Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold25
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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 6276 characters in sequence are not A, C, G, or T
File 16 of 56
Found at i:3023838 original size:45 final size:47
Alignment explanation
Indices: 3023761--3023851 Score: 168
Period size: 45 Copynumber: 2.0 Consensus size: 47
3023751 TTTTGTTATA
3023761 TTAATTTTTAATATTTTTTTATTATAGTCTATGAAATAT-ATATATG
1 TTAATTTTTAATATTTTTTTATTATAGTCTATGAAATATAATATATG
3023807 TTAATTTTTAATA-TTTTTTATTATAGTCTATGAAATATAATATAT
1 TTAATTTTTAATATTTTTTTATTATAGTCTATGAAATATAATATAT
3023852 ATATATATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 25 0.57
46 19 0.43
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.56
Consensus pattern (47 bp):
TTAATTTTTAATATTTTTTTATTATAGTCTATGAAATATAATATATG
Found at i:3027086 original size:11 final size:11
Alignment explanation
Indices: 3027047--3027091 Score: 53
Period size: 10 Copynumber: 4.5 Consensus size: 11
3027037 GAGATAAGAC
3027047 ATATTTATAA-
1 ATATTTATAAT
3027057 A-ATTTAT-AT
1 ATATTTATAAT
*
3027066 AAATTT-TAAT
1 ATATTTATAAT
3027076 ATATTTATAAT
1 ATATTTATAAT
3027087 ATATT
1 ATATT
3027092 ATATTTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
8 1 0.03
9 8 0.27
10 12 0.40
11 9 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATATTTATAAT
Found at i:3027142 original size:21 final size:22
Alignment explanation
Indices: 3027116--3027156 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3027106 TTTTAATATA
*
3027116 ATATTATATTT-TAATTATTTT
1 ATATTATATTTAAAATTATTTT
3027137 ATATTATATTTAAAATTATT
1 ATATTATATTTAAAATTATT
3027157 AAATTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATTATATTTAAAATTATTTT
Found at i:3027144 original size:29 final size:28
Alignment explanation
Indices: 3027068--3027140 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
3027058 ATTTATATAA
3027068 ATTTTAA-TATATTTATA-AT-ATATTAT
1 ATTTTAATTAT-TTTATATATAATATTAT
*
3027094 ATTTAAATTAATTTT-TAATATAATATTAT
1 ATTTTAATT-ATTTTAT-ATATAATATTAT
3027123 ATTTTAATTATTTTATAT
1 ATTTTAATTATTTTATAT
3027141 TATATTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
26 7 0.18
27 5 0.13
28 11 0.28
29 16 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTTTAATTATTTTATATATAATATTAT
Found at i:3029623 original size:2 final size:2
Alignment explanation
Indices: 3029616--3029646 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3029606 TTTTGCTCCA
3029616 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
3029647 AGTTATAAAT
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:3031705 original size:17 final size:17
Alignment explanation
Indices: 3031678--3031712 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3031668 ATTATTACTA
3031678 AATTAAATAATAAAATTT
1 AATTAAATAAT-AAATTT
3031696 AATT-AATAATAAATTT
1 AATTAAATAATAAATTT
3031712 A
1 A
3031713 TTTATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 6 0.35
18 4 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTAAATAATAAATTT
Found at i:3032016 original size:5 final size:5
Alignment explanation
Indices: 3032006--3032069 Score: 58
Period size: 5 Copynumber: 12.4 Consensus size: 5
3031996 AAATTCATAA
* * *
3032006 AATAT AATAT AAAAAT AATATT AATAT AATAT AATAT ATATAT ATTAA
1 AATAT AATAT -AATAT AATA-T AATAT AATAT AATAT A-ATAT AATAT
*
3032054 AAT-T AATAT AACAT AA
1 AATAT AATAT AATAT AA
3032070 ATTATTATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
4 3 0.06
5 31 0.65
6 14 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:3032025 original size:11 final size:11
Alignment explanation
Indices: 3032002--3032064 Score: 54
Period size: 11 Copynumber: 5.4 Consensus size: 11
3031992 TGGTAAATTC
3032002 ATAAAATATAAT
1 ATAAAA-ATAAT
3032014 ATAAAAATAAT
1 ATAAAAATAAT
* *
3032025 ATTAATATAAT
1 ATAAAAATAAT
*
3032036 ATAATATATATAT
1 ATAA-AAATA-AT
*
3032049 ATTAAAATTAAT
1 A-TAAAAATAAT
3032061 ATAA
1 ATAA
3032065 CATAAATTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
11 20 0.47
12 14 0.33
13 6 0.14
14 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATAAAAATAAT
Found at i:3032039 original size:16 final size:16
Alignment explanation
Indices: 3032006--3032073 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
3031996 AAATTCATAA
*
3032006 AATA-TAATATAAAAAT
1 AATATTAATAT-AATAT
3032022 AATATTAATATAATAT
1 AATATTAATATAATAT
3032038 AATA-T-ATAT-ATATT
1 AATATTAATATAATA-T
* *
3032052 AAAATTAATATAACAT
1 AATATTAATATAATAT
3032068 AA-ATTA
1 AATATTA
3032074 TTATTTTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
13 3 0.07
14 8 0.18
15 6 0.14
16 19 0.43
17 8 0.18
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATTAATATAATAT
Found at i:3032048 original size:22 final size:22
Alignment explanation
Indices: 3032006--3032064 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 22
3031996 AAATTCATAA
3032006 AATATAATATAAAAATAATATT
1 AATATAATATAAAAATAATATT
*
3032028 AATATAATATAATATATATATATT
1 AATATAATATAA-AAATA-ATATT
*
3032052 AAAATTAATATAA
1 AATA-TAATATAA
3032065 CATAAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 12 0.38
23 4 0.12
24 8 0.25
25 8 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AATATAATATAAAAATAATATT
Found at i:3033259 original size:4 final size:4
Alignment explanation
Indices: 3033252--3033283 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
3033242 TATATATATA
3033252 TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG
3033284 GGTTGCTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:3043013 original size:30 final size:32
Alignment explanation
Indices: 3042979--3043044 Score: 100
Period size: 30 Copynumber: 2.1 Consensus size: 32
3042969 AAAAAATTAT
*
3042979 AATATTAATTATTA-TATTTTA-AAAATAAAA
1 AATATTAATTATTATTATTTAATAAAATAAAA
*
3043009 AATATTTATTATTATTATTTAATAAAATAAAA
1 AATATTAATTATTATTATTTAATAAAATAAAA
3043041 AATA
1 AATA
3043045 ATATTTAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 13 0.41
31 6 0.19
32 13 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
AATATTAATTATTATTATTTAATAAAATAAAA
Found at i:3043060 original size:110 final size:108
Alignment explanation
Indices: 3042801--3043052 Score: 357
Period size: 110 Copynumber: 2.3 Consensus size: 108
3042791 TAAAAAAAGT
* * *
3042801 TTATTATTTTTTAATAAAATTAAAAATAATATTTAATTAAGGTTAAAAAAATTACATTAATAATT
1 TTATTA-TTTTTAATAAAATAAAAAATAATATTTAATTAAGGTTAAAAAAATTACATTAAAAAAT
* *
3042866 TAAAATATTAATTATTATGTTTTTATAAAATAAAAAAGGTTTTTTA
65 TAAAATATTAATTATTATGATTTTATAAAATAAAAAA-G-TATTTA
* * **
3042912 TTATAATTTTTAATAAAATAAAAAATAATATTTAATTAAGTTTAAAAATTTTACATTAAAAAATT
1 TTATTATTTTTAATAAAATAAAAAATAATATTTAATTAAGGTTAAAAAAATTACATTAAAAAATT
*
3042977 ATAATATTAATTATTAT-ATTTTA-AAAATAAAAAA-TATTTA
66 AAAATATTAATTATTATGATTTTATAAAATAAAAAAGTATTTA
3043017 TTATTATTATTTAATAAAATAAAAAATAATATTTAA
1 TTATTATT-TTTAATAAAATAAAAAATAATATTTAA
3043053 AGAATTAAAA
Statistics
Matches: 129, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
105 12 0.09
106 27 0.21
108 11 0.09
109 5 0.04
110 69 0.53
111 5 0.04
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (108 bp):
TTATTATTTTTAATAAAATAAAAAATAATATTTAATTAAGGTTAAAAAAATTACATTAAAAAATT
AAAATATTAATTATTATGATTTTATAAAATAAAAAAGTATTTA
Found at i:3047263 original size:90 final size:90
Alignment explanation
Indices: 3047131--3047475 Score: 381
Period size: 87 Copynumber: 3.9 Consensus size: 90
3047121 TAATATGTAA
* *
3047131 AATCAATCAACTTTTCTACTTTTCTAT-AAAAAGAAATTTGATTCT-TAAATATAA-TCTATGCA
1 AATCAATCAACTTTT-T-CTTTTCTATAAAAAAG-AATATGATTCTCT-GATATAATTC-ATGCA
*
3047193 TTAGTCTAATCTTTATAGTTTGACATTTAC
61 TTAGTCTAATCTTTACAGTTTGACATTTAC
3047223 AATCAATCAACTTTTTCTTTTCTATAAAAAAGAATATGATTCTCTGATATAATTCATGCATTAGT
1 AATCAATCAACTTTTTCTTTTCTATAAAAAAGAATATGATTCTCTGATATAATTCATGCATTAGT
* * * *
3047288 CTAATCTTTGCAGTCTGATATTTAT
66 CTAATCTTTACAGTTTGACATTTAC
* * *
3047313 ACTCAATCAAC-TTTT-TTTT-TATAAAAAAGAATCTGAATCTCTGATATAATTCATGCATTAGT
1 AATCAATCAACTTTTTCTTTTCTATAAAAAAGAATATGATTCTCTGATATAATTCATGCATTAGT
* * *
3047375 TTAATCCTTACAGTTTAACATTTAC
66 CTAATCTTTACAGTTTGACATTTAC
* * * * *
3047400 ACTCAATCAAC--TTT-TTTTATA-AAAAAAGAAT-TCGATT-TCAGATACAATTAATGCATTAG
1 AATCAATCAACTTTTTCTTTTCTATAAAAAAGAATAT-GATTCTCTGATATAATTCATGCATTAG
*
3047459 TCTAATCCTTACAGTTT
65 TCTAATCTTTACAGTTT
3047476 TTCTTTTTTT
Statistics
Matches: 226, Mismatches: 22, Indels: 17
0.85 0.08 0.06
Matches are distributed among these distances:
85 36 0.16
86 20 0.09
87 72 0.32
88 4 0.02
89 4 0.02
90 65 0.29
91 10 0.04
92 15 0.07
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42
Consensus pattern (90 bp):
AATCAATCAACTTTTTCTTTTCTATAAAAAAGAATATGATTCTCTGATATAATTCATGCATTAGT
CTAATCTTTACAGTTTGACATTTAC
Found at i:3047484 original size:155 final size:155
Alignment explanation
Indices: 3047323--3047628 Score: 420
Period size: 155 Copynumber: 2.0 Consensus size: 155
3047313 ACTCAATCAA
* * *
3047323 CTTTTTTTTTATAAAAAAGAATCTGAATCTCTGATATAATTCATGCATTAGTTTAATCCTTACAG
1 CTTTTTTTCTATAAAAAAGAATCTGAATCTC-AATATAATTCATGCATTAGTCT-ATCCTTACAG
* * *
3047388 TTTAACATTTACACTCAATCAACTTTTTTTATA-AAAAAAGAAT-TCGATT-TCAGATACAATTA
64 TCTAACATTTACAATCAATCAACTTTTTTTATATAAAAAAGAATCT-GATTCTCAAATACAATTA
3047450 ATGCATTAGTCTAATCCTTACAGTTTTT
128 ATGCATTAGTCTAATCCTTACAGTTTTT
* * *
3047478 CTTTTTTTCTATAAAAAAGAATCTGATTCTCAATATAATTCATGCATTAGTCTATTCTTGCAGTC
1 CTTTTTTTCTATAAAAAAGAATCTGAATCTCAATATAATTCATGCATTAGTCTATCCTTACAGTC
* * * * * *
3047543 TGACATTTACAATCAATCAACTTTTTTTCTATCAATAAGAATCTGATTCTCAAATATAATTCATG
66 TAACATTTACAATCAATCAACTTTTTTTATATAAAAAAGAATCTGATTCTCAAATACAATTAATG
*
3047608 CATTAGTCTAATCTTTACAGT
131 CATTAGTCTAATCCTTACAGT
3047629 CTGACATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
153 37 0.28
154 32 0.24
155 63 0.48
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (155 bp):
CTTTTTTTCTATAAAAAAGAATCTGAATCTCAATATAATTCATGCATTAGTCTATCCTTACAGTC
TAACATTTACAATCAATCAACTTTTTTTATATAAAAAAGAATCTGATTCTCAAATACAATTAATG
CATTAGTCTAATCCTTACAGTTTTT
Found at i:3047651 original size:87 final size:86
Alignment explanation
Indices: 3047478--3047878 Score: 451
Period size: 85 Copynumber: 4.7 Consensus size: 86
3047468 TACAGTTTTT
*
3047478 CTTTTTTTCTATAAAAAAGAATCTGATTCTC-AATATAATTCATGCATTAGTCT-ATTCTTGCAG
1 CTTTTTTTCTAT-AAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTGCAG
3047541 TCTGACATTTACAATCAATCAA
65 TCTGACATTTACAATCAATCAA
* * *
3047563 CTTTTTTTCTATCAATAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCTTTACAG
1 CTTTTTTTCTAT-AAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTGCAG
*
3047628 TCTGACATTTACAATCAAACAA
65 TCTGACATTTACAATCAATCAA
* * * *
3047650 CTTTTTTTCTACAAAAACGAATAC-AATTCTCTAATATAA-TCATGCATTAGTTTAATCCTTGCA
1 CTTTTTTTCTATAAAAA-GAAT-CTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTGCA
* * * *
3047713 GTCTGATATTTATACTCATTCAA
64 GTCTGACATTTACAATCAATCAA
* * ** * * *
3047736 CTTTTTTT-TATAAAAAAAATCTGAATCTCTGATATAATTTATTCATTAGTCTAATCCTTGTAGT
1 CTTTTTTTCTATAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTGCAGT
* * * *
3047800 CTAATATTTACACTCAATTAA
66 CTGACATTTACAATCAATCAA
* *
3047821 CTTTTTTT-TAATAAAAA-AAT-TCGATT-TCAAATACAATTCATGCATTTGTCTAATCCTT
1 CTTTTTTTCT-ATAAAAAGAATCT-GATTCTCAAATATAATTCATGCATTAGTCTAATCCTT
3047879 ACCGTCTTTT
Statistics
Matches: 270, Mismatches: 38, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
83 1 0.00
84 42 0.16
85 90 0.33
86 80 0.30
87 56 0.21
88 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.42
Consensus pattern (86 bp):
CTTTTTTTCTATAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTGCAGT
CTGACATTTACAATCAATCAA
Found at i:3047811 original size:171 final size:172
Alignment explanation
Indices: 3047478--3048316 Score: 524
Period size: 174 Copynumber: 5.0 Consensus size: 172
3047468 TACAGTTTTT
* * *
3047478 CTTTTTTTCTATAAAAAAGAATCTGATTCTCAATATAATTCATGCATTAGTCTATTCTTGCAGTC
1 CTTTTTTTCTACAAAAAAGAATCTAATTCTCAATATAATTCATGCATTAGTCTATCCTTGCAGTC
* * *
3047543 TGACATTTACAATCAATCAACTTTTTTTCTATCAATAAGAATCTGATTCTCAAATATAATTCATG
66 TGACATTTACAATCAATCAACTTTTTTTCTATCAAAAAAAATCTGAATCTCAAATATAATTCATG
* *
3047608 CATTAGTCTAATCTTTACAGTCTGACATTTACAATCAAACAA
131 CATTAGTCTAATCCTTACAGTCTAACATTTACAATCAAACAA
* *
3047650 CTTTTTTTCTACAAAAACGAATAC-AATTCTCTAATATAA-TCATGCATTAGTTTAATCCTTGCA
1 CTTTTTTTCTACAAAAAAGAAT-CTAATTCTC-AATATAATTCATGCATTAGTCT-ATCCTTGCA
* * * * ** *
3047713 GTCTGATATTTATACTCATTCAACTTTTTTT-TAT-AAAAAAAATCTGAATCTCTGATATAATTT
63 GTCTGACATTTACAATCAATCAACTTTTTTTCTATCAAAAAAAATCTGAATCTCAAATATAATTC
* ** * * **
3047776 ATTCATTAGTCTAATCCTTGTAGTCTAATATTTACACTCAATTAA
128 ATGCATTAGTCTAATCCTTACAGTCTAACATTTACAATCAAACAA
* * *
3047821 CTTTTTTT-TA-ATAAAAA-AAT-TCGATT-TCAAATACAATTCATGCATTTGTCTAATCCTT--
1 CTTTTTTTCTACA-AAAAAGAATCT-AATTCTC-AATATAATTCATGCATTAGTCT-ATCCTTGC
* * * * * * * *
3047879 A--C---C--GT-C--T---T---TTTTTTTTCTATAAGAAAGAATCTAATTCTCATATATAATT
62 AGTCTGACATTTACAATCAATCAACTTTTTTTCTATCAAAAAAAATCTGAATCTCAAATATAATT
** * * * * *
3047928 ATTTCATTAGTCTAATCCCTACAGTATGACATTTACAATCAATCAA
127 CATGCATTAGTCTAATCCTTACAGTCTAACATTTACAATCAAACAA
* * * ** * *
3047974 CTTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATCATTCATATATTAGTCTAATCTTTACAG
1 CTTTTTTTCTACAAAAAAGAATCTAATTCTC-AATATAATTCATGCATTAGTCT-ATCCTTGCAG
* * * * * * * ***
3048039 TCTAAAATTTA-TATACAATCAACTTTTTTTTCTAT-AAAAAAGAGTTTCATTCTTTGATATAAT
64 TCTGACATTTACAAT-CAATCAAC-TTTTTTTCTATCAAAAAA-AATCTGAATCTCAAATATAAT
* * * * * * **
3048102 TTAT-CATAAGTCTAATCGTTGCAGTTTAACATTTACACTCAATTAA
126 TCATGCATTAGTCTAATCCTTACAGTCTAACATTTACAATCAAACAA
* * * * *
3048148 CCTCTTTTTTATAAAAAAAAAGAATCTGATTTTCAAATATAATTCATGCAGTAGTCTAAT-CTT-
1 -CT-TTTTTTCT-ACAAAAAAGAATCTAATTCTC-AATATAATTCATGCATTAGTCT-ATCCTTG
* * * * *
3048211 -TG-CTGACATTTACAATCAATCAACTATCTTTTTCTAT-AAAAAAGAATCTGATTATTAGATAT
61 CAGTCTGACATTTACAATCAATCAACT-T-TTTTTCTATCAAAAAA-AATCTGAATCTCAAATAT
** * *
3048273 AATTCATGCATTAGTCTAATCCTTGTAATCTGACATTTACAATC
123 AATTCATGCATTAGTCTAATCCTTACAGTCTAACATTTACAATC
3048317 CATGCATTAT
Statistics
Matches: 523, Mismatches: 102, Indels: 81
0.74 0.14 0.11
Matches are distributed among these distances:
151 7 0.01
152 3 0.01
153 66 0.13
154 8 0.02
155 8 0.02
156 27 0.05
157 1 0.00
158 1 0.00
160 2 0.00
165 2 0.00
167 2 0.00
168 8 0.02
169 26 0.05
170 6 0.01
171 68 0.13
172 43 0.08
173 60 0.11
174 76 0.15
175 59 0.11
176 9 0.02
177 41 0.08
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.41
Consensus pattern (172 bp):
CTTTTTTTCTACAAAAAAGAATCTAATTCTCAATATAATTCATGCATTAGTCTATCCTTGCAGTC
TGACATTTACAATCAATCAACTTTTTTTCTATCAAAAAAAATCTGAATCTCAAATATAATTCATG
CATTAGTCTAATCCTTACAGTCTAACATTTACAATCAAACAA
Found at i:3047962 original size:153 final size:154
Alignment explanation
Indices: 3047737--3048041 Score: 356
Period size: 153 Copynumber: 2.0 Consensus size: 154
3047727 CTCATTCAAC
* ** *
3047737 TTTTTTTTATAAAAAAAATCTGAATCTCTGATATAATTTATTCATTAGTCTAATCCTTGTAGTCT
1 TTTTTTTTATAAAAAAAATCTGAATCTCTGATATAATTTATTCATTAGTCTAATCCCTACAGTAT
* * * *
3047802 AATATTTACACTCAATTAACTTTTTTT-TAATAAAAAA-ATTC-GATT-TCAAATA-CAATTCAT
66 AACATTTACAATCAATCAACTTTTTTTCT-ATAAAAAAGAATCTGATTCTCAAATATC-ATTCAT
* * *
3047862 GCATTTGTCTAATCCTTACCGTCTTT
129 ACATTAGTCTAATCCTTACAGTCTTT
*
3047888 TTTTTTTCTATAAGAAAGAATCT-AATTCTCAT-ATATAA-TTATTTCATTAGTCTAATCCCTAC
1 TTTTTTT-TATAA-AAAAAATCTGAA-TCTC-TGATATAATTTA-TTCATTAGTCTAATCCCTAC
*
3047950 AGTATGACATTTACAATCAATCAACTTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATCATT
61 AGTATAACATTTACAATCAATCAACTTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATCATT
* *
3048015 CATATATTAGTCTAATCTTTACAGTCT
126 CATACATTAGTCTAATCCTTACAGTCT
3048042 AAAATTTATA
Statistics
Matches: 129, Mismatches: 15, Indels: 15
0.81 0.09 0.09
Matches are distributed among these distances:
151 7 0.05
152 10 0.08
153 70 0.54
154 5 0.04
155 4 0.03
156 32 0.25
157 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.44
Consensus pattern (154 bp):
TTTTTTTTATAAAAAAAATCTGAATCTCTGATATAATTTATTCATTAGTCTAATCCCTACAGTAT
AACATTTACAATCAATCAACTTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATCATTCATAC
ATTAGTCTAATCCTTACAGTCTTT
Found at i:3047962 original size:324 final size:333
Alignment explanation
Indices: 3047564--3048208 Score: 823
Period size: 324 Copynumber: 2.0 Consensus size: 333
3047554 ATCAATCAAC
* * **
3047564 TTTTTTTCTATCAATAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCTTTACAGT
1 TTTTTTTCTATCAAAAAGAATCTAATTCTCAAATATAATTCATGCATTAGTCTAATCCCTACAGT
* * *
3047629 CTGACATTTACAATCAAACAACTTTTTTTCTACAAAAACGAATAC-AATTCTCTAATAT-AATCA
66 ATGACATTTACAATCAAACAACTTTTTTTCTACAAAAAAGAAT-CTAATTCTCAAATATCAATCA
* * * * * *
3047692 TGCATTAGTTTAATCCTTGCAGTCTGATATTTATACT-CATTCAAC-TTTTTTT-TATAAAAAA-
130 TACATTAGTCTAATCCTTACAGTCTAAAATTTATA-TACAATCAACTTTTTTTTCTATAAAAAAG
* * * *
3047753 AATCTGAATCTCTGATATAATTTATTCATTAGTCTAATCCTTGTAGTCTAATATTTACACTCAAT
194 AATCTCAATCTCTGATATAATTTA-TCATAAGTCTAATCCTTGCAGTCTAACATTTACACTCAAT
* * * *
3047818 TAA-CT-TTTTTT-TAATAAAAAA-ATTC-GA-TTTCAAATACAATTCATGCATTTGTCTAATCC
258 TAACCTCTTTTTTATAAAAAAAAAGAATCTGATTTTCAAATACAATTCATGCAGTAGTCTAATCC
3047877 TTACCGTCTTT
323 TTACCGTCTTT
* *
3047888 TTTTTTTCTAT-AAGAAAGAATCTAATTCTCATATATAATT-ATTTCATTAGTCTAATCCCTACA
1 TTTTTTTCTATCAA-AAAGAATCTAATTCTCAAATATAATTCA-TGCATTAGTCTAATCCCTACA
* * * *
3047951 GTATGACATTTACAATCAATCAACTTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATCATTC
64 GTATGACATTTACAATCAAACAACTTTTTTTCTACAAAAAAGAATCTAATTCTCAAATATCAATC
* *
3048016 ATATATTAGTCTAATCTTTACAGTCTAAAATTTATATACAATCAACTTTTTTTTCTATAAAAAAG
129 ATACATTAGTCTAATCCTTACAGTCTAAAATTTATATACAATCAACTTTTTTTTCTATAAAAAAG
* * * * * *
3048081 AGTTTCATTCTTTGATATAATTTATCATAAGTCTAATCGTTGCAGTTTAACATTTACACTCAATT
194 AATCTCAATCTCTGATATAATTTATCATAAGTCTAATCCTTGCAGTCTAACATTTACACTCAATT
*
3048146 AACCTCTTTTTTATAAAAAAAAAGAATCTGATTTTCAAATATAATTCATGCAGTAGTCTAATC
259 AACCTCTTTTTTATAAAAAAAAAGAATCTGATTTTCAAATACAATTCATGCAGTAGTCTAATC
3048209 TTTGCTGACA
Statistics
Matches: 271, Mismatches: 36, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
323 4 0.01
324 105 0.39
325 39 0.14
326 7 0.03
327 47 0.17
328 21 0.08
329 6 0.02
330 9 0.03
331 3 0.01
332 2 0.01
333 28 0.10
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.42
Consensus pattern (333 bp):
TTTTTTTCTATCAAAAAGAATCTAATTCTCAAATATAATTCATGCATTAGTCTAATCCCTACAGT
ATGACATTTACAATCAAACAACTTTTTTTCTACAAAAAAGAATCTAATTCTCAAATATCAATCAT
ACATTAGTCTAATCCTTACAGTCTAAAATTTATATACAATCAACTTTTTTTTCTATAAAAAAGAA
TCTCAATCTCTGATATAATTTATCATAAGTCTAATCCTTGCAGTCTAACATTTACACTCAATTAA
CCTCTTTTTTATAAAAAAAAAGAATCTGATTTTCAAATACAATTCATGCAGTAGTCTAATCCTTA
CCGTCTTT
Found at i:3047962 original size:411 final size:414
Alignment explanation
Indices: 3047150--3048296 Score: 1392
Period size: 411 Copynumber: 2.8 Consensus size: 414
3047140 ACTTTTCTAC
* * * *
3047150 TTTTCTATAAAAAGAAATTTGATTCTTAAATATAA-TCTATGCATTAGTCTAATCTTTATAGTTT
1 TTTTCTATAAAAAG-AATCTGATTCTCAAATATAATTC-ATGCATTAGTCTAATCTTTACAGTCT
** *
3047214 GACATTTACAATCAATCAACTTTTTCTTTTCTATAAAAAAGAATATGATTCTCTGATATAATTCA
64 GACATTTACAATCAATCAAC-TTTT-TTTTCTATAAAAAAGAATACAATTCTCTAATATAATTCA
*
3047279 TGCATTAGTCTAATCTTTGCAGTCTGATATTTATACTCAATCAACTTTTTTTTTATAAAAAAGAA
127 TGCATTAGTCTAATCCTTGCAGTCTGATATTTATACTCAATCAACTTTTTTTTTATAAAAAAGAA
* *
3047344 TCTGAATCTCTGATATAATTCATGCATTAGTTTAATCCTTACAGTTTAACATTTACACTCAATCA
192 TCTGAATCTCTGATATAATTCATGCATTAGTCTAATCCTTACAGTCTAACATTTACACTCAATCA
*
3047409 ACTTTTTTTATAAAAAAAGAATTCGATTTCAGATACAATTAATGCATTAGTCTAATCCTTACAGT
257 ACTTTTTTTATAAAAAAAGAATTCGATTTCAAATACAATTAATGCATTAGTCTAATCCTTACAGT
* * * * *
3047474 TTTTCTTTTTTTCTATAAAAAAGAATCTGATTCTCAATATAATTCATGCATTAGTCTATTCTTGC
322 CTTTCTTTTTTTCTATAAAAAAGAATCTAATTCTCAATATAATTCATGCATTAGTCTATCCCTAC
*
3047539 AGTCTGACATTTACAATCAATCAACTTT
387 AGTATGACATTTACAATCAATCAACTTT
*
3047567 TTTTCTATCAATAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCTTTACAGTCTG
1 TTTTCTAT-AAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCTTTACAGTCTG
* * *
3047632 ACATTTACAATCAAACAAC-TTTTTTTCTACAAAAACGAATACAATTCTCTAATATAA-TCATGC
65 ACATTTACAATCAATCAACTTTTTTTTCTATAAAAAAGAATACAATTCTCTAATATAATTCATGC
* *
3047695 ATTAGTTTAATCCTTGCAGTCTGATATTTATACTCATTCAAC-TTTTTTTTATAAAAAA-AATCT
130 ATTAGTCTAATCCTTGCAGTCTGATATTTATACTCAATCAACTTTTTTTTTATAAAAAAGAATCT
* * ** * *
3047758 GAATCTCTGATATAATTTATTCATTAGTCTAATCCTTGTAGTCTAATATTTACACTCAATTAACT
195 GAATCTCTGATATAATTCATGCATTAGTCTAATCCTTACAGTCTAACATTTACACTCAATCAACT
* * *
3047823 TTTTTT-TAATAAAAA-AATTCGATTTCAAATACAATTCATGCATTTGTCTAATCCTTACCGTCT
260 TTTTTTATAA-AAAAAGAATTCGATTTCAAATACAATTAATGCATTAGTCTAATCCTTACAGTCT
* *
3047886 TT-TTTTTTTCTATAAGAAAGAATCTAATTCTCATATATAATT-ATTTCATTAGTCTAATCCCTA
324 TTCTTTTTTTCTATAAAAAAGAATCTAATTCTCA-ATATAATTCA-TGCATTAGTCT-ATCCCTA
3047949 CAGTATGACATTTACAATCAATCAACTTT
386 CAGTATGACATTTACAATCAATCAACTTT
* ** *
3047978 TTTTCTATAAAAAAGAATCTGATTCTCAAATATCATTCATATATTAGTCTAATCTTTACAGTCTA
1 TTTTCTAT-AAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCTTTACAGTCTG
* * * * * * *
3048043 AAATTTA-TATACAATCAACTTTTTTTTCTATAAAAAAGAGTTTC-ATTCTTTGATATAATTTAT
65 ACATTTACAAT-CAATCAACTTTTTTTTCTATAAAAAAGA-ATACAATTCTCTAATATAATTCAT
* * * * * * * * *
3048106 -CATAAGTCTAATCGTTGCAGTTTAACATTTACACTCAATTAACCTCTTTTTTATAAAAAAAAAG
128 GCATTAGTCTAATCCTTGCAGTCTGATATTTATACTCAATCAA-CT-TTTTTT-TTATAAAAAAG
* * ** * * * *
3048170 AATCTGATTTTCAAATATAATTCATGCAGTAGTCTAAT-CTT--TG-CTGACATTTACAATCAAT
190 AATCTGAATCTCTGATATAATTCATGCATTAGTCTAATCCTTACAGTCTAACATTTACACTCAAT
* * * * *
3048231 CAACTATCTTTTTCTATAAAAAAGAA-TCTGATTATTAGATATAATTCATGCATTAGTCTAATCC
255 CAACT-T-TTTTTATA-AAAAAAGAATTC-GATT-TCAAATACAATTAATGCATTAGTCTAATCC
3048295 TT
315 TT
3048297 GTAATCTGAC
Statistics
Matches: 631, Mismatches: 77, Indels: 43
0.84 0.10 0.06
Matches are distributed among these distances:
409 30 0.05
410 68 0.11
411 177 0.28
412 78 0.12
413 70 0.11
414 32 0.05
415 14 0.02
416 20 0.03
417 107 0.17
418 35 0.06
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (414 bp):
TTTTCTATAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCTTTACAGTCTGA
CATTTACAATCAATCAACTTTTTTTTCTATAAAAAAGAATACAATTCTCTAATATAATTCATGCA
TTAGTCTAATCCTTGCAGTCTGATATTTATACTCAATCAACTTTTTTTTTATAAAAAAGAATCTG
AATCTCTGATATAATTCATGCATTAGTCTAATCCTTACAGTCTAACATTTACACTCAATCAACTT
TTTTTATAAAAAAAGAATTCGATTTCAAATACAATTAATGCATTAGTCTAATCCTTACAGTCTTT
CTTTTTTTCTATAAAAAAGAATCTAATTCTCAATATAATTCATGCATTAGTCTATCCCTACAGTA
TGACATTTACAATCAATCAACTTT
Found at i:3047987 original size:87 final size:88
Alignment explanation
Indices: 3047888--3048294 Score: 341
Period size: 87 Copynumber: 4.7 Consensus size: 88
3047878 TACCGTCTTT
* * *
3047888 TTTTTTTCTATAAGAAAGAATCTAATTCTCATATATAATT-ATTTCATTAGTCTAATCCCTACAG
1 TTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATTTCATTAGTCTAATCCCTACAG
* *
3047952 TATGACATTTACAATCAATCAAC
66 TCTAACATTTACAATCAATCAAC
* * **
3047975 TTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATCATTCATAT-ATTAGTCTAATCTTTACAG
1 TTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATTTCATTAGTCTAATCCCTACAG
* *
3048039 TCTAAAATTTA-TATACAATCAAC
66 TCTAACATTTACAAT-CAATCAAC
* * * *** * * ** *
3048062 TTTTTTTTCTATAAAAAAGAGTTTCATTCTTTGATATAATT--TATCATAAGTCTAATCGTTGCA
1 -TTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATTTCATTAGTCTAATCCCTACA
* * *
3048125 GTTTAACATTTACACTCAATTAACC
65 GTCTAACATTTACAATCAATCAA-C
* * * * * *
3048150 TCTTTTTTATAAAAAAAAAGAATCTGATTTTCAAATATAATTCA-TGCAGTAGTCTAAT--CT-T
1 T-TTTTTTCT-ATAAAAAAGAATCTGATTCTCAAATATAATTCATTTCATTAGTCTAATCCCTAC
* *
3048211 TG-CTGACATTTACAATCAATCAAC
64 AGTCTAACATTTACAATCAATCAAC
* * * *
3048235 TATCTTTTTCTATAAAAAAGAATCTGATTATTAGATATAATTCA-TGCATTAGTCTAATCC
1 T-T-TTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATTTCATTAGTCTAATCC
3048295 TTGTAATCTG
Statistics
Matches: 254, Mismatches: 53, Indels: 26
0.76 0.16 0.08
Matches are distributed among these distances:
85 45 0.18
86 28 0.11
87 102 0.40
88 46 0.18
89 23 0.09
90 10 0.04
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (88 bp):
TTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATTTCATTAGTCTAATCCCTACAG
TCTAACATTTACAATCAATCAAC
Found at i:3049064 original size:15 final size:15
Alignment explanation
Indices: 3049044--3049073 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3049034 TTATAATAAT
3049044 TTTTTTAATTTAAAA
1 TTTTTTAATTTAAAA
*
3049059 TTTTTTATTTTAAAA
1 TTTTTTAATTTAAAA
3049074 AACATAATAA
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTTAATTTAAAA
Found at i:3049285 original size:125 final size:129
Alignment explanation
Indices: 3049044--3049285 Score: 327
Period size: 125 Copynumber: 1.9 Consensus size: 129
3049034 TTATAATAAT
*
3049044 TTTTTTAATTTAAAATTTTTTATTTTAAAAAACATAATAATTAATATTTTAATTTATTAATATAA
1 TTTTTTAATTTAAAATTTTTTATTTT-AAAAACATAATAATTAATATTTTAATTTATGAATATAA
* * *
3049109 TTTTTTAAAATTTAATTAAATATTATTTTTATTTTATTTAAAAATAATAATAATAAACCCTTTTT
65 TTTTTTAAAACTTAATTAAATATTATTTTTATATTA-TAAAAAATAATAATAATAAACCCTTTTT
3049174 A
129 A
* *
3049175 TTTTTT-ATTT-AAATTTTTTATTTT-AAAA-A-AATAATTAATATTTTAATTTGTGAATGTAAA
1 TTTTTTAATTTAAAATTTTTTATTTTAAAAACATAATAATTAATATTTTAATTTATGAATAT-AA
*
3049235 TTTTTTTAAACTTAATTAAATATTATTTTT-TATTA-AAAATAATAATTAATA
65 TTTTTTAAAACTTAATTAAATATTATTTTTATATTATAAAA-AATAA-TAATA
3049286 CATTATCATT
Statistics
Matches: 101, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
123 3 0.03
124 5 0.05
125 34 0.34
126 31 0.31
127 4 0.04
129 14 0.14
130 4 0.04
131 6 0.06
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (129 bp):
TTTTTTAATTTAAAATTTTTTATTTTAAAAACATAATAATTAATATTTTAATTTATGAATATAAT
TTTTTAAAACTTAATTAAATATTATTTTTATATTATAAAAAATAATAATAATAAACCCTTTTTA
Found at i:3049302 original size:115 final size:123
Alignment explanation
Indices: 3049051--3049309 Score: 295
Period size: 126 Copynumber: 2.1 Consensus size: 123
3049041 AATTTTTTTA
*
3049051 ATTTAAAATTTTTTATTTTAAAAAACATAATAATTAATATTTTAATTTATTAATATAATTTTTTA
1 ATTT-AAATTTTTTATTTT-AAAAACATAATAATTAATATTTTAATTTATGAATATAATTTTTTA
* * **
3049116 AAATTTAATTAAATATTATTTTTATTTTATTTAAAAATAATAATAATAAACCCTTTTTATTTTTT
64 AAACTTAATTAAATATTA--TTTATTTTATTTAAAAATAATAATAAT-AA-CC-TATTATCATTT
* * *
3049181 ATTTAAATTTTTTATTTT-AAAA-A-AATAATTAATATTTTAATTTGTGAATGTAAATTTTTTTA
1 ATTTAAATTTTTTATTTTAAAAACATAATAATTAATATTTTAATTTATGAATAT-AATTTTTTAA
3049243 AACTTAATTAAATATTA-TT-TTTTA-TTAAAAATAATAATTAAT-A-C-ATTATCATTT
65 AACTTAATTAAATATTATTTATTTTATTTAAAAATAATAA-TAATAACCTATTATCATTT
3049297 A-TTAAATTTTTTA
1 ATTTAAATTTTTTA
3049310 AATTTAATTA
Statistics
Matches: 119, Mismatches: 8, Indels: 19
0.82 0.05 0.13
Matches are distributed among these distances:
115 12 0.10
116 8 0.07
118 1 0.01
120 1 0.01
121 13 0.11
122 9 0.08
123 2 0.02
125 25 0.21
126 26 0.22
127 4 0.03
129 14 0.12
130 4 0.03
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (123 bp):
ATTTAAATTTTTTATTTTAAAAACATAATAATTAATATTTTAATTTATGAATATAATTTTTTAAA
ACTTAATTAAATATTATTTATTTTATTTAAAAATAATAATAATAACCTATTATCATTT
Found at i:3049330 original size:125 final size:123
Alignment explanation
Indices: 3049079--3049331 Score: 282
Period size: 125 Copynumber: 2.0 Consensus size: 123
3049069 TAAAAAACAT
* *
3049079 AATAATTAATATTTTAATTTATTAATATAATTTTTTAAAATTTAATTAAATATTATTTTTATTTT
1 AATAATTAATATTTTAATTTATGAATATAATTTTTTAAAACTTAATTAAATATTA--TTTATTTT
* ** * *
3049144 ATTTAAAAATAATAATAATAAACCCTTTTTATTTTTTATTTAAATTTTTTATTTTAAAAA
64 ATTTAAAAATAATAATAATAAACCATTTTTATAATTTATTTAAATTTATTAATTTAAAAA
* * *
3049204 AATAATTAATATTTTAATTTGTGAATGTAAATTTTTTTAAACTTAATTAAATATTA-TT-TTTTA
1 AATAATTAATATTTTAATTTATGAATAT-AATTTTTTAAAACTTAATTAAATATTATTTATTTTA
*
3049267 -TTAAAAATAATAATTAATACATTATCATTTATTA-AATTT-TTTAAATTTAATTAATTTATAAA
65 TTTAAAAATAATAA-TAATA-A--ACCATTT-TTATAATTTATTTAAATTT-ATTAATTTA-AAA
3049329 A
123 A
3049330 AA
1 AA
3049332 ATAGACAATT
Statistics
Matches: 109, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
121 13 0.12
122 10 0.09
123 3 0.03
124 9 0.08
125 40 0.37
126 34 0.31
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (123 bp):
AATAATTAATATTTTAATTTATGAATATAATTTTTTAAAACTTAATTAAATATTATTTATTTTAT
TTAAAAATAATAATAATAAACCATTTTTATAATTTATTTAAATTTATTAATTTAAAAA
Found at i:3050005 original size:9 final size:9
Alignment explanation
Indices: 3049991--3050040 Score: 54
Period size: 9 Copynumber: 6.0 Consensus size: 9
3049981 TAAAAAAATA
3049991 ATATTTAAT
1 ATATTTAAT
3050000 ATATTTAA-
1 ATATTTAAT
3050008 A-ATTTAA-
1 ATATTTAAT
3050015 A-ATTTAAT
1 ATATTTAAT
*
3050023 ATTTTTAAT
1 ATATTTAAT
*
3050032 ATTTTTAAT
1 ATATTTAAT
3050041 TTTTAAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
7 13 0.34
8 2 0.05
9 23 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATATTTAAT
Found at i:3051853 original size:2 final size:2
Alignment explanation
Indices: 3051846--3051889 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3051836 ACCATCAATC
3051846 AT AT AT AT AT 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
3051888 AT
1 AT
3051890 TTCCGTTCCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3052169 original size:15 final size:15
Alignment explanation
Indices: 3052149--3052189 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
3052139 GTATAAATTT
3052149 TTAAATATATAAAAA
1 TTAAATATATAAAAA
*
3052164 TTAAATATATTAAAA
1 TTAAATATATAAAAA
*
3052179 TTAAATTTATA
1 TTAAATATATA
3052190 TTTATATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAATATATAAAAA
Found at i:3052340 original size:18 final size:18
Alignment explanation
Indices: 3052297--3052341 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3052287 TGATATTTAA
**
3052297 TAAATTAAATATTTATTTT
1 TAAATT-AATATTTATAAT
*
3052316 TATATTAATATTTATAAT
1 TAAATTAATATTTATAAT
3052334 TAAATTAA
1 TAAATTAA
3052342 AATATAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAAATTAATATTTATAAT
Found at i:3052404 original size:14 final size:15
Alignment explanation
Indices: 3052387--3052415 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3052377 TAATTGAGCC
3052387 AATTCA-ATTTAAAA
1 AATTCATATTTAAAA
3052401 AATTCATATTTAAAA
1 AATTCATATTTAAAA
3052416 TTAATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTCATATTTAAAA
Found at i:3053170 original size:16 final size:15
Alignment explanation
Indices: 3053145--3053195 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
3053135 TTTTTTATAA
*
3053145 TTTTAAATTTGATTT
1 TTTTAAATTTAATTT
*
3053160 TTTTAAAATTTAAATTA
1 TTTT-AAATTT-AATTT
3053177 TTTTAAATTTAATTT
1 TTTTAAATTTAATTT
3053192 TTTT
1 TTTT
3053196 TAAGTTTAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 12 0.39
16 12 0.39
17 7 0.23
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTTAAATTTAATTT
Found at i:3053171 original size:22 final size:23
Alignment explanation
Indices: 3053132--3053175 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
3053122 GGTTGATTCG
*
3053132 GATTTTTTTATAATTTTAAATTT
1 GATTTTTTTATAAATTTAAATTT
3053155 GATTTTTTTA-AAATTTAAATT
1 GATTTTTTTATAAATTTAAATT
3053176 ATTTTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (23 bp):
GATTTTTTTATAAATTTAAATTT
Found at i:3053196 original size:16 final size:16
Alignment explanation
Indices: 3053145--3053203 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
3053135 TTTTTTATAA
*
3053145 TTTTAAATTTGATTTT
1 TTTTAAATTTAATTTT
* * *
3053161 TTTAAAATTTAAATTA
1 TTTTAAATTTAATTTT
3053177 TTTTAAATTTAATTTT
1 TTTTAAATTTAATTTT
*
3053193 TTTTAAGTTTA
1 TTTTAAATTTA
3053204 GCACGAATTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
TTTTAAATTTAATTTT
Found at i:3053305 original size:16 final size:16
Alignment explanation
Indices: 3053284--3053315 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3053274 GTTCTTCAAA
3053284 TTTAAATTTAAATTTT
1 TTTAAATTTAAATTTT
*
3053300 TTTAAATTTTAATTTT
1 TTTAAATTTAAATTTT
3053316 CTTGATCAAA
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:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTAAATTTAAATTTT
Found at i:3053551 original size:2 final size:2
Alignment explanation
Indices: 3053544--3053578 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3053534 ATAAGTGTAC
3053544 AT 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 AT A
3053579 AAATAAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3056047 original size:14 final size:16
Alignment explanation
Indices: 3056015--3056062 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
3056005 ACAGGTTAAA
3056015 AAAATATTATAAATATT
1 AAAAT-TTATAAATATT
3056032 AAAATTTA-AAAT-TT
1 AAAATTTATAAATATT
3056046 AAAA-TTATTAAATATT
1 AAAATTTA-TAAATATT
3056062 A
1 A
3056063 TTTCTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.11
14 6 0.21
15 8 0.29
16 6 0.21
17 5 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAATTTATAAATATT
Found at i:3056286 original size:3 final size:3
Alignment explanation
Indices: 3056278--3056312 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3056268 TTTTACTGTC
*
3056278 ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3056313 CCTTGAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3057010 original size:26 final size:25
Alignment explanation
Indices: 3056964--3057040 Score: 59
Period size: 25 Copynumber: 3.1 Consensus size: 25
3056954 ATTAATTTAA
** *
3056964 TTTAATTTAATTAATAAAAATATAT
1 TTTAATTTAATTTTTATAAATATAT
*
3056989 TTTAATTTTAATTTTTATAAAT-TAAA
1 TTTAA-TTTAATTTTTATAAATAT-AT
* * *
3057015 TTAAATTTAAATTTGATAAA-ATAT
1 TTTAATTTAATTTTTATAAATATAT
3057039 TT
1 TT
3057041 AAAAAAAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
24 3 0.07
25 20 0.49
26 18 0.44
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (25 bp):
TTTAATTTAATTTTTATAAATATAT
Found at i:3057160 original size:2 final size:2
Alignment explanation
Indices: 3057153--3057185 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3057143 AAACTCCAAA
3057153 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
3057186 GGCATGCATG
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:3058929 original size:2 final size:2
Alignment explanation
Indices: 3058916--3058956 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
3058906 CATATAAAAC
* *
3058916 AT AT AT AC AT AT AT AT GT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3058957 TTTTGAGCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3059564 original size:24 final size:26
Alignment explanation
Indices: 3059515--3059563 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
3059505 ATTATAAATA
3059515 AAAAAAATATTAAATTATATTATTTT
1 AAAAAAATATTAAATTATATTATTTT
3059541 AAAAAAAT-TT-AATTAT-TTATTTT
1 AAAAAAATATTAAATTATATTATTTT
3059564 TGATTTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.30
24 6 0.26
25 2 0.09
26 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
AAAAAAATATTAAATTATATTATTTT
Found at i:3060420 original size:13 final size:14
Alignment explanation
Indices: 3060402--3060434 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
3060392 AGTATAAAAT
3060402 TTTTAATTTAAT-A
1 TTTTAATTTAATAA
3060415 TTTTAATTTAATAA
1 TTTTAATTTAATAA
3060429 TTTTAA
1 TTTTAA
3060435 ATTTCGAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTAATTTAATAA
Found at i:3061988 original size:2 final size:2
Alignment explanation
Indices: 3061983--3062007 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3061973 TTGTTCCCCC
3061983 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
3062008 ACACACACAC
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:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3064532 original size:2 final size:2
Alignment explanation
Indices: 3064525--3064551 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3064515 GTATGCCATT
3064525 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3064552 GACTATTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3066030 original size:43 final size:44
Alignment explanation
Indices: 3065968--3066076 Score: 109
Period size: 44 Copynumber: 2.5 Consensus size: 44
3065958 ATTAAGTTTA
* * *
3065968 ATTTTAATAATAATTATAA-ATTAAAATAATATATTT-TTATTTAA-
1 ATTTTATTAAAAATAATAATATTAAAATAA-A-ATTTATT-TTTAAT
* *
3066012 ATTTTATTATAAA-AATAAATATTAATATAAAATTTATTTTTAAT
1 ATTTTATTAAAAATAAT-AATATTAAAATAAAATTTATTTTTAAT
3066056 ATTTTATTAAAAATAATAATA
1 ATTTTATTAAAAATAATAATA
3066077 ATTTTTTAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
43 11 0.20
44 31 0.57
45 12 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (44 bp):
ATTTTATTAAAAATAATAATATTAAAATAAAATTTATTTTTAAT
Found at i:3066040 original size:18 final size:18
Alignment explanation
Indices: 3066009--3066043 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3065999 TATTTTTATT
* *
3066009 TAAATTTTATTATAAAAA
1 TAAATATTAATATAAAAA
3066027 TAAATATTAATATAAAA
1 TAAATATTAATATAAAA
3066044 TTTATTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATATTAATATAAAAA
Found at i:3066085 original size:20 final size:20
Alignment explanation
Indices: 3066052--3066089 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3066042 AATTTATTTT
3066052 TAATATTTTATTAAAAATAA
1 TAATATTTTATTAAAAATAA
3066072 TAATAATTTT-TTAAAAAT
1 TAAT-ATTTTATTAAAAAT
3066090 TGAAGCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATATTTTATTAAAAATAA
Found at i:3066415 original size:10 final size:10
Alignment explanation
Indices: 3066400--3066441 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
3066390 CATTTTAATT
3066400 TTTATATCAA
1 TTTATATCAA
3066410 TTTATATCAA
1 TTTATATCAA
*
3066420 -TTGTATCAA
1 TTTATATCAA
* *
3066429 TTCATATTAA
1 TTTATATCAA
3066439 TTT
1 TTT
3066442 GTACTGATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (10 bp):
TTTATATCAA
Found at i:3066428 original size:19 final size:19
Alignment explanation
Indices: 3066404--3066440 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3066394 TTAATTTTTA
*
3066404 TATCAATTTATATCAATTG
1 TATCAATTCATATCAATTG
*
3066423 TATCAATTCATATTAATT
1 TATCAATTCATATCAATT
3066441 TGTACTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.49
Consensus pattern (19 bp):
TATCAATTCATATCAATTG
Found at i:3066513 original size:20 final size:21
Alignment explanation
Indices: 3066490--3066541 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
3066480 TTTTTTTAAA
*
3066490 AAATTATTTATTTAATTTT-T
1 AAATTATTTATTAAATTTTAT
3066510 AAATTAATTT-TTAAATTTTAT
1 AAATT-ATTTATTAAATTTTAT
3066531 AAATGTATTTA
1 AAAT-TATTTA
3066542 AAAAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 13 0.48
21 13 0.48
22 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
AAATTATTTATTAAATTTTAT
Found at i:3066516 original size:12 final size:12
Alignment explanation
Indices: 3066501--3066526 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3066491 AATTATTTAT
3066501 TTAATTTTTAAA
1 TTAATTTTTAAA
3066513 TTAATTTTTAAA
1 TTAATTTTTAAA
3066525 TT
1 TT
3066527 TTATAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTAATTTTTAAA
Found at i:3066847 original size:41 final size:41
Alignment explanation
Indices: 3066802--3066883 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
3066792 TCTAACACTT
3066802 TCTTTTGTGTTTCTCTCTTATCAATCCAATTACCTATCCCA
1 TCTTTTGTGTTTCTCTCTTATCAATCCAATTACCTATCCCA
3066843 TCTTTTGTGTTTCTCTCTTATCAATCCAATTACCTATCCCA
1 TCTTTTGTGTTTCTCTCTTATCAATCCAATTACCTATCCCA
3066884 CTTCCTTCGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.20, C:0.29, G:0.05, T:0.46
Consensus pattern (41 bp):
TCTTTTGTGTTTCTCTCTTATCAATCCAATTACCTATCCCA
Found at i:3068855 original size:99 final size:98
Alignment explanation
Indices: 3068738--3068996 Score: 322
Period size: 99 Copynumber: 2.6 Consensus size: 98
3068728 CAATACTTAA
3068738 CCTGCTTATAGGGGCATCATCACTGCTACTTGGCCAGCTTATAGGAGCATCATCCCTACTACTTG
1 CCTGCTTATAGGGGCATCATC-CTGCTACTTGGCCAGCTTATAGGAGCATCATCCCTACTACTTG
* *
3068803 GGCTCCTTATAGGAGCATCATCCCTGCTACTTGG
65 GGCTCCTTATAGGAGCATCATCCCTACTACTTCG
* * * *
3068837 GCTGCTTATAGGGGCATCATTCCTGCTACTTGGCCTGCTTATAAGAGCATCATCCCTAGTACTTG
1 CCTGCTTATAGGGGCATCA-TCCTGCTACTTGGCCAGCTTATAGGAGCATCATCCCTACTACTTG
* * * *
3068902 GGCTGCTTATAGGGGCATCATCCCTACTGCTTCT
65 GGCTCCTTATAGGAGCATCATCCCTACTACTTCG
* * * * * * *
3068936 CCAGCTTAAAGGAGCATCATCCGTACTACTTGTCCAGCTAAGAGGAGCAGT-ATCCCTACTA
1 CCTGCTTATAGGGGCATCATCC-TGCTACTTGGCCAGCTTATAGGAGCA-TCATCCCTACTA
3068997 ATTATCCTGC
Statistics
Matches: 136, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
98 3 0.02
99 130 0.96
100 3 0.02
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (98 bp):
CCTGCTTATAGGGGCATCATCCTGCTACTTGGCCAGCTTATAGGAGCATCATCCCTACTACTTGG
GCTCCTTATAGGAGCATCATCCCTACTACTTCG
Found at i:3068972 original size:33 final size:33
Alignment explanation
Indices: 3068738--3068996 Score: 277
Period size: 33 Copynumber: 7.8 Consensus size: 33
3068728 CAATACTTAA
* * *
3068738 CCTGCTTATAGGGGCATCATCACTGCTACTTGG
1 CCTGCTTATAGGAGCATCATCCCTACTACTTGG
*
3068771 CCAGCTTATAGGAGCATCATCCCTACTACTTGG
1 CCTGCTTATAGGAGCATCATCCCTACTACTTGG
* * *
3068804 GCTCCTTATAGGAGCATCATCCCTGCTACTTGG
1 CCTGCTTATAGGAGCATCATCCCTACTACTTGG
* * * *
3068837 GCTGCTTATAGGGGCATCATTCCTGCTACTTGG
1 CCTGCTTATAGGAGCATCATCCCTACTACTTGG
* *
3068870 CCTGCTTATAAGAGCATCATCCCTAGTACTTGG
1 CCTGCTTATAGGAGCATCATCCCTACTACTTGG
* * * **
3068903 GCTGCTTATAGGGGCATCATCCCTACTGCTTCT
1 CCTGCTTATAGGAGCATCATCCCTACTACTTGG
* * * *
3068936 CCAGCTTAAAGGAGCATCATCCGTACTACTTGT
1 CCTGCTTATAGGAGCATCATCCCTACTACTTGG
* * *
3068969 CCAGCTAAGAGGAGCAGT-ATCCCTACTA
1 CCTGCTTATAGGAGCA-TCATCCCTACTA
3068997 ATTATCCTGC
Statistics
Matches: 191, Mismatches: 34, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
33 190 0.99
34 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (33 bp):
CCTGCTTATAGGAGCATCATCCCTACTACTTGG
Found at i:3075135 original size:14 final size:14
Alignment explanation
Indices: 3075112--3075144 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3075102 TTTTTTCAAA
*
3075112 AAAT-AAAATAATT
1 AAATAAAAATAAAT
3075125 AAATAAAAATAAAT
1 AAATAAAAATAAAT
3075139 AAATAA
1 AAATAA
3075145 TATTTTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:3075187 original size:184 final size:184
Alignment explanation
Indices: 3074890--3075236 Score: 586
Period size: 184 Copynumber: 1.9 Consensus size: 184
3074880 AAATACTAAA
*
3074890 AATTTAAAAAAGAAAATTGAGCAATAAATTTAAAAAAAAAACAAAATTATTAAATAAAAATAAAT
1 AATTTAAAAAAGAAAATTGAGCAATAAATTTAAAAAAAAAACAAAATAATTAAATAAAAATAAAT
* *
3074955 AAATAATATTTTATGTTATTTTTTGATATTAAAATTTAATTTATCTTTTTAATTATATTTATTAA
66 AAATAATATTTTATGTTATTATTTGATATTAAAATTTAATTGATCTTTTTAATTATATTTATTAA
3075020 ATTTGTGTCAAATGGTTTATGACATAAATTTTGAGTAATTTAAAAAATATTAGC
131 ATTTGTGTCAAATGGTTTATGACATAAATTTTGAGTAATTTAAAAAATATTAGC
* **** *
3075074 AATTTAAAGAAGAAAATTGAGCAATAAATTTTTTCAAAAAATAAAATAATTAAATAAAAATAAAT
1 AATTTAAAAAAGAAAATTGAGCAATAAATTTAAAAAAAAAACAAAATAATTAAATAAAAATAAAT
* * *
3075139 AAATAATATTTTATGTTATTATTTGATATTAAATTTTAATTGATCTTTTTTATTATTTTTATTAA
66 AAATAATATTTTATGTTATTATTTGATATTAAAATTTAATTGATCTTTTTAATTATATTTATTAA
3075204 ATTTGTGTCAAATGGTTTATGACATAAATTTTG
131 ATTTGTGTCAAATGGTTTATGACATAAATTTTG
3075237 GCACATCTTC
Statistics
Matches: 151, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
184 151 1.00
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (184 bp):
AATTTAAAAAAGAAAATTGAGCAATAAATTTAAAAAAAAAACAAAATAATTAAATAAAAATAAAT
AAATAATATTTTATGTTATTATTTGATATTAAAATTTAATTGATCTTTTTAATTATATTTATTAA
ATTTGTGTCAAATGGTTTATGACATAAATTTTGAGTAATTTAAAAAATATTAGC
Found at i:3075590 original size:20 final size:21
Alignment explanation
Indices: 3075548--3075593 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
3075538 TATGAAAACA
3075548 TTATTAATAATATAAATAGTT
1 TTATTAATAATATAAATAGTT
* *
3075569 TTATTAAT-ATATATATATTT
1 TTATTAATAATATAAATAGTT
3075589 TTATT
1 TTATT
3075594 TATTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTATTAATAATATAAATAGTT
Found at i:3076984 original size:27 final size:28
Alignment explanation
Indices: 3076929--3076984 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
3076919 AATAAATAAA
* *
3076929 ATTATTAAATTATTATATTAGATATAAT
1 ATTATTAAATAATTATATTAGATACAAT
* *
3076957 ATTA-TAAATAATTATTTTATATACAAT
1 ATTATTAAATAATTATATTAGATACAAT
3076984 A
1 A
3076985 ATAAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (28 bp):
ATTATTAAATAATTATATTAGATACAAT
Found at i:3077014 original size:14 final size:14
Alignment explanation
Indices: 3076983--3077018 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3076973 TTATATACAA
3076983 TAATAAAA-AAAAT
1 TAATAAAATAAAAT
3076996 T--TAAAATAAAAT
1 TAATAAAATAAAAT
3077008 TAATAAAATAA
1 TAATAAAATAA
3077019 CTTGTATCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
11 5 0.25
12 6 0.30
13 1 0.05
14 8 0.40
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
TAATAAAATAAAAT
Found at i:3079837 original size:17 final size:17
Alignment explanation
Indices: 3079815--3079848 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3079805 AAATGAGTAA
*
3079815 TTAATATAATTATATAT
1 TTAATATAAGTATATAT
*
3079832 TTAATATGAGTATATAT
1 TTAATATAAGTATATAT
3079849 AAATTTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
TTAATATAAGTATATAT
Found at i:3081595 original size:39 final size:37
Alignment explanation
Indices: 3081511--3081597 Score: 95
Period size: 39 Copynumber: 2.3 Consensus size: 37
3081501 TTGTTATTAT
*
3081511 ATAATAAAATAAAATTTTTATTTAAATTTAATTATAA
1 ATAATAATATAAAATTTTTATTTAAATTTAATTATAA
* * * *
3081548 ATATTAATATATAATTTTTTATTTTTAATATT-ATTTTAA
1 ATAATAATATA-AAATTTTTA-TTTAAAT-TTAATTATAA
3081587 ATAATAATATA
1 ATAATAATATA
3081598 GACTTTGACA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
37 9 0.22
38 8 0.20
39 22 0.54
40 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
ATAATAATATAAAATTTTTATTTAAATTTAATTATAA
Found at i:3081794 original size:2 final size:2
Alignment explanation
Indices: 3081787--3081812 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3081777 CAAGCTTGGC
3081787 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
3081813 GCAGTTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3085580 original size:6 final size:6
Alignment explanation
Indices: 3085562--3085667 Score: 50
Period size: 6 Copynumber: 18.7 Consensus size: 6
3085552 GATATAAATA
* * **
3085562 ATATTC ATA-TT ATATTT ATATTT -TAATT ATATTT ATATAA AT-TTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
* * *
3085607 AATATATT AATATAT ATATTT ATA-TA ATA-TT ATATTT -TAATT -T-TTT
1 -ATAT-TT -ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
*
3085653 ATA-TT CTATTT ATAT
1 ATATTT ATATTT ATAT
3085668 GATGTTATTA
Statistics
Matches: 76, Mismatches: 15, Indels: 18
0.70 0.14 0.17
Matches are distributed among these distances:
4 2 0.03
5 27 0.36
6 38 0.50
7 2 0.03
8 7 0.09
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (6 bp):
ATATTT
Found at i:3085614 original size:20 final size:21
Alignment explanation
Indices: 3085581--3085638 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
3085571 TTATATTTAT
*
3085581 ATTTTAATTATATTTATATAA
1 ATTTTAATTATATTAATATAA
*
3085602 ATTTTAA-TATATTAATATAT
1 ATTTTAATTATATTAATATAA
*
3085622 ATATTTATATAATATTA
1 AT-TTTA-ATTATATTA
3085639 TATTTTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 13 0.42
21 11 0.35
22 1 0.03
23 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTTAATTATATTAATATAA
Found at i:3088194 original size:54 final size:55
Alignment explanation
Indices: 3088109--3088216 Score: 137
Period size: 54 Copynumber: 2.0 Consensus size: 55
3088099 TAGCTTCACG
** * * * *
3088109 TTGCTTAAAGACATTTTTGGAAGTGATTTGCCTAGCTAAGAAAGATTCAATGTTC
1 TTGCTTAAAGACATCATCGGAAGTGACTTGCCGAGCTAAGAAAGAATCAATGTTC
* *
3088164 TTGCTTAAAGACA-CATCGGAAGTGACTTGCCGAGGTATGAAAGAATCAATGTT
1 TTGCTTAAAGACATCATCGGAAGTGACTTGCCGAGCTAAGAAAGAATCAATGTT
3088217 TTTGTTTCTT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
54 32 0.71
55 13 0.29
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.31
Consensus pattern (55 bp):
TTGCTTAAAGACATCATCGGAAGTGACTTGCCGAGCTAAGAAAGAATCAATGTTC
Found at i:3090884 original size:19 final size:18
Alignment explanation
Indices: 3090860--3090897 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
3090850 ATTATATTTT
*
3090860 AAATATTATATATTTAATA
1 AAATATAATATA-TTAATA
3090879 AAATATAATATATTAATA
1 AAATATAATATATTAATA
3090897 A
1 A
3090898 TTTATGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATAATATATTAATA
Found at i:3091573 original size:15 final size:16
Alignment explanation
Indices: 3091553--3091582 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3091543 AATTTATTTG
3091553 ATTTAA-TAAATTTAT
1 ATTTAATTAAATTTAT
3091568 ATTTAATTAAATTTA
1 ATTTAATTAAATTTA
3091583 AATATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTAATTAAATTTAT
Found at i:3091674 original size:22 final size:21
Alignment explanation
Indices: 3091642--3091694 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
3091632 CTTATTTAAA
* *
3091642 AAAATAT-TTAAATTTAATTAT
1 AAAATATATT-AATATAAATAT
3091663 AAAATATATTAATATAAATAT
1 AAAATATATTAATATAAATAT
3091684 AAAATAATATT
1 AAAAT-ATATT
3091695 TTAATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATATATTAATATAAATAT
Found at i:3092214 original size:5 final size:5
Alignment explanation
Indices: 3092204--3092248 Score: 60
Period size: 5 Copynumber: 9.4 Consensus size: 5
3092194 ACCTTAATTT
3092204 TTATA TTATA TTATA TTATA -TATAA TTATA TT-T- TTATA TTATA TT
1 TTATA TTATA TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA TT
3092249 CAAAATTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 2 0.06
4 5 0.14
5 26 0.72
6 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:3097303 original size:22 final size:23
Alignment explanation
Indices: 3097266--3097308 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3097256 TTTATATATA
*
3097266 AATAATTTATTATTATATTTAAT
1 AATAATATATTATTATATTTAAT
3097289 AATAATAT-TTATTATATTTA
1 AATAATATATTATTATATTTA
3097309 TACATTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AATAATATATTATTATATTTAAT
Found at i:3097467 original size:17 final size:18
Alignment explanation
Indices: 3097445--3097479 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3097435 AAAATCATTC
3097445 AAAAATAACTTA-TTTTT
1 AAAAATAACTTACTTTTT
*
3097462 AAAAATAATTTACTTTTT
1 AAAAATAACTTACTTTTT
3097480 TTTACAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAAATAACTTACTTTTT
Found at i:3097476 original size:21 final size:21
Alignment explanation
Indices: 3097452--3097492 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3097442 TTCAAAAATA
3097452 ACTTATTTTTA-AAAATAATTT
1 ACTTATTTTTACAAAA-AATTT
*
3097473 ACTTTTTTTTACAAAAAATT
1 ACTTATTTTTACAAAAAATT
3097493 AAAACCATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (21 bp):
ACTTATTTTTACAAAAAATTT
Found at i:3098758 original size:11 final size:11
Alignment explanation
Indices: 3098729--3098817 Score: 51
Period size: 11 Copynumber: 8.1 Consensus size: 11
3098719 TGTGTAATAA
* *
3098729 TTATATTTAAT
1 TTATATATATT
3098740 TTATTATATATT
1 TTA-TATATATT
*
3098752 TTATATAAATT
1 TTATATATATT
**
3098763 TTA-ATACGTT
1 TTATATATATT
* *
3098773 ATTA-ATTTATG
1 -TTATATATATT
3098784 TTATATA-ATT
1 TTATATATATT
3098794 TTA-ATATATAT
1 TTATATATAT-T
3098805 TTATATTATATT
1 TTATA-TATATT
3098817 T
1 T
3098818 ATTTTATTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
9 3 0.05
10 15 0.25
11 25 0.42
12 12 0.20
13 5 0.08
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (11 bp):
TTATATATATT
Found at i:3098814 original size:13 final size:14
Alignment explanation
Indices: 3098771--3098815 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
3098761 TTTTAATACG
*
3098771 TTAT-TAATTTATG
1 TTATATAATTTATA
3098784 TTATATAATTT-TA
1 TTATATAATTTATA
*
3098797 ATATAT-ATTTATA
1 TTATATAATTTATA
3098810 TTATAT
1 TTATAT
3098816 TTATTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 4 0.15
13 17 0.63
14 6 0.22
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTATATAATTTATA
Found at i:3098818 original size:11 final size:11
Alignment explanation
Indices: 3098800--3098838 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3098790 AATTTTAATA
3098800 TATATTTATAT
1 TATATTTATAT
*
3098811 TATATTTATTT
1 TATATTTATAT
* *
3098822 TATTTTTTTAT
1 TATATTTATAT
3098833 TATATT
1 TATATT
3098839 ATAACTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATATTTATAT
Found at i:3099100 original size:2 final size:2
Alignment explanation
Indices: 3099059--3099085 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3099049 GAAACAAATA
3099059 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 A
3099086 AATTGGCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3100009 original size:19 final size:19
Alignment explanation
Indices: 3099985--3100021 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3099975 AGGTGGAGAT
3099985 TTATGGTGGATGGCTATCC
1 TTATGGTGGATGGCTATCC
*
3100004 TTATGGTGGGTGGCTATC
1 TTATGGTGGATGGCTATC
3100022 TTTAGTCAAC
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:0.14, C:0.14, G:0.35, T:0.38
Consensus pattern (19 bp):
TTATGGTGGATGGCTATCC
Found at i:3100457 original size:10 final size:10
Alignment explanation
Indices: 3100414--3100512 Score: 53
Period size: 11 Copynumber: 9.3 Consensus size: 10
3100404 ATTTTTAAGT
3100414 AAATAAATTTA
1 AAATAAA-TTA
3100425 AAATTACAATTA
1 AAA-TA-AATTA
*
3100437 AAAT-TATTA
1 AAATAAATTA
*
3100446 TAATAAATT-
1 AAATAAATTA
*
3100455 ATATAAAATATA
1 AAAT-AAAT-TA
3100467 AAATAAATTA
1 AAATAAATTA
3100477 AAATATAA-TA
1 AAATA-AATTA
3100487 CAAATATAATATGA
1 -AAATA-AAT-T-A
3100501 AAA-AAATTA
1 AAATAAATTA
3100510 AAA
1 AAA
3100513 AATTGACATC
Statistics
Matches: 71, Mismatches: 6, Indels: 24
0.70 0.06 0.24
Matches are distributed among these distances:
9 13 0.18
10 17 0.24
11 22 0.31
12 12 0.17
13 6 0.08
14 1 0.01
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (10 bp):
AAATAAATTA
Found at i:3103620 original size:16 final size:15
Alignment explanation
Indices: 3103601--3103634 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3103591 TTAATTTAGA
3103601 TTTGACTTATTTTAAG
1 TTTGACTT-TTTTAAG
*
3103617 TTTGAGTTTTTTAAG
1 TTTGACTTTTTTAAG
3103632 TTT
1 TTT
3103635 AACAGTTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.21, C:0.03, G:0.15, T:0.62
Consensus pattern (15 bp):
TTTGACTTTTTTAAG
Found at i:3104731 original size:16 final size:16
Alignment explanation
Indices: 3104707--3104737 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3104697 ACTAATAATT
3104707 ATTAAAATAAAATAAA
1 ATTAAAATAAAATAAA
*
3104723 ATTATAATAAAATAA
1 ATTAAAATAAAATAA
3104738 TTATTTTATA
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATTAAAATAAAATAAA
Found at i:3110218 original size:21 final size:21
Alignment explanation
Indices: 3110189--3110238 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3110179 ATCAAATTAT
3110189 TATTT-AATTAA-TAAAAAAA
1 TATTTAAATTAATTAAAAAAA
*
3110208 CTATTTAAATTAATTATAAAAA
1 -TATTTAAATTAATTAAAAAAA
*
3110230 TATTAAAAT
1 TATTTAAAT
3110239 AAAAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.19
21 14 0.54
22 7 0.27
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TATTTAAATTAATTAAAAAAA
Found at i:3110271 original size:17 final size:16
Alignment explanation
Indices: 3110245--3110278 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3110235 AAATAAAAAT
*
3110245 ATTTTTTAATATTTTA
1 ATTTTTTAATAATTTA
3110261 ATTTTTATAATAATTTA
1 ATTTTT-TAATAATTTA
3110278 A
1 A
3110279 AATTATAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTTTAATAATTTA
Found at i:3111168 original size:8 final size:9
Alignment explanation
Indices: 3111128--3111169 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
3111118 CATATTTAAA
3111128 TATATTATAT
1 TATATT-TAT
*
3111138 CATATTTAT
1 TATATTTAT
*
3111147 TAAATTTAT
1 TATATTTAT
3111156 TATATTT-T
1 TATATTTAT
3111164 TATATT
1 TATATT
3111170 GTAGACAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 7 0.25
9 16 0.57
10 5 0.18
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (9 bp):
TATATTTAT
Found at i:3111815 original size:10 final size:10
Alignment explanation
Indices: 3111800--3111838 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
3111790 TGAATCTATA
3111800 AAAAATTGAT
1 AAAAATTGAT
*
3111810 AAAAATCGAT
1 AAAAATTGAT
3111820 AAAAATTGATT
1 AAAAATTGA-T
3111831 AAAAATTG
1 AAAAATTG
3111839 GGTTTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.28
Consensus pattern (10 bp):
AAAAATTGAT
Found at i:3112863 original size:44 final size:44
Alignment explanation
Indices: 3112764--3112893 Score: 107
Period size: 44 Copynumber: 2.9 Consensus size: 44
3112754 ATTAACATGT
** ** * * * *
3112764 TTAAAATTGATCTTTTAAATTTAATACGATATGATTACGACACAG
1 TTAAAATTGATCCGTTAACGTTAATACGACACGA-CACGACACAA
* *
3112809 TTAAAATTGATCTGTTAACGTTTATACGACACGACACGACACAA
1 TTAAAATTGATCCGTTAACGTTAATACGACACGACACGACACAA
** * * * *
3112853 TTAAGCTTGATCCGTTTATGTTAATATGATACGACACGACA
1 TTAAAATTGATCCGTTAACGTTAATACGACACGACACGACA
3112894 TTATTATAAT
Statistics
Matches: 69, Mismatches: 16, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
44 41 0.59
45 28 0.41
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (44 bp):
TTAAAATTGATCCGTTAACGTTAATACGACACGACACGACACAA
Found at i:3119919 original size:17 final size:18
Alignment explanation
Indices: 3119897--3119946 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
3119887 CGATACATGA
*
3119897 ATTTTCATTCAATTT-TT
1 ATTTTCATTCAATTTGAT
*
3119914 ATTTTC-TACAATTTGAT
1 ATTTTCATTCAATTTGAT
*
3119931 ACTTTCCATTCAATTT
1 A-TTTTCATTCAATTT
3119947 ATTTATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.27
17 8 0.31
18 4 0.15
19 7 0.27
ACGTcount: A:0.26, C:0.16, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTTTCATTCAATTTGAT
Found at i:3123342 original size:20 final size:21
Alignment explanation
Indices: 3123317--3123363 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
3123307 GTTCGTATTC
**
3123317 TTATATTTTTTATA-TTATAA
1 TTATATTTAATATATTTATAA
*
3123337 TTATATTTAATATATTTATAT
1 TTATATTTAATATATTTATAA
3123358 TTATAT
1 TTATAT
3123364 AAATTTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATATTTAATATATTTATAA
Found at i:3123355 original size:15 final size:15
Alignment explanation
Indices: 3123332--3123391 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 15
3123322 TTTTTTATAT
*
3123332 TATAATTATATTTAA
1 TATATTTATATTTAA
3123347 TATATTTATATTTATA
1 TATATTTATATTTA-A
*
3123363 TAAATTTTGATATATTAA
1 TATA-TTT-ATAT-TTAA
3123381 TA-ATTTATATT
1 TATATTTATATT
3123392 ATATAAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 1 0.03
15 17 0.44
16 7 0.18
17 4 0.10
18 7 0.18
19 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
TATATTTATATTTAA
Found at i:3123394 original size:32 final size:35
Alignment explanation
Indices: 3123338--3123404 Score: 113
Period size: 32 Copynumber: 2.0 Consensus size: 35
3123328 ATATTATAAT
3123338 TATATTTAATATATTTATATTTATATAAATTTTGA
1 TATATTTAATATATTTATATTTATATAAATTTTGA
3123373 TATA-TTAATA-ATTTATA-TTATATAAATTTTGA
1 TATATTTAATATATTTATATTTATATAAATTTTGA
3123405 AACATTCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 15 0.47
33 7 0.22
34 6 0.19
35 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (35 bp):
TATATTTAATATATTTATATTTATATAAATTTTGA
Found at i:3124237 original size:15 final size:16
Alignment explanation
Indices: 3124217--3124247 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3124207 TAGTTATTTC
3124217 GTTTT-AATTATTAAA
1 GTTTTAAATTATTAAA
3124232 GTTTTAAATTATTAAA
1 GTTTTAAATTATTAAA
3124248 AAAAGTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
GTTTTAAATTATTAAA
Found at i:3125301 original size:20 final size:20
Alignment explanation
Indices: 3125254--3125306 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
3125244 ATAAAAGTAG
* *
3125254 AAAAAAAAACTATTTACTTT
1 AAAAAAAAACTATTCACATT
***
3125274 ACTTAAAAACTATTCACATT
1 AAAAAAAAACTATTCACATT
3125294 -AAAAAAAACTATT
1 AAAAAAAAACTATT
3125307 TTTTTAATCT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAAAAAACTATTCACATT
Found at i:3126285 original size:14 final size:15
Alignment explanation
Indices: 3126260--3126288 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3126250 TAATTATAAA
3126260 AATATCTAAAATATT
1 AATATCTAAAATATT
3126275 AATAT-TAAAATATT
1 AATATCTAAAATATT
3126289 TTTAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AATATCTAAAATATT
Found at i:3126295 original size:17 final size:18
Alignment explanation
Indices: 3126273--3126326 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
3126263 ATCTAAAATA
3126273 TTAATATTAAAATATT-T
1 TTAATATTAAAATATTAT
**
3126290 TTAATATTTTAATATTAT
1 TTAATATTAAAATATTAT
*
3126308 TTAAATAATAAAAT-TTAT
1 TT-AATATTAAAATATTAT
3126326 T
1 T
3126327 GTTAAGCTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 14 0.47
18 8 0.27
19 8 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAATATTAAAATATTAT
Found at i:3127811 original size:14 final size:15
Alignment explanation
Indices: 3127787--3127830 Score: 63
Period size: 14 Copynumber: 2.9 Consensus size: 15
3127777 TTATTATAAA
3127787 AAAATTATAAATATT
1 AAAATTATAAATATT
*
3127802 AAAATT-TAAATTTT
1 AAAATTATAAATATT
3127816 AAAATTATTAAATAT
1 AAAATTA-TAAATAT
3127831 CACTTATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 13 0.52
15 6 0.24
16 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:3128651 original size:38 final size:38
Alignment explanation
Indices: 3128580--3128652 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
3128570 AAAATATCAT
*
3128580 ATTATTAAAAATAAAATTATTTTTATTTATTTTTAAAA
1 ATTATTAAAAATAAAATTATTTTAATTTATTTTTAAAA
*
3128618 ATTATTAATAAGATAACATTA-TTTAATTT-TTTTTA
1 ATTATTAA-AA-ATAAAATTATTTTAATTTATTTTTA
3128653 CGATATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 14 0.45
39 9 0.29
40 8 0.26
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (38 bp):
ATTATTAAAAATAAAATTATTTTAATTTATTTTTAAAA
Found at i:3132914 original size:27 final size:27
Alignment explanation
Indices: 3132862--3132914 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
3132852 TGCAACCTCC
* **
3132862 ACTGTTTCAAATTGAATTTCGTAATTT
1 ACTGTTTCAAATTGAATGTCAAAATTT
3132889 ACTGTTTCAAATTGAATGTCAAAATT
1 ACTGTTTCAAATTGAATGTCAAAATT
3132915 GGCAGCACAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (27 bp):
ACTGTTTCAAATTGAATGTCAAAATTT
Found at i:3139864 original size:14 final size:13
Alignment explanation
Indices: 3139820--3139867 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
3139810 TTTATTTTTT
3139820 AAATT-ATTAATC
1 AAATTAATTAATC
*
3139832 AAATTAAATTAAAC
1 AAATT-AATTAATC
3139846 TAAATTAATTAAGTC
1 -AAATTAATTAA-TC
3139861 AAATTAA
1 AAATTAA
3139868 AATTATCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 5 0.17
14 19 0.63
15 6 0.20
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.35
Consensus pattern (13 bp):
AAATTAATTAATC
Found at i:3140330 original size:15 final size:15
Alignment explanation
Indices: 3140310--3140345 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3140300 AATGTTAAAT
3140310 TTTTAAAATTATTAA
1 TTTTAAAATTATTAA
* *
3140325 TTTTAAATTTTTTAA
1 TTTTAAAATTATTAA
3140340 TTTTAA
1 TTTTAA
3140346 TAACATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTAAAATTATTAA
Found at i:3142162 original size:27 final size:29
Alignment explanation
Indices: 3142125--3142181 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
3142115 AACATATAAA
* *
3142125 TATTATTAATAAACTTAAAATTTTTTATAT
1 TATTAATAATAAA-ATAAAATTTTTTATAT
3142155 T-TTAAATAATAAAATAAAATTTTTTAT
1 TATT-AATAATAAAATAAAATTTTTTAT
3142182 TAATTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
TATTAATAATAAAATAAAATTTTTTATAT
Found at i:3142188 original size:29 final size:31
Alignment explanation
Indices: 3142129--3142212 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 31
3142119 TATAAATATT
* *
3142129 ATTAATAAACTTAAAATTTTTTA-TATTTTAA
1 ATTAATAAA-ATAAAATTTTTTATTATATTAA
3142160 A-TAATAAAATAAAATTTTTTATTA-ATTAA
1 ATTAATAAAATAAAATTTTTTATTATATTAA
3142189 ATTTAA-ATAAAT-AAATTTTTTATT
1 A-TTAATA-AAATAAAATTTTTTATT
3142213 TAAATTTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
29 17 0.36
30 22 0.47
31 8 0.17
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (31 bp):
ATTAATAAAATAAAATTTTTTATTATATTAA
Found at i:3142218 original size:27 final size:30
Alignment explanation
Indices: 3142140--3142221 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 30
3142130 TTAATAAACT
*
3142140 TAAAATTTTTTATATTTTAAA--T-AATAAAA
1 TAAAATTTTTTAT-TATTAAATTTAAAT-AAA
3142169 TAAAATTTTTTATTAATTAAATTTAAATAAA
1 TAAAATTTTTTATT-ATTAAATTTAAATAAA
3142200 T-AAATTTTTTA-T-TTAAATTTAA
1 TAAAATTTTTTATTATTAAATTTAA
3142222 TCCTATCTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
27 10 0.21
28 1 0.02
29 19 0.40
30 10 0.21
31 5 0.10
32 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TAAAATTTTTTATTATTAAATTTAAATAAA
Found at i:3143129 original size:23 final size:23
Alignment explanation
Indices: 3143083--3143138 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
3143073 AATAAATTAA
* *
3143083 AAATTAAAAATTTATTTGAATAT
1 AAATTAAGAATTTATTTCAATAT
3143106 AAATTAAGAATTTA-TTCAAGTAT
1 AAATTAAGAATTTATTTCAA-TAT
3143129 AAATTGAAGA
1 AAATT-AAGA
3143139 TTAAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 4 0.14
23 21 0.72
24 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.38
Consensus pattern (23 bp):
AAATTAAGAATTTATTTCAATAT
Found at i:3146572 original size:2 final size:2
Alignment explanation
Indices: 3146561--3146589 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3146551 ACACATACAC
3146561 AT AT -T 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
3146590 TGTAGGGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3151006 original size:21 final size:21
Alignment explanation
Indices: 3150973--3151015 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3150963 ATTATAAAAA
* *
3150973 TATATAAAATTAATTTAATTT
1 TATATAAAATTAAATGAATTT
* *
3150994 TATATTAATTTAAATGAATTT
1 TATATAAAATTAAATGAATTT
3151015 T
1 T
3151016 TTTTGTATAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TATATAAAATTAAATGAATTT
Found at i:3153524 original size:6 final size:6
Alignment explanation
Indices: 3153515--3153540 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3153505 AATAAAAAAA
3153515 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
3153541 AATAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:3153630 original size:15 final size:16
Alignment explanation
Indices: 3153606--3153639 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3153596 ACCTTAAAAA
*
3153606 ATTTTTAAAAAT-ATT
1 ATTTTAAAAAATAATT
3153621 ATTTTAAAAAATAATT
1 ATTTTAAAAAATAATT
3153637 ATT
1 ATT
3153640 AATCATCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAAAAAATAATT
Found at i:3162020 original size:21 final size:20
Alignment explanation
Indices: 3161991--3162032 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3161981 ATAAAAAATT
3161991 TATTAATATATATTTATATTA
1 TATTAATATATATTTAT-TTA
* *
3162012 TATTGATATATTTTTATTTA
1 TATTAATATATATTTATTTA
3162032 T
1 T
3162033 GATAATTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTAATATATATTTATTTA
Found at i:3162277 original size:26 final size:28
Alignment explanation
Indices: 3162225--3162278 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
3162215 GATATTATAA
*
3162225 AAATAATATAAAATATTAATTTTATTATT
1 AAATAATATAAAATATT-ATTTAATTATT
*
3162254 AAATAAT-TAATATATT-TTTAATTAT
1 AAATAATATAAAATATTATTTAATTAT
3162279 ATTAAATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 8 0.35
28 8 0.35
29 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
AAATAATATAAAATATTATTTAATTATT
Found at i:3163473 original size:20 final size:20
Alignment explanation
Indices: 3163437--3163475 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3163427 ATATAATTAT
*
3163437 TTTGTTAAATCTACAATCGA
1 TTTGTTAAATATACAATCGA
3163457 TTTGTT-AATATATCAATCG
1 TTTGTTAAATATA-CAATCG
3163476 TATGTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (20 bp):
TTTGTTAAATATACAATCGA
Found at i:3165011 original size:16 final size:16
Alignment explanation
Indices: 3164990--3165020 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3164980 TATACACAAC
*
3164990 AAAATTATAATATAAA
1 AAAATTAAAATATAAA
3165006 AAAATTAAAATATAA
1 AAAATTAAAATATAA
3165021 TATAAATATA
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTAAAATATAAA
Found at i:3165124 original size:18 final size:18
Alignment explanation
Indices: 3165088--3165127 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3165078 TTATATAAAT
3165088 ATAAAATATTTAAAATATA
1 ATAAAATATTT-AAATATA
3165107 ATAAAATATATT-AATATA
1 ATAAAATAT-TTAAATATA
3165125 ATA
1 ATA
3165128 TAAACACACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 9 0.45
20 2 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAAATATTTAAATATA
Found at i:3166771 original size:16 final size:16
Alignment explanation
Indices: 3166750--3166780 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3166740 AATGTAACAC
3166750 AATAAAATTATTTATG
1 AATAAAATTATTTATG
3166766 AATAAAATTATTTAT
1 AATAAAATTATTTAT
3166781 TTAAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AATAAAATTATTTATG
Found at i:3166809 original size:18 final size:20
Alignment explanation
Indices: 3166757--3166810 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 20
3166747 CACAATAAAA
3166757 TTATTT-ATGAATAAAATTAT
1 TTATTTAATG-ATAAAATTAT
*
3166777 TTATTTAAAT-TTAAAA-T-T
1 TTATTT-AATGATAAAATTAT
3166795 TTATTTAATGATAAAA
1 TTATTTAATGATAAAA
3166811 AATTAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 3 0.10
18 12 0.41
19 1 0.03
20 11 0.38
22 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (20 bp):
TTATTTAATGATAAAATTAT
Found at i:3167253 original size:19 final size:21
Alignment explanation
Indices: 3167215--3167254 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
3167205 ATGAATATTT
3167215 TTATTTATTAATGATAAAATA
1 TTATTTATTAATGATAAAATA
*
3167236 TTATTT-TT-ATGCTAAAATA
1 TTATTTATTAATGATAAAATA
3167255 CAAGTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 2 0.11
21 6 0.33
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (21 bp):
TTATTTATTAATGATAAAATA
Found at i:3167749 original size:16 final size:16
Alignment explanation
Indices: 3167713--3167754 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
3167703 TTAAATTAAA
3167713 TATATTTTA-ATTATT
1 TATATTTTATATTATT
3167728 TAATATTTTATATGTA-T
1 T-ATATTTTATAT-TATT
3167745 TATATTTTAT
1 TATATTTTAT
3167755 TTAAAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 4 0.17
18 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TATATTTTATATTATT
Found at i:3168632 original size:28 final size:26
Alignment explanation
Indices: 3168589--3168640 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 26
3168579 TATATTAATT
3168589 TTAAAAGATTGAGAAAATTTGAAAATAA
1 TTAAAAGATTGAG-AAATTT-AAAATAA
3168617 TTAAAAGATT-ACGAAATTTAAAAT
1 TTAAAAGATTGA-GAAATTTAAAAT
3168641 TTAAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 5 0.22
27 7 0.30
28 11 0.48
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.31
Consensus pattern (26 bp):
TTAAAAGATTGAGAAATTTAAAATAA
Found at i:3169594 original size:15 final size:16
Alignment explanation
Indices: 3169574--3169603 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3169564 TATTAAATTT
3169574 ATTTTTTAA-ATTAAA
1 ATTTTTTAATATTAAA
3169589 ATTTTTTAATATTAA
1 ATTTTTTAATATTAA
3169604 TGAGTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTTTAATATTAAA
Found at i:3171623 original size:28 final size:28
Alignment explanation
Indices: 3171582--3171656 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
3171572 TTTATTAAAA
*
3171582 AAATAAAATTTAAT-ATCAAAATTCAATC
1 AAATAAAATATAATAAT-AAAATTCAATC
* *
3171610 AAATAAAGTATAATAATAAAATTCAATATTA
1 AAATAAAATATAATAATAAAATTC-A-A-TC
3171641 AAATAAAATATAATAA
1 AAATAAAATATAATAA
3171657 CAAATTTGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
28 19 0.49
29 3 0.08
30 1 0.03
31 16 0.41
ACGTcount: A:0.63, C:0.05, G:0.01, T:0.31
Consensus pattern (28 bp):
AAATAAAATATAATAATAAAATTCAATC
Found at i:3171777 original size:3 final size:3
Alignment explanation
Indices: 3171769--3171806 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3171759 ACCTCAACAA
3171769 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3171807 ATCGATAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3172575 original size:6 final size:6
Alignment explanation
Indices: 3172564--3172594 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3172554 TTATTATTTG
3172564 ATCCAA ATCCAA ATCCAA ATCCAA ATCCAA A
1 ATCCAA ATCCAA ATCCAA ATCCAA ATCCAA A
3172595 GAAGAGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (6 bp):
ATCCAA
Done.