTAATT
1 TTTTTAATA
5900575 TGTTTTATAGTA
1 T-TTTTA-A-TA
5900587 TTTTTAATA
1 TTTTTAATA
5900596 TTTTTAAT
1 TTTTTAAT
5900604 TTAAAATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
9 24 0.57
10 10 0.24
11 6 0.14
12 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (9 bp):
TTTTTAATA
Found at i:5900582 original size:30 final size:30
Alignment explanation
Indices: 5900546--5900605 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
5900536 TTTATTATTA
5900546 GTTTTATAATATTTTTAATATTTTTAATTT
1 GTTTTATAATATTTTTAATATTTTTAATTT
*
5900576 GTTTTATAGTATTTTTAATATTTTTAATTT
1 GTTTTATAATATTTTTAATATTTTTAATTT
5900606 AAAATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (30 bp):
GTTTTATAATATTTTTAATATTTTTAATTT
Found at i:5900628 original size:7 final size:7
Alignment explanation
Indices: 5900616--5900642 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5900606 AAAATATATA
5900616 TTTTTAT
1 TTTTTAT
5900623 TTTTTAT
1 TTTTTAT
5900630 TTTTTAT
1 TTTTTAT
5900637 TTTTTA
1 TTTTTA
5900643 ATATATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTAT
Found at i:5900646 original size:34 final size:35
Alignment explanation
Indices: 5900585--5900655 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 35
5900575 TGTTTTATAG
5900585 TATTTTTAATATTTTTAATTTAAAATATATATTTT
1 TATTTTTAATATTTTTAATTTAAAATATATATTTT
* * **
5900620 TATTTTTTAT-TTTTTATTTTTTAATATATATTTT
1 TATTTTTAATATTTTTAATTTAAAATATATATTTT
5900654 TA
1 TA
5900656 AATAAATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 23 0.72
35 9 0.28
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (35 bp):
TATTTTTAATATTTTTAATTTAAAATATATATTTT
Found at i:5900801 original size:13 final size:13
Alignment explanation
Indices: 5900783--5900807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5900773 ATCTTTAAAA
5900783 ATAATTTAAAATC
1 ATAATTTAAAATC
5900796 ATAATTTAAAAT
1 ATAATTTAAAAT
5900808 ATTAAAAAAC
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATTTAAAATC
Found at i:5900822 original size:21 final size:21
Alignment explanation
Indices: 5900780--5900832 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
5900770 AATATCTTTA
* *
5900780 AAAATAATTTAAAATCATAATTT
1 AAAAT-ATTAAAAAACATAA-TT
5900803 AAAATATTAAAAAACA-AATT
1 AAAATATTAAAAAACATAATT
5900823 ATAAATATTA
1 A-AAATATTA
5900833 TAAATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 3 0.11
21 10 0.37
22 9 0.33
23 5 0.19
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAATATTAAAAAACATAATT
Found at i:5900832 original size:9 final size:9
Alignment explanation
Indices: 5900820--5900845 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5900810 TAAAAAACAA
5900820 ATTATAAAT
1 ATTATAAAT
5900829 ATTATAAAT
1 ATTATAAAT
5900838 ATTATAAA
1 ATTATAAA
5900846 ACTAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
ATTATAAAT
Found at i:5900956 original size:22 final size:21
Alignment explanation
Indices: 5900903--5900976 Score: 105
Period size: 21 Copynumber: 3.5 Consensus size: 21
5900893 TTATATTATT
* *
5900903 AAAAAT-ATATTTAATATTTA
1 AAAAATAATTTTTAAAATTTA
5900923 AAAAATAATTTTTAAAATTTA
1 AAAAATAATTTTTAAAATTTA
*
5900944 AAAAATAATTTTTAAAATTTTT
1 AAAAATAATTTTTAAAA-TTTA
5900966 AAAAATAATTT
1 AAAAATAATTT
5900977 AAAAATAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
20 6 0.12
21 29 0.59
22 14 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAAATAATTTTTAAAATTTA
Found at i:5900961 original size:33 final size:32
Alignment explanation
Indices: 5900929--5901005 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 32
5900919 TTTAAAAAAT
*
5900929 AATTTTT-AAAAT-TTAAAAAATAATTTTTAA
1 AATTTTTAAAAATATTAAAAAATAATATTTAA
*
5900959 AATTTTTAAAAATAATTTAAAAATAATATTTAA
1 AATTTTTAAAAAT-ATTAAAAAATAATATTTAA
*
5900992 AATTTTAAAAAATA
1 AATTTTTAAAAATA
5901006 ATTTCAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
30 7 0.17
31 5 0.12
32 1 0.02
33 28 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
AATTTTTAAAAATATTAAAAAATAATATTTAA
Found at i:5901032 original size:54 final size:53
Alignment explanation
Indices: 5900904--5901041 Score: 147
Period size: 54 Copynumber: 2.6 Consensus size: 53
5900894 TATATTATTA
* * *
5900904 AAAATATAT-TTAATATTTAAAAAATAATTTTTAAAATTTAAAAAATAATTTTT
1 AAAATATATATTAA-ATTTTAAAAATAATATTTAAAATTTAAAAAATAATTTTC
* * *
5900957 AAAATTTTTA-AAAATAATTTAAAAATAATATTTAAAATTTTAAAAAATAA-TTTC
1 AAAATATATATTAAAT--TTTAAAAATAATATTTAAAA-TTTAAAAAATAATTTTC
*
5901011 AAATATATATATTAAATTTTAAAAAAAATAT
1 AAA-ATATATATTAAATTTTAAAAATAATAT
5901042 ATACTATAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
52 2 0.03
53 9 0.13
54 37 0.54
55 17 0.25
56 4 0.06
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (53 bp):
AAAATATATATTAAATTTTAAAAATAATATTTAAAATTTAAAAAATAATTTTC
Found at i:5901037 original size:34 final size:33
Alignment explanation
Indices: 5900938--5901036 Score: 130
Period size: 33 Copynumber: 3.0 Consensus size: 33
5900928 TAATTTTTAA
* *
5900938 AATTTAAAAAATAATTTTTAAAATTTTTAAAAAT
1 AATTT-AAAAATAATATTTAAAATTTTAAAAAAT
5900972 AATTTAAAAATAATATTTAAAATTTTAAAAAAT
1 AATTTAAAAATAATATTTAAAATTTTAAAAAAT
*
5901005 AATTT-CAAATATATATATT-AAATTTTAAAAAA
1 AATTTAAAAATA-ATAT-TTAAAATTTTAAAAAA
5901037 AATATATACT
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
32 5 0.08
33 48 0.80
34 7 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (33 bp):
AATTTAAAAATAATATTTAAAATTTTAAAAAAT
Found at i:5901158 original size:25 final size:25
Alignment explanation
Indices: 5901137--5901200 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
5901127 AGACAAAACT
5901137 TAAAAAAAAAAGTAA-A-AACAAAA
1 TAAAAAAAAAAGTAATAGAACAAAA
* *
5901160 AAAAAAGAAAAAG-AATAGGACAAAA
1 TAAAAA-AAAAAGTAATAGAACAAAA
5901185 GTAAAAAAAAAAGTAA
1 -TAAAAAAAAAAGTAA
5901201 CAAGGTGTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
23 7 0.21
24 7 0.21
25 12 0.36
26 7 0.21
ACGTcount: A:0.78, C:0.03, G:0.11, T:0.08
Consensus pattern (25 bp):
TAAAAAAAAAAGTAATAGAACAAAA
Found at i:5901170 original size:17 final size:18
Alignment explanation
Indices: 5901138--5901171 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5901128 GACAAAACTT
5901138 AAAAAAAAAAGTAAAAAC
1 AAAAAAAAAAGTAAAAAC
5901156 AAAAAAAAAAG-AAAAA
1 AAAAAAAAAAGTAAAAA
5901172 GAATAGGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.88, C:0.03, G:0.06, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAAGTAAAAAC
Found at i:5904246 original size:16 final size:16
Alignment explanation
Indices: 5904227--5904258 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5904217 AAGATACCAT
*
5904227 GGCAGCCTGATATGAA
1 GGCAACCTGATATGAA
5904243 GGCAACCTGATATGAA
1 GGCAACCTGATATGAA
5904259 ATGTGTAAGA
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:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (16 bp):
GGCAACCTGATATGAA
Found at i:5904272 original size:46 final size:46
Alignment explanation
Indices: 5904243--5904476 Score: 326
Period size: 46 Copynumber: 5.1 Consensus size: 46
5904233 CTGATATGAA
5904243 GGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCAT
1 GGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCAT
* ***
5904289 GGCAACGTGATATGAAATGAACAAGACCATGGTTGAAAGATACCAT
1 GGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCAT
5904335 GGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCAT
1 GGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCAT
* ***
5904381 GGCAACGTGATATGAAATGAACAAGACCATGGTTGAAAGATACCAT
1 GGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCAT
* * * * * *
5904427 GGCAACATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTAT
1 GGCAACCTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCAT
5904473 GGCA
1 GGCA
5904477 TCATGTCTAA
Statistics
Matches: 168, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 1 0.01
46 167 0.99
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
GGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCAT
Found at i:5904284 original size:62 final size:62
Alignment explanation
Indices: 5904187--5904304 Score: 218
Period size: 62 Copynumber: 1.9 Consensus size: 62
5904177 AGTGTGCTTT
*
5904187 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAGGCAAC
*
5904249 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAA
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAA
5904305 ATGAACAAGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.24
Consensus pattern (62 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAGGCAAC
Found at i:5904379 original size:92 final size:92
Alignment explanation
Indices: 5904243--5904476 Score: 398
Period size: 92 Copynumber: 2.5 Consensus size: 92
5904233 CTGATATGAA
5904243 GGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATG
1 GGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATG
5904308 AACAAGACCATGGTTGAAAGATACCAT
66 AACAAGACCATGGTTGAAAGATACCAT
5904335 GGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATG
1 GGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATG
5904400 AACAAGACCATGGTTGAAAGATACCAT
66 AACAAGACCATGGTTGAAAGATACCAT
* * * * * *
5904427 GGCAACATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 GGCAACCTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
5904477 TCATGTCTAA
Statistics
Matches: 135, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
91 1 0.01
92 134 0.99
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (92 bp):
GGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATG
AACAAGACCATGGTTGAAAGATACCAT
Found at i:5904507 original size:45 final size:45
Alignment explanation
Indices: 5904403--5904544 Score: 194
Period size: 45 Copynumber: 3.1 Consensus size: 45
5904393 TGAAATGAAC
* * * * * * * *
5904403 AAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGT
1 AAGACCATAGTTGAAAGACACTATGGCATCATGTCA-AAGATAAAT
*
5904449 AAGACCATAGTTGAAAGACACTATGGCATCATGTCTAAGATAAAT
1 AAGACCATAGTTGAAAGACACTATGGCATCATGTCAAAGATAAAT
5904494 AAGACCATAGTTGAAAGACACTATGGCATCATGTCAAAGATAAAT
1 AAGACCATAGTTGAAAGACACTATGGCATCATGTCAAAGATAAAT
5904539 AAGACC
1 AAGACC
5904545 GTAGATGGGA
Statistics
Matches: 86, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
45 56 0.65
46 30 0.35
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (45 bp):
AAGACCATAGTTGAAAGACACTATGGCATCATGTCAAAGATAAAT
Found at i:5907216 original size:60 final size:60
Alignment explanation
Indices: 5906864--5907218 Score: 373
Period size: 60 Copynumber: 6.0 Consensus size: 60
5906854 CAAGTATATG
* * * * * *
5906864 TTATTACACGCGAACCATTGTTCATGCAAGTCAATGATATG-----ACATGCGAGTC-CA
1 TTATTACATGTGAACCACTGTTTATGCGAGTCAATGATATGTTATTACATGCGAGTCAAA
* * * ** *
5906918 TTATTACATGTGAACCACTGTTAATGTGAGTCAATGATATGTTATTATATGTAAGTCACA
1 TTATTACATGTGAACCACTGTTTATGCGAGTCAATGATATGTTATTACATGCGAGTCAAA
* * * * *
5906978 TTATTACATGTGAATCATTGTTTATGCTAGTCAATAATATGTTATTACATGCGAGTCACA
1 TTATTACATGTGAACCACTGTTTATGCGAGTCAATGATATGTTATTACATGCGAGTCAAA
* * * *
5907038 TTATTACATGTGAACCACTATTTATGCGAGGCAATGATATGTTATTACATACGAATCACAA
1 TTATTACATGTGAACCACTGTTTATGCGAGTCAATGATATGTTATTACATGCGAGTCA-AA
* * * * *
5907099 -TATTACATGTGAATCACTATTTATGCGAGTAAATGATATGCTAGTACATGCGAGTCAAA
1 TTATTACATGTGAACCACTGTTTATGCGAGTCAATGATATGTTATTACATGCGAGTCAAA
* * * * *
5907158 TTATTACATGTGAACCACCGTTTCTACGAGTCAATGATATGTTACTATATGCGAGTCAAA
1 TTATTACATGTGAACCACTGTTTATGCGAGTCAATGATATGTTATTACATGCGAGTCAAA
5907218 T
1 T
5907219 ATATGTTATT
Statistics
Matches: 250, Mismatches: 43, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
54 35 0.14
59 10 0.04
60 204 0.82
61 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (60 bp):
TTATTACATGTGAACCACTGTTTATGCGAGTCAATGATATGTTATTACATGCGAGTCAAA
Found at i:5907222 original size:25 final size:26
Alignment explanation
Indices: 5907184--5907240 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 26
5907174 ACCGTTTCTA
*
5907184 CGAGTC-AATGATATGTTACTATATG
1 CGAGTCAAATGATATGTTACTACATG
*
5907209 CGAGTCAAAT-ATATGTTATTACATG
1 CGAGTCAAATGATATGTTACTACATG
5907234 CGAGTCA
1 CGAGTCA
5907241 CTTATCTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 26 0.90
26 3 0.10
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (26 bp):
CGAGTCAAATGATATGTTACTACATG
Found at i:5907250 original size:25 final size:24
Alignment explanation
Indices: 5907222--5907290 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 24
5907212 GTCAAATATA
*
5907222 TGTTATTACATGCGAGTCACTTAT
1 TGTTATTACATGCGAATCACTTAT
* *
5907246 CTGTTATTACATGC-AAACCCTTTAT
1 -TGTTATTACATGCGAATCAC-TTAT
5907271 TGTTATTACATGCGAATCAC
1 TGTTATTACATGCGAATCAC
5907291 CTGTATATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 16 0.43
25 21 0.57
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (24 bp):
TGTTATTACATGCGAATCACTTAT
Found at i:5907302 original size:49 final size:49
Alignment explanation
Indices: 5907222--5907315 Score: 125
Period size: 49 Copynumber: 1.9 Consensus size: 49
5907212 GTCAAATATA
* * * * *
5907222 TGTTATTACATGCGAGTCACTTATCTGTTATTACATGCAAACCCTTTAT
1 TGTTATTACATGCGAATCACCTATATATTATTACACGCAAACCCTTTAT
* *
5907271 TGTTATTACATGCGAATCACCTGTATATTATTACACGCGAACCCT
1 TGTTATTACATGCGAATCACCTATATATTATTACACGCAAACCCT
5907316 AAGAACTATG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 38 1.00
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (49 bp):
TGTTATTACATGCGAATCACCTATATATTATTACACGCAAACCCTTTAT
Found at i:5910353 original size:26 final size:26
Alignment explanation
Indices: 5910295--5910358 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
5910285 CTCAATTGAG
* *
5910295 TTTGTTTATTTTAGTTTATGTAATTC
1 TTTGTTTATTTTAATTTATGTAATTA
* *
5910321 TTTGTTTCTTTTAATTTAT-TTATTA
1 TTTGTTTATTTTAATTTATGTAATTA
*
5910346 TTTAGTTTTTTTT
1 TTT-GTTTATTTT
5910359 TTAAAAACCG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 7 0.22
26 25 0.78
ACGTcount: A:0.17, C:0.03, G:0.08, T:0.72
Consensus pattern (26 bp):
TTTGTTTATTTTAATTTATGTAATTA
Found at i:5910588 original size:29 final size:26
Alignment explanation
Indices: 5910555--5910630 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 26
5910545 CTTCTACATT
*
5910555 ATTATTTTTATATATGTTATTTATATTAA
1 ATTATTTTTA-A-AT-TTATGTATATTAA
5910584 ATTATTTTTAAATTTATGTATATT--
1 ATTATTTTTAAATTTATGTATATTAA
* *
5910608 ATT-TGTTTAAATTAATGTATATT
1 ATTATTTTTAAATTTATGTATATT
5910631 TTTTTATATT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
23 18 0.41
24 3 0.07
26 10 0.23
27 2 0.05
28 1 0.02
29 10 0.23
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (26 bp):
ATTATTTTTAAATTTATGTATATTAA
Found at i:5910610 original size:21 final size:21
Alignment explanation
Indices: 5910584--5910641 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 21
5910574 TTTATATTAA
*
5910584 ATTATTTTTAAATTTATGTAT
1 ATTATTTTTAAATTAATGTAT
5910605 ATTATTTGTTTAAATTAATGTAT
1 ATTA-TT-TTTAAATTAATGTAT
*
5910628 ATT-TTTTTATATTA
1 ATTATTTTTAAATTA
5910642 CTTACTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 8 0.24
21 6 0.18
22 2 0.06
23 17 0.52
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
ATTATTTTTAAATTAATGTAT
Found at i:5911995 original size:18 final size:18
Alignment explanation
Indices: 5911972--5912008 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5911962 AGAATAGAAC
5911972 TTAAGAAAATTGAGAGAT
1 TTAAGAAAATTGAGAGAT
* *
5911990 TTAAGAGAGTTGAGAGAT
1 TTAAGAAAATTGAGAGAT
5912008 T
1 T
5912009 AGAAAGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (18 bp):
TTAAGAAAATTGAGAGAT
Found at i:5918911 original size:25 final size:26
Alignment explanation
Indices: 5918859--5918915 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 26
5918849 TTTTTCTTAA
5918859 ATTATTTTATTTATGTTCTTAATAAT
1 ATTATTTTATTTATGTTCTTAATAAT
5918885 ATTATTTATATTTAT-TT-TT-ATATAT
1 ATTATTT-TATTTATGTTCTTAATA-AT
5918910 ATTATT
1 ATTATT
5918916 GATTTAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.10
25 10 0.34
26 9 0.31
27 7 0.24
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (26 bp):
ATTATTTTATTTATGTTCTTAATAAT
Found at i:5920399 original size:12 final size:13
Alignment explanation
Indices: 5920380--5920410 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5920370 GTCACTTTCT
*
5920380 CTTTTTTTTTTTA
1 CTTTTTTATTTTA
5920393 CTTTTTTATTTTA
1 CTTTTTTATTTTA
5920406 CTTTT
1 CTTTT
5920411 GTCTTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (13 bp):
CTTTTTTATTTTA
Found at i:5920822 original size:18 final size:17
Alignment explanation
Indices: 5920790--5920831 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
5920780 TCTTTTGCCT
5920790 TTTTCTTTAAATTTTTTTC
1 TTTT-TTTAAA-TTTTTTC
*
5920809 TTTTTTTAAGTTTTTTC
1 TTTTTTTAAATTTTTTC
5920826 TTTTTT
1 TTTTTT
5920832 CTTGTTTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.59
18 5 0.23
19 4 0.18
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTTTTTAAATTTTTTC
Found at i:5921162 original size:12 final size:13
Alignment explanation
Indices: 5921108--5921162 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 13
5921098 AAACATTTGA
5921108 ATATCTTTAAAATT
1 ATAT-TTTAAAATT
5921122 A-ATTTTAAAATT
1 ATATTTTAAAATT
5921134 AATAATTTATAAAAATT
1 -AT-ATTT-T-AAAATT
5921151 ATA-TTTAAAATT
1 ATATTTTAAAATT
5921163 TAAAAAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
12 15 0.42
13 4 0.11
14 3 0.08
15 5 0.14
16 3 0.08
17 6 0.17
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATTTTAAAATT
Found at i:5921257 original size:24 final size:24
Alignment explanation
Indices: 5921216--5921279 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
5921206 ATGTCATATC
* * *
5921216 TTTAAAACTAATATATTTTAAATAA
1 TTTAAAAATCATA-ATTTAAAATAA
*
5921241 TTTCAAAATCATAATTTAAAATAA
1 TTTAAAAATCATAATTTAAAATAA
5921265 TTTAAAAATCATAAT
1 TTTAAAAATCATAAT
5921280 AAAAAATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 24 0.71
25 10 0.29
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (24 bp):
TTTAAAAATCATAATTTAAAATAA
Found at i:5921285 original size:24 final size:24
Alignment explanation
Indices: 5921235--5921286 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5921225 AATATATTTT
* **
5921235 AAATAATTTCAAAATCATAATTTA
1 AAATAATTTAAAAATCATAATAAA
5921259 AAATAATTTAAAAATCATAATAAA
1 AAATAATTTAAAAATCATAATAAA
5921283 AAAT
1 AAAT
5921287 TATAAAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATAATTTAAAAATCATAATAAA
Found at i:5921399 original size:21 final size:21
Alignment explanation
Indices: 5921375--5921422 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
5921365 TAAATGTTTT
5921375 ATATTATTAAAAAT-ATATTTA
1 ATATT-TTAAAAATAATATTTA
*
5921396 ATATTTAAAAAATAATATTTA
1 ATATTTTAAAAATAATATTTA
5921417 A-ATTTT
1 ATATTTT
5921423 TAAACAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATTTTAAAAATAATATTTA
Found at i:5921400 original size:18 final size:21
Alignment explanation
Indices: 5921383--5921421 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
5921373 TTATATTATT
5921383 AAAAAT-ATATTTAATATTTA
1 AAAAATAATATTTAATATTTA
5921403 AAAAATAATATTTAA-ATTT
1 AAAAATAATATTTAATATTT
5921422 TTAAACAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAAATAATATTTAATATTTA
Found at i:5921454 original size:34 final size:34
Alignment explanation
Indices: 5921398--5921498 Score: 118
Period size: 33 Copynumber: 3.0 Consensus size: 34
5921388 TATATTTAAT
* * *
5921398 ATTTAAAAAATAATATTTAAATTTTTA-AACAATG
1 ATTTAAAAAATAATATTTAAA-ATTTAGAAAAATA
5921432 ATTT-AAAAATAATATTTAAAATTTAGAAAAATA
1 ATTTAAAAAATAATATTTAAAATTTAGAAAAATA
* *
5921465 ATTTCAAATATATATATTTAAAATTTA-AAAAATA
1 ATTTAAAAAATA-ATATTTAAAATTTAGAAAAATA
5921499 TAAATTATAA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
32 4 0.07
33 25 0.42
34 17 0.28
35 14 0.23
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (34 bp):
ATTTAAAAAATAATATTTAAAATTTAGAAAAATA
Found at i:5921490 original size:22 final size:23
Alignment explanation
Indices: 5921464--5921510 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
5921454 TTAGAAAAAT
* * *
5921464 AATTTCAAATATATATATT-TAA
1 AATTTAAAAAATATAAATTATAA
5921486 AATTTAAAAAATATAAATTATAA
1 AATTTAAAAAATATAAATTATAA
5921509 AA
1 AA
5921511 CATTTTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AATTTAAAAAATATAAATTATAA
Found at i:5921566 original size:13 final size:13
Alignment explanation
Indices: 5921548--5921592 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
5921538 TAAAAGTAAT
5921548 AATAAATAAATAA
1 AATAAATAAATAA
5921561 AATAAATAAATAA
1 AATAAATAAATAA
*
5921574 AGATAAAGAAA-AA
1 A-ATAAATAAATAA
5921587 AATAAA
1 AATAAA
5921593 AAAAGTCAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 5 0.17
13 17 0.57
14 8 0.27
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (13 bp):
AATAAATAAATAA
Found at i:5921592 original size:22 final size:23
Alignment explanation
Indices: 5921553--5921597 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
5921543 GTAATAATAA
* *
5921553 ATAAATAAAATAAATAAATAAAG
1 ATAAAGAAAATAAATAAAAAAAG
5921576 ATAAAGAAAA-AAATAAAAAAAG
1 ATAAAGAAAATAAATAAAAAAAG
5921598 TCAGAGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.16
Consensus pattern (23 bp):
ATAAAGAAAATAAATAAAAAAAG
Found at i:5921665 original size:22 final size:21
Alignment explanation
Indices: 5921633--5921698 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
5921623 AAGTAAAAAA
*
5921633 AAAATTT-AAAAATATATATTT
1 AAAATTTAAAAAATA-ATATTC
**
5921654 AATGTTTAAAAAATAATATTC
1 AAAATTTAAAAAATAATATTC
5921675 AAAATTTAAAAAATAA-ATT-
1 AAAATTTAAAAAATAATATTC
5921694 AAAAT
1 AAAAT
5921699 AATATTTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 5 0.13
20 3 0.08
21 24 0.62
22 7 0.18
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAATTTAAAAAATAATATTC
Found at i:5921993 original size:14 final size:15
Alignment explanation
Indices: 5921974--5922002 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5921964 TTTGAATATC
5921974 TTTAAAAT-TTATAA
1 TTTAAAATATTATAA
5921988 TTTAAAATATTATAA
1 TTTAAAATATTATAA
5922003 AACAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTAAAATATTATAA
Found at i:5922115 original size:30 final size:31
Alignment explanation
Indices: 5922054--5922132 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 31
5922044 AAATTTGAAG
*
5922054 TTTAAAATATTTAAATATTAAAAAAATAATA
1 TTTAAAATATTTAAAAATTAAAAAAATAATA
5922085 TTTAAAAT-TTTAAAAATTAAATTCAAAATATATA
1 TTTAAAATATTTAAAAATTAAA---AAAATA-ATA
5922119 TTAATAAAATATTT
1 TT--TAAAATATTT
5922133 CAAATATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
30 12 0.30
31 8 0.20
33 6 0.15
34 5 0.12
36 6 0.15
37 3 0.08
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTAAAATATTTAAAAATTAAAAAAATAATA
Found at i:5925711 original size:5 final size:5
Alignment explanation
Indices: 5925701--5925731 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
5925691 TGAACATTCG
5925701 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
5925732 AATTTTCGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:5926377 original size:17 final size:16
Alignment explanation
Indices: 5926357--5926392 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5926347 AAAATTTAGG
5926357 GAGAAATAAAAAGTTTT
1 GAGAAAT-AAAAGTTTT
*
5926374 GAGAGATAAAAGTTTT
1 GAGAAATAAAAGTTTT
5926390 GAG
1 GAG
5926393 GGAAAGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.25, T:0.28
Consensus pattern (16 bp):
GAGAAATAAAAGTTTT
Found at i:5926767 original size:9 final size:9
Alignment explanation
Indices: 5926749--5926785 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
5926739 TATAGTTTGA
*
5926749 TATTCAAAT
1 TATTCGAAT
5926758 TATTCGAAT
1 TATTCGAAT
*
5926767 TATTCGAGT
1 TATTCGAAT
5926776 TATTCGAAT
1 TATTCGAAT
5926785 T
1 T
5926786 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:5928329 original size:14 final size:15
Alignment explanation
Indices: 5928310--5928339 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5928300 ATATTTGACT
5928310 TGTTCTTAATT-TTG
1 TGTTCTTAATTCTTG
5928324 TGTTCTTAATTCTTG
1 TGTTCTTAATTCTTG
5928339 T
1 T
5928340 TTTAATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.13, C:0.10, G:0.13, T:0.63
Consensus pattern (15 bp):
TGTTCTTAATTCTTG
Found at i:5929070 original size:19 final size:19
Alignment explanation
Indices: 5929046--5929092 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5929036 AGCCATTCTA
5929046 TTTTATTTTCAATTT-AAAT
1 TTTTATTTTC-ATTTCAAAT
* *
5929065 TTTTATTTTCTTTTCTAAT
1 TTTTATTTTCATTTCAAAT
5929084 TTTTATTTT
1 TTTTATTTT
5929093 AATCATTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATTTTCATTTCAAAT
Found at i:5931700 original size:15 final size:16
Alignment explanation
Indices: 5931682--5931719 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
5931672 TAAAAGTCTG
5931682 TAATATAAA-GAATAA
1 TAATATAAATGAATAA
5931697 TAATAGATAAATGAATAA
1 TAAT--ATAAATGAATAA
5931715 TAATA
1 TAATA
5931720 ATAGGTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 4 0.20
16 1 0.05
17 5 0.25
18 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (16 bp):
TAATATAAATGAATAA
Found at i:5931714 original size:18 final size:17
Alignment explanation
Indices: 5931686--5931719 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
5931676 AGTCTGTAAT
5931686 ATAAAGAATAATAATAG
1 ATAAAGAATAATAATAG
5931703 ATAAATGAATAATAATA
1 ATAAA-GAATAATAATA
5931720 ATAGGTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (17 bp):
ATAAAGAATAATAATAG
Found at i:5931734 original size:21 final size:21
Alignment explanation
Indices: 5931692--5931734 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5931682 TAATATAAAG
**
5931692 AATAATAATAGATAAATGAAT
1 AATAATAATAGATAAACAAAT
*
5931713 AATAATAATAGGTAAACAAAT
1 AATAATAATAGATAAACAAAT
5931734 A
1 A
5931735 CAAAGAAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (21 bp):
AATAATAATAGATAAACAAAT
Found at i:5948254 original size:3 final size:3
Alignment explanation
Indices: 5948246--5948275 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5948236 ATTCAATACC
5948246 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5948276 CTTACCATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5948910 original size:4 final size:4
Alignment explanation
Indices: 5948901--5948931 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
5948891 CCTTTTCTCC
5948901 CTTT CTTT CTTT CTTT CTTT CCTTT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CT
5948932 CCCCTGTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
CTTT
Found at i:5949162 original size:3 final size:3
Alignment explanation
Indices: 5949136--5949216 Score: 50
Period size: 3 Copynumber: 28.3 Consensus size: 3
5949126 TTATTTAATT
* * *
5949136 TAA TAA T-A TAA T-A TCAA TTA -AA TAA TAA TAA CAA TAA CAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
5949179 TAA T-T TAA T-A TAA -AA CT-A TAA TAA TAAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA T-AA TAA TAA TAA T
5949217 TTAATATATT
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
2 11 0.18
3 44 0.73
4 5 0.08
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5949212 original size:21 final size:21
Alignment explanation
Indices: 5949136--5949215 Score: 67
Period size: 21 Copynumber: 3.7 Consensus size: 21
5949126 TTATTTAATT
*
5949136 TAATAAT-ATAATATCAATTAAA
1 TAATAATAATAATAACAA-T-AA
*
5949158 TAATAATAACAATAACAATAA
1 TAATAATAATAATAACAATAA
*
5949179 TAATTTAAT-ATAA-AACTATAA
1 TAA--TAATAATAATAACAATAA
5949200 TAATAAATAATAATAA
1 TAAT-AATAATAATAA
5949216 TTTAATATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
19 1 0.02
20 3 0.06
21 19 0.40
22 13 0.27
23 12 0.25
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATAATAATAATAACAATAA
Found at i:5954359 original size:48 final size:51
Alignment explanation
Indices: 5954304--5954416 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 51
5954294 GGGTAACAGT
* *
5954304 AACAGTAACAGTAGCGGT-A-A-ACAAAGTACCTCATCGGAACAAATCCGA
1 AACAGTAACAGTAGCAGTCAGATACAAAGTACCTCATCAGAACAAATCCGA
* ** * *
5954352 AACAGTAACAGTAACAGTCAGATACGGAGTACCTCTTCAGAACAAATCCGG
1 AACAGTAACAGTAGCAGTCAGATACAAAGTACCTCATCAGAACAAATCCGA
*
5954403 AACAGTCACAGTAG
1 AACAGTAACAGTAG
5954417 TCGACACATA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
48 16 0.30
49 1 0.02
50 1 0.02
51 35 0.66
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (51 bp):
AACAGTAACAGTAGCAGTCAGATACAAAGTACCTCATCAGAACAAATCCGA
Found at i:5954727 original size:3 final size:3
Alignment explanation
Indices: 5954719--5954748 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5954709 ATTCAATACC
5954719 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5954749 CTTACCATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5955693 original size:21 final size:21
Alignment explanation
Indices: 5955617--5955694 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 21
5955607 TTATTTAATT
*
5955617 TAATAAT-ATAATATCAATTAAA
1 TAATAATAATAATAACAA-T-AA
*
5955639 TAATAATAACAATAACAATAA
1 TAATAATAATAATAACAATAA
*
5955660 TAATTTAAT-ATAA-AACTATAA
1 TAA--TAATAATAATAACAATAA
5955681 TAATAAATAATAAT
1 TAAT-AATAATAAT
5955695 TTAATATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 19 0.41
22 11 0.24
23 12 0.26
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATAATAATAATAACAATAA
Found at i:5961409 original size:20 final size:20
Alignment explanation
Indices: 5961384--5961434 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 20
5961374 CTNGCTTTGA
*
5961384 AGAAATTTTCCATCTTCACC
1 AGAAATTTTCCATCTTAACC
5961404 AGAAA-TTT---TCTTAACC
1 AGAAATTTTCCATCTTAACC
5961420 AGAAATTTTCCATCT
1 AGAAATTTTCCATCT
5961435 GTACACCCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
16 12 0.46
17 3 0.12
19 3 0.12
20 8 0.31
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (20 bp):
AGAAATTTTCCATCTTAACC
Found at i:5962893 original size:79 final size:79
Alignment explanation
Indices: 5962797--5963001 Score: 234
Period size: 79 Copynumber: 2.6 Consensus size: 79
5962787 GCTCGATTGT
* * * * *
5962797 CTTCGGGACATAGCCCGGTTATAGTAATTCACACAATTGCCTTCGGGAATTAGCCCGGATTTAGT
1 CTTCGGGACTTAACCCGGTTATAGTAACTCACACAAATGCCTTCGGGAATTAACCC-GATTTAGT
5962862 AACTCGCAC-AATGC
65 AACTCGCACAAATGC
* * * * *
5962876 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGACTTAACCCGATTTGGTA
1 CTTCGGGACTTAACCCGGTTATAGTAACTCACACAAATGCCTTCGGGAATTAACCCGATTTAGTA
5962941 ACTCGCACAAATGC
66 ACTCGCACAAATGC
* * * * *
5962955 CTTCGGGAATTGACCCGGATT-TAGTCACTTAGCACAAAAGCCTTCGG
1 CTTCGGGACTTAACCCGG-TTATAGTAACTCA-CACAAATGCCTTCGG
5963002 ACTTAGCCCG
Statistics
Matches: 106, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
78 16 0.15
79 74 0.70
80 16 0.15
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (79 bp):
CTTCGGGACTTAACCCGGTTATAGTAACTCACACAAATGCCTTCGGGAATTAACCCGATTTAGTA
ACTCGCACAAATGC
Found at i:5963012 original size:40 final size:40
Alignment explanation
Indices: 5962797--5963013 Score: 246
Period size: 39 Copynumber: 5.5 Consensus size: 40
5962787 GCTCGATTGT
* * * *
5962797 CTTCGGGACATAGCCCGG-TTATAGTAATTCACACAATTGC
1 CTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGC
*
5962837 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCAC-AATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* * *
5962876 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* *
5962916 CTTCGGGACTTAACCC-GATTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* * * *
5962955 CTTCGGGAATT-GACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACTTAG-CCCGGATTTAGTAAC-TCGCACAAATGC
5962996 CTTC-GGACTTAGCCCGGA
1 CTTCGGGACTTAGCCCGGA
5963014 CATCATTCGA
Statistics
Matches: 154, Mismatches: 17, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
39 69 0.45
40 68 0.44
41 17 0.11
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
Found at i:5970936 original size:40 final size:39
Alignment explanation
Indices: 5970892--5971110 Score: 226
Period size: 40 Copynumber: 5.5 Consensus size: 39
5970882 GCTCGATTGT
* *
5970892 CTTCGGGACATAGCCCGGTTATAGTAATTCGCACAATTGC
1 CTTCGGGACATAGCCCGGTT-TAGTAACTCGCACAAATGC
5970932 CTTCGGGA-ATTAGCCCGGATTTAGTAACTCGCACAAATGC
1 CTTCGGGACA-TAGCCCGG-TTTAGTAACTCGCACAAATGC
* * *
5970972 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACATAGCCCGG-TTTAGTAACTCGCACAAATGC
* * * *
5971012 CTTCGGGACTTAACCCGATTTTGGTAACTCGCACAAATGC
1 CTTCGGGACATAGCCCG-GTTTAGTAACTCGCACAAATGC
* * * *
5971052 CTTCGGGA-ATTGACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACATAG-CCCGG-TTTAGTAAC-TCGCACAAATGC
*
5971093 CTTCGGGACTTAGCCCGG
1 CTTCGGGACATAGCCCGG
5971111 ACATCATTCG
Statistics
Matches: 154, Mismatches: 17, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
39 2 0.01
40 125 0.81
41 25 0.16
42 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (39 bp):
CTTCGGGACATAGCCCGGTTTAGTAACTCGCACAAATGC
Found at i:5970991 original size:80 final size:80
Alignment explanation
Indices: 5970892--5971111 Score: 273
Period size: 80 Copynumber: 2.7 Consensus size: 80
5970882 GCTCGATTGT
* * * *
5970892 CTTCGGGACATAGCCCGGTTATAGTAATTCGCACAATTGCCTTCGGGAATTAGCCCGGA-TTTAG
1 CTTCGGGACTTAACCCGGTT-TAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTTAG
5970956 TAACTCGCACAAATGC
65 TAACTCGCACAAATGC
* * * *
5970972 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGACTTAACCC-GATTTTGG
1 CTTCGGGACTTAACCCGG-TTTAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTTAG
5971036 TAACTCGCACAAATGC
65 TAACTCGCACAAATGC
* * * * *
5971052 CTTCGGGAATTGACCCGGATTTAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGA
1 CTTCGGGACTTAACCCGG-TTTAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCGGA
5971112 CATCATTCGA
Statistics
Matches: 119, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
79 2 0.02
80 87 0.73
81 28 0.24
82 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (80 bp):
CTTCGGGACTTAACCCGGTTTAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTTAGT
AACTCGCACAAATGC
Found at i:5971070 original size:120 final size:121
Alignment explanation
Indices: 5970892--5971110 Score: 316
Period size: 120 Copynumber: 1.8 Consensus size: 121
5970882 GCTCGATTGT
* * * *
5970892 CTTCGGGACATAGCCCGGTTATAGTAATTCGCACAATTGCCTTCGGGAATTAGCCCGGATTTAGT
1 CTTCGGGACATAACCCGATTATAGTAACTCGCACAAATGCCTTCGGGAATTAGCCCGGATTTAGT
* *
5970957 AAC-TCGCACAAATGCCTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
66 AACTTAGCACAAAAGCCTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
* * *
5971012 CTTCGGGACTTAACCCGATTTTGGTAACTCGCACAAATGCCTTCGGGAATT-GACCCGGATTTAG
1 CTTCGGGACATAACCCGATTATAGTAACTCGCACAAATGCCTTCGGGAATTAG-CCCGGATTTAG
* *
5971076 TCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGG
65 TAACTTAGCACAAAAGCCTTCGGGACTTAACCCGG
5971111 ACATCATTCG
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
119 1 0.01
120 58 0.67
121 27 0.31
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (121 bp):
CTTCGGGACATAACCCGATTATAGTAACTCGCACAAATGCCTTCGGGAATTAGCCCGGATTTAGT
AACTTAGCACAAAAGCCTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
Found at i:5978618 original size:2 final size:2
Alignment explanation
Indices: 5978611--5978641 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5978601 TAAGTTATTA
5978611 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5978642 AAGTAAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5978736 original size:15 final size:15
Alignment explanation
Indices: 5978710--5978747 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5978700 AGAGAGTAGG
*
5978710 GGAAAGAAAGAAGGAA
1 GGAAA-AAAGAAAGAA
5978726 GGAAAAAAGAAAGAA
1 GGAAAAAAGAAAGAA
5978741 GGAAAAA
1 GGAAAAA
5978748 GGGAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (15 bp):
GGAAAAAAGAAAGAA
Found at i:5980864 original size:46 final size:46
Alignment explanation
Indices: 5980812--5980988 Score: 309
Period size: 46 Copynumber: 3.8 Consensus size: 46
5980802 AGTGTGCTCT
5980812 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
5980858 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
5980904 CTAACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
5980950 ATGATATGAAATGAATAAGACCATGGTTGAAAGATACCA
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCA
5980989 ATGAATAAGA
Statistics
Matches: 124, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 124 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:5980994 original size:29 final size:29
Alignment explanation
Indices: 5980959--5981017 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
5980949 CATGATATGA
5980959 AATGAATAAGACCATGGTTGAAAGATACC
1 AATGAATAAGACCATGGTTGAAAGATACC
5980988 AATGAATAAGACCATGGTTGAAAGATACC
1 AATGAATAAGACCATGGTTGAAAGATACC
5981017 A
1 A
5981018 TGGCAACGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (29 bp):
AATGAATAAGACCATGGTTGAAAGATACC
Found at i:5981007 original size:75 final size:75
Alignment explanation
Indices: 5980919--5981063 Score: 263
Period size: 75 Copynumber: 1.9 Consensus size: 75
5980909 ATGAAATGTG
* *
5980919 TAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAATAAGACCATGGTTGAAAGA
5980984 TACCAATGAA
66 TACCAATGAA
*
5980994 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAATAAGACCATGGTTGAAAGA
5981059 TACCA
66 TACCA
5981064 TGGCAACCTA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.20
Consensus pattern (75 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAATAAGACCATGGTTGAAAGA
TACCAATGAA
Found at i:5981043 original size:46 final size:46
Alignment explanation
Indices: 5980991--5981210 Score: 316
Period size: 46 Copynumber: 4.7 Consensus size: 46
5980981 AGATACCAAT
5980991 GAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAA
1 GAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAA
* * * *
5981037 GAATAAGACCATGGTTGAAAGATACCATGGCAACCTAATATGAAAT
1 GAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAA
5981083 GAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAA
1 GAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAA
*
5981129 GAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAA
1 GAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAA
* * *
5981174 TGAAAGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 -G--A-A-TAAGACCATGGTTGAAAGATACCATGGCA
5981211 TCATGTCAAA
Statistics
Matches: 157, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
45 5 0.03
46 124 0.79
48 1 0.01
49 1 0.01
50 26 0.17
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.18
Consensus pattern (46 bp):
GAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAA
Found at i:5981087 original size:121 final size:121
Alignment explanation
Indices: 5980873--5981109 Score: 411
Period size: 121 Copynumber: 2.0 Consensus size: 121
5980863 ATGAAATGTG
* **
5980873 TAAGACCATGGTTGAAAGATACCATGGCAACCTAACATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTAACATGAAAAGAATAAGACCATGGTTGAAAGA
*
5980938 TACCATGGCAACATGATATGAAATGAATAAGACCATGGTTGAAAGATACCAATGAA
66 TACCATGGCAACATAATATGAAATGAATAAGACCATGGTTGAAAGATACCAATGAA
* *
5980994 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTAACATGAAAAGAATAAGACCATGGTTGAAAGA
*
5981059 TACCATGGCAACCTAATATGAAATGAATAAGACCATGGTTGAAAGATACCA
66 TACCATGGCAACATAATATGAAATGAATAAGACCATGGTTGAAAGATACCA
5981110 TGGCAACGTG
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 109 1.00
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.21
Consensus pattern (121 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACCTAACATGAAAAGAATAAGACCATGGTTGAAAGA
TACCATGGCAACATAATATGAAATGAATAAGACCATGGTTGAAAGATACCAATGAA
Found at i:5981093 original size:92 final size:92
Alignment explanation
Indices: 5980988--5981162 Score: 350
Period size: 92 Copynumber: 1.9 Consensus size: 92
5980978 GAAAGATACC
5980988 AATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTT
1 AATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTT
5981053 GAAAGATACCATGGCAACCTAATATGA
66 GAAAGATACCATGGCAACCTAATATGA
5981080 AATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTT
1 AATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTT
5981145 GAAAGATACCATGGCAAC
66 GAAAGATACCATGGCAAC
5981163 ATGACAGAAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 83 1.00
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.19
Consensus pattern (92 bp):
AATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTT
GAAAGATACCATGGCAACCTAATATGA
Found at i:5981103 original size:167 final size:167
Alignment explanation
Indices: 5980827--5981155 Score: 559
Period size: 167 Copynumber: 2.0 Consensus size: 167
5980817 ATGAAATGTG
* * **
5980827 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACCATGGTTGAAAGA
** *
5980892 TACCATGGCAACCTAACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAT
66 TACCATGGCAACCTAACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAT
*
5980957 GAAATGAATAAGACCATGGTTGAAAGATACCAATGAA
131 GAAAAGAATAAGACCATGGTTGAAAGATACCAATGAA
*
5980994 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACCATGGTTGAAAGA
* *
5981059 TACCATGGCAACCTAATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACAT
66 TACCATGGCAACCTAACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAT
5981124 GAAAAGAATAAGACCATGGTTGAAAGATACCA
131 GAAAAGAATAAGACCATGGTTGAAAGATACCA
5981156 TGGCAACATG
Statistics
Matches: 151, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
167 151 1.00
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (167 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACCATGGTTGAAAGA
TACCATGGCAACCTAACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAT
GAAAAGAATAAGACCATGGTTGAAAGATACCAATGAA
Found at i:5984043 original size:27 final size:27
Alignment explanation
Indices: 5984024--5984180 Score: 197
Period size: 27 Copynumber: 5.8 Consensus size: 27
5984014 ATTACCAAAG
*
5984024 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
5984051 TACCCTCAATTTACAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
5984078 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * **
5984105 TACCCTCGATTTATAAAATTACTATTT
1 TACCCTCGATTTACAGAATTACCGTTT
** * * *
5984132 TACCCTTAATTTACAAAATTACTGTGT
1 TACCCTCGATTTACAGAATTACCGTTT
*
5984159 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
5984181 TAAAATACCC
Statistics
Matches: 114, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 114 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:5984057 original size:54 final size:52
Alignment explanation
Indices: 5983999--5984208 Score: 150
Period size: 54 Copynumber: 3.9 Consensus size: 52
5983989 TACTGAAATG
*
5983999 CCCTCAAATTGTAAAATTACCAAAGTACCCTCGATTTATAGAATTACCGTTTTA
1 CCCTC-AATT-TAAAATTACCAAAGTACCCTCGATTTACAGAATTACCGTTTTA
* ****
5984053 CCCTCAATTTACAGAATTATCGTTTTACCCTCGATTTACAGAATTACCGTTTTA
1 CCCTCAATTTA-A-AATTACCAAAGTACCCTCGATTTACAGAATTACCGTTTTA
* * *** ** * * *
5984107 CCCTCGATTTATAAAATTACTATTTTACCCTTAATTTACAAAATTACTGTGTTA
1 CCCTC-AATT-TAAAATTACCAAAGTACCCTCGATTTACAGAATTACCGTTTTA
* * * * * *
5984161 CCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACC
1 CCCTCAATTT--AAAATTACCAAAGTACCCTCGATTTACAGAATTACC
5984209 AAAATACCCT
Statistics
Matches: 127, Mismatches: 23, Indels: 12
0.78 0.14 0.07
Matches are distributed among these distances:
52 3 0.02
53 7 0.06
54 111 0.87
55 4 0.03
56 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (52 bp):
CCCTCAATTTAAAATTACCAAAGTACCCTCGATTTACAGAATTACCGTTTTA
Found at i:5984189 original size:27 final size:27
Alignment explanation
Indices: 5984159--5984516 Score: 201
Period size: 27 Copynumber: 13.2 Consensus size: 27
5984149 ATTACTGTGT
* *
5984159 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* * *
5984186 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
*
5984213 TACCCTCGA-TCAGTAAAATTACCAAAA
1 TACCCTCGATTTA-TAAAATTACCAAAA
* * * * *
5984240 TACCCTAG-TCTGTAAAATTGCTAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* * **
5984266 TACCC-CTAGTTTGTAAAATTACCGGAA
1 TACCCTCGA-TTTATAAAATTACCAAAA
* *
5984293 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* *
5984320 TACCC-CTAGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTATAAAATTACCAAAA
* * * *
5984347 TACCACT-GGTTTGTGAAATTACCGAAA
1 TACC-CTCGATTTATAAAATTACCAAAA
* *
5984374 TACCTTCAATTTATAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
*
5984401 TACCC-CTGATTT-TCAAAGTTA-CAGAAA
1 TACCCTC-GATTTAT-AAAATTACCA-AAA
* * ***
5984428 TACCCTTGACTTTCTAAAAATTATGGAAA
1 TACCCTCGA-TTTAT-AAAATTACCAAAA
* * * * **
5984457 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* * * *
5984484 TACCCTTGATTTGTAGATTTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
*
5984511 CACCCT
1 TACCCT
5984517 TGTAGGATGA
Statistics
Matches: 258, Mismatches: 57, Indels: 32
0.74 0.16 0.09
Matches are distributed among these distances:
26 26 0.10
27 206 0.80
28 9 0.03
29 17 0.07
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
TACCCTCGATTTATAAAATTACCAAAA
Found at i:5984190 original size:81 final size:81
Alignment explanation
Indices: 5984011--5984209 Score: 238
Period size: 81 Copynumber: 2.5 Consensus size: 81
5984001 CTCAAATTGT
* * * *
5984011 AAAATTACCAAAGTACCCTCGATTTATAGAATTACCGTTTTACCCTCAATTTACAGAATTATCGT
1 AAAATTACCAAAATACCCTCGATTTATAAAATTACCATTTTACCCTCAATTTACAAAATTATCGT
*
5984076 TTTACCCTCGATTTAC
66 GTTACCCTCGATTTAC
* **** * *
5984092 AGAATTACCGTTTTACCCTCGATTTATAAAATTACTATTTTACCCTTAATTTACAAAATTA-CTG
1 AAAATTACCAAAATACCCTCGATTTATAAAATTACCATTTTACCCTCAATTTACAAAATTATC-G
5984156 TGTTACCCTCGATTTAC
65 TGTTACCCTCGATTTAC
* * * *
5984173 AAAATTACTAAAATACCCTTGGTTTACAAAATTACCA
1 AAAATTACCAAAATACCCTCGATTTATAAAATTACCA
5984210 AAATACCCTC
Statistics
Matches: 96, Mismatches: 21, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
80 1 0.01
81 95 0.99
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.37
Consensus pattern (81 bp):
AAAATTACCAAAATACCCTCGATTTATAAAATTACCATTTTACCCTCAATTTACAAAATTATCGT
GTTACCCTCGATTTAC
Found at i:5984217 original size:54 final size:54
Alignment explanation
Indices: 5984105--5984518 Score: 237
Period size: 54 Copynumber: 7.6 Consensus size: 54
5984095 ATTACCGTTT
* *** ** *****
5984105 TACCCTCGATTTATAAAATTACTATTTTACCCTTAATTTACAAAATTACTGTGT
1 TACCCTCGATTTATAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAA
* *
5984159 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAA
* * * ** * *
5984213 TACCCTCGA-TCAGTAAAATTACCAAAATACCC-TAGTCTGTAAAATTGCTAAAA
1 TACCCTCGATTTA-TAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAA
* * ** *** **
5984266 TACCC-CTAGTTTGTAAAATTACCGGAATACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTATAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAA
* * *** *
5984320 TACCC-CTAGTTTGTAAAATTACCAAAATACCAC-TGGTTTGTGAAATTACCGAAA
1 TACCCTCGA-TTTATAAAATTACCAAAATACC-CTTGGTTTACAAAATTACCAAAA
* * * * * *
5984374 TACCTTCAATTTATAAAATTACCAAAATACCCCTGATTTTCAAAGTTA-CAGAAA
1 TACCCTCGATTTATAAAATTACCAAAATACCCTTGGTTTACAAAATTACCA-AAA
* * *** * **
5984428 TACCCTTGACTTTCTAAAAATTATGGAAATACCATTGGTTTACAAAATTACTGAAA
1 TACCCTCGA-TTTAT-AAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAA
* * * * *
5984484 TACCCTTGATTTGTAGATTTACCAAAACACCCTTG
1 TACCCTCGATTTATAAAATTACCAAAATACCCTTG
5984519 TAGGATGAAA
Statistics
Matches: 281, Mismatches: 68, Indels: 22
0.76 0.18 0.06
Matches are distributed among these distances:
52 2 0.01
53 41 0.15
54 189 0.67
55 11 0.04
56 38 0.14
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (54 bp):
TACCCTCGATTTATAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAA
Found at i:5984244 original size:81 final size:80
Alignment explanation
Indices: 5984159--5984435 Score: 274
Period size: 81 Copynumber: 3.4 Consensus size: 80
5984149 ATTACTGTGT
* ** * * *
5984159 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCGATC
1 TACCC-CGATTTGCAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCGAAATACCCTCAATT
5984224 AGTAAAATTACCAAAA
65 AGTAAAATTACCAAAA
* * * * * * *
5984240 TA-CCCTAGTCTGTAAAATTGCTAAAATACCCCTAGTTTGTAAAATTACCGGAATACCCTCAATT
1 TACCCCGA-TTTGCAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCGAAATACCCTCAATT
*
5984304 TGTAAAATTACCAAAA
65 AGTAAAATTACCAAAA
* * * * *
5984320 TACCCCTAGTTTGTAAAATTACCAAAATACCAC-TGGTTTGTGAAATTACCGAAATACCTTCAAT
1 TACCCCGA-TTTGCAAAATTACTAAAATACC-CTTGGTTTGTAAAATTACCGAAATACCCTCAA-
5984384 TTA-TAAAATTACCAAAA
63 TTAGTAAAATTACCAAAA
* *
5984401 TACCCCTGATTTTCAAAGTTAC-AGAAATACCCTTG
1 TACCCC-GATTTGCAAAATTACTA-AAATACCCTTG
5984436 ACTTTCTAAA
Statistics
Matches: 163, Mismatches: 26, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
79 2 0.01
80 65 0.40
81 92 0.56
82 4 0.02
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.30
Consensus pattern (80 bp):
TACCCCGATTTGCAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCGAAATACCCTCAATTA
GTAAAATTACCAAAA
Found at i:5985464 original size:52 final size:52
Alignment explanation
Indices: 5985386--5985537 Score: 281
Period size: 52 Copynumber: 3.0 Consensus size: 52
5985376 TTACATTGGG
5985386 TTGAAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTA
1 TTGAAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTA
5985438 TTGAAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTA
1 TTGAAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTA
*
5985490 TTGAAAAGGGCTT-TGCCCCAGTTTACCGAAAAGGGCTT-TACCCCAGTT
1 TTGAAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTT
5985538 GTTAAAGAGG
Statistics
Matches: 99, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
50 9 0.09
51 25 0.25
52 65 0.66
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (52 bp):
TTGAAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTA
Found at i:5985512 original size:25 final size:26
Alignment explanation
Indices: 5985388--5985537 Score: 241
Period size: 26 Copynumber: 5.8 Consensus size: 26
5985378 ACATTGGGTT
5985388 GAAAAGGGCTTATGCCCCAGTTTACC
1 GAAAAGGGCTTATGCCCCAGTTTACC
**
5985414 GAAAAGGGCTTATGCCCCAGTTTATT
1 GAAAAGGGCTTATGCCCCAGTTTACC
5985440 GAAAAGGGCTTATGCCCCAGTTTACC
1 GAAAAGGGCTTATGCCCCAGTTTACC
**
5985466 GAAAAGGGCTTATGCCCCAGTTTATT
1 GAAAAGGGCTTATGCCCCAGTTTACC
5985492 GAAAAGGGCTT-TGCCCCAGTTTACC
1 GAAAAGGGCTTATGCCCCAGTTTACC
*
5985517 GAAAAGGGCTT-TACCCCAGTT
1 GAAAAGGGCTTATGCCCCAGTT
5985538 GTTAAAGAGG
Statistics
Matches: 115, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
25 32 0.28
26 83 0.72
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (26 bp):
GAAAAGGGCTTATGCCCCAGTTTACC
Found at i:5985905 original size:26 final size:26
Alignment explanation
Indices: 5985876--5985957 Score: 121
Period size: 26 Copynumber: 3.2 Consensus size: 26
5985866 TGGTACAAAT
*
5985876 TGATAATGGGTTAGGTAAATGTTCTA
1 TGATAATGGATTAGGTAAATGTTCTA
5985902 TGATAATGGATTAGGTAAATGTT-TCA
1 TGATAATGGATTAGGTAAATGTTCT-A
* *
5985928 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCTA
5985954 TGAT
1 TGAT
5985958 GGGCATTTCA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
25 1 0.02
26 50 0.98
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCTA
Found at i:5988772 original size:42 final size:42
Alignment explanation
Indices: 5988713--5988804 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
5988703 TAGTCTCCCC
* ** *
5988713 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
5988755 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
5988797 AAATGGGC
1 AAATGGGC
5988805 CTAAGGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:5990928 original size:2 final size:2
Alignment explanation
Indices: 5990917--5990951 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5990907 TTATTATTAT
5990917 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5990952 AAAGAAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5990980 original size:23 final size:24
Alignment explanation
Indices: 5990951--5990995 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
5990941 ATATATATAT
5990951 AAAAGAAAAGAAAAA-AAAGAAGA
1 AAAAGAAAAGAAAAAGAAAGAAGA
*
5990974 AAAAGAATAGAAAAAGAAAGAA
1 AAAAGAAAAGAAAAAGAAAGAA
5990996 AGGATGAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (24 bp):
AAAAGAAAAGAAAAAGAAAGAAGA
Found at i:5990985 original size:11 final size:11
Alignment explanation
Indices: 5990951--5990996 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
5990941 ATATATATAT
5990951 AAAAGAAAAGA
1 AAAAGAAAAGA
*
5990962 AAAAAAAGAAGA
1 AAAAGAA-AAGA
*
5990974 AAAAGAATAGA
1 AAAAGAAAAGA
5990985 AAAAG-AAAGA
1 AAAAGAAAAGA
5990995 AA
1 AA
5990997 GGATGAAACG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 6 0.20
11 14 0.47
12 10 0.33
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:5991065 original size:16 final size:16
Alignment explanation
Indices: 5991021--5991059 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
5991011 AGAGAGCAGG
*
5991021 GGAAAGAAA-GAAGGAA
1 GGAAA-AAACGAAAGAA
5991037 GGAAAAAACGAAAGAA
1 GGAAAAAACGAAAGAA
5991053 GGAAAAA
1 GGAAAAA
5991060 GGGAAAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.67, C:0.03, G:0.31, T:0.00
Consensus pattern (16 bp):
GGAAAAAACGAAAGAA
Found at i:5997457 original size:59 final size:54
Alignment explanation
Indices: 5997384--5997518 Score: 166
Period size: 54 Copynumber: 2.4 Consensus size: 54
5997374 TAGGGTCTGA
* *
5997384 ATTTAGCCTGGACTGGTAATTCAGATCCAA-GCTC-ATTAGAGTAATTATCATTACAGGGG
1 ATTTAGCCTGGACTGGTAATCCAGA--CAATACTCTA-T-GAGT--TTAT-ATTACAGGGG
*
5997443 ATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTACAGGGG
1 ATTTAGCCTGGACTGGTAATCCAGACAATACTCTATGAGTTTATATTACAGGGG
5997497 ATTTAGCCTGGACTGGTAATCC
1 ATTTAGCCTGGACTGGTAATCC
5997519 CACTGTAAGG
Statistics
Matches: 71, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
54 32 0.45
55 4 0.06
57 7 0.10
58 4 0.06
59 24 0.34
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (54 bp):
ATTTAGCCTGGACTGGTAATCCAGACAATACTCTATGAGTTTATATTACAGGGG
Found at i:5997605 original size:46 final size:46
Alignment explanation
Indices: 5997553--5997874 Score: 491
Period size: 46 Copynumber: 7.0 Consensus size: 46
5997543 AGTGTGCTCT
** *
5997553 CTGATATGAAATGTGTAAGACCATGATTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
**
5997599 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* **
5997645 CTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
*
5997691 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
5997737 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* *
5997783 CTAATATGAAATAAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
5997829 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
5997875 ATGACAGAAA
Statistics
Matches: 258, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 258 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
Done.