Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 24 of 25
Found at i:3820038 original size:17 final size:17
Alignment explanation
Indices: 3820018--3820071 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
3820008 TATTGAATAC
3820018 ATTT-TAAATATTAACTT
1 ATTTATAAATATTAA-TT
* *
3820035 ATTTATTAATTTTAATT
1 ATTTATAAATATTAATT
3820052 ATTTATAAAATATATAATT
1 ATTTAT-AAATAT-TAATT
3820071 A
1 A
3820072 ATTTTTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 12 0.40
18 12 0.40
19 6 0.20
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTATAAATATTAATT
Found at i:3821925 original size:21 final size:21
Alignment explanation
Indices: 3821901--3821940 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3821891 TATTTTTATT
*
3821901 TAAAT-TTTATTATAAAATATA
1 TAAATATTAATTA-AAAATATA
3821922 TAAATATTAATTAAAAATA
1 TAAATATTAATTAAAAATA
3821941 ATTTTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATATTAATTAAAAATATA
Found at i:3823242 original size:16 final size:16
Alignment explanation
Indices: 3823206--3823244 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3823196 TTATGTGATG
3823206 TTTAAAAATTTTAAAT
1 TTTAAAAATTTTAAAT
*
3823222 ATTAAAAA-TTTATAAT
1 TTTAAAAATTTTA-AAT
3823238 TTTAAAA
1 TTTAAAA
3823245 TTTGTATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTAAAAATTTTAAAT
Found at i:3824877 original size:20 final size:21
Alignment explanation
Indices: 3824852--3824890 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3824842 TTCATTGTCT
3824852 TTAATAT-TTTTATAATAATA
1 TTAATATATTTTATAATAATA
3824872 TTAATATATTTTATAATAA
1 TTAATATATTTTATAATAA
3824891 AATTTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAATATATTTTATAATAATA
Found at i:3824897 original size:22 final size:21
Alignment explanation
Indices: 3824851--3824897 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
3824841 ATTCATTGTC
*
3824851 TTTAATATTTTTATAATAATA
1 TTTAATATTTTTATAATAAAA
3824872 -TTAATATATTTTATAATAAAA
1 TTTAATAT-TTTTATAATAAAA
3824893 TTTAA
1 TTTAA
3824898 ATAAAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 12 0.52
22 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTAATATTTTTATAATAAAA
Found at i:3825303 original size:37 final size:41
Alignment explanation
Indices: 3825261--3825348 Score: 112
Period size: 43 Copynumber: 2.2 Consensus size: 41
3825251 TAATCTTATA
*
3825261 ATTAATTTTATCTCA-CTCAT-TA-T-ATTTAGTATAATAT
1 ATTAATTTTATCTCATCTCATCTATTAATTTAATATAATAT
*
3825298 ATTAATTTTATCTCATTCTCGTCTATTTAATTTAATATAATAT
1 ATTAATTTTATCTCA-TCTCATCTA-TTAATTTAATATAATAT
3825341 ATTAATTT
1 ATTAATTT
3825349 AATATTATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
37 15 0.35
39 4 0.09
40 2 0.05
42 1 0.02
43 21 0.49
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.53
Consensus pattern (41 bp):
ATTAATTTTATCTCATCTCATCTATTAATTTAATATAATAT
Found at i:3825474 original size:17 final size:18
Alignment explanation
Indices: 3825442--3825480 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
3825432 TTATAAATAT
3825442 ATTTACTTATCATTTTTA
1 ATTTACTTATCATTTTTA
*
3825460 ATTTA-TTATCTTTTTTA
1 ATTTACTTATCATTTTTA
3825477 ATTT
1 ATTT
3825481 TGTTATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTACTTATCATTTTTA
Found at i:3826429 original size:2 final size:2
Alignment explanation
Indices: 3826422--3826470 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
3826412 AGTATTCTTT
*
3826422 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TT 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
*
3826463 AA TA TA TA
1 TA TA TA TA
3826471 AAAGCTAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3828423 original size:14 final size:15
Alignment explanation
Indices: 3828399--3828427 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3828389 AAAATACAAC
3828399 TTATCTCCTAAGTTA
1 TTATCTCCTAAGTTA
3828414 TTAT-TCCTAAGTTA
1 TTATCTCCTAAGTTA
3828428 ATTTTAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (15 bp):
TTATCTCCTAAGTTA
Found at i:3828604 original size:28 final size:29
Alignment explanation
Indices: 3828560--3828627 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 29
3828550 ATTATTATTA
*
3828560 AATT-AAAT-TATTATT-AAGTTATATTCT
1 AATTCAAATATATTATTAAATTTAT-TTCT
*
3828587 AATTCAAATATATT-TTAAATTTATTTTT
1 AATTCAAATATATTATTAAATTTATTTCT
*
3828615 AATTCAATTATAT
1 AATTCAAATATAT
3828628 AATAACTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 4 0.11
28 21 0.60
29 10 0.29
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (29 bp):
AATTCAAATATATTATTAAATTTATTTCT
Found at i:3828893 original size:17 final size:16
Alignment explanation
Indices: 3828855--3828893 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
3828845 GAAAAATATT
3828855 ATTTTTTATTTTAATCA
1 ATTTTTTATTTTAA-CA
3828872 ATTTTTTATCTTTAA-A
1 ATTTTTTAT-TTTAACA
3828888 ATTTTT
1 ATTTTT
3828894 AAAATAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 9 0.43
18 5 0.24
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTTTTATTTTAACA
Found at i:3829181 original size:14 final size:13
Alignment explanation
Indices: 3829164--3829194 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
3829154 AAATATTTTT
3829164 TAAAAAAATTAAAA
1 TAAAAAAA-TAAAA
3829178 TAAAAAAATAAAA
1 TAAAAAAATAAAA
3829191 TAAA
1 TAAA
3829195 TAATTGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
TAAAAAAATAAAA
Found at i:3829182 original size:13 final size:13
Alignment explanation
Indices: 3829166--3829199 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3829156 ATATTTTTTA
3829166 AAAAAATTAAAAT
1 AAAAAATTAAAAT
*
3829179 AAAAAAATAAAAT
1 AAAAAATTAAAAT
*
3829192 AAATAATT
1 AAAAAATT
3829200 GATAAATGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAAATTAAAAT
Found at i:3831072 original size:25 final size:27
Alignment explanation
Indices: 3831029--3831083 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
3831019 TATCTTTAAA
** *
3831029 ATTTTTAAAATAATGATAAT-TAATTT
1 ATTTTTAAAATAAAAATAATATAATAT
3831055 ATTTTT-AAATAAAAATAATATAATAT
1 ATTTTTAAAATAAAAATAATATAATAT
3831081 ATT
1 ATT
3831084 AATTTTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
ATTTTTAAAATAAAAATAATATAATAT
Found at i:3831933 original size:24 final size:24
Alignment explanation
Indices: 3831904--3831956 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
3831894 TACTTCCATA
3831904 AAAAAACCTATC-ATCTTTTTACTT
1 AAAAAACCTATCAATCTTTTTA-TT
** *
3831928 AAAAAAGTTTTCAATCTTTTTATT
1 AAAAAACCTATCAATCTTTTTATT
3831952 AAAAA
1 AAAAA
3831957 TATATTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.42
Consensus pattern (24 bp):
AAAAAACCTATCAATCTTTTTATT
Found at i:3832230 original size:17 final size:18
Alignment explanation
Indices: 3832197--3832231 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3832187 CATGATTATT
3832197 TAAAATAATATTAAAATA
1 TAAAATAATATTAAAATA
*
3832215 TAAAAT-ATATTTAAATA
1 TAAAATAATATTAAAATA
3832232 AAATTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATAATATTAAAATA
Found at i:3833596 original size:26 final size:23
Alignment explanation
Indices: 3833552--3833612 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 23
3833542 TAAAATTTAT
*
3833552 CAATTTTTGTTAATGATGCAAATG
1 CAATTTTTTTTAATGATGCAAA-G
*
3833576 TAATTTTTTTTAATGAAATGCAAAG
1 CAATTTTTTTTAATG--ATGCAAAG
3833601 CAAGTTTTTTTT
1 CAA-TTTTTTTT
3833613 TATTTATCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 13 0.42
25 3 0.10
26 15 0.48
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (23 bp):
CAATTTTTTTTAATGATGCAAAG
Found at i:3833982 original size:19 final size:19
Alignment explanation
Indices: 3833958--3834025 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
3833948 AATTCAACAA
3833958 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3833977 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3833992 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3834009 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3834026 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3833997 original size:13 final size:13
Alignment explanation
Indices: 3833979--3834003 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3833969 ACATAAGTTT
3833979 TGTATCGATACAA
1 TGTATCGATACAA
3833992 TGTATCGATACA
1 TGTATCGATACA
3834004 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3834001 original size:32 final size:32
Alignment explanation
Indices: 3833960--3834022 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3833950 TTCAACAATT
*
3833960 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3833992 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3834023 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3834087 original size:33 final size:33
Alignment explanation
Indices: 3834045--3834111 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
3834035 GCCAAGGAAA
* **
3834045 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTTTACAATGTATCGATACAT
3834078 TGTATCGATACATTTTACAATGTATCGATACAT
1 TGTATCGATACATTTTACAATGTATCGATACAT
3834111 T
1 T
3834112 CAGGCATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATTTTACAATGTATCGATACAT
Found at i:3834096 original size:20 final size:20
Alignment explanation
Indices: 3834073--3834111 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3834063 TGTGTATCGA
*
3834073 TACATTGTATCGATACATTT
1 TACAATGTATCGATACATTT
3834093 TACAATGTATCGATACATT
1 TACAATGTATCGATACATT
3834112 CAGGCATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (20 bp):
TACAATGTATCGATACATTT
Found at i:3834109 original size:13 final size:13
Alignment explanation
Indices: 3834065--3834091 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3834055 CATTTTTCTG
3834065 TGTATCGATACAT
1 TGTATCGATACAT
3834078 TGTATCGATACAT
1 TGTATCGATACAT
3834091 T
1 T
3834092 TTACAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3836464 original size:51 final size:53
Alignment explanation
Indices: 3836395--3836736 Score: 199
Period size: 52 Copynumber: 6.5 Consensus size: 53
3836385 AGTTTATCAA
* * * * *
3836395 TTCTCCACAATCGAGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
3836446 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * *** * * *
3836500 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAAT
** *** * * *
3836553 CCCGTT-ATTTTCGAGGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAAT
1 TTC-TTCACAATC--GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAAT
* * **
3836607 TT-TTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAATGCCAATT
1 TTCTT-CACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAA-T
* *
3836660 TTCCTT--TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
3836712 TT-TTCACAATCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
3836737 CTCGTTATTT
Statistics
Matches: 220, Mismatches: 47, Indels: 47
0.70 0.15 0.15
Matches are distributed among these distances:
50 4 0.02
51 35 0.16
52 80 0.36
53 38 0.17
54 38 0.17
55 22 0.10
57 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:3836622 original size:107 final size:106
Alignment explanation
Indices: 3836458--3836850 Score: 327
Period size: 107 Copynumber: 3.7 Consensus size: 106
3836448 TTCTATAATC
*
3836458 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACTCCGATTTTA-TTCC-AAAAACACCAATTT-TTCACAATCGGGGATACTCC
3836523 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTTCGA
63 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTTCGA
* * *
3836567 GGGGATACTCCAACTCCGGTTTTA-TCGCTAAAACACTAATTTTTCCACAATCGGGGATACTCCA
1 GGGGATACTCCAACTCCGATTTTATTC-CAAAAACACCAATTTTT-CACAATCGGGGATACTCCA
** * ** * * ** **
3836631 ATCCTGGTTTTATTTTC----AAAATGCCAATTTTCC-TT-TAATC--
64 A-CCCCG-TTAATCATCGGGGATACT-CCAA--CCCCGTTATTTTCGA
* *
3836671 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTA-TTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
* * * *
3836736 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
65 CCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTATTTTCGA
* ** * * *** * * *
3836779 GGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
3836844 CCCGTTA
66 CCCGTTA
3836851 TTTTCGAAGG
Statistics
Matches: 221, Mismatches: 45, Indels: 38
0.73 0.15 0.12
Matches are distributed among these distances:
102 2 0.01
103 7 0.03
104 44 0.20
105 19 0.09
106 16 0.07
107 78 0.35
108 27 0.12
109 28 0.13
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (106 bp):
GGGGATACTCCAACTCCGATTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTTCGA
Found at i:3836720 original size:104 final size:102
Alignment explanation
Indices: 3836400--3836735 Score: 281
Period size: 104 Copynumber: 3.2 Consensus size: 102
3836390 ATCAATTCTC
* * *
3836400 CACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAA-CACTAATTTT-CTATAATCGGGGA
1 CACAATCGAGGATACTCCAA-TCCGGTTTTATTTTCAAAATC-C-AATTTTCCTTTAATCGGGGA
*
3836463 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
63 TACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTT-TT
* * * * ** * * ** **
3836505 CACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAA--CCCCGTTATTTTCGA
1 CACAATCGAGGATACTCCAATCCGGTTTTATTTTC----AAAATCCAATTTTCC-TT-TAATC--
* * *
3836567 GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTT
58 GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAATTTTT
*
3836611 CCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAAAATGCCAATTTTCCTTTAATCGGGGA
1 -CACAATCGAGGATACTCCAATCC-GGTTTTATTTTCAAAAT-CCAATTTTCCTTTAATCGGGGA
*
3836676 TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
63 TACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
3836716 CACAATCGAGGATACTCCAA
1 CACAATCGAGGATACTCCAA
3836736 CCTCGTTATT
Statistics
Matches: 177, Mismatches: 35, Indels: 39
0.71 0.14 0.16
Matches are distributed among these distances:
103 6 0.03
104 44 0.25
105 36 0.20
106 14 0.08
107 44 0.25
108 5 0.03
109 28 0.16
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (102 bp):
CACAATCGAGGATACTCCAATCCGGTTTTATTTTCAAAATCCAATTTTCCTTTAATCGGGGATAC
TCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
Found at i:3836756 original size:28 final size:28
Alignment explanation
Indices: 3836720--3836796 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
3836710 ATTTTTCACA
* * *
3836720 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
3836748 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
3836776 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
3836797 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:3836765 original size:212 final size:212
Alignment explanation
Indices: 3836398--3836803 Score: 620
Period size: 212 Copynumber: 1.9 Consensus size: 212
3836388 TTATCAATTC
* *
3836398 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* *
3836463 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * * *
3836528 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACTCCGGTTTTATC
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
3836593 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * ** *
3836610 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAATGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGAGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
*
3836674 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
3836737 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
3836802 AT
193 AT
3836804 TCCCAAAATA
Statistics
Matches: 175, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 31 0.18
212 109 0.62
213 35 0.20
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (212 bp):
TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
GCTAAAACACTAATTTT
Found at i:3836929 original size:78 final size:79
Alignment explanation
Indices: 3836750--3836951 Score: 230
Period size: 78 Copynumber: 2.6 Consensus size: 79
3836740 GTTATTTCAT
* * * *
3836750 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGATTTATTCCCAAAATAT
* * *
3836815 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * ** *
3836829 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCC-GATTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGATTTATTCCCAAAAT-A
3836892 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* *
3836907 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
3836952 TGTTATTATC
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
77 8 0.08
78 55 0.53
79 41 0.39
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGATTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:3838005 original size:31 final size:33
Alignment explanation
Indices: 3837944--3838006 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
3837934 CATGAGCAAT
*
3837944 ATAATATAAATAACAAAAACACATATTATAAAA
1 ATAATATAAATAACAAAAACACATAATATAAAA
*
3837977 ATAATATAAATGAC-AAAA-ACATAATATAAA
1 ATAATATAAATAACAAAAACACATAATATAAA
3838007 TCATAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 11 0.39
32 4 0.14
33 13 0.46
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.24
Consensus pattern (33 bp):
ATAATATAAATAACAAAAACACATAATATAAAA
Found at i:3838014 original size:20 final size:19
Alignment explanation
Indices: 3837973--3838015 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
3837963 CACATATTAT
*
3837973 AAAAATAATATAAATGACA
1 AAAAATAATATAAATCACA
*
3837992 AAAACATAATATAAATCATA
1 AAAA-ATAATATAAATCACA
3838012 AAAA
1 AAAA
3838016 TACATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAAATAATATAAATCACA
Found at i:3838040 original size:24 final size:22
Alignment explanation
Indices: 3837977--3838040 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 22
3837967 TATTATAAAA
*
3837977 ATAATATAAATG--ACAAAAAC
1 ATAATATAAATGATACAAATAC
* *
3837997 ATAATATAAATCATAAAAATAC
1 ATAATATAAATGATACAAATAC
3838019 ATATTATATAAATGATACAAAT
1 ATA--ATATAAATGATACAAAT
3838041 GATAGAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 11 0.31
22 9 0.26
24 15 0.43
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.28
Consensus pattern (22 bp):
ATAATATAAATGATACAAATAC
Found at i:3840541 original size:21 final size:22
Alignment explanation
Indices: 3840500--3840542 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
3840490 ACATAGTTTT
3840500 CAATAAAAAATAAACTTAATTA
1 CAATAAAAAATAAACTTAATTA
* *
3840522 CAATAATAAA-AAATTTAATTA
1 CAATAAAAAATAAACTTAATTA
3840543 TTACAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (22 bp):
CAATAAAAAATAAACTTAATTA
Found at i:3841052 original size:73 final size:73
Alignment explanation
Indices: 3841004--3841197 Score: 196
Period size: 73 Copynumber: 2.7 Consensus size: 73
3840994 CAAACTAATC
* *
3841004 TTACAAAT-AAAATAAATCATATCTTAAAAAATTTAAACTCGTATAATTAAACTATAAAATAAAT
1 TTACAAATAAAAATAAATCATATATTAAAAAATTTAAACTCATATAATTAAACTATAAAATAAAT
*
3841068 TTAAACTT
66 TCAAACTT
* * * *
3841076 TTACAAATAAAAATAAATCATATATTGAATAATTTAAATTCATATAATTATACT-TAAAAATAAA
1 TTACAAATAAAAATAAATCATATATTAAAAAATTTAAACTCATATAATTAAACTAT-AAAATAAA
* ***
3841140 TTTAGGGGTT
65 TTCA-AACTT
* * ** * *
3841150 CTATAAATAAAAATAAATCATA-CCTAAAAAAATCAAACTCATATAATT
1 TTACAAATAAAAATAAATCATATATTAAAAAATTTAAACTCATATAATT
3841198 CTTTTAAATT
Statistics
Matches: 101, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
72 9 0.09
73 70 0.69
74 22 0.22
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.34
Consensus pattern (73 bp):
TTACAAATAAAAATAAATCATATATTAAAAAATTTAAACTCATATAATTAAACTATAAAATAAAT
TCAAACTT
Found at i:3842499 original size:20 final size:21
Alignment explanation
Indices: 3842453--3842499 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
3842443 AATGTGTTAA
3842453 AATTATATAAAATAAATTATT
1 AATTATATAAAATAAATTATT
*
3842474 AA-TATATCAAAATTAA-TA-T
1 AATTATAT-AAAATAAATTATT
3842493 AATTATA
1 AATTATA
3842500 ATATTTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 3 0.13
20 11 0.48
21 9 0.39
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTATATAAAATAAATTATT
Found at i:3844314 original size:24 final size:25
Alignment explanation
Indices: 3844268--3844314 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
3844258 TTAAAAAAAT
* *
3844268 AATAATAAAGAAATTGATTGAAAGA
1 AATAATAAAGAAATAGATAGAAAGA
*
3844293 AATAATGAA-AAATAGATAGAAA
1 AATAATAAAGAAATAGATAGAAA
3844315 ATAAAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (25 bp):
AATAATAAAGAAATAGATAGAAAGA
Found at i:3845369 original size:23 final size:23
Alignment explanation
Indices: 3845345--3845387 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3845335 CAACCCTCAT
3845345 TTTA-TTTTAT-TTTTAATTTTCA
1 TTTATTTTTATATTTT-ATTTTCA
3845367 TTTATTTTTATATTTTATTTT
1 TTTATTTTTATATTTTATTTT
3845388 GTGTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTATTTTTATATTTTATTTTCA
Found at i:3845370 original size:17 final size:17
Alignment explanation
Indices: 3845343--3845386 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
3845333 GTCAACCCTC
3845343 ATTTTATTTTATTTTTA-
1 ATTTTA-TTTATTTTTAT
3845360 ATTTTCATTTATTTTTAT
1 ATTTT-ATTTATTTTTAT
3845378 ATTTTATTT
1 ATTTTATTT
3845387 TGTGTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTATTTATTTTTAT
Found at i:3846512 original size:29 final size:30
Alignment explanation
Indices: 3846480--3846546 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
3846470 TGTTGTCATA
* *
3846480 TTATTTTTTT-ATGTTG-TGTTATATTTTAG
1 TTATTTTTTTCAT-ATGATGTTACATTTTAG
*
3846509 TTATTTTTTTCATATGATGTTGCATTTTAG
1 TTATTTTTTTCATATGATGTTACATTTTAG
3846539 TTATTTTT
1 TTATTTTT
3846547 CATATCTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 12 0.36
30 21 0.64
ACGTcount: A:0.18, C:0.03, G:0.12, T:0.67
Consensus pattern (30 bp):
TTATTTTTTTCATATGATGTTACATTTTAG
Found at i:3846789 original size:27 final size:26
Alignment explanation
Indices: 3846758--3846825 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
3846748 ATAAATTTTT
3846758 AAATATTTTAAATG-TTAAATCAAAAA
1 AAATATTTTAAATGATTAAAT-AAAAA
* *
3846784 CAAATATTAT-AATGATTAAATGAAAA
1 -AAATATTTTAAATGATTAAATAAAAA
*
3846810 AACTATTTTAAATGAT
1 AAATATTTTAAATGAT
3846826 GTCATAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 7 0.20
26 14 0.40
27 14 0.40
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.35
Consensus pattern (26 bp):
AAATATTTTAAATGATTAAATAAAAA
Found at i:3846823 original size:26 final size:26
Alignment explanation
Indices: 3846760--3846825 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
3846750 AAATTTTTAA
*
3846760 ATATTTTAAATG-TTAAATCAAAAAC
1 ATATTTTAAATGATTAAATAAAAAAC
* *
3846785 AAATATTATAATGATTAAATGAAAAAAC
1 ATATTTTA-AATGATTAAAT-AAAAAAC
3846813 -TATTTTAAATGAT
1 ATATTTTAAATGAT
3846826 GTCATAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
25 6 0.18
26 10 0.30
27 11 0.33
28 6 0.18
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (26 bp):
ATATTTTAAATGATTAAATAAAAAAC
Found at i:3846877 original size:10 final size:10
Alignment explanation
Indices: 3846862--3846893 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3846852 GTTGTTCGAG
3846862 TTATATTTTA
1 TTATATTTTA
3846872 TTATATTTTA
1 TTATATTTTA
3846882 TT-T-TTTTA
1 TTATATTTTA
3846890 TTAT
1 TTAT
3846894 GAAATATAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 7 0.33
9 2 0.10
10 12 0.57
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
TTATATTTTA
Found at i:3848995 original size:20 final size:20
Alignment explanation
Indices: 3848959--3849011 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
3848949 ATTATAAAAG
*
3848959 TTTCAATTTATTTTTATTGT
1 TTTCAATTTATTCTTATTGT
*
3848979 TTTCAATATTA-TCTTATTAT
1 TTTCAAT-TTATTCTTATTGT
*
3848999 TAT-AATTTATTCT
1 TTTCAATTTATTCT
3849012 ATGTATCCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.11
19 6 0.21
20 16 0.57
21 3 0.11
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTCAATTTATTCTTATTGT
Found at i:3849791 original size:15 final size:15
Alignment explanation
Indices: 3849771--3849809 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3849761 TTTCTCTATT
*
3849771 TTTTATTTTTTTATG
1 TTTTATTTATTTATG
*
3849786 TTTTATTTATTTATT
1 TTTTATTTATTTATG
3849801 TATTTATTT
1 T-TTTATTT
3849810 CCCACCATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTATTTATTTATG
Found at i:3849796 original size:4 final size:4
Alignment explanation
Indices: 3849767--3849809 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
3849757 TCTTTTTCTC
* *
3849767 TATT T-TT TATT TTTT TATG T-TT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT T
3849810 CCCACCATGC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 5 0.15
4 28 0.85
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (4 bp):
TATT
Found at i:3851757 original size:16 final size:16
Alignment explanation
Indices: 3851738--3851768 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3851728 ATTTCTATAA
3851738 AATTAAATTTTAATTT
1 AATTAAATTTTAATTT
*
3851754 AATTATATTTTAATT
1 AATTAAATTTTAATT
3851769 CAAGAAAATA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTAAATTTTAATTT
Found at i:3851841 original size:83 final size:84
Alignment explanation
Indices: 3851754--3851926 Score: 235
Period size: 83 Copynumber: 2.1 Consensus size: 84
3851744 ATTTTAATTT
* *
3851754 AATTATATTTTAATTCAAGAAAATATTAAATATTTTAAAA-TTATTTAT-AGTTAAATTATATTA
1 AATTATATTTTAATTCAAGAAAATAATAAATA-TTTAAAATTTATTTATAAGTTAAATAATATTA
*
3851817 A-TTTAGACATAAATTCATTA
65 ACTTT-CACATAAATTCATTA
* * * * *
3851837 AATTATATTTTAATTTAAGTAAATAATAAATATTTAAAATTTATTTTTAATTTAACTAATATTAA
1 AATTATATTTTAATTCAAGAAAATAATAAATATTTAAAATTTATTTATAAGTTAAATAATATTAA
3851902 CTTTCACATAAATTCATTA
66 CTTTCACATAAATTCATTA
3851921 AATTAT
1 AATTAT
3851927 TTTGATTTAA
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
82 7 0.09
83 36 0.46
84 33 0.42
85 3 0.04
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (84 bp):
AATTATATTTTAATTCAAGAAAATAATAAATATTTAAAATTTATTTATAAGTTAAATAATATTAA
CTTTCACATAAATTCATTA
Found at i:3852079 original size:29 final size:26
Alignment explanation
Indices: 3852046--3852106 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 26
3852036 CTTATGTAAG
*
3852046 ATTTTATTAAAAATATACTTAAAATTATA
1 ATTTT-TTAAAAA-ATAATTAAAATTA-A
*
3852075 ATTTTTTAAAAAATAATTAATATTAA
1 ATTTTTTAAAAAATAATTAAAATTAA
3852101 ATTTTT
1 ATTTTT
3852107 ATAATTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 7 0.23
27 11 0.37
28 7 0.23
29 5 0.17
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTTTTAAAAAATAATTAAAATTAA
Found at i:3852132 original size:20 final size:20
Alignment explanation
Indices: 3852087--3852124 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3852077 TTTTTAAAAA
3852087 ATAATTAATATTAAATTTTT
1 ATAATTAATATTAAATTTTT
3852107 ATAATTAA-ATTAATATTT
1 ATAATTAATATTAA-ATTT
3852125 ATTTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATAATTAATATTAAATTTTT
Found at i:3852846 original size:17 final size:16
Alignment explanation
Indices: 3852809--3852852 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
3852799 AATACTCCAA
3852809 AAAAAATTTTAAAAAT
1 AAAAAATTTTAAAAAT
3852825 AAAAAATTATT-AAAAT
1 AAAAAATT-TTAAAAAT
*
3852841 AGAAAATGTTTA
1 AAAAAAT-TTTA
3852853 TATATACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 21 0.88
17 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
AAAAAATTTTAAAAAT
Found at i:3854129 original size:29 final size:28
Alignment explanation
Indices: 3854076--3854146 Score: 81
Period size: 30 Copynumber: 2.5 Consensus size: 28
3854066 ATTAATCTTA
* * *
3854076 AAAAAATTAATATATATTTTGTCAAACTTT
1 AAAAAATAAATAAATGTTTTGTCAAAC--T
*
3854106 AAAAGATAAATAAATGTTTT-TCAAACT
1 AAAAAATAAATAAATGTTTTGTCAAACT
3854133 AAAAAATAAATAAA
1 AAAAAATAAATAAA
3854147 ATTTTTATCA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 14 0.39
29 6 0.17
30 16 0.44
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.34
Consensus pattern (28 bp):
AAAAAATAAATAAATGTTTTGTCAAACT
Found at i:3855486 original size:2 final size:2
Alignment explanation
Indices: 3855474--3855521 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
3855464 ATTACTACAA
* * * * *
3855474 AT AT AT CT AT AT AC AT AT TT AT AT TT AT AT AC 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
3855516 AT AT AT
1 AT AT AT
3855522 GTATTCAAGT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3855502 original size:18 final size:18
Alignment explanation
Indices: 3855474--3855521 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
3855464 ATTACTACAA
*
3855474 ATATATCTATATACATAT
1 ATATATATATATACATAT
* *
3855492 TTATATTTATATACATAT
1 ATATATATATATACATAT
3855510 ATATATATATAT
1 ATATATATATAT
3855522 GTATTCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATATATATACATAT
Found at i:3861652 original size:15 final size:15
Alignment explanation
Indices: 3861632--3861664 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3861622 AGAATATTTC
3861632 AAGGAAAAAAAAAGA
1 AAGGAAAAAAAAAGA
*
3861647 AAGGAAAATAAAAGA
1 AAGGAAAAAAAAAGA
3861662 AAG
1 AAG
3861665 AGGGAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (15 bp):
AAGGAAAAAAAAAGA
Found at i:3863537 original size:6 final size:6
Alignment explanation
Indices: 3863457--3863549 Score: 55
Period size: 6 Copynumber: 15.0 Consensus size: 6
3863447 GTTCAGCCAT
* * * * *
3863457 ATATTA AT-TTA AGATTT ATACTTA ATCTTAA ATGATTA TTATAA AT-TTA
1 ATATTA ATATTA ATATTA ATA-TTA ATATT-A AT-ATTA ATATTA ATATTA
* * *
3863506 ATTTTT ATAATTA ATATAA TATATTA ATATTA ATATTA ATATTA
1 ATATTA AT-ATTA ATATTA -ATATTA ATATTA ATATTA ATATTA
3863550 TTTCAATATA
Statistics
Matches: 65, Mismatches: 15, Indels: 14
0.69 0.16 0.15
Matches are distributed among these distances:
5 8 0.12
6 37 0.57
7 18 0.28
8 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
ATATTA
Found at i:3863625 original size:26 final size:27
Alignment explanation
Indices: 3863592--3863646 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
3863582 ATAATCATTT
**
3863592 AATAAAA-TTTATTTTAAAATTAATTA
1 AATAAAATTTTATTTTAAAAAAAATTA
3863618 AATAAAATTTTATTTTAAAAAAAATTA
1 AATAAAATTTTATTTTAAAAAAAATTA
3863645 AA
1 AA
3863647 ACTCCAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AATAAAATTTTATTTTAAAAAAAATTA
Found at i:3864287 original size:17 final size:17
Alignment explanation
Indices: 3864265--3864299 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3864255 GTGAGGAGCT
3864265 AAATTGAAAAAATTGAA
1 AAATTGAAAAAATTGAA
* *
3864282 AAATTGGAGAAATTGAA
1 AAATTGAAAAAATTGAA
3864299 A
1 A
3864300 TTGGAGGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (17 bp):
AAATTGAAAAAATTGAA
Found at i:3864302 original size:15 final size:15
Alignment explanation
Indices: 3864282--3864317 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3864272 AAAAATTGAA
3864282 AAATTGGAGAAATTG
1 AAATTGGAGAAATTG
*
3864297 AAATTGGAGGAATTG
1 AAATTGGAGAAATTG
*
3864312 GAATTG
1 AAATTG
3864318 AAAAGTTGAA
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:0.42, C:0.00, G:0.31, T:0.28
Consensus pattern (15 bp):
AAATTGGAGAAATTG
Found at i:3872001 original size:16 final size:17
Alignment explanation
Indices: 3871982--3872013 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3871972 AAAATATTTT
3871982 AAATAAAAA-TAATAAA
1 AAATAAAAATTAATAAA
3871998 AAATAAAAATTAATAA
1 AAATAAAAATTAATAA
3872014 TTAACAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
AAATAAAAATTAATAAA
Found at i:3872570 original size:18 final size:18
Alignment explanation
Indices: 3872544--3872578 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3872534 TATTTTTAAA
*
3872544 TTATCATTATAAAATTTT
1 TTATCATTAAAAAATTTT
*
3872562 TTATTATTAAAAAATTT
1 TTATCATTAAAAAATTT
3872579 ATCTATTTTA
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:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATCATTAAAAAATTTT
Found at i:3873392 original size:15 final size:14
Alignment explanation
Indices: 3873372--3873403 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
3873362 TAATAACATC
3873372 AAAATAATATATTTA
1 AAAATAATAT-TTTA
3873387 AAAATAATATTTTA
1 AAAATAATATTTTA
3873401 AAA
1 AAA
3873404 GTTATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATAATATTTTA
Found at i:3873500 original size:12 final size:12
Alignment explanation
Indices: 3873469--3873542 Score: 60
Period size: 12 Copynumber: 7.0 Consensus size: 12
3873459 ATAATTTAAT
3873469 ATTAATAATAT-
1 ATTAATAATATA
3873480 ATT-A-AATATA
1 ATTAATAATATA
*
3873490 ATTAATGATATA
1 ATTAATAATATA
*
3873502 CTTAATAATAT-
1 ATTAATAATATA
3873513 ATT--TAA-AT-
1 ATTAATAATATA
3873521 ATTAAT--TATA
1 ATTAATAATATA
3873531 ATTAATAATATA
1 ATTAATAATATA
3873543 TATTTTTTGG
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
8 5 0.10
9 10 0.20
10 11 0.22
11 6 0.12
12 18 0.36
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (12 bp):
ATTAATAATATA
Found at i:3873737 original size:12 final size:11
Alignment explanation
Indices: 3873720--3874083 Score: 180
Period size: 10 Copynumber: 34.0 Consensus size: 11
3873710 TGAATCAACC
3873720 AATAATATACTT
1 AATAATATA-TT
3873732 AATAATATATT
1 AATAATATATT
3873743 AA-AAT-TATTGT
1 AATAATATA-T-T
3873754 AATAATTATATT
1 AATAA-TATATT
*
3873766 TATAATAT-TT
1 AATAATATATT
* *
3873776 AATGATATGTT
1 AATAATATATT
* *
3873787 ACGT-A-ACATT
1 A-ATAATATATT
3873797 --TAATA-ATT
1 AATAATATATT
3873805 AAT-ATATATT
1 AATAATATATT
*
3873815 -ATAATATTTT
1 AATAATATATT
*
3873825 AATAGTAT-TT
1 AATAATATATT
3873835 AATAATAT-TT
1 AATAATATATT
* *
3873845 AATATTATACT
1 AATAATATATT
* * *
3873856 AA-ATTGTTTT
1 AATAATATATT
3873866 AATAATATATTT
1 AATAATATA-TT
* * *
3873878 TATATTTTATT
1 AATAATATATT
*
3873889 AA-AATATTTTGAT
1 AATAATA-TAT--T
3873902 AATAATATATT
1 AATAATATATT
* *
3873913 CA-AATATTTT
1 AATAATATATT
*
3873923 AATATTTATATT
1 AATA-ATATATT
**
3873935 TGTAATAT-TT
1 AATAATATATT
*
3873945 AATGATATATT
1 AATAATATATT
* *
3873956 TATAACAT-TT
1 AATAATATATT
3873966 AATAATATATT
1 AATAATATATT
* *
3873977 AA-CATATTTT
1 AATAATATATT
3873987 AATAATATATT
1 AATAATATATT
*
3873998 AAAAATAT-TT
1 AATAATATATT
*
3874008 AATAATATGTT
1 AATAATATATT
3874019 AA-AATAT-TT
1 AATAATATATT
3874028 AATAATATATT
1 AATAATATATT
3874039 -ATAATAT-TT
1 AATAATATATT
3874048 AATAATAATATAT
1 AATAAT-ATAT-T
* *
3874061 TATAATATTTT
1 AATAATATATT
3874072 AATAATAATATT
1 AATAAT-ATATT
3874084 TAAATAAATA
Statistics
Matches: 267, Mismatches: 51, Indels: 68
0.69 0.13 0.18
Matches are distributed among these distances:
7 1 0.00
8 4 0.01
9 14 0.05
10 114 0.43
11 75 0.28
12 40 0.15
13 13 0.05
14 6 0.02
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (11 bp):
AATAATATATT
Found at i:3873841 original size:21 final size:19
Alignment explanation
Indices: 3873797--3874075 Score: 131
Period size: 21 Copynumber: 13.6 Consensus size: 19
3873787 ACGTAACATT
*
3873797 TAATAATTAATATATATTA
1 TAATATTTAATATATATTA
3873816 TAATATTTTAATAGTAT-TTAA
1 TAATA-TTTAATA-TATATT-A
*
3873837 TAATATTTAATATTATACTA
1 TAATATTTAATA-TATATTA
*
3873857 -AATTGTTTTAATAATATATT-
1 TAA-T-ATTTAAT-ATATATTA
* * * *
3873877 TTATATTTTATTAAAATATTT
1 TAATA-TTTAAT-ATATATTA
* * *
3873898 TGATA-ATAATATAT-TCA
1 TAATATTTAATATATATTA
*
3873915 -AATATTTTAATATTTATATTTG
1 TAATA-TTTAATA--TATA-TTA
3873937 TAATATTTAATGATATATTTA
1 TAATATTTAAT-ATATA-TTA
*
3873958 TAACATTTAATAATATATTA
1 TAATATTTAAT-ATATATTA
3873978 -ACATATTTTAATAATATATTAA
1 TA-ATA-TTTAAT-ATATATT-A
* *
3874000 AAATATTTAATAATATGTTA
1 TAATATTTAAT-ATATATTA
*
3874020 AAATATTTAATAATATATTA
1 TAATATTTAAT-ATATATTA
3874040 TAATATTTAATAATAATATATTA
1 TAATA-TT--TAAT-ATATATTA
3874063 TAATATTTTAATA
1 TAATA-TTTAATA
3874076 ATAATATTTA
Statistics
Matches: 209, Mismatches: 26, Indels: 49
0.74 0.09 0.17
Matches are distributed among these distances:
16 3 0.01
17 1 0.00
18 8 0.04
19 11 0.05
20 66 0.32
21 81 0.39
22 12 0.06
23 27 0.13
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.50
Consensus pattern (19 bp):
TAATATTTAATATATATTA
Found at i:3873904 original size:33 final size:33
Alignment explanation
Indices: 3873834--3874075 Score: 84
Period size: 33 Copynumber: 7.4 Consensus size: 33
3873824 TAATAGTATT
* *
3873834 TAATAATATTTAATATTATACTAAATTGTTTTAA
1 TAAT-ATATTTAATATTATACTAAAATATTTTAA
* * *
3873868 TAATATATTTTATATTTTATTAAAATATTTTGATAA
1 TAATATATTTAATATTATACTAAAATA-TTT--TAA
* *
3873904 TAATATATTCAAATATT-T--T--AATATTTATAT
1 TAATATATT-TAATATTATACTAAAATATTT-TAA
** * * *
3873934 TTGTAATATTTAATGA-TATATTTATAACA-TTTAA
1 TAAT-ATATTTAAT-ATTATA-CTAAAATATTTTAA
* *
3873968 TAATATATTAACATATT-T--TAATAATATATTAA
1 TAATATATTTA-ATATTATACTAA-AATATTTTAA
* **
3874000 -AA-ATATTTAATAATATGTTAAAATA-TTTAA
1 TAATATATTTAATATTATACTAAAATATTTTAA
* *
3874030 TAATATATTATAATATT-TAATAATAATATATT-A
1 TAATATATT-TAATATTATACTAA-AATATTTTAA
3874063 TAATAT-TTTAATA
1 TAATATATTTAATA
3874076 ATAATATTTA
Statistics
Matches: 158, Mismatches: 26, Indels: 51
0.67 0.11 0.22
Matches are distributed among these distances:
29 4 0.03
30 22 0.14
31 26 0.16
32 22 0.14
33 43 0.27
34 18 0.11
35 2 0.01
36 16 0.10
37 5 0.03
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (33 bp):
TAATATATTTAATATTATACTAAAATATTTTAA
Found at i:3873942 original size:15 final size:14
Alignment explanation
Indices: 3873916--3873945 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3873906 ATATATTCAA
3873916 ATATTTTAATATTT
1 ATATTTTAATATTT
3873930 ATATTTGTAATATTT
1 ATATTT-TAATATTT
3873945 A
1 A
3873946 ATGATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (14 bp):
ATATTTTAATATTT
Found at i:3873976 original size:64 final size:61
Alignment explanation
Indices: 3873901--3874087 Score: 198
Period size: 62 Copynumber: 2.9 Consensus size: 61
3873891 AATATTTTGA
* *
3873901 TAATAATATATTCAAATATTTTAATATTTATATTTGTAATATTTAATGATATATTTATAACATT
1 TAATAATATATT-AAATATTTTAATA-TTATATTTATAATATTTAAT-ATATATTTAAAACATT
* * * *
3873965 TAATAATATATTAACATATTTTAATAATATATTAAAAATATTTAATA-ATATGTTAAAATATT
1 TAATAATATATTAA-ATATTTTAATATTATATTTATAATATTTAATATATAT-TTAAAACATT
*
3874027 TAATAATATATTATAATA-TTTAATAATAATATATTATAATATTTTAATAATAATATTTAAA
1 TAATAATATATTA-AATATTTTAAT-ATTATAT-TTATAATA-TTTAAT-AT-ATATTTAAA
3874088 TAAATAATAT
Statistics
Matches: 104, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
61 10 0.10
62 30 0.29
63 25 0.24
64 29 0.28
65 1 0.01
66 5 0.05
67 4 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (61 bp):
TAATAATATATTAAATATTTTAATATTATATTTATAATATTTAATATATATTTAAAACATT
Found at i:3874009 original size:85 final size:84
Alignment explanation
Indices: 3873901--3874089 Score: 217
Period size: 85 Copynumber: 2.2 Consensus size: 84
3873891 AATATTTTGA
* ** *
3873901 TAATAATATATTCAAATATTTTAATATTTATAT-TTGTAATATTTAATGATATATTTATAACA-T
1 TAATAATATATTAAAATATTTTAATA---ATATGTTAAAATATTTAATAATATA-TTATAACATT
3873964 T-TAATAATATATTA-ACATATTT
62 TATAATAATATATTATA-ATATTT
*
3873986 TAATAATATATTAAAA-ATATTTAATAATATGTTAAAATATTTAATAATATATTATAATATTTAA
1 TAATAATATATTAAAATAT-TTTAATAATATGTTAAAATATTTAATAATATATTATAACATTT-A
3874050 TAATAATATATTATAATATTT
64 TAATAATATATTATAATATTT
*
3874071 TAATAATAATATTTAAATA
1 TAATAAT-ATATTAAAATA
3874090 AATAATATGA
Statistics
Matches: 90, Mismatches: 6, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
82 11 0.12
83 19 0.21
84 2 0.02
85 48 0.53
86 9 0.10
87 1 0.01
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (84 bp):
TAATAATATATTAAAATATTTTAATAATATGTTAAAATATTTAATAATATATTATAACATTTATA
ATAATATATTATAATATTT
Found at i:3874076 original size:21 final size:21
Alignment explanation
Indices: 3873901--3874083 Score: 180
Period size: 21 Copynumber: 8.6 Consensus size: 21
3873891 AATATTTTGA
3873901 TAATAATATATTCA-AATATTT
1 TAATAATATATT-ATAATATTT
* *
3873922 TAATATTTATATTTGTAATA-TT
1 TAATA-ATATA-TTATAATATTT
* *
3873944 TAATGATATATTTATAACA-TT
1 TAATAATATA-TTATAATATTT
3873965 TAATAATATATTA-ACATATTT
1 TAATAATATATTATA-ATATTT
*
3873986 TAATAATATATTA-AAAATATT
1 TAATAATATATTATAATAT-TT
* *
3874007 TAATAATATGTTAAAATA-TT
1 TAATAATATATTATAATATTT
3874027 TAATAATATATTATAATATTT
1 TAATAATATATTATAATATTT
3874048 AATAATAATATATTATAATATTT
1 --TAATAATATATTATAATATTT
3874071 TAATAATAATATT
1 TAATAAT-ATATT
3874084 TAAATAAATA
Statistics
Matches: 138, Mismatches: 13, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
19 1 0.01
20 26 0.19
21 66 0.48
22 18 0.13
23 27 0.20
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
TAATAATATATTATAATATTT
Found at i:3874574 original size:2 final size:2
Alignment explanation
Indices: 3874567--3874599 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3874557 TCCCAGCTCC
3874567 CT CT CT CT 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 CT CT CT CT C
3874600 GCTCGTCTTT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3876089 original size:13 final size:13
Alignment explanation
Indices: 3876071--3876098 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3876061 GGATTTATAG
3876071 CAGTATGTGCAAT
1 CAGTATGTGCAAT
3876084 CAGTATGTGCAAT
1 CAGTATGTGCAAT
3876097 CA
1 CA
3876099 ATCTTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (13 bp):
CAGTATGTGCAAT
Found at i:3883796 original size:16 final size:16
Alignment explanation
Indices: 3883777--3883809 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3883767 ATTATACGGA
3883777 TTCGAGCTTATTCAGG
1 TTCGAGCTTATTCAGG
3883793 TTCGAGCTTATTCAGG
1 TTCGAGCTTATTCAGG
3883809 T
1 T
3883810 CGGTTTCGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (16 bp):
TTCGAGCTTATTCAGG
Found at i:3884268 original size:14 final size:14
Alignment explanation
Indices: 3884249--3884300 Score: 70
Period size: 14 Copynumber: 3.6 Consensus size: 14
3884239 TAAACTCAAT
3884249 TAAAAAAAACGAAA
1 TAAAAAAAACGAAA
*
3884263 TAAAAAAAAATC-AAT
1 T-AAAAAAAA-CGAAA
3884278 TAAAAAAAACGAAA
1 TAAAAAAAACGAAA
3884292 TAAAAAAAA
1 TAAAAAAAA
3884301 ATCAAAATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 1 0.03
14 20 0.61
15 11 0.33
16 1 0.03
ACGTcount: A:0.79, C:0.06, G:0.04, T:0.12
Consensus pattern (14 bp):
TAAAAAAAACGAAA
Found at i:3884268 original size:15 final size:15
Alignment explanation
Indices: 3884250--3884301 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
3884240 AAACTCAATT
3884250 AAAAAAAACGAAATA
1 AAAAAAAACGAAATA
*
3884265 AAAAAAAATC--AATT
1 AAAAAAAA-CGAAATA
3884279 AAAAAAAACGAAATA
1 AAAAAAAACGAAATA
3884294 AAAAAAAA
1 AAAAAAAA
3884302 TCAAAATCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 1 0.03
14 11 0.34
15 19 0.59
16 1 0.03
ACGTcount: A:0.81, C:0.06, G:0.04, T:0.10
Consensus pattern (15 bp):
AAAAAAAACGAAATA
Found at i:3884276 original size:29 final size:29
Alignment explanation
Indices: 3884244--3884305 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
3884234 TCACGTAAAC
3884244 TCAATTAAAAAAAACGAAATAAAAAAAAA
1 TCAATTAAAAAAAACGAAATAAAAAAAAA
3884273 TCAATTAAAAAAAACGAAATAAAAAAAAA
1 TCAATTAAAAAAAACGAAATAAAAAAAAA
3884302 TCAA
1 TCAA
3884306 AATCTTTAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.15
Consensus pattern (29 bp):
TCAATTAAAAAAAACGAAATAAAAAAAAA
Found at i:3884717 original size:16 final size:15
Alignment explanation
Indices: 3884690--3884719 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3884680 ATGTTAACTT
3884690 TATATTCTATTCTAC
1 TATATTCTATTCTAC
3884705 TATATTGCTATTCTA
1 TATATT-CTATTCTA
3884720 AGTATAACAT
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:0.27, C:0.17, G:0.03, T:0.53
Consensus pattern (15 bp):
TATATTCTATTCTAC
Found at i:3885221 original size:16 final size:16
Alignment explanation
Indices: 3885202--3885299 Score: 83
Period size: 16 Copynumber: 6.2 Consensus size: 16
3885192 GTTCTGGTTC
*
3885202 TTTCGGGTTCGAGATT
1 TTTCGAGTTCGAGATT
*
3885218 TTTCGGGTTCGA-ACTT
1 TTTCGAGTTCGAGA-TT
*
3885234 TTTCGAGTTCGAGCTT
1 TTTCGAGTTCGAGATT
* * * *
3885250 TCTCGGGTTCGAGCTG
1 TTTCGAGTTCGAGATT
* * *
3885266 TCTCGAGTTCGAGCTA
1 TTTCGAGTTCGAGATT
3885282 TTTCGAGTTCGA-ATT
1 TTTCGAGTTCGAGATT
3885297 TTT
1 TTT
3885300 GACTTTTTGA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
15 5 0.07
16 65 0.93
ACGTcount: A:0.13, C:0.18, G:0.27, T:0.42
Consensus pattern (16 bp):
TTTCGAGTTCGAGATT
Found at i:3885238 original size:32 final size:32
Alignment explanation
Indices: 3885202--3885299 Score: 117
Period size: 32 Copynumber: 3.1 Consensus size: 32
3885192 GTTCTGGTTC
* *
3885202 TTTCGGGTTCGAGATTTTTCGGGTTCGAACTT
1 TTTCGAGTTCGAGCTTTTTCGGGTTCGAACTT
* * *
3885234 TTTCGAGTTCGAGCTTTCTCGGGTTCGAGCTG
1 TTTCGAGTTCGAGCTTTTTCGGGTTCGAACTT
* * *
3885266 TCTCGAGTTCGAGCTATTTCGAGTTCGAA-TT
1 TTTCGAGTTCGAGCTTTTTCGGGTTCGAACTT
3885297 TTT
1 TTT
3885300 GACTTTTTGA
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
31 3 0.06
32 51 0.94
ACGTcount: A:0.13, C:0.18, G:0.27, T:0.42
Consensus pattern (32 bp):
TTTCGAGTTCGAGCTTTTTCGGGTTCGAACTT
Found at i:3886291 original size:3 final size:3
Alignment explanation
Indices: 3886276--3886319 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
3886266 GAGAGAAATT
* *
3886276 GAA GAA TAA GAA GAA GAT GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
3886320 CGAATGCAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.05
Consensus pattern (3 bp):
GAA
Found at i:3900357 original size:365 final size:364
Alignment explanation
Indices: 3899360--3900460 Score: 1991
Period size: 365 Copynumber: 3.0 Consensus size: 364
3899350 GAGCACCGGG
3899360 AGGATACGAAAGGTTTTTATTACTTTAAAATCGTAAAATATCCGATTTTCATTTTGAAAAGGGAG
1 AGGATACGAAAGGTTTTTATTACTTTAAAATCGTAAAATATCCGATTTTCATTTTGAAAAGGGAG
3899425 TTTCATCGTTAAAATAACCTGTAAAA---CTCCTATATATATATATGGATGGGAGAAATTTCACG
66 TTTCATCGTTAAAATAACCTGTAAAACTCCTCCTATATATATATATGGATGGGAGAAATTTCACG
3899487 TACCATTTTAACTTCGAGACATTGCCTTTATCTTTTAAAAGATCCAAATTTTATTTAAAACTCGA
131 TACCATTTTAACTTCGAGACATTGCCTTTATCTTTTAAAAGATCCAAATTTTATTTAAAACTCGA
*
3899552 TTTTGAAAAGAATTACAAAAATATCCCTAAGGGTATACTTTGACGTAAAAGCATCCCGGAACATT
196 TTTTGAAAAGAATTATAAAAATATCCCTAAGGGTATACTTTGACGTAAAAGCATCCCGGAACATT
3899617 GAAAAAATGATTAATAAAATAATTTTATCCTAAATGGGTAATTTTCAAGAATTACGTATAAATGT
261 GAAAAAATGATTAATAAAATAATTTTATCCTAAATGGGTAA-TTTCAAGAATTACGTATAAATGT
3899682 CTATGTTTTAAAAATTCATCTCGTTCTCGATGGAACACTA
325 CTATGTTTTAAAAATTCATCTCGTTCTCGATGGAACACTA
*
3899722 AGGATATGAAAGGTTTTTATTACTTTAAAATCGTAAAATATCCGATTTTC-TATTTGAAAAGGGA
1 AGGATACGAAAGGTTTTTATTACTTTAAAATCGTAAAATATCCGATTTTCAT-TTTGAAAAGGGA
3899786 GTTTCATCGTTAAAATAACCTGTAAAACTCCTCC--TATATATATATGGATGGGAGAAATTTCAC
65 GTTTCATCGTTAAAATAACCTGTAAAACTCCTCCTATATATATATATGGATGGGAGAAATTTCAC
* *
3899849 GTACCATTTTAACTTCGAGACATTGCTTTTATCTTTTAAAAAATCCAAATTTTATTTAAAACTCG
130 GTACCATTTTAACTTCGAGACATTGCCTTTATCTTTTAAAAGATCCAAATTTTATTTAAAACTCG
3899914 ATTTTGAAAAGAATTATAAAAATATCCCTAAGGGTATACTTTGACGTAAAAGCATCCCGGAACAT
195 ATTTTGAAAAGAATTATAAAAATATCCCTAAGGGTATACTTTGACGTAAAAGCATCCCGGAACAT
* *
3899979 TGAAAAAATGATTAATAAAATAATTTTATCCTCAATGAGTAA-TTCAAGAATTACGTATAAATGT
260 TGAAAAAATGATTAATAAAATAATTTTATCCTAAATGGGTAATTTCAAGAATTACGTATAAATGT
3900043 CTATGTTTTAAAAATTCATCTCGTTCTCGATGGAACACTA
325 CTATGTTTTAAAAATTCATCTCGTTCTCGATGGAACACTA
* *
3900083 AGGATACGAAAGGTTTTTATTACTTTAAAATTGTAAAATATCTGATTTTCATTTTGAAAAGGGAG
1 AGGATACGAAAGGTTTTTATTACTTTAAAATCGTAAAATATCCGATTTTCATTTTGAAAAGGGAG
3900148 TTTCATCGTTAAAATAACCTGTAAAACTCCTCCTATATATATATATATGGATGGGAGAAATTTCA
66 TTTCATCGTTAAAATAACCTGTAAAACTCCTCC--TATATATATATATGGATGGGAGAAATTTCA
*
3900213 CGTACCATTTTAACTTCGAGACATTGCCTTTATCTTTTAAAAGATTCAAATTTTATTTAAAACTC
129 CGTACCATTTTAACTTCGAGACATTGCCTTTATCTTTTAAAAGATCCAAATTTTATTTAAAACTC
* *
3900278 GATTTTGAAAAGAATTATAAAAATATCCCTAAAGGTATACTTTGATGTAAAAGCATCCCGGAACA
194 GATTTTGAAAAGAATTATAAAAATATCCCTAAGGGTATACTTTGACGTAAAAGCATCCCGGAACA
3900343 TTGAAAAAATGATTAATAAAATAATTTTATCCTAAATGGGTAATTTTCAAGAATTACGTATAAAT
259 TTGAAAAAATGATTAATAAAATAATTTTATCCTAAATGGGTAA-TTTCAAGAATTACGTATAAAT
*
3900408 GTCTATGTTTTAAAAATTTATCTCGTTCTCGATGGAACACTA
323 GTCTATGTTTTAAAAATTCATCTCGTTCTCGATGGAACACTA
3900450 AGAGATACGAA
1 AG-GATACGAA
3900461 TTTTAGGGAT
Statistics
Matches: 710, Mismatches: 17, Indels: 18
0.95 0.02 0.02
Matches are distributed among these distances:
361 156 0.22
362 89 0.13
363 196 0.28
365 198 0.28
367 63 0.09
368 8 0.01
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (364 bp):
AGGATACGAAAGGTTTTTATTACTTTAAAATCGTAAAATATCCGATTTTCATTTTGAAAAGGGAG
TTTCATCGTTAAAATAACCTGTAAAACTCCTCCTATATATATATATGGATGGGAGAAATTTCACG
TACCATTTTAACTTCGAGACATTGCCTTTATCTTTTAAAAGATCCAAATTTTATTTAAAACTCGA
TTTTGAAAAGAATTATAAAAATATCCCTAAGGGTATACTTTGACGTAAAAGCATCCCGGAACATT
GAAAAAATGATTAATAAAATAATTTTATCCTAAATGGGTAATTTCAAGAATTACGTATAAATGTC
TATGTTTTAAAAATTCATCTCGTTCTCGATGGAACACTA
Found at i:3900769 original size:138 final size:138
Alignment explanation
Indices: 3900513--3900798 Score: 464
Period size: 138 Copynumber: 2.1 Consensus size: 138
3900503 CCCCCCACAT
* ** *
3900513 ATTGCATACTTCATGATTTTCTCCATGTGGCCTTTAATTTATTTTGTTTATCATATGTTTCTTCA
1 ATTGCATGCTTCATGATTTTCTCCATGTGGCCTCCAATTCATTTTGTTTATCATATGTTTCTTCA
* * *
3900578 TGATTTGCATCTCCTATCACTTTTTCATTTGCACGTTATTTTGCTTTCTTTTCATTTGCTTGTGT
66 TGATTTGCATCTCCCATCACTTTTTCATTTGCACGTTACTTTGCTTTCTTTTCATTTGCTTGTAT
*
3900643 TCCTTATG
131 TCCTCATG
* *
3900651 ATTGTATGCTTCATGATTTTCTCCATGTGGCCTCCAATTCATTTTGTTTGTCATATGTTTCTTCA
1 ATTGCATGCTTCATGATTTTCTCCATGTGGCCTCCAATTCATTTTGTTTATCATATGTTTCTTCA
* *
3900716 TGATTTGCATCTCCCATCACTTTTTTATTTGCACGTTGCTTTGCTTTCTTTTCATTTGCTTGTAT
66 TGATTTGCATCTCCCATCACTTTTTCATTTGCACGTTACTTTGCTTTCTTTTCATTTGCTTGTAT
3900781 TCCTCATG
131 TCCTCATG
3900789 ATTGCATGCT
1 ATTGCATGCT
3900799 ACATTATATT
Statistics
Matches: 135, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
138 135 1.00
ACGTcount: A:0.15, C:0.20, G:0.13, T:0.52
Consensus pattern (138 bp):
ATTGCATGCTTCATGATTTTCTCCATGTGGCCTCCAATTCATTTTGTTTATCATATGTTTCTTCA
TGATTTGCATCTCCCATCACTTTTTCATTTGCACGTTACTTTGCTTTCTTTTCATTTGCTTGTAT
TCCTCATG
Found at i:3901403 original size:43 final size:43
Alignment explanation
Indices: 3901336--3901706 Score: 313
Period size: 43 Copynumber: 8.7 Consensus size: 43
3901326 AGGCAGTTTT
* * * *
3901336 CAGGGTCAAAGCTGACAAGCAGACTGAGGGATAGAAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTC
* * * * *
3901379 TAGGGTCACAGTCGACAGGTAGACTTTAGAGGATAGGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGAC-TAAG-GGATAGGAAAGTCTC
* * * * * * *
3901424 CAGGGTCAAAGCTGGCAGCCAGACTAAAGG-TAAGAAAAGTTTT
1 CAGGGTCAAAGCCGACAGGCAGACTAAGGGAT-AGGAAAGTCTC
** * * * *
3901467 CAGGGTCAAAGTTGACAGGCAGACTAAGAGATAGGAAGGTTTT
1 CAGGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTC
* ** * *
3901510 CAGGGTCAAAGTCGGTAGACAGACTAAGGGATAGGAAAGTCCC
1 CAGGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTC
* *
3901553 CAAGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTT
1 CAGGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTC
* * * * *
3901596 CAGGGTCAAAGCCGACAGGCAAACTGAGAGA-AAGAAAGTTTC
1 CAGGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTC
*
3901638 CAGGGTC-AA-CCGACAGGCAGACTAAGGG--AGAAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTC
* * * *
3901677 CAGAGTTAAAGCTGACAGGTAGACTGAAGG
1 CAGGGTCAAAGCCGACAGGCAGACT-AAGG
3901707 TCAAAAAGAA
Statistics
Matches: 261, Mismatches: 60, Indels: 15
0.78 0.18 0.04
Matches are distributed among these distances:
39 13 0.05
40 18 0.07
41 14 0.05
42 20 0.08
43 159 0.61
44 6 0.02
45 31 0.12
ACGTcount: A:0.36, C:0.17, G:0.31, T:0.16
Consensus pattern (43 bp):
CAGGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTC
Found at i:3909482 original size:22 final size:22
Alignment explanation
Indices: 3909435--3909476 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3909425 CTTTATACAC
*
3909435 ATTTTATTAATTTTTAATATAT
1 ATTTTATTAATTTTAAATATAT
3909457 ATTTTATT-ATTTATAAATAT
1 ATTTTATTAATTT-TAAATAT
3909477 TAATTTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTTATTAATTTTAAATATAT
Found at i:3909873 original size:18 final size:18
Alignment explanation
Indices: 3909847--3909882 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3909837 ATATTGAATT
*
3909847 AAATTAAATTTACATTTA
1 AAATAAAATTTACATTTA
*
3909865 AAATAAAATTTATATTTA
1 AAATAAAATTTACATTTA
3909883 TTTAACTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATAAAATTTACATTTA
Found at i:3915537 original size:20 final size:21
Alignment explanation
Indices: 3915512--3915563 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
3915502 ATAGGGTCTA
*
3915512 GTATCGATACATTCA-TT-TAT
1 GTATCGATACATTAACTTGT-T
3915532 GTATCGATACATTAACTTGTT
1 GTATCGATACATTAACTTGTT
3915553 GTATCGATACA
1 GTATCGATACA
3915564 AATTATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 14 0.48
21 14 0.48
22 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (21 bp):
GTATCGATACATTAACTTGTT
Found at i:3923101 original size:16 final size:15
Alignment explanation
Indices: 3923082--3923172 Score: 53
Period size: 16 Copynumber: 5.9 Consensus size: 15
3923072 ATTTTAAATA
3923082 AATTTAATTATTTTAT
1 AATTT-ATTATTTTAT
*
3923098 AATTT-TTATTTTTT
1 AATTTATTATTTTAT
3923112 ATATTT-TTA-TTTAT
1 A-ATTTATTATTTTAT
* *
3923126 AAATTAATAAATTTTAT
1 -AATTTAT-TATTTTAT
* * *
3923143 GATTTTATAATTTTACA
1 -AATTTATTATTTTA-T
3923160 AATTTATTATTTT
1 AATTTATTATTTT
3923173 TATTAATATA
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
14 16 0.27
15 9 0.15
16 24 0.41
17 10 0.17
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (15 bp):
AATTTATTATTTTAT
Found at i:3923108 original size:14 final size:14
Alignment explanation
Indices: 3923089--3923127 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
3923079 ATAAATTTAA
3923089 TTATTTTATAATTT
1 TTATTTTATAATTT
*
3923103 TTATTTTTTATATTT
1 TTATTTTATA-ATTT
3923118 TTA-TTTATAA
1 TTATTTTATAA
3923128 ATTAATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 1 0.05
14 14 0.64
15 7 0.32
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATTTTATAATTT
Found at i:3923117 original size:15 final size:16
Alignment explanation
Indices: 3923092--3923123 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3923082 AATTTAATTA
3923092 TTTTATAATTTTTATT
1 TTTTATAATTTTTATT
3923108 TTTTAT-ATTTTTATT
1 TTTTATAATTTTTATT
3923123 T
1 T
3923124 ATAAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTATAATTTTTATT
Found at i:3924125 original size:15 final size:16
Alignment explanation
Indices: 3924096--3924127 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3924086 ATTAATATAT
3924096 TAAAATTTATTTTAAA
1 TAAAATTTATTTTAAA
3924112 TAAAATTT-TTTTAAA
1 TAAAATTTATTTTAAA
3924127 T
1 T
3924128 TTAACTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAAATTTATTTTAAA
Found at i:3925016 original size:18 final size:18
Alignment explanation
Indices: 3924995--3925052 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
3924985 TAAATAATTT
*
3924995 AAAATTTGTAAAA-TAAA
1 AAAAATTGTAAAATTAAA
*
3925012 AAAAATTG-AAAATTTTAA
1 AAAAATTGTAAAA-TTAAA
*
3925030 AAAAATTGTAAAGAGTAAA
1 AAAAATTGTAAA-ATTAAA
3925049 AAAA
1 AAAA
3925053 TAAAGGTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 4 0.12
17 7 0.21
18 11 0.33
19 10 0.30
20 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
AAAAATTGTAAAATTAAA
Found at i:3925403 original size:16 final size:16
Alignment explanation
Indices: 3925384--3925439 Score: 69
Period size: 17 Copynumber: 3.5 Consensus size: 16
3925374 AATTTGATGA
*
3925384 AATAAAAAATAATTAT
1 AATAAAAAATAATAAT
3925400 AATAAAATAATAATAAT
1 AATAAAA-AATAATAAT
*
3925417 ATTAAAAAATAA-AAT
1 AATAAAAAATAATAAT
*
3925432 AAGAAAAA
1 AATAAAAA
3925440 TATGTAGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 9 0.26
16 12 0.34
17 14 0.40
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (16 bp):
AATAAAAAATAATAAT
Found at i:3925408 original size:14 final size:14
Alignment explanation
Indices: 3925384--3925417 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3925374 AATTTGATGA
3925384 AATAA-AAAATAAT
1 AATAATAAAATAAT
*
3925397 TATAATAAAATAAT
1 AATAATAAAATAAT
3925411 AATAATA
1 AATAATA
3925418 TTAAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AATAATAAAATAAT
Found at i:3929760 original size:3 final size:3
Alignment explanation
Indices: 3929752--3929782 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3929742 TATATTTTTG
*
3929752 TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3929783 TATTTATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3930637 original size:24 final size:24
Alignment explanation
Indices: 3930610--3930657 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3930600 AAGTTCAGTT
3930610 TAACAAGCAGC-AAAGCTAAATCCA
1 TAACAAGCAGCAAAAG-TAAATCCA
3930634 TAACAAGCAGCAAAAGTAAATCCA
1 TAACAAGCAGCAAAAGTAAATCCA
3930658 ATTTCCTCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.52, C:0.23, G:0.12, T:0.12
Consensus pattern (24 bp):
TAACAAGCAGCAAAAGTAAATCCA
Found at i:3930933 original size:3 final size:3
Alignment explanation
Indices: 3930925--3930956 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3930915 GGTTTGACTA
3930925 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3930957 TAGTAGTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:3933493 original size:19 final size:19
Alignment explanation
Indices: 3933454--3933493 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3933444 TATATAAAAT
*
3933454 AATATGTATTAAAATTTTA
1 AATATGTATTAAAATTATA
3933473 AATAT-TATTAAAATATATA
1 AATATGTATTAAAAT-TATA
3933492 AA
1 AA
3933494 AATAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
AATATGTATTAAAATTATA
Found at i:3934211 original size:15 final size:16
Alignment explanation
Indices: 3934191--3934222 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3934181 TAGTCATATC
3934191 ATATTTA-AAATTATT
1 ATATTTATAAATTATT
3934206 ATATTTATAAATTATT
1 ATATTTATAAATTATT
3934222 A
1 A
3934223 ATTATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTTATAAATTATT
Found at i:3934596 original size:21 final size:21
Alignment explanation
Indices: 3934572--3934624 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
3934562 TATTAAATTA
*
3934572 ATTATTTTA-AATATTATTATG
1 ATTAATTTATAATA-TATTATG
3934593 ATTAATTTATAATATATTAT-
1 ATTAATTTATAATATATTATG
3934613 ATT--TTTATAATA
1 ATTAATTTATAATA
3934625 AATTCTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 9 0.30
20 3 0.10
21 14 0.47
22 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTAATTTATAATATATTATG
Found at i:3934786 original size:19 final size:19
Alignment explanation
Indices: 3934764--3934805 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
3934754 TAATTTTATT
*
3934764 TTTAAATATAAA-TATTTAA
1 TTTAAATAAAAATTA-TTAA
*
3934783 TTTATATAAAAATTATTAA
1 TTTAAATAAAAATTATTAA
3934802 TTTA
1 TTTA
3934806 TCATAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAAATAAAAATTATTAA
Found at i:3934876 original size:16 final size:16
Alignment explanation
Indices: 3934850--3934907 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
3934840 ACTCAAATAA
*
3934850 AATTTAAATTTAAAAT
1 AATTAAAATTTAAAAT
*
3934866 AATCAAAATTTAAAAT
1 AATTAAAATTTAAAAT
* *
3934882 AAATTTAAATTTTAAAT
1 -AATTAAAATTTAAAAT
3934899 AATTAAAAT
1 AATTAAAAT
3934908 AATATAAACT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 22 0.63
17 13 0.37
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTAAAATTTAAAAT
Found at i:3934886 original size:33 final size:34
Alignment explanation
Indices: 3934844--3934907 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
3934834 ATTTAAACTC
3934844 AAATAAAATTTAAATTTAAAATAATCAAAATTTA
1 AAATAAAATTTAAATTTAAAATAATCAAAATTTA
* *
3934878 AAAT-AAATTTAAATTTTAAATAATTAAAAT
1 AAATAAAATTTAAATTTAAAATAATCAAAAT
3934908 AATATAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (34 bp):
AAATAAAATTTAAATTTAAAATAATCAAAATTTA
Found at i:3934893 original size:17 final size:17
Alignment explanation
Indices: 3934844--3934900 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
3934834 ATTTAAACTC
3934844 AAATAAAATTTAAATTTA
1 AAAT-AAATTTAAATTTA
**
3934862 AAAT-AATCAAAATTTA
1 AAATAAATTTAAATTTA
*
3934878 AAATAAATTTAAATTTT
1 AAATAAATTTAAATTTA
3934895 AAATAA
1 AAATAA
3934901 TTAAAATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
16 14 0.42
17 15 0.45
18 4 0.12
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATAAATTTAAATTTA
Found at i:3936314 original size:10 final size:10
Alignment explanation
Indices: 3936299--3936328 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3936289 AAAATGCTAC
3936299 TTAAATTTAT
1 TTAAATTTAT
*
3936309 TTAAATTTGT
1 TTAAATTTAT
3936319 TTAAATTTAT
1 TTAAATTTAT
3936329 AAAAATACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (10 bp):
TTAAATTTAT
Found at i:3937779 original size:17 final size:18
Alignment explanation
Indices: 3937749--3937782 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3937739 CTTGTCTACC
3937749 TTTTTCTAATTATTATTA
1 TTTTTCTAATTATTATTA
*
3937767 TTTTTTTAA-TATTATT
1 TTTTTCTAATTATTATT
3937783 TCACATTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTCTAATTATTATTA
Found at i:3938013 original size:17 final size:18
Alignment explanation
Indices: 3937984--3938023 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
3937974 AATATAATTG
3937984 ATTAAATTAATATCATCA
1 ATTAAATTAATATCATCA
*
3938002 ATTAAA-TAATATTATCA
1 ATTAAATTAATATCATCA
3938019 ATTAA
1 ATTAA
3938024 TAAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTAAATTAATATCATCA
Found at i:3938561 original size:23 final size:23
Alignment explanation
Indices: 3938528--3938581 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
3938518 ATAAATAAAT
3938528 TCATTTA-TAGTTCATTTAAAGC
1 TCATTTATTAGTTCATTTAAAGC
** *
3938550 TCATTTATTAGTTTGTTTAAAGT
1 TCATTTATTAGTTCATTTAAAGC
*
3938573 TCGTTTATT
1 TCATTTATT
3938582 GTACTATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (23 bp):
TCATTTATTAGTTCATTTAAAGC
Found at i:3945236 original size:14 final size:14
Alignment explanation
Indices: 3945214--3945245 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3945204 GTATCATTCG
*
3945214 TATCGATTGGTTTC
1 TATCCATTGGTTTC
3945228 TATCCATTGGTTTC
1 TATCCATTGGTTTC
3945242 TATC
1 TATC
3945246 AATTTTGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50
Consensus pattern (14 bp):
TATCCATTGGTTTC
Found at i:3949992 original size:15 final size:15
Alignment explanation
Indices: 3949972--3950002 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3949962 AATCTGAAAC
*
3949972 AAAAACAAAAATAAA
1 AAAAACAAAAACAAA
3949987 AAAAACAAAAACAAA
1 AAAAACAAAAACAAA
3950002 A
1 A
3950003 TCAAACCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.10, G:0.00, T:0.03
Consensus pattern (15 bp):
AAAAACAAAAACAAA
Found at i:3950713 original size:19 final size:20
Alignment explanation
Indices: 3950689--3950733 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
3950679 AGGAATTAAG
3950689 ATTTATTTAATTATTATAT-
1 ATTTATTTAATTATTATATA
* *
3950708 ATTTATTTTATTATTTTATA
1 ATTTATTTAATTATTATATA
3950728 ATTTAT
1 ATTTAT
3950734 ATTTAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTATTTAATTATTATATA
Found at i:3950719 original size:24 final size:21
Alignment explanation
Indices: 3950692--3950738 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
3950682 AATTAAGATT
*
3950692 TATTTAATTATTATAT-ATTTA
1 TATTT-ATTATTTTATAATTTA
3950713 T-TTTATTATTTTATAATTTA
1 TATTTATTATTTTATAATTTA
3950733 TATTTA
1 TATTTA
3950739 AATTTTGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 9 0.39
21 5 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTTATTATTTTATAATTTA
Found at i:3950743 original size:20 final size:20
Alignment explanation
Indices: 3950692--3950749 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
3950682 AATTAAGATT
3950692 TATTT-AATTATTATATATTTA
1 TATTTAAATT-TTATA-ATTTA
*
3950713 T-TTTATTATTTTATAATTTA
1 TATTTA-AATTTTATAATTTA
*
3950733 TATTTAAATTTTGTAAT
1 TATTTAAATTTTATAAT
3950750 AATTTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 18 0.58
21 10 0.32
22 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TATTTAAATTTTATAATTTA
Found at i:3951087 original size:18 final size:19
Alignment explanation
Indices: 3951064--3951099 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3951054 GATTTTATGA
3951064 ATTTTTATATTA-TATTAG
1 ATTTTTATATTATTATTAG
*
3951082 ATTTTTTTATTATTATTA
1 ATTTTTATATTATTATTA
3951100 TTATTATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
ATTTTTATATTATTATTAG
Found at i:3951094 original size:3 final size:3
Alignment explanation
Indices: 3951088--3951115 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3951078 TTAGATTTTT
3951088 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3951116 ATAATACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3954316 original size:3 final size:3
Alignment explanation
Indices: 3954308--3954347 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
3954298 ACCCACCTGG
* * *
3954308 TGA TGA TGA TGA TAA TGA TGA TAA TGA TGA TAA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
3954348 AATATAACTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.25, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:3954325 original size:9 final size:9
Alignment explanation
Indices: 3954308--3954350 Score: 77
Period size: 9 Copynumber: 4.8 Consensus size: 9
3954298 ACCCACCTGG
*
3954308 TGATGATGA
1 TGATAATGA
3954317 TGATAATGA
1 TGATAATGA
3954326 TGATAATGA
1 TGATAATGA
3954335 TGATAATGA
1 TGATAATGA
3954344 TGATAAT
1 TGATAAT
3954351 ATAACTATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (9 bp):
TGATAATGA
Found at i:3957866 original size:13 final size:13
Alignment explanation
Indices: 3957848--3957874 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3957838 GATGACCAGC
3957848 AAAGTGACACTAT
1 AAAGTGACACTAT
3957861 AAAGTGACACTAT
1 AAAGTGACACTAT
3957874 A
1 A
3957875 CTCAATAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (13 bp):
AAAGTGACACTAT
Found at i:3958485 original size:28 final size:28
Alignment explanation
Indices: 3958449--3958503 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
3958439 ATGATTTTTT
*
3958449 TATTTTATTAAAATTA-TTTATATATTTG
1 TATTGTATTAAAATTATTTTAT-TATTTG
* *
3958477 TATTGTATTTATATTATTTTATTATTT
1 TATTGTATTAAAATTATTTTATTATTT
3958504 CAATCGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (28 bp):
TATTGTATTAAAATTATTTTATTATTTG
Found at i:3958487 original size:19 final size:19
Alignment explanation
Indices: 3958463--3958499 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3958453 TTATTAAAAT
3958463 TATTTATA-TATTTGTATTG
1 TATTTATATTATTT-TATTG
3958482 TATTTATATTATTTTATT
1 TATTTATATTATTTTATT
3958500 ATTTCAATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
TATTTATATTATTTTATTG
Found at i:3962046 original size:20 final size:21
Alignment explanation
Indices: 3962010--3962048 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
3962000 ATATAATAAT
3962010 AAAATTAAATAAATATAAATC
1 AAAATTAAATAAATATAAATC
3962031 AAAA-TAAA-AAATTATAAA
1 AAAATTAAATAAA-TATAAA
3962049 ATTAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 10 0.59
21 4 0.24
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAATTAAATAAATATAAATC
Found at i:3962096 original size:2 final size:2
Alignment explanation
Indices: 3962089--3962117 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3962079 ACAAATCCAT
3962089 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3962118 ATACATACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.