Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 100 of 204
Found at i:31084334 original size:63 final size:62
Alignment explanation
Indices: 31084207--31084765 Score: 561
Period size: 63 Copynumber: 9.3 Consensus size: 62
31084197 ACATAAATTA
* *
31084207 GGTTAGGGTTTTTAATT-A--AAA-TATGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTAAGTTAG
* *
31084266 AGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAAGTTAG
1 GGTTAGGGTTTTTAATT-AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAG
*
31084329 GGTTAGGGTTTTTAATT-A--AAA-TAGGTTAGGGTTAGGGTTTTAAATTAAATTAAATTAGGTT
1 GGTTAGGGTTTTTAATTAATTAAATTAGGTTAGGGTTAGGG-TTT---TT-AATTAAATTAAGTT
31084390 AG
61 AG
* * * *
31084392 AGTTAGGGTTTTTAATTAA-T---TTAGGTTAGAGTTAGGGTTTTTAAATAAATTAAATTA-
1 GGTTAGGGTTTTTAATTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAG
*
31084449 GGTTA-GGTTTTTAATT-A--AAA-TAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAG
* * * *
31084506 GGTTAGGG--TTT--TTAATTAAATTAGGCTAGGGTTACGGTTTTTAATTAAAATAGGTTAG
1 GGTTAGGGTTTTTAATTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAG
* *
31084564 GGTTAGGGTTTTTAATTAAATTAAATTAGGCTAAGGGTTAGGGTTTTTAATTAAATTAAATTA-
1 GGTTAGGGTTTTTAATT-AATTAAATTAGG-TTAGGGTTAGGGTTTTTAATTAAATTAAGTTAG
* * *
31084627 GGCTAGGGTTAGGGTTT--TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAATAAATTAAATT-
1 GGTTAGGGTT----TTTAATTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTA
31084689 G
62 G
* *
31084690 GGTTAGGATTTTTAATTAAATT-AA--A--TTA-GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATT-AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAG
*
31084747 GGTTTAGGGTTTTTTATTA
1 GG-TTAGGGTTTTTAATTA
31084766 CGGTTAGGGG
Statistics
Matches: 426, Mismatches: 36, Indels: 78
0.79 0.07 0.14
Matches are distributed among these distances:
54 2 0.00
55 2 0.00
56 70 0.16
57 19 0.04
58 85 0.20
59 28 0.07
60 3 0.01
61 6 0.01
62 11 0.03
63 147 0.35
64 48 0.11
65 2 0.00
67 3 0.01
ACGTcount: A:0.32, C:0.01, G:0.24, T:0.44
Consensus pattern (62 bp):
GGTTAGGGTTTTTAATTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAGTTAG
Found at i:31084478 original size:241 final size:243
Alignment explanation
Indices: 31084200--31084765 Score: 862
Period size: 241 Copynumber: 2.3 Consensus size: 243
31084190 GGTTTTTACA
*
31084200 TAAATTAGGTTAGGGTTTTTAATTAAAATATGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTA
1 TAAATTAGGTTA-GGTTTTTAATTAAAATAAGTTAGGG-TTAGGGTTTTTAATTAAATTAGGTTA
* * *
31084265 GAGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAATAAGTTAGG
64 GGGTTAGGGTTTTT-ATTAAATTAAATTAGGCTAGGGTTACGGTTTTTAATTAAAATAAGTTAGG
* *
31084330 GTTAGGGTTTTTAATT-A-AAA-TAGG-TTAGGGTTAGGGTTTTAAATTAAATTAAATTAGGTTA
128 GTTAGGGTTTTTAATTAATAAATTAGGCTAAGGGTTAGGGTTTTAAATTAAATTAAATTAGGCTA
*
31084391 GAGTTAGGGTTTTTAATTAATTTAGGTTAGAGTTAGGGTTTTTAAATAAAT
193 GAGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAAATAAAT
*
31084442 TAAATTAGGTTAGGTTTTTAATTAAAATAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGG
1 TAAATTAGGTTAGGTTTTTAATTAAAATAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGG
*
31084507 GTTAGGG--TTT-TT-AATTAAATTAGGCTAGGGTTACGGTTTTTAATTAAAATAGGTTAGGGTT
66 GTTAGGGTTTTTATTAAATTAAATTAGGCTAGGGTTACGGTTTTTAATTAAAATAAGTTAGGGTT
*
31084568 AGGGTTTTTAATTAAATTAAATTAGGCTAAGGGTTAGGGTTTTTAATTAAATTAAATTAGGCTAG
131 AGGGTTTTTAATT-AA-TAAATTAGGCTAAGGGTTAGGGTTTTAAATTAAATTAAATTAGGCTAG
* *
31084633 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAATAAAT
194 AGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAAATAAAT
* * *
31084683 TAAATTGGGTTAGGATTTTTAATTAAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 TAAATTAGGTTAGG-TTTTTAATTAAAATAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAG
31084747 GGTTTAGGGTTTTTTATTA
65 GG-TTAGGG-TTTTTATTA
31084766 CGGTTAGGGG
Statistics
Matches: 296, Mismatches: 15, Indels: 21
0.89 0.05 0.06
Matches are distributed among these distances:
235 59 0.20
236 2 0.01
237 1 0.00
238 3 0.01
239 3 0.01
240 38 0.13
241 150 0.51
242 35 0.12
245 3 0.01
246 2 0.01
ACGTcount: A:0.32, C:0.01, G:0.23, T:0.44
Consensus pattern (243 bp):
TAAATTAGGTTAGGTTTTTAATTAAAATAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGG
GTTAGGGTTTTTATTAAATTAAATTAGGCTAGGGTTACGGTTTTTAATTAAAATAAGTTAGGGTT
AGGGTTTTTAATTAATAAATTAGGCTAAGGGTTAGGGTTTTAAATTAAATTAAATTAGGCTAGAG
TTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAAATAAAT
Found at i:31084772 original size:26 final size:25
Alignment explanation
Indices: 31084737--31084786 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
31084727 TTTTAATTAA
*
31084737 ATTAGGTTAGGGTTTAGGGTTTTTT
1 ATTAGGTTAGGGGTTAGGGTTTTTT
31084762 ATTACGGTTAGGGGTTAGGGTTTTT
1 ATTA-GGTTAGGGGTTAGGGTTTTT
31084787 AAATAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.16, C:0.02, G:0.34, T:0.48
Consensus pattern (25 bp):
ATTAGGTTAGGGGTTAGGGTTTTTT
Found at i:31086968 original size:14 final size:15
Alignment explanation
Indices: 31086951--31086983 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
31086941 TAATAATTAT
31086951 ATAAAAATA-CATAA
1 ATAAAAATATCATAA
*
31086965 ATAAAAATATCTTAA
1 ATAAAAATATCATAA
31086980 ATAA
1 ATAA
31086984 TATTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAAAAATATCATAA
Found at i:31087102 original size:10 final size:10
Alignment explanation
Indices: 31087089--31087138 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
31087079 ATATTAAAAA
31087089 ATTTAAAATT
1 ATTTAAAATT
**
31087099 ATTTTAAAAAA
1 A-TTTAAAATT
*
31087110 ATATAAAATT
1 ATTTAAAATT
31087120 ATTTAAAATT
1 ATTTAAAATT
31087130 ATCTTAAAA
1 AT-TTAAAA
31087139 AATGAAATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
10 18 0.56
11 14 0.44
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (10 bp):
ATTTAAAATT
Found at i:31087111 original size:31 final size:31
Alignment explanation
Indices: 31087076--31087140 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
31087066 GCCATTGTTG
*
31087076 AAAATATTAAAA-AATTTAAAATTATTTTAAA
1 AAAATA-TAAAATAATTTAAAATTATCTTAAA
*
31087107 AAAATATAAAATTATTTAAAATTATCTTAAA
1 AAAATATAAAATAATTTAAAATTATCTTAAA
31087138 AAA
1 AAA
31087141 TGAAATTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (31 bp):
AAAATATAAAATAATTTAAAATTATCTTAAA
Found at i:31087138 original size:21 final size:21
Alignment explanation
Indices: 31087084--31087127 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
31087074 TGAAAATATT
31087084 AAAAAATTTAAAATTATTTTA
1 AAAAAATTTAAAATTATTTTA
*
31087105 AAAAAATATAAAATTA-TTTA
1 AAAAAATTTAAAATTATTTTA
31087125 AAA
1 AAA
31087128 TTATCTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAAATTTAAAATTATTTTA
Found at i:31087162 original size:17 final size:18
Alignment explanation
Indices: 31087136--31087169 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
31087126 AATTATCTTA
31087136 AAAAATGAAATTGAATAG
1 AAAAATGAAATTGAATAG
*
31087154 AAAAA-GAAATTTAATA
1 AAAAATGAAATTGAATA
31087170 TGGATTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (18 bp):
AAAAATGAAATTGAATAG
Found at i:31087209 original size:22 final size:22
Alignment explanation
Indices: 31087184--31087225 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
31087174 TTTTAGAGAT
31087184 TTTTGGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
31087206 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
31087226 TTTGAGAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.31
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:31091156 original size:26 final size:25
Alignment explanation
Indices: 31091127--31091224 Score: 70
Period size: 26 Copynumber: 3.6 Consensus size: 25
31091117 ATCTTTTTGA
31091127 TTTTTTATTTGTTTGTCCTTTTTCCTT
1 TTTTTTATTTGTTTGTCCTTTTT-C-T
* * * * *
31091154 TTTCCTTTTTTTCTTTATTTCATTTTTTT
1 TTT--TTTATTT-GTT-TGTCCTTTTTCT
31091183 ATTTTTTTATTTGTTTGTCCTTTTTCT
1 -T-TTTTTATTTGTTTGTCCTTTTTCT
31091210 TATTTTTATTTGTTT
1 T-TTTTTATTTGTTT
31091225 TTCTTTATTT
Statistics
Matches: 54, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
26 14 0.26
27 12 0.22
28 2 0.04
29 13 0.24
30 3 0.06
31 10 0.19
ACGTcount: A:0.07, C:0.11, G:0.05, T:0.77
Consensus pattern (25 bp):
TTTTTTATTTGTTTGTCCTTTTTCT
Found at i:31091189 original size:7 final size:8
Alignment explanation
Indices: 31091159--31091311 Score: 62
Period size: 9 Copynumber: 17.9 Consensus size: 8
31091149 TCCTTTTTCC
*
31091159 TTTTTTTC
1 TTTTTTTA
*
31091167 TTTATTTCA
1 TTT-TTTTA
31091176 TTTTTTTA
1 TTTTTTTA
31091184 TTTTTTTA
1 TTTTTTTA
*
31091192 TTTGTTTGTCC
1 TTT-TTT-T-A
31091203 TTTTTCTTA
1 TTTTT-TTA
31091212 TTTTTATT-
1 TTTTT-TTA
* *
31091220 TGTTTTTC
1 TTTTTTTA
*
31091228 TTTATTTCA
1 TTT-TTTTA
31091237 TTTTTCTCT-
1 TTTTT-T-TA
31091246 TTTTTTTA
1 TTTTTTTA
31091254 TTTGTTTT-
1 TTT-TTTTA
*
31091262 TCTTTATTTC
1 T-TTT-TTTA
*
31091272 TTTATTTCA
1 TTT-TTTTA
*
31091281 TTTTTCTA
1 TTTTTTTA
31091289 -TTTTTTA
1 TTTTTTTA
*
31091296 TTTGTTTA
1 TTTTTTTA
31091304 TTATTTTT
1 TT-TTTTT
31091312 TATAATATTT
Statistics
Matches: 110, Mismatches: 18, Indels: 33
0.68 0.11 0.20
Matches are distributed among these distances:
7 9 0.08
8 43 0.39
9 48 0.44
10 6 0.05
11 4 0.04
ACGTcount: A:0.10, C:0.08, G:0.03, T:0.78
Consensus pattern (8 bp):
TTTTTTTA
Found at i:31091208 original size:58 final size:60
Alignment explanation
Indices: 31091110--31091260 Score: 193
Period size: 58 Copynumber: 2.5 Consensus size: 60
31091100 TTCTACTACC
* * *
31091110 TATTGTCATCTTTTTGA-TTTTTTATTTGTTTGTCCTTTTTC-CTTTTTCCTT-TTTTTCTT
1 TATT-TCAT-TTTTTTATTTTTTTATTTGTTTGTCCTTTTTCTATTTTTACTTGTTTTTCTT
*
31091169 TATTTCATTTTTTTATTTTTTTATTTGTTTGTCCTTTTTCTTATTTTTATTTGTTTTTCTT
1 TATTTCATTTTTTTATTTTTTTATTTGTTTGTCCTTTTTC-TATTTTTACTTGTTTTTCTT
31091230 TATTTCATTTTTCTCT-TTTTTTTATTTGTTT
1 TATTTCATTTTT-T-TATTTTTTTATTTGTTT
31091261 TTCTTTATTT
Statistics
Matches: 82, Mismatches: 4, Indels: 9
0.86 0.04 0.09
Matches are distributed among these distances:
57 6 0.07
58 28 0.34
59 4 0.05
60 7 0.09
61 20 0.24
62 16 0.20
63 1 0.01
ACGTcount: A:0.09, C:0.11, G:0.05, T:0.75
Consensus pattern (60 bp):
TATTTCATTTTTTTATTTTTTTATTTGTTTGTCCTTTTTCTATTTTTACTTGTTTTTCTT
Found at i:31091285 original size:36 final size:34
Alignment explanation
Indices: 31091152--31091305 Score: 134
Period size: 36 Copynumber: 4.4 Consensus size: 34
31091142 TCCTTTTTCC
* *
31091152 TTTTTCCTTTTTTTCTTTATTTCATTTTTTTATTT-
1 TTTTT-CTTTATTTCTTT-TTTCTTTTTTTTATTTG
* *
31091187 TTTTAT-TTGT-TTGTCCTTTTTCTTATTTTTATTTG
1 TTTT-TCTT-TATT-TCTTTTTTCTTTTTTTTATTTG
31091222 TTTTTCTTTATTTCATTTTTCTCTTTTTTTTATTTG
1 TTTTTCTTTATTTC-TTTTT-TCTTTTTTTTATTTG
* * *
31091258 TTTTTCTTTATTTCTTTATTTCATTTTTCTATTTT
1 TTTTTCTTTATTTCTTT-TTTCTTTTTTTTATTTG
*
31091293 TTATTTGTTTATT
1 TT-TTTCTTTATT
31091306 ATTTTTTATA
Statistics
Matches: 100, Mismatches: 9, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
34 22 0.22
35 38 0.38
36 40 0.40
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.77
Consensus pattern (34 bp):
TTTTTCTTTATTTCTTTTTTCTTTTTTTTATTTG
Found at i:31091298 original size:84 final size:84
Alignment explanation
Indices: 31091128--31091283 Score: 199
Period size: 84 Copynumber: 1.8 Consensus size: 84
31091118 TCTTTTTGAT
* * *
31091128 TTTTTATTTGTTTGTCCTTTTTCCTTTTTCCTTTTTTTCTTTATTTCATTTTTTTATTTTTTTAT
1 TTTTTATTTGTTTGTCCTTTTTCATTTTTCCTCTTTTTCTTTATTTCATTTTTTTATTTCTTTAT
*
31091193 TTGTTTGTCCTTTTTCTTA
66 TTATTTGTCCTTTTTCTTA
* * **
31091212 TTTTTATTTGTTTTTCTTTATTTCATTTTT-CTCTTTTT-TTTATTTGTTTTTCTTTATTTCTTT
1 TTTTTATTTGTTTGTCCTT-TTTCATTTTTCCTCTTTTTCTTTATTTCATTTT-TTTATTTCTTT
31091275 ATTTCATTT
64 ATTT-ATTT
31091284 TTCTATTTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
83 11 0.18
84 38 0.62
85 12 0.20
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.76
Consensus pattern (84 bp):
TTTTTATTTGTTTGTCCTTTTTCATTTTTCCTCTTTTTCTTTATTTCATTTTTTTATTTCTTTAT
TTATTTGTCCTTTTTCTTA
Found at i:31091529 original size:11 final size:10
Alignment explanation
Indices: 31091507--31091550 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 10
31091497 ATGGAGGACC
*
31091507 AAAAAATAAA
1 AAAAAATGAA
31091517 AAAAAACTGAA
1 AAAAAA-TGAA
31091528 AAAAAATGAGA
1 AAAAAATGA-A
31091539 AAAAAATTGAA
1 AAAAAA-TGAA
31091550 A
1 A
31091551 GTTGAATTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 9 0.30
11 18 0.60
12 3 0.10
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.11
Consensus pattern (10 bp):
AAAAAATGAA
Found at i:31097718 original size:21 final size:21
Alignment explanation
Indices: 31097679--31097744 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
31097669 CTTTAAAAAT
31097679 AATTTTAAAAAATTATATTTAA
1 AATTTTAAAAAA-TATATTTAA
31097701 AATTTTAAAAAA-AGTATTTAA
1 AATTTTAAAAAATA-TATTTAA
* * *
31097722 ACTTCTTAAAATATACATTTAA
1 AATT-TTAAAAAATATATTTAA
31097744 A
1 A
31097745 TGTTATAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.03
21 10 0.26
22 26 0.68
23 1 0.03
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (21 bp):
AATTTTAAAAAATATATTTAA
Found at i:31097829 original size:23 final size:23
Alignment explanation
Indices: 31097802--31097867 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
31097792 ATATATTTTA
*
31097802 AATATTTTATAACATTAAAAAAT
1 AATATTTTAAAACATTAAAAAAT
* **
31097825 TATA-TTTAAAATTTTAAAAAAT
1 AATATTTTAAAACATTAAAAAAT
* *
31097847 AATATTATAAAACATTTAAAA
1 AATATTTTAAAACATTAAAAA
31097868 TATACATTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 18 0.55
23 15 0.45
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (23 bp):
AATATTTTAAAACATTAAAAAAT
Found at i:31097841 original size:22 final size:22
Alignment explanation
Indices: 31097816--31097890 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
31097806 TTTTATAACA
31097816 TTAAAAAATTATATTTAAAATT
1 TTAAAAAATTATATTTAAAATT
* *
31097838 TTAAAAAATAATATTATAAAACAT
1 TTAAAAAATTATATT-TAAAA-TT
* *
31097862 TTAAAATA-TACATTTAAAATAT
1 TTAAAAAATTATATTTAAAAT-T
*
31097884 TTTAAAA
1 TTAAAAA
31097891 CAAATAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
22 25 0.60
23 9 0.21
24 8 0.19
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAAAATTATATTTAAAATT
Found at i:31097861 original size:45 final size:46
Alignment explanation
Indices: 31097802--31097890 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 46
31097792 ATATATTTTA
* * *
31097802 AATATTTTATAACATTAAAAA-ATTATATTTAAAAT-TTTAAAAAAT
1 AATATTATAAAACATTAAAAATA-TACATTTAAAATATTTAAAAAAT
* *
31097847 AATATTATAAAACATTTAAAATATACATTTAAAATATTTTAAAA
1 AATATTATAAAACATTAAAAATATACATTTAAAATATTTAAAAA
31097891 CAAATAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
45 29 0.78
46 8 0.22
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (46 bp):
AATATTATAAAACATTAAAAATATACATTTAAAATATTTAAAAAAT
Found at i:31097874 original size:13 final size:13
Alignment explanation
Indices: 31097858--31097883 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31097848 ATATTATAAA
31097858 ACATTTAAAATAT
1 ACATTTAAAATAT
31097871 ACATTTAAAATAT
1 ACATTTAAAATAT
31097884 TTTAAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATTTAAAATAT
Found at i:31097887 original size:23 final size:22
Alignment explanation
Indices: 31097820--31097890 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 22
31097810 ATAACATTAA
31097820 AAAAT-TATATTT-AAAATTTT
1 AAAATATATATTTAAAAATTTT
*
31097840 AAAAAATAATATTATAAAACA-TTT
1 AAAATAT-ATATT-TAAAA-ATTTT
*
31097864 AAAATATACATTTAAAATATTTT
1 AAAATATATATTTAAAA-ATTTT
31097887 AAAA
1 AAAA
31097891 CAAATAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
20 4 0.10
21 1 0.02
22 11 0.27
23 12 0.29
24 12 0.29
25 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATATATATTTAAAAATTTT
Found at i:31097933 original size:24 final size:23
Alignment explanation
Indices: 31097890--31097934 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
31097880 ATATTTTAAA
* *
31097890 ACAAATAAAAAAACATAAAAATG
1 ACAAACAAAAAAACAGAAAAATG
31097913 ACAAACAATAAAAACAGAAAAA
1 ACAAACAA-AAAAACAGAAAAA
31097935 ATAATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.76, C:0.11, G:0.04, T:0.09
Consensus pattern (23 bp):
ACAAACAAAAAAACAGAAAAATG
Found at i:31099798 original size:25 final size:24
Alignment explanation
Indices: 31099770--31099885 Score: 135
Period size: 25 Copynumber: 4.7 Consensus size: 24
31099760 TCCCAATAAA
* *
31099770 TGGCTCTCTTGAGCTTTCCGTTATT
1 TGGCTCTCATGAGCTTCCCGTTA-T
*
31099795 TGGCTCTCACGAGCTTCCCGTTAAT
1 TGGCTCTCATGAGCTTCCCGTT-AT
*
31099820 TGGCTCTCATGAGCTTCCCGATTAA
1 TGGCTCTCATGAGCTTCCCG-TTAT
*
31099845 TGGCTCTCCA-GAGCTTCCCGATAT
1 TGGCTCT-CATGAGCTTCCCGTTAT
*
31099869 TGGCTCGCATGAGCTTC
1 TGGCTCTCATGAGCTTC
31099886 TCGAATTTGA
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
23 2 0.03
24 15 0.19
25 57 0.72
26 5 0.06
ACGTcount: A:0.15, C:0.29, G:0.22, T:0.34
Consensus pattern (24 bp):
TGGCTCTCATGAGCTTCCCGTTAT
Found at i:31102184 original size:26 final size:26
Alignment explanation
Indices: 31102155--31102208 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
31102145 TAAAAAGAAG
31102155 ATAGAGACATGAATATTGATTGTTAA
1 ATAGAGACATGAATATTGATTGTTAA
31102181 ATAGAGACATGAATATTGATTGTTAA
1 ATAGAGACATGAATATTGATTGTTAA
31102207 AT
1 AT
31102209 CAGAAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.35
Consensus pattern (26 bp):
ATAGAGACATGAATATTGATTGTTAA
Found at i:31102400 original size:21 final size:22
Alignment explanation
Indices: 31102376--31102424 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
31102366 CCCATTGCTT
*
31102376 GTGGCTATACAA-TTGTTTGCA
1 GTGGCTATACAATTTATTTGCA
*
31102397 GTGGCTATATAATTTATTTGCA
1 GTGGCTATACAATTTATTTGCA
31102419 GTGGCT
1 GTGGCT
31102425 CCATCTGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.41
Consensus pattern (22 bp):
GTGGCTATACAATTTATTTGCA
Found at i:31107501 original size:26 final size:27
Alignment explanation
Indices: 31107466--31107542 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
31107456 ACATTTTATG
*
31107466 AAATTATATTTAATAATAATTAT-TTT
1 AAATTATATTTAATAATAATTATAATT
* *
31107492 AAATTGTATTTAATCATATATT-TAATT
1 AAATTATATTTAATAATA-ATTATAATT
* *
31107519 AAAATATATTTAATATTAATTATA
1 AAATTATATTTAATAATAATTATA
31107543 GTATCATATA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
26 20 0.49
27 21 0.51
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
AAATTATATTTAATAATAATTATAATT
Found at i:31107623 original size:18 final size:17
Alignment explanation
Indices: 31107595--31107629 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31107585 ATTATTAAGA
*
31107595 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
31107612 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
31107630 TTAATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:31107718 original size:120 final size:119
Alignment explanation
Indices: 31107507--31107766 Score: 402
Period size: 120 Copynumber: 2.2 Consensus size: 119
31107497 GTATTTAATC
* * *
31107507 ATATATTTAATTAAAATATAT-TTAATATTA-A--TTATAGTATCATATATTATGATTTGAATAA
1 ATATATTTAATAAAAAT-TATGTTAAT-TTATATTTTACAATATCATATATTATGATTTGAATAA
31107568 ATTATATAAGAATATGAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
64 ATTATATAAGAATATGAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
* * *
31107624 ATATATTTAATAATATTTATGTTAATTTATATTTTACAATATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAAAAATTATGTTAATTTATATTTTACAATATCATATATTATGATTTGAATAAAT
*
31107689 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 T-ATATAAGAATATGAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
31107744 ATATATTTAATAAAAATTATGTT
1 ATATATTTAATAAAAATTATGTT
31107767 TAAATATGAT
Statistics
Matches: 129, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
116 6 0.05
117 20 0.16
119 30 0.23
120 73 0.57
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (119 bp):
ATATATTTAATAAAAATTATGTTAATTTATATTTTACAATATCATATATTATGATTTGAATAAAT
TATATAAGAATATGAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
Found at i:31107743 original size:18 final size:17
Alignment explanation
Indices: 31107715--31107749 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31107705 ATTATTAAGA
*
31107715 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
31107732 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
31107750 TTAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:31107749 original size:16 final size:16
Alignment explanation
Indices: 31107715--31107769 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
31107705 ATTATTAAGA
31107715 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
31107732 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
31107748 A-TTTAATAAAAAT-T
1 ATTTTAATTAAAATAT
31107762 ATGTTTAA
1 AT-TTTAA
31107770 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:31107902 original size:155 final size:157
Alignment explanation
Indices: 31107703--31108017 Score: 553
Period size: 155 Copynumber: 2.0 Consensus size: 157
31107693 ATAAGAATAT
31107703 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAATTATGTTT
* *
31107768 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
31107833 TAATCATTTACCAAAACAAATTTATGC
131 TAATCATTTACCAAAACAAATTTATAC
* *
31107860 TAATTA-TAAGAA-TTTATTAAATTGTATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAATTATGTTT
*
31107923 AAATATGTTTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
31107988 TAATCATTTACCAAAACAATTTTATAC
131 TAATCATTTACCAAAACAAATTTATAC
31108015 TAA
1 TAA
31108018 GGGTATTCTA
Statistics
Matches: 151, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
155 139 0.92
156 6 0.04
157 6 0.04
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAATTATGTTT
AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATCATTTACCAAAACAAATTTATAC
Found at i:31108134 original size:44 final size:45
Alignment explanation
Indices: 31108069--31108159 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
31108059 ACCTTTATTC
* * *
31108069 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
31108113 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
31108158 CA
1 CA
31108160 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:31108161 original size:16 final size:16
Alignment explanation
Indices: 31108140--31108175 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
31108130 GATTAGCTAT
31108140 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
31108156 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
31108172 TACA
1 TACA
31108176 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:31111599 original size:39 final size:39
Alignment explanation
Indices: 31111556--31111630 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
31111546 TCACTCTTCC
*
31111556 CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCTCA
1 CTGATAAGATAAGTGTAGCTAAAGCTACCACTTATCTCA
31111595 CTGATAAGATAAGTGTAGCTAAAGCTACCACTTATC
1 CTGATAAGATAAGTGTAGCTAAAGCTACCACTTATC
31111631 ACTTGTCACT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (39 bp):
CTGATAAGATAAGTGTAGCTAAAGCTACCACTTATCTCA
Found at i:31111656 original size:51 final size:51
Alignment explanation
Indices: 31111592--31111742 Score: 257
Period size: 51 Copynumber: 3.0 Consensus size: 51
31111582 ACCACTTATC
* *
31111592 TCACTGATAAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTG
1 TCACTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTGTCACTTG
* *
31111643 TCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTTG
1 TCACTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTGTCACTTG
*
31111694 TCACTGATCAGATAAGTGTAGCTGAAGCTACTACTTATCACTTGTCACT
1 TCACTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTGTCACT
31111743 GATCAGAAGT
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 93 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (51 bp):
TCACTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTGTCACTTG
Found at i:31115939 original size:12 final size:12
Alignment explanation
Indices: 31115922--31115948 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31115912 AGTTAGAACT
31115922 AAATTAATAATA
1 AAATTAATAATA
31115934 AAATTAATAATA
1 AAATTAATAATA
31115946 AAA
1 AAA
31115949 CAAAAGTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTAATAATA
Found at i:31116052 original size:34 final size:35
Alignment explanation
Indices: 31116014--31116088 Score: 86
Period size: 34 Copynumber: 2.2 Consensus size: 35
31116004 AATAACTGCG
* *
31116014 AAACAACAAT-AAAACACCA-CAAAAAGCAGCACCA
1 AAACAACAATCAAAACACCATAAAAAAACAGCA-CA
*
31116048 AAACAAC-ATCAAAACAGCATAAAAAAACAGCACA
1 AAACAACAATCAAAACACCATAAAAAAACAGCACA
31116082 AAA-AACA
1 AAACAACA
31116089 GTATCACCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
33 5 0.14
34 20 0.57
35 10 0.29
ACGTcount: A:0.65, C:0.25, G:0.05, T:0.04
Consensus pattern (35 bp):
AAACAACAATCAAAACACCATAAAAAAACAGCACA
Found at i:31120618 original size:12 final size:12
Alignment explanation
Indices: 31120601--31120627 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31120591 AGTTAGAACT
31120601 AAATTAATAATA
1 AAATTAATAATA
31120613 AAATTAATAATA
1 AAATTAATAATA
31120625 AAA
1 AAA
31120628 CAAAAGTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTAATAATA
Found at i:31120731 original size:34 final size:35
Alignment explanation
Indices: 31120693--31120767 Score: 86
Period size: 34 Copynumber: 2.2 Consensus size: 35
31120683 AATAACTGCG
* *
31120693 AAACAACAAT-AAAACACCA-CAAAAAGCAGCACCA
1 AAACAACAATCAAAACACCATAAAAAAACAGCA-CA
*
31120727 AAACAAC-ATCAAAACAGCATAAAAAAACAGCACA
1 AAACAACAATCAAAACACCATAAAAAAACAGCACA
31120761 AAA-AACA
1 AAACAACA
31120768 GTATCACCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
33 5 0.14
34 20 0.57
35 10 0.29
ACGTcount: A:0.65, C:0.25, G:0.05, T:0.04
Consensus pattern (35 bp):
AAACAACAATCAAAACACCATAAAAAAACAGCACA
Found at i:31128176 original size:22 final size:22
Alignment explanation
Indices: 31128151--31128199 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
31128141 GCAAAAATTG
*
31128151 ATCAATCATGTATACTTACCAT
1 ATCAATCATGCATACTTACCAT
31128173 ATCAATCATGCATACTTACCAT
1 ATCAATCATGCATACTTACCAT
*
31128195 TTCAA
1 ATCAA
31128200 CCCCCCACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (22 bp):
ATCAATCATGCATACTTACCAT
Found at i:31139414 original size:17 final size:18
Alignment explanation
Indices: 31139387--31139420 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
31139377 ATTTACAAAC
*
31139387 TATGTATATATATATAAG
1 TATGTATATATAAATAAG
31139405 TATG-ATATATAAATAA
1 TATGTATATATAAATAA
31139421 ATTTTGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (18 bp):
TATGTATATATAAATAAG
Found at i:31139744 original size:22 final size:22
Alignment explanation
Indices: 31139691--31139745 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
31139681 ACAAAAGTTT
*
31139691 AAAATATACATATATATTATAAA
1 AAAATATGCATATATATTAT-AA
31139714 GAAAATATGCATATATA-TATTAA
1 -AAAATATGCATATATATTA-TAA
*
31139737 AAACTATGC
1 AAAATATGC
31139746 GTGTGTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 8 0.29
23 4 0.14
24 16 0.57
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (22 bp):
AAAATATGCATATATATTATAA
Found at i:31139821 original size:6 final size:6
Alignment explanation
Indices: 31139779--31139817 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
31139769 AATAAAAACG
*
31139779 TAACAA TAACAA TAACAA TAACAA TAACAA TAATAA TAA
1 TAACAA TAACAA TAACAA TAACAA TAACAA TAACAA TAA
31139818 TAATGCAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.21
Consensus pattern (6 bp):
TAACAA
Found at i:31141898 original size:19 final size:19
Alignment explanation
Indices: 31141874--31141922 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
31141864 TGAGAGTTTC
*
31141874 TTTTATATTTCTTCTTCTG
1 TTTTATATTTCCTCTTCTG
*
31141893 TTTTATTAGTTCCTCTTCTG
1 TTTTA-TATTTCCTCTTCTG
*
31141913 TTTAATATTT
1 TTTTATATTT
31141923 TGAAGCTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.14, C:0.14, G:0.06, T:0.65
Consensus pattern (19 bp):
TTTTATATTTCCTCTTCTG
Found at i:31151936 original size:17 final size:17
Alignment explanation
Indices: 31151916--31151950 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
31151906 AATGGCATAA
31151916 AAATAATAT-AAACAAAT
1 AAATAA-ATGAAACAAAT
31151933 AAATAAATGAAACAAAT
1 AAATAAATGAAACAAAT
31151950 A
1 A
31151951 TACATAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (17 bp):
AAATAAATGAAACAAAT
Found at i:31152383 original size:22 final size:22
Alignment explanation
Indices: 31152324--31152386 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
31152314 AAATATATAT
*
31152324 ATATGTATAGAT-TAAAAAT-A
1 ATATGTATATATATAAAAATAA
** *
31152344 ATAAATACAT-TATCAAAAATAA
1 ATATGTATATATAT-AAAAATAA
31152366 ATATGTATATATATAAAAATA
1 ATATGTATATATATAAAAATA
31152387 TTAGTTTGAG
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
19 1 0.03
20 7 0.22
21 6 0.19
22 15 0.47
23 3 0.09
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (22 bp):
ATATGTATATATATAAAAATAA
Found at i:31154999 original size:7 final size:7
Alignment explanation
Indices: 31154987--31155011 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31154977 TAGTCGATTG
31154987 GTATTTA
1 GTATTTA
31154994 GTATTTA
1 GTATTTA
31155001 GTATTTA
1 GTATTTA
31155008 GTAT
1 GTAT
31155012 CATGTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
GTATTTA
Found at i:31155690 original size:18 final size:18
Alignment explanation
Indices: 31155663--31155702 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
31155653 CAGGTGCGTT
*
31155663 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
31155681 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
31155699 TCCT
1 TCCT
31155703 TTTCCGAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:31156159 original size:25 final size:24
Alignment explanation
Indices: 31156131--31156248 Score: 129
Period size: 25 Copynumber: 5.0 Consensus size: 24
31156121 TATTTTGATA
31156131 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAA-T
31156156 TTATTTGATGTAATAAAATAGAAT
1 TTATTTGATGTAATAAAATAGAAT
* * ** *
31156180 TT-TTT--T-TAGTTATTTTG-AT
1 TTATTTGATGTAATAAAATAGAAT
31156199 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAA-T
31156225 TTATTTGATGTAATAAAATAGAAT
1 TTATTTGATGTAATAAAATAGAAT
31156249 ATTTTGAATA
Statistics
Matches: 76, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
19 2 0.03
20 8 0.11
21 4 0.05
23 4 0.05
24 10 0.13
25 47 0.62
26 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.46
Consensus pattern (24 bp):
TTATTTGATGTAATAAAATAGAAT
Found at i:31156203 original size:69 final size:69
Alignment explanation
Indices: 31156121--31156253 Score: 257
Period size: 69 Copynumber: 1.9 Consensus size: 69
31156111 ATATTTTGAA
*
31156121 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAATTTTTTT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAATATTTTT
31156186 TAGT
66 TAGT
31156190 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAATATTTT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAATATTTT
31156254 GAATATTTTG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (69 bp):
TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAATATTTTT
TAGT
Found at i:31156259 original size:9 final size:9
Alignment explanation
Indices: 31156245--31156286 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
31156235 TAATAAAATA
31156245 GAATATTTT
1 GAATATTTT
31156254 GAATATTTT
1 GAATATTTT
31156263 GAATATTTT
1 GAATATTTT
* *
31156272 AAATATATT
1 GAATATTTT
31156281 G-ATATT
1 GAATATT
31156287 ATTTGAGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
8 4 0.14
9 25 0.86
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (9 bp):
GAATATTTT
Found at i:31156348 original size:23 final size:23
Alignment explanation
Indices: 31156317--31156600 Score: 322
Period size: 23 Copynumber: 12.6 Consensus size: 23
31156307 ATTAATACCC
*
31156317 TTAACTTAAAAATCCTAACCTAAT
1 TTAA-TTAAAAACCCTAACCTAAT
*
31156341 TTAATTAAAAACCTTAACCTAAT
1 TTAATTAAAAACCCTAACCTAAT
*
31156364 TTAATTAAAAACCCTAACCTGAT
1 TTAATTAAAAACCCTAACCTAAT
*
31156387 TTAATTAAAAACCCTAACC---C
1 TTAATTAAAAACCCTAACCTAAT
*
31156407 TTAACCCT-AAAACCCTAACCTAAT
1 TTAA--TTAAAAACCCTAACCTAAT
*
31156431 TTAATTAAAAACCCTAACC---C
1 TTAATTAAAAACCCTAACCTAAT
* *
31156451 TTAACCCT-CAAACCCTAACCTAAT
1 TTAA--TTAAAAACCCTAACCTAAT
31156475 TTAATTAAAAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAAT
31156498 TTAATTAAAAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAAT
*
31156521 TAAATTAAAAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAAT
*
31156544 TTAATTAAAAACCCTAACC---C
1 TTAATTAAAAACCCTAACCTAAT
*
31156564 TTAACCCT-AAAACCCTAACCTAAT
1 TTAA--TTAAAAACCCTAACCTAAT
31156588 TTAATTAAAAACC
1 TTAATTAAAAACC
31156601 TTTGGTCATG
Statistics
Matches: 222, Mismatches: 20, Indels: 37
0.80 0.07 0.13
Matches are distributed among these distances:
20 12 0.05
21 35 0.16
22 6 0.03
23 153 0.69
24 16 0.07
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.28
Consensus pattern (23 bp):
TTAATTAAAAACCCTAACCTAAT
Found at i:31156420 original size:21 final size:21
Alignment explanation
Indices: 31156394--31156470 Score: 77
Period size: 21 Copynumber: 3.6 Consensus size: 21
31156384 GATTTAATTA
31156394 AAAACCCTAACCCTTAACCCT
1 AAAACCCTAACCCTTAACCCT
* *
31156415 AAAACCCTAACCTAATTTAA--TT
1 AAAACCCTAACC---CTTAACCCT
31156437 AAAAACCCTAACCCTTAACCCT
1 -AAAACCCTAACCCTTAACCCT
*
31156459 CAAACCCTAACC
1 AAAACCCTAACC
31156471 TAATTTAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
20 4 0.09
21 23 0.51
22 2 0.04
23 12 0.27
24 4 0.09
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAACCCTAACCCTTAACCCT
Found at i:31156432 original size:67 final size:66
Alignment explanation
Indices: 31156317--31156600 Score: 235
Period size: 67 Copynumber: 4.2 Consensus size: 66
31156307 ATTAATACCC
* * * *
31156317 TTAACTTAAAAATCCTAACCTAATTTAATTAAAAACCTTAACCTAATTTAATTAAAAACCCTAAC
1 TTAA-TTAAAAACCCTAACC--ACTTAACTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAC
31156382 CTGAT
63 CT-AT
31156387 TTAATTAAAAACCCTAACC-CTTAACCCT-AAAACCCTAACCTAATTTAATTAAAAACCCTAACC
1 TTAATTAAAAACCCTAACCACTTAA--CTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACC
*
31156450 --C
64 TAT
* * * *
31156451 TTAACCCT-CAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
1 TTAA--TTAAAAACCCTAACC--ACTTAACTAAAAACCCTAACCTAATTTAATTAAAAACCCTAA
31156515 CCTAAT
62 CCT-AT
* * * * *
31156521 TAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACC---CTTAACCCT-AAAACCCTAA
1 TTAATTAAAAACCCTAACC--ACTTAACTAAAAACCCTAACCTAATTTAA--TTAAAAACCCTAA
31156582 CCTAAT
62 CCT-AT
31156588 TTAATTAAAAACC
1 TTAATTAAAAACC
31156601 TTTGGTCATG
Statistics
Matches: 184, Mismatches: 16, Indels: 31
0.80 0.07 0.13
Matches are distributed among these distances:
64 4 0.02
65 11 0.06
66 10 0.05
67 97 0.53
68 7 0.04
69 48 0.26
70 7 0.04
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.28
Consensus pattern (66 bp):
TTAATTAAAAACCCTAACCACTTAACTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTA
T
Found at i:31159458 original size:123 final size:124
Alignment explanation
Indices: 31159163--31159538 Score: 549
Period size: 123 Copynumber: 3.0 Consensus size: 124
31159153 CCCAAACATG
* *
31159163 CTACTGTAGTAAAATCGCGTCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGA-TTTCACAAATTCTTCTCAAATAGCATCCTG
*
31159228 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
65 CTAGAAGCGATTTTATACTATTTGATCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
* * * *
31159288 CGACTGTAGCAAAAGCGTGTCCACGAGGGCGCGATTTTACAAGTTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
31159353 TAGAAGC-ATTTTTATACTATTTGTTTAGAAACGTCAAAAAAAA-TATTTCTTCCATGAC
66 TAGAAGCGA-TTTTATACTATTTGATCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
* * * *
31159411 CTACTGTAGCAAAAGCACGTCTACGAGGGCGGGATTTCACAAATTCTTCTCAAATAGCATCATGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *** *
31159476 TAGAAGCGATTTTATACTATTTGATCAGAAATGTCAACTCGAAATTATTTCTTCCAAGAC
66 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAA-AAAAAATTATTTCTTCCATGAC
31159536 CTA
1 CTA
31159539 AAACCCTAAA
Statistics
Matches: 224, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
123 105 0.47
124 72 0.32
125 47 0.21
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
Found at i:31160808 original size:6 final size:6
Alignment explanation
Indices: 31160797--31160824 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
31160787 ATTTTAGCTA
31160797 ATAATT ATAATT ATAATT ATAATT ATAA
1 ATAATT ATAATT ATAATT ATAATT ATAA
31160825 CTATCTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATAATT
Found at i:31169183 original size:20 final size:20
Alignment explanation
Indices: 31169139--31169206 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
31169129 TAGGCACTGT
*
31169139 AGTGCAAATAGAGGCA--AA
1 AGTGCAATTAGAGGCACCAA
*
31169157 ATTGTGCAATTAGAGGCACCGA
1 A--GTGCAATTAGAGGCACCAA
*
31169179 AGTGCAAATAGAGGCACCAA
1 AGTGCAATTAGAGGCACCAA
31169199 AGTGCAAT
1 AGTGCAAT
31169207 CTCGTACAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
18 1 0.02
20 38 0.93
22 2 0.05
ACGTcount: A:0.41, C:0.16, G:0.26, T:0.16
Consensus pattern (20 bp):
AGTGCAATTAGAGGCACCAA
Found at i:31180644 original size:40 final size:40
Alignment explanation
Indices: 31180589--31181176 Score: 1005
Period size: 40 Copynumber: 14.7 Consensus size: 40
31180579 GAGCATTGGA
31180589 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
31180629 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
31180669 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
31180709 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
31180749 ATATGTCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
31180789 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
31180829 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
31180869 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
31180909 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
31180949 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
31180989 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
31181029 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
31181069 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
31181109 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
31181149 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
31181177 AGGTGTTTGC
Statistics
Matches: 517, Mismatches: 31, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 517 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:31188437 original size:40 final size:40
Alignment explanation
Indices: 31188340--31188968 Score: 1014
Period size: 40 Copynumber: 15.7 Consensus size: 40
31188330 TGAGCATTGG
31188340 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
31188380 AGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 A-ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
31188421 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
31188461 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
31188501 AATATGTCCGGGCTAAGACCCGAAGGCAATTATTGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTA-TGCGAGTT
31188542 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
31188582 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* *
31188622 AATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
31188662 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
31188702 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* * *
31188742 AATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGAT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* *
31188782 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* * *
31188822 GATATGTCCGGGCTATGATCCCGAAGGCAATTATGCGAG--
1 AATATATCCGGGCTAAGA-CCCGAAGGCAATTATGCGAGTT
*
31188861 -ATGATATCC-GGCTAAGACCCGAAGGCAATTATGCGAGAT
1 AAT-ATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* *
31188900 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* * *
31188940 GATATGTCCGGGTTAAGACCCGAAGGCAA
1 AATATATCCGGGCTAAGACCCGAAGGCAA
31188969 AGGTGTTTGC
Statistics
Matches: 552, Mismatches: 29, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
37 20 0.04
38 9 0.02
39 11 0.02
40 414 0.75
41 98 0.18
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
Found at i:31192350 original size:16 final size:16
Alignment explanation
Indices: 31192329--31192359 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31192319 ATCAGGTTGA
*
31192329 GAAAATTATTTAATTG
1 GAAAATTAATTAATTG
31192345 GAAAATTAATTAATT
1 GAAAATTAATTAATT
31192360 TATAATGTTT
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:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
GAAAATTAATTAATTG
Found at i:31195891 original size:13 final size:14
Alignment explanation
Indices: 31195868--31195902 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
31195858 CACGTTAACA
31195868 CTGTATATCTGTAT
1 CTGTATATCTGTAT
31195882 CTGT-TATCTGTAT
1 CTGTATATCTGTAT
*
31195895 ATGTATAT
1 CTGTATAT
31195903 GGGGCGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.51
Consensus pattern (14 bp):
CTGTATATCTGTAT
Found at i:31196909 original size:21 final size:21
Alignment explanation
Indices: 31196866--31196927 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
31196856 CGAATACACC
*
31196866 AACAAAAGCTTG-AA-AGCTG
1 AACAAAAGCTCGTAAGAGCTG
*
31196885 AACAAAAGCTCGTAAGAGTTG
1 AACAAAAGCTCGTAAGAGCTG
* *
31196906 AACAGAAGCTCATAAGAGCTG
1 AACAAAAGCTCGTAAGAGCTG
31196927 A
1 A
31196928 TCCACCCAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
19 11 0.31
20 2 0.06
21 23 0.64
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.16
Consensus pattern (21 bp):
AACAAAAGCTCGTAAGAGCTG
Found at i:31230194 original size:71 final size:68
Alignment explanation
Indices: 31229990--31230214 Score: 261
Period size: 70 Copynumber: 3.2 Consensus size: 68
31229980 TTTTTAACTT
* * * * * * *
31229990 TCGCTAACTATTTTGGAGGCTACGGTTTTTATTCTGCGAGCCTTAGTATGACAACTTGGTGTTTT
1 TCGCTAACTATGTTGAAGGCTACGTTTTTTATCCTGCGAGCCTTAGTATGAC-AGTTGGAGCTTT
31230055 GCTC
65 GCTC
* * * *
31230059 TCGCTAACTTTGTTGAAGGCTGCCGTTTTTTATCCTGCGAGCCTTAGTATGAGAGCTAGGAGCTT
1 TCGCTAACTATGTTGAAGGCT-ACGTTTTTTATCCTGCGAGCCTTAGTATGACAG-TTGGAGCTT
31230124 TGCTC
64 TGCTC
* *
31230129 TCGCTAACTGTGTTGAAGGCTACGATTTTTTTATCCTGCGAGTCTTAGTATGACAGTTGGGAGCT
1 TCGCTAACTATGTTGAAGGCTACG--TTTTTTATCCTGCGAGCCTTAGTATGACAGTT-GGAGCT
31230194 TTGCTC
63 TTGCTC
* *
31230200 TCACTAGCTATGTTG
1 TCGCTAACTATGTTG
31230215 GTGGCTGCAA
Statistics
Matches: 132, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
69 21 0.16
70 59 0.45
71 52 0.39
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (68 bp):
TCGCTAACTATGTTGAAGGCTACGTTTTTTATCCTGCGAGCCTTAGTATGACAGTTGGAGCTTTG
CTC
Found at i:31230228 original size:71 final size:69
Alignment explanation
Indices: 31230015--31230253 Score: 253
Period size: 70 Copynumber: 3.4 Consensus size: 69
31230005 GAGGCTACGG
* * * * *
31230015 TTTTTATTCTGCGAGCCTTAGTATGACAACTTGGTGTTTTGCTCTCGCTAACTTTGTTGAAGGCT
1 TTTTTATCCTGCGAGCCTTAGTATGAC-AGTTGGAGCTTTGCTCTCGCTAACTATGTTGAAGGCT
**
31230080 GCCGT
65 GCATT
* * *
31230085 TTTTTATCCTGCGAGCCTTAGTATGAGAGCTAGGAGCTTTGCTCTCGCTAACTGTGTTGAAGGCT
1 TTTTTATCCTGCGAGCCTTAGTATGACAG-TTGGAGCTTTGCTCTCGCTAACTATGTTGAAGGCT
*
31230150 ACGATT
65 GC-ATT
* * * **
31230156 TTTTTATCCTGCGAGTCTTAGTATGACAGTTGGGAGCTTTGCTCTCACTAGCTATGTTGGTGGCT
1 TTTTTATCCTGCGAGCCTTAGTATGACAGTT-GGAGCTTTGCTCTCGCTAACTATGTTGAAGGCT
*
31230221 GCAAT
65 GCATT
* * * *
31230226 TTTTTATCTTACCAACCTTAGTATGACA
1 TTTTTATCCTGCGAGCCTTAGTATGACA
31230254 CAAATGTTGT
Statistics
Matches: 141, Mismatches: 25, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
69 1 0.01
70 83 0.59
71 57 0.40
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.39
Consensus pattern (69 bp):
TTTTTATCCTGCGAGCCTTAGTATGACAGTTGGAGCTTTGCTCTCGCTAACTATGTTGAAGGCTG
CATT
Found at i:31230245 original size:141 final size:139
Alignment explanation
Indices: 31229990--31230251 Score: 310
Period size: 141 Copynumber: 1.9 Consensus size: 139
31229980 TTTTTAACTT
* * * * *
31229990 TCGCTAACTATTTTGGAGGCTACGGTTTTTATTCTGCGAGCCTTAGTATGACAACTTGGTGTTTT
1 TCGCTAACTATGTTGAAGGCTACGGTTTTTATCCTGCGAGCCTTAGTATGACAACTTGGAGCTTT
* * ** * * *
31230055 GCTCTCGCTAACTTTGTTGAAGGCTGCCGTTTTTTATCCTGCGAGCCTTAGTATGAGAGCTAGGA
66 GCTCTCACTAACTATGTTGAAGGCTGCAATTTTTTATCCTACCAACCTTAGTATGAGAGCTAGGA
31230120 GCTTTGCTC
131 GCTTTGCTC
* * * *
31230129 TCGCTAACTGTGTTGAAGGCTACGATTTTTTTATCCTGCGAGTCTTAGTATGAC-AGTTGGGAGC
1 TCGCTAACTATGTTGAAGGCTACG--GTTTTTATCCTGCGAGCCTTAGTATGACAACTT-GGAGC
* ** *
31230193 TTTGCTCTCACTAGCTATGTTGGTGGCTGCAATTTTTTATCTTACCAACCTTAGTATGA
63 TTTGCTCTCACTAACTATGTTGAAGGCTGCAATTTTTTATCCTACCAACCTTAGTATGA
31230252 CACAAATGTT
Statistics
Matches: 100, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
139 21 0.21
140 3 0.03
141 76 0.76
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (139 bp):
TCGCTAACTATGTTGAAGGCTACGGTTTTTATCCTGCGAGCCTTAGTATGACAACTTGGAGCTTT
GCTCTCACTAACTATGTTGAAGGCTGCAATTTTTTATCCTACCAACCTTAGTATGAGAGCTAGGA
GCTTTGCTC
Found at i:31239410 original size:15 final size:15
Alignment explanation
Indices: 31239390--31239427 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
31239380 AACTCGACAT
31239390 TTACTTGTCACTTTA
1 TTACTTGTCACTTTA
31239405 TTACTTGTCACTTTA
1 TTACTTGTCACTTTA
31239420 TTACTTGT
1 TTACTTGT
31239428 TGCGATTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.55
Consensus pattern (15 bp):
TTACTTGTCACTTTA
Found at i:31251275 original size:16 final size:18
Alignment explanation
Indices: 31251254--31251290 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
31251244 GAAATCAATC
31251254 AATTTTT-CAAAACCC-T
1 AATTTTTACAAAACCCGT
*
31251270 AATTTTTATAAAACCCGT
1 AATTTTTACAAAACCCGT
31251288 AAT
1 AAT
31251291 CCACAGTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 7 0.39
18 4 0.22
ACGTcount: A:0.41, C:0.19, G:0.03, T:0.38
Consensus pattern (18 bp):
AATTTTTACAAAACCCGT
Found at i:31258364 original size:22 final size:22
Alignment explanation
Indices: 31258339--31258383 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
31258329 AATTTTTGTA
31258339 TTAATTCATAATATAA-TTAATT
1 TTAATT-ATAATATAATTTAATT
* *
31258361 TTAATTTTAATCTAATTTAATT
1 TTAATTATAATATAATTTAATT
31258383 T
1 T
31258384 GAGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTATAATATAATTTAATT
Found at i:31270711 original size:6 final size:6
Alignment explanation
Indices: 31270700--31270741 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
31270690 CCCCCTCTTG
* *
31270700 AATATA AATATA AATATC AATATC AATATC AATATC AATATC
1 AATATC AATATC AATATC AATATC AATATC AATATC AATATC
31270742 TTCAATTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (6 bp):
AATATC
Found at i:31276343 original size:17 final size:17
Alignment explanation
Indices: 31276321--31276353 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31276311 CCCATTAGTG
31276321 AAATAAACT-AAATAAAC
1 AAATAAA-TAAAATAAAC
31276338 AAATAAATAAAATAAA
1 AAATAAATAAAATAAA
31276354 ACCAAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATAAATAAAATAAAC
Found at i:31278313 original size:111 final size:111
Alignment explanation
Indices: 31278187--31278407 Score: 361
Period size: 111 Copynumber: 2.0 Consensus size: 111
31278177 TAAATAATCG
* * *
31278187 AAAATTTTCTACAATCAAAGCGAATAAACCAAAAACTCACTTTCGGGAATTTGATACGCCGTGTC
1 AAAATTTTCTACAATCAAAACGAATAAACCAAAAACTCACTTTCGGGAATTCGATACGCCATGTC
* *
31278252 CTAATGTATTGAATGTGATGTGTCGTTTTCTCGAAATGAAGATTTT
66 CTAATGTATTGAATATGACGTGTCGTTTTCTCGAAATGAAGATTTT
* * *
31278298 AAAATTTTCTACAATCAAAACGCATAAACCAAAAACTCACTTTCGGGCATTCGATACGTCATGTC
1 AAAATTTTCTACAATCAAAACGAATAAACCAAAAACTCACTTTCGGGAATTCGATACGCCATGTC
*
31278363 CTAATGTATTGGATATGACGTGTCGTTTTCTCGAAATGAAGATTT
66 CTAATGTATTGAATATGACGTGTCGTTTTCTCGAAATGAAGATTT
31278408 AAATAATAAG
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
111 101 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (111 bp):
AAAATTTTCTACAATCAAAACGAATAAACCAAAAACTCACTTTCGGGAATTCGATACGCCATGTC
CTAATGTATTGAATATGACGTGTCGTTTTCTCGAAATGAAGATTTT
Found at i:31278991 original size:25 final size:25
Alignment explanation
Indices: 31278962--31279025 Score: 119
Period size: 25 Copynumber: 2.6 Consensus size: 25
31278952 TCACCGTCTT
*
31278962 CTCCTCTAACATCCAGTGTGTTCTG
1 CTCCTCTAACATCCAGTGTGTTCTA
31278987 CTCCTCTAACATCCAGTGTGTTCTA
1 CTCCTCTAACATCCAGTGTGTTCTA
31279012 CTCCTCTAACATCC
1 CTCCTCTAACATCC
31279026 TCTGGCATAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.19, C:0.36, G:0.11, T:0.34
Consensus pattern (25 bp):
CTCCTCTAACATCCAGTGTGTTCTA
Found at i:31281519 original size:54 final size:54
Alignment explanation
Indices: 31281456--31281688 Score: 234
Period size: 54 Copynumber: 4.1 Consensus size: 54
31281446 AGTATCATAT
*
31281456 ATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
*
31281510 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * * * * *
31281564 ATTATATATTTTAATTATAATAT-ATTTAATAATAATTATGTTAATTTATATTTTATAGTATCAT
1 ATTAT-GA-TTTGAGTA-AAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTT-TA-T-T-A-
31281628 A
54 A
*
31281629 TATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 -ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
31281684 ATTAT
1 ATTAT
31281689 ATATTTTAAT
Statistics
Matches: 143, Mismatches: 22, Indels: 28
0.74 0.11 0.15
Matches are distributed among these distances:
54 62 0.43
55 2 0.01
56 7 0.05
57 12 0.08
58 5 0.03
59 4 0.03
60 16 0.11
61 4 0.03
62 5 0.03
63 12 0.08
64 7 0.05
65 2 0.01
66 5 0.03
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.48
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:31281556 original size:28 final size:27
Alignment explanation
Indices: 31281471--31281556 Score: 63
Period size: 28 Copynumber: 3.1 Consensus size: 27
31281461 GATTTGAGTA
*
31281471 AATTCATATAAAAATATTAATTATTAAG
1 AATTCATAT-AAAATATTGATTATTAAG
* * *
31281499 AATT-TTATTAAAT-TATGA-T-TTGAG
1 AATTCATATAAAATAT-TGATTATTAAG
31281523 TAAATTCATATAAGAATATTGATTATTAAG
1 --AATTCATATAA-AATATTGATTATTAAG
31281553 AATT
1 AATT
31281557 TTATTAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 16
0.65 0.11 0.24
Matches are distributed among these distances:
24 4 0.09
25 2 0.05
26 10 0.23
27 7 0.16
28 14 0.33
29 2 0.05
30 4 0.09
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (27 bp):
AATTCATATAAAATATTGATTATTAAG
Found at i:31281593 original size:15 final size:15
Alignment explanation
Indices: 31281558--31281609 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
31281548 TTAAGAATTT
*
31281558 TATTAAATTAT-ATA
1 TATTTAATTATAATA
31281572 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
31281586 TATTTAATAATAAT-
1 TATTTAATTATAATA
31281600 TATGTTAATT
1 TAT-TTAATT
31281610 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:31281635 original size:120 final size:120
Alignment explanation
Indices: 31281510--31281725 Score: 432
Period size: 120 Copynumber: 1.8 Consensus size: 120
31281500 ATTTTATTAA
31281510 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
1 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
31281575 TAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATAT
66 TAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATAT
31281630 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
1 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
31281695 TAATTATAATATATTTAATAATAATTATGTT
66 TAATTATAATATATTTAATAATAATTATGTT
31281726 TAAATATGAT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 96 1.00
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.50
Consensus pattern (120 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
TAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATAT
Found at i:31281708 original size:16 final size:16
Alignment explanation
Indices: 31281687--31281728 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
31281677 TTATTAAATT
*
31281687 ATATATTTTAATTATA
1 ATATATTTTAATAATA
31281703 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
31281718 AT-TATGTTTAA
1 ATATAT-TTTAA
31281729 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:31281713 original size:15 final size:15
Alignment explanation
Indices: 31281678--31281719 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
31281668 TTAAGAATTT
*
31281678 TATTAAATTAT-ATA
1 TATTTAATTATAATA
31281692 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
31281706 TATTTAATAATAAT
1 TATTTAATTATAAT
31281720 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:31281939 original size:45 final size:43
Alignment explanation
Indices: 31281839--31281949 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 43
31281829 TTTTCCATTA
31281839 TGCTATTACACCTCTATT-C---CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
* * ***
31281878 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCA-TACATTCAACCAAACACAAGA-T
31281923 TGCTATTACACCTCTATTCCAATACAT
1 TGCTATTACACCTCTATTCC-ATACAT
31281950 CTCTATTCCA
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 24 0.41
46 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.33
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
Found at i:31281953 original size:16 final size:16
Alignment explanation
Indices: 31281929--31281996 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
31281919 GATTTGCTAT
*
31281929 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
* *
31281945 TACATCTCTATTCCAA
1 TACACCTCTAATCCAA
31281961 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
31281977 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
31281993 TACA
1 TACA
31281997 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:31294187 original size:44 final size:44
Alignment explanation
Indices: 31293724--31294158 Score: 593
Period size: 44 Copynumber: 9.9 Consensus size: 44
31293714 AATCACAAAA
* * *
31293724 CCTAGCTCCCT-ATCCAGTAGTGGAATAGGTTGAAGATTGTAAGT
1 CCTAACTCCCTGA-CCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * *
31293768 CCTAGCTCCCTGACGAGCAGTGGAATAGGTTGAAGATTGTAAGT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * * * *
31293812 CCTATCTCCCTGACCAACAGAGGAATAGGTAGAAGATCGCAAGT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* *
31293856 CCTAACTACCTAACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * *
31293900 CCTAACTCCCTGACCAGTAGAGGAATAGGTAGAAGATTGCAAGT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* *
31293944 CCTAACTTCCTGACCAACAGTGGAATAGGTTGAAGATTGCAAGT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* *
31293988 CCTAACTCCCTGACCAGCAGTGGAATAGGTAGAAGATTTCAAGT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
*
31294032 CCTAACTCCCTGACCAGAAGTGGAATAGGTTGAAGATTGCAAGT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * *
31294076 CCTAACTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTATGT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* ** * *
31294120 CCTATCTCCCTGAAAAACTGTGGAATAGGTTGAAGATTG
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
31294159 TGGATCCTGT
Statistics
Matches: 347, Mismatches: 43, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
44 346 1.00
45 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (44 bp):
CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
Found at i:31296439 original size:111 final size:111
Alignment explanation
Indices: 31296323--31296543 Score: 370
Period size: 111 Copynumber: 2.0 Consensus size: 111
31296313 TAAATAATCG
* *
31296323 AAAATTTTCTACAATCAAAGCGAATAAACCAAAAACTCACTTTCGGGAATTCGATACGCCGTGTC
1 AAAATTTTCTACAATCAAAACGAATAAACCAAAAACTCACTTTCGGGAATTCGATACGCCATGTC
* *
31296388 CTAATGTATTGAATGTGATGTGTCGTTTTCTCGAAATGAAGATTTT
66 CTAATGTATTGAATATGACGTGTCGTTTTCTCGAAATGAAGATTTT
* * *
31296434 AAAATTTTCTACAATCAAAACGCATAAACCAAAAACTCACTTTCGGGCATTCGATACGTCATGTC
1 AAAATTTTCTACAATCAAAACGAATAAACCAAAAACTCACTTTCGGGAATTCGATACGCCATGTC
*
31296499 CTAATGTATTGGATATGACGTGTCGTTTTCTCGAAATGAAGATTT
66 CTAATGTATTGAATATGACGTGTCGTTTTCTCGAAATGAAGATTT
31296544 AAATAATAAG
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 102 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Consensus pattern (111 bp):
AAAATTTTCTACAATCAAAACGAATAAACCAAAAACTCACTTTCGGGAATTCGATACGCCATGTC
CTAATGTATTGAATATGACGTGTCGTTTTCTCGAAATGAAGATTTT
Found at i:31307687 original size:387 final size:386
Alignment explanation
Indices: 31306966--31307727 Score: 1355
Period size: 387 Copynumber: 2.0 Consensus size: 386
31306956 CATTGGGTTG
31306966 GGATTACTGGATGAATCTTTAGTTCCTTTAATGACCAAGGCATTATCCTGATTAGATTTACTATT
1 GGATTACTGGATGAATCTTTAGTTCCTTTAATGACCAAGGCATTATCCTGATTAGATTTACTATT
* *
31307031 TCATTTGATTTGCGCTATTTTAAAACTTATGCATGTAGTCTCTAGACATAGATGAATATATGGTA
66 TCATTTGATTTGCGCTATTTTAAAACGTATGCATGCAGTCTCTAGACATAGATGAATATATGGTA
31307096 TGTCCATAAACTTGATTTAATTCTGAAAAGGTTAGATGAGTTCGATTGTGATCGAATGATACAAG
131 TGTCCATAAACTTGATTTAATTCTGAAAAGGTTAGATGAGTTCGATTGTGATCGAATGATACAAG
* *
31307161 CGAGTATTCGATAGAATAGTCATAGCACTCTAGACATAGAGCTGCGCTCTGTACAGAGAAAGGAA
196 CGAGTATTCGACAGAATAGTCATAGCACTCTAGACATAGAGCTACGCTCTGTACAGAGAAAGGAA
* * * *
31307226 GAAACAATGATGGGTATCCTTTTTAAATCTTGTAGATATGCAAAGTCTTAGGTAGGGTAGCTTGA
261 GAAACAATGATAGGTATCCTTCTTAAAGCTTGTAGATATGCAAAGCCTTAGGTAGGGTAGCTTGA
* *
31307291 AGTCTGACTCTCGAAAGAAGCAGACTACCTTAGATATGTTGTTGAATGATACTTTTTATTTT
326 AGTCTGACTCTCGAAAGAAGCAGACTACCTTAGATATATT-CTGAATGATACTTTTTATTTT
*
31307353 GGATTATTGGATGAATCTTTAGTTCCTTTAATGACCAAGGCATTATCCTGATTAGATTTACTATT
1 GGATTACTGGATGAATCTTTAGTTCCTTTAATGACCAAGGCATTATCCTGATTAGATTTACTATT
31307418 TCATTTGATTTGCGCTATTTTAAAACGTATGCATGCAGTCTCTAGACATAGATGAATATATGGTA
66 TCATTTGATTTGCGCTATTTTAAAACGTATGCATGCAGTCTCTAGACATAGATGAATATATGGTA
* *
31307483 TGTCCATAAACTTGATTTAATTCTGAAAAGGTTAGATGAGTTGGATTGTGATTGAATGATACAAG
131 TGTCCATAAACTTGATTTAATTCTGAAAAGGTTAGATGAGTTCGATTGTGATCGAATGATACAAG
* *
31307548 CGAGTATTCGACAGAATAGTCGTAGCACTCTAGACATAGAGCTACGCTTTGTACA-AGGAAAGGA
196 CGAGTATTCGACAGAATAGTCATAGCACTCTAGACATAGAGCTACGCTCTGTACAGA-GAAAGGA
*
31307612 AGAAACAGTGATAGGTATCCTTCTTAAAGCTTGTAGATATGCAAAGCCTTAGGTAGGGTAGCTTG
260 AGAAACAATGATAGGTATCCTTCTTAAAGCTTGTAGATATGCAAAGCCTTAGGTAGGGTAGCTTG
31307677 AAGTCTGACTCTCGAAAGAAGCAGACTACCTTAGATATATTCTGAATGATA
325 AAGTCTGACTCTCGAAAGAAGCAGACTACCTTAGATATATTCTGAATGATA
31307728 GATTTGTTAA
Statistics
Matches: 358, Mismatches: 16, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
386 10 0.03
387 348 0.97
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (386 bp):
GGATTACTGGATGAATCTTTAGTTCCTTTAATGACCAAGGCATTATCCTGATTAGATTTACTATT
TCATTTGATTTGCGCTATTTTAAAACGTATGCATGCAGTCTCTAGACATAGATGAATATATGGTA
TGTCCATAAACTTGATTTAATTCTGAAAAGGTTAGATGAGTTCGATTGTGATCGAATGATACAAG
CGAGTATTCGACAGAATAGTCATAGCACTCTAGACATAGAGCTACGCTCTGTACAGAGAAAGGAA
GAAACAATGATAGGTATCCTTCTTAAAGCTTGTAGATATGCAAAGCCTTAGGTAGGGTAGCTTGA
AGTCTGACTCTCGAAAGAAGCAGACTACCTTAGATATATTCTGAATGATACTTTTTATTTT
Found at i:31308338 original size:19 final size:20
Alignment explanation
Indices: 31308316--31308369 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
31308306 CACTCATTCA
31308316 ATGCTTTTATTCACTCA-CT
1 ATGCTTTTATTCACTCACCT
*
31308335 ATGCTTTTA-TCCCTCACCT
1 ATGCTTTTATTCACTCACCT
31308354 -TGCTTTTATTCACTCA
1 ATGCTTTTATTCACTCA
31308370 ATTTTTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.19, C:0.30, G:0.06, T:0.46
Consensus pattern (20 bp):
ATGCTTTTATTCACTCACCT
Found at i:31308357 original size:18 final size:18
Alignment explanation
Indices: 31308289--31308369 Score: 69
Period size: 19 Copynumber: 4.4 Consensus size: 18
31308279 GTCACTCTTT
*
31308289 TCACTCACAATGC-TTTA
1 TCACTCACTATGCTTTTA
*
31308306 -CACTCATTCAATGCTTTTA
1 TCACTCA--CTATGCTTTTA
31308325 TTCACTCACTATGCTTTTA
1 -TCACTCACTATGCTTTTA
*
31308344 TCCCTCACCT-TGCTTTTA
1 TCACTCA-CTATGCTTTTA
31308362 TTCACTCA
1 -TCACTCA
31308370 ATTTTTTTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
16 6 0.11
18 20 0.37
19 22 0.41
21 6 0.11
ACGTcount: A:0.22, C:0.31, G:0.05, T:0.42
Consensus pattern (18 bp):
TCACTCACTATGCTTTTA
Found at i:31311834 original size:12 final size:12
Alignment explanation
Indices: 31311809--31311847 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
31311799 ACTCACTTCT
* *
31311809 TTACTTACTCAC
1 TTACTTGCTTAC
*
31311821 TTACTTGTTTAC
1 TTACTTGCTTAC
31311833 TTACTTGCTTAC
1 TTACTTGCTTAC
31311845 TTA
1 TTA
31311848 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:31312171 original size:50 final size:50
Alignment explanation
Indices: 31312096--31312284 Score: 184
Period size: 50 Copynumber: 3.7 Consensus size: 50
31312086 TTTTCTGTAT
* * **
31312096 TGCCAGTGCCATATCCCAGAT-ATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAG-TCATGGTCTTACATGGGACCTCTCATATCGG
* ** * *
31312146 TGCCCATGCCATGTCCCAGTCATGGTCTTACGGGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGTCATGGTCTTACATGGGACCTCTCATATCGG
* * *
31312196 TGCCAATGCCATGTACCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGTCATGGTCTTACATGGGACCTCTCAT-A--TC---GG
31312252 TGCCAATGCCATGTCCC-GTACATGGTCTTACAT
1 TGCCAATGCCATGTCCCAGT-CATGGTCTTACAT
31312285 AGTATCCCAT
Statistics
Matches: 112, Mismatches: 19, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
49 1 0.01
50 78 0.70
53 2 0.02
55 1 0.01
56 30 0.27
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGTCATGGTCTTACATGGGACCTCTCATATCGG
Found at i:31312258 original size:56 final size:49
Alignment explanation
Indices: 31312046--31312284 Score: 169
Period size: 50 Copynumber: 4.7 Consensus size: 49
31312036 CTGATAATAC
* * * * *
31312046 ATGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGA--TGTTTTCT-G
1 ATGCCAATGCCATGT-CCAGACATGGTCTTACATGGGACCTCTTATCTCG
* * * ** * *
31312093 TATTGCCAGTGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCG
1 -A-TGCCAATGCCATGT-CCAGACATGGTCTTACATGGGACCTCTTATCTCG
* * * **
31312145 GTGCCCATGCCATGTCCCAGTCATGGTCTTACGGGGGACCTCTTATCTCG
1 ATGCCAATGCCATGT-CCAGACATGGTCTTACATGGGACCTCTTATCTCG
*
31312195 GTGCCAATGCCATGTACCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATG
1 ATGCCAATGCCATGT-CCAGACATGGTCTTACATGGGACCTCT--T-ATCTC---G
*
31312251 ATGCCAATGCCATGTCCCGTACATGGTCTTACAT
1 ATGCCAATGCCATGTCCAG-ACATGGTCTTACAT
31312285 AGTATCCCAT
Statistics
Matches: 151, Mismatches: 29, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
48 1 0.01
49 31 0.21
50 76 0.50
51 4 0.03
52 2 0.01
53 5 0.03
55 3 0.02
56 29 0.19
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (49 bp):
ATGCCAATGCCATGTCCAGACATGGTCTTACATGGGACCTCTTATCTCG
Found at i:31314111 original size:27 final size:27
Alignment explanation
Indices: 31314040--31314111 Score: 126
Period size: 27 Copynumber: 2.7 Consensus size: 27
31314030 CCCAGTATTT
* *
31314040 GTAAAATGACTGTAATAACCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
31314067 GTAAAATGACCGTAATACCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
31314094 GTAAAATGACCGTAATAC
1 GTAAAATGACCGTAATAC
31314112 TGGTAGCTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.24
Consensus pattern (27 bp):
GTAAAATGACCGTAATACCCCTGTAGG
Found at i:31315779 original size:27 final size:27
Alignment explanation
Indices: 31315750--31315926 Score: 221
Period size: 27 Copynumber: 6.6 Consensus size: 27
31315740 AAAATGATCT
* * **
31315750 TGTAGAGTAAAATGACCGTAATACCTT
1 TGTAGGGTAAAATGACCGTAATGCCCC
*
31315777 TGTAGGGT-AAATAACCGTAATGCCCC
1 TGTAGGGTAAAATGACCGTAATGCCCC
* * *
31315803 TATAGGGTAAAATGACCATAATACCCC
1 TGTAGGGTAAAATGACCGTAATGCCCC
* *
31315830 TGTAGGGTAAAATGGCCGTAACGCCCC
1 TGTAGGGTAAAATGACCGTAATGCCCC
* *
31315857 TGTATGGTAAAATGATCGTAATGCCCC
1 TGTAGGGTAAAATGACCGTAATGCCCC
* *
31315884 TGTAGGGTAAAATAACCATAATGCCCC
1 TGTAGGGTAAAATGACCGTAATGCCCC
31315911 TGTAGGGTAAAATGAC
1 TGTAGGGTAAAATGAC
31315927 TATTTTGCCT
Statistics
Matches: 126, Mismatches: 23, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
26 21 0.17
27 105 0.83
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (27 bp):
TGTAGGGTAAAATGACCGTAATGCCCC
Found at i:31315978 original size:24 final size:24
Alignment explanation
Indices: 31315947--31316063 Score: 146
Period size: 24 Copynumber: 4.9 Consensus size: 24
31315937 ATCGGGGTTG
31315947 AATGATTGATTTGTCTGTGATGTA
1 AATGATTGATTTGTCTGTGATGTA
*
31315971 AATAATTGATTTGTCTGTGATGTA
1 AATGATTGATTTGTCTGTGATGTA
** * *
31315995 AATGACCGATTTGTCTCTGATTTA
1 AATGATTGATTTGTCTGTGATGTA
*
31316019 AATGATTGATTTGTTTGTGAT-TA
1 AATGATTGATTTGTCTGTGATGTA
* *
31316042 GTATGACTGATTTGTCTGTGAT
1 -AATGATTGATTTGTCTGTGAT
31316064 TTGTATGACT
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
23 2 0.03
24 77 0.97
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.46
Consensus pattern (24 bp):
AATGATTGATTTGTCTGTGATGTA
Found at i:31316222 original size:26 final size:26
Alignment explanation
Indices: 31316193--31316246 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
31316183 TTGGCCACAT
* * *
31316193 ATACTGCTGCTGGCAGTTTTGCTGCG
1 ATACTGCTGCTAGCAGCTATGCTGCG
*
31316219 ATACTGTTGCTAGCAGCTATGCTGCG
1 ATACTGCTGCTAGCAGCTATGCTGCG
31316245 AT
1 AT
31316247 GCTACTGATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (26 bp):
ATACTGCTGCTAGCAGCTATGCTGCG
Found at i:31316290 original size:32 final size:32
Alignment explanation
Indices: 31316249--31316355 Score: 146
Period size: 32 Copynumber: 3.4 Consensus size: 32
31316239 GCTGCGATGC
31316249 TACTGATGGCTTTGTGCCAATCATATTA-TCAT
1 TACTGATGGCTTTGTGCCAATCATATTACT-AT
* * **
31316281 TACTGATGGCTGTGTGTCGGTCATATTACTAT
1 TACTGATGGCTTTGTGCCAATCATATTACTAT
31316313 TACTGATGGCTTTGTGCCAATCATATTACTA-
1 TACTGATGGCTTTGTGCCAATCATATTACTAT
*
31316344 TACTTATGGCTT
1 TACTGATGGCTT
31316356 GTAGCCATTC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
31 11 0.17
32 53 0.82
33 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCAATCATATTACTAT
Found at i:31324193 original size:20 final size:18
Alignment explanation
Indices: 31324158--31324197 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
31324148 TGTTTTAAAG
31324158 TTTATAGTTTAATTTTAT
1 TTTATAGTTTAATTTTAT
*
31324176 TTTATAGGTATTAGTTTTAT
1 TTTATA-GT-TTAATTTTAT
31324196 TT
1 TT
31324198 ATCTTTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 2 0.11
20 11 0.58
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (18 bp):
TTTATAGTTTAATTTTAT
Found at i:31324212 original size:25 final size:25
Alignment explanation
Indices: 31324162--31324212 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
31324152 TTAAAGTTTA
*
31324162 TAGTTTAATTTTATTTTATAGGTAT
1 TAGTTTAATTTTATTTTATAGATAT
* *
31324187 TAGTTTTATTTATCTTTTA-AGATAT
1 TAGTTTAATTT-TATTTTATAGATAT
31324212 T
1 T
31324213 GTACTTATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (25 bp):
TAGTTTAATTTTATTTTATAGATAT
Found at i:31335794 original size:19 final size:18
Alignment explanation
Indices: 31335745--31335795 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
31335735 AAATCGTGTC
31335745 ATTCATTTCCAACA-CATT
1 ATTCATTTCCAA-ATCATT
*
31335763 ATTCATTTACAAATCATT
1 ATTCATTTCCAAATCATT
31335781 ATTCAATTTCCAAAT
1 ATTC-ATTTCCAAAT
31335796 GTTTTTTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 1 0.03
18 19 0.66
19 9 0.31
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTCATTTCCAAATCATT
Found at i:31340103 original size:24 final size:24
Alignment explanation
Indices: 31340071--31340121 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
31340061 TGATATCCTT
31340071 AACTGTAGAGTCCACAGAATCTAA
1 AACTGTAGAGTCCACAGAATCTAA
* *
31340095 AACTGTAGAGTCCTCAGAATCTGA
1 AACTGTAGAGTCCACAGAATCTAA
31340119 AAC
1 AAC
31340122 ACTTACATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.22
Consensus pattern (24 bp):
AACTGTAGAGTCCACAGAATCTAA
Found at i:31341602 original size:19 final size:18
Alignment explanation
Indices: 31341553--31341606 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
31341543 AAATTGTGTC
*
31341553 ATTCGTTTCCAAAACATT
1 ATTCATTTCCAAAACATT
* * *
31341571 ATTCATTTACAAATCGTT
1 ATTCATTTCCAAAACATT
31341589 ATTCAATTTCC-AAACATT
1 ATTC-ATTTCCAAAACATT
31341607 TTTTTATTAC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (18 bp):
ATTCATTTCCAAAACATT
Found at i:31342581 original size:17 final size:18
Alignment explanation
Indices: 31342546--31342581 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
31342536 CATGATGTTC
*
31342546 GCTCGTGTAGGCGCACAT
1 GCTCGTGTAGGCCCACAT
31342564 GCTCGTGT-GGCCCACAT
1 GCTCGTGTAGGCCCACAT
31342581 G
1 G
31342582 GCCCAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.22
Consensus pattern (18 bp):
GCTCGTGTAGGCCCACAT
Found at i:31351744 original size:26 final size:26
Alignment explanation
Indices: 31351715--31351772 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
31351705 TGATGGTTTA
31351715 ATTATTGTAGAA-TTGAGAGTTAAACC
1 ATTATTGTAGAATTTG-GAGTTAAACC
*
31351741 ATTATTGTAGAATTTGTAGTTAAACC
1 ATTATTGTAGAATTTGGAGTTAAACC
31351767 ATTATT
1 ATTATT
31351773 CTAGTATGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 27 0.90
27 3 0.10
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (26 bp):
ATTATTGTAGAATTTGGAGTTAAACC
Found at i:31353895 original size:45 final size:45
Alignment explanation
Indices: 31353826--31353951 Score: 153
Period size: 45 Copynumber: 2.8 Consensus size: 45
31353816 GTTGGTTGAA
* * * *
31353826 AAACAAGTAAGACCATAGCTGAAAGACGTTATGGCATCACAGTTC
1 AAACGAGTAAGACCATAGTTGAAAGACGCTATGGCATCACAATTC
* * **
31353871 ATACGAGTAAGACCATAGTTGAAAGACGCTATGACATTGCAATTC
1 AAACGAGTAAGACCATAGTTGAAAGACGCTATGGCATCACAATTC
* * *
31353916 AAACGTGTAAGACCATTGTTGAAAGACACTATGGCA
1 AAACGAGTAAGACCATAGTTGAAAGACGCTATGGCA
31353952 ACAAGACGAA
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 68 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (45 bp):
AAACGAGTAAGACCATAGTTGAAAGACGCTATGGCATCACAATTC
Found at i:31354035 original size:92 final size:90
Alignment explanation
Indices: 31353923--31354133 Score: 262
Period size: 91 Copynumber: 2.3 Consensus size: 90
31353913 TTCAAACGTG
* *
31353923 TAAGACCATTGTTGAAAGACACTATGGCAACAAGACGAAAAATGAAGAAAACTATAGTTGAAAGA
1 TAAGACCATTGTTGAAAGACACTATGACAACAAGAC-AAAAATGAAGAAAACCATAGTTGAAAGA
*
31353988 CACTATGACAAT-ATAACGGAAAATAAA
65 CACTATGAC-ATCACAACGG-AAATAAA
* * * *
31354015 TAAGACCATTGTTGAAAGACACTATGACAACATGACAAAAATGGATAAGACCATAGTTGAAAGAC
1 TAAGACCATTGTTGAAAGACACTATGACAACAAGACAAAAATGAAGAAAACCATAGTTGAAAGAC
* * *
31354080 ACTATGGCATCACGATGGAAATAAA
66 ACTATGACATCACAACGGAAATAAA
* * * *
31354105 TAAGACCATGGATGAAAGACGCTACGACA
1 TAAGACCATTGTTGAAAGACACTATGACA
31354134 TTCTTTGAAA
Statistics
Matches: 104, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
90 34 0.33
91 36 0.35
92 34 0.33
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.18
Consensus pattern (90 bp):
TAAGACCATTGTTGAAAGACACTATGACAACAAGACAAAAATGAAGAAAACCATAGTTGAAAGAC
ACTATGACATCACAACGGAAATAAA
Found at i:31354074 original size:45 final size:46
Alignment explanation
Indices: 31353923--31354085 Score: 211
Period size: 46 Copynumber: 3.6 Consensus size: 46
31353913 TTCAAACGTG
* * *
31353923 TAAGACCATTGTTGAAAGACACTATGGCAACAAGACGAAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGACAACATGACGAAAAATGAA
* * * * * * *
31353969 GAAAACTATAGTTGAAAGACACTATGACAATATAACGGAAAATAAA
1 TAAGACCATAGTTGAAAGACACTATGACAACATGACGAAAAATGAA
* *
31354015 TAAGACCATTGTTGAAAGACACTATGACAACATGAC-AAAAATGGA
1 TAAGACCATAGTTGAAAGACACTATGACAACATGACGAAAAATGAA
31354060 TAAGACCATAGTTGAAAGACACTATG
1 TAAGACCATAGTTGAAAGACACTATG
31354086 GCATCACGAT
Statistics
Matches: 97, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
45 31 0.32
46 66 0.68
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (46 bp):
TAAGACCATAGTTGAAAGACACTATGACAACATGACGAAAAATGAA
Found at i:31354108 original size:45 final size:45
Alignment explanation
Indices: 31353923--31354133 Score: 206
Period size: 45 Copynumber: 4.6 Consensus size: 45
31353913 TTCAAACGTG
* * * *
31353923 TAAGACCATTGTTGAAAGACACTATGGCAACAAGACGAAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGACAACATGACG-AAAATAAA
* * * * *
31353969 GAAAACTATAGTTGAAAGACACTATGACAATATAACGGAAAATAAA
1 TAAGACCATAGTTGAAAGACACTATGACAACATGAC-GAAAATAAA
* * **
31354015 TAAGACCATTGTTGAAAGACACTATGACAACATGACAAAAATGGA
1 TAAGACCATAGTTGAAAGACACTATGACAACATGACGAAAATAAA
* * * * *
31354060 TAAGACCATAGTTGAAAGACACTATGGCATCACGATGGAAATAAA
1 TAAGACCATAGTTGAAAGACACTATGACAACATGACGAAAATAAA
* * * *
31354105 TAAGACCATGGATGAAAGACGCTACGACA
1 TAAGACCATAGTTGAAAGACACTATGACA
31354134 TTCTTTGAAA
Statistics
Matches: 132, Mismatches: 32, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
45 66 0.50
46 65 0.49
47 1 0.01
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.18
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGACAACATGACGAAAATAAA
Found at i:31356480 original size:1 final size:1
Alignment explanation
Indices: 31356476--31356546 Score: 70
Period size: 1 Copynumber: 71.0 Consensus size: 1
31356466 AAAAAATATG
* * * * * * * *
31356476 TTTTTTTTTTGTTTTTTGTTTTTTTGTTTTTTTGTTTTTGTTTTTGTTTTTGTTTTTTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
31356541 TTTTTT
1 TTTTTT
31356547 GTAATGGTTA
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:31356490 original size:6 final size:6
Alignment explanation
Indices: 31356474--31356544 Score: 94
Period size: 6 Copynumber: 12.2 Consensus size: 6
31356464 CAAAAAAATA
*
31356474 TGTTTT T-TTTT TGTTTTT TGTTTT T-TTGT T-TTTT TGTTTT TGTTTT
1 TGTTTT TGTTTT TG-TTTT TGTTTT TGTTTT TGTTTT TGTTTT TGTTTT
*
31356520 TGTTTT TGTTTT TTTTTT TGTTTT T
1 TGTTTT TGTTTT TGTTTT TGTTTT T
31356545 TTGTAATGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
5 13 0.22
6 39 0.67
7 6 0.10
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (6 bp):
TGTTTT
Found at i:31356492 original size:8 final size:8
Alignment explanation
Indices: 31356479--31356548 Score: 87
Period size: 8 Copynumber: 9.1 Consensus size: 8
31356469 AAATATGTTT
31356479 TTTTTTTG
1 TTTTTTTG
31356487 -TTTTTTG
1 TTTTTTTG
31356494 TTTTTTTG
1 TTTTTTTG
31356502 TTTTTTTG
1 TTTTTTTG
31356510 --TTTTTG
1 TTTTTTTG
31356516 TTTTTGTT-
1 TTTTT-TTG
31356524 TTTGTTTT-
1 TTT-TTTTG
31356532 TTTTTTTG
1 TTTTTTTG
31356540 TTTTTTTG
1 TTTTTTTG
31356548 T
1 T
31356549 AATGGTTAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.11
7 11 0.20
8 35 0.62
9 4 0.07
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (8 bp):
TTTTTTTG
Found at i:31363860 original size:26 final size:27
Alignment explanation
Indices: 31363784--31363867 Score: 79
Period size: 26 Copynumber: 3.3 Consensus size: 27
31363774 AGGGAATCTT
* *
31363784 CGAAGAGCCA-ATAATCAAGATGCTCA
1 CGAAGAGCCATATAATCAGGAAGCTCA
* *
31363810 CAAAGAGCC-TTTAATC-GGAAAGCTCA
1 CGAAGAGCCATATAATCAGG-AAGCTCA
*
31363836 CGAAGAGCCATAT-ATCAGGACGCTCA
1 CGAAGAGCCATATAATCAGGAAGCTCA
31363862 -GAAGAG
1 CGAAGAG
31363868 TGTGGTGTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
25 7 0.15
26 36 0.77
27 4 0.09
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.15
Consensus pattern (27 bp):
CGAAGAGCCATATAATCAGGAAGCTCA
Found at i:31364849 original size:13 final size:13
Alignment explanation
Indices: 31364831--31364858 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31364821 TTTTATTTTA
31364831 TTATTTATCATCT
1 TTATTTATCATCT
31364844 TTATTTATCATCT
1 TTATTTATCATCT
31364857 TT
1 TT
31364859 CTAATTTTAT
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:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTTATCATCT
Found at i:31366847 original size:27 final size:27
Alignment explanation
Indices: 31366817--31366891 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
31366807 AGCCTATGAG
*
31366817 GGTATTTTGATCATTTTACCTTACAGA
1 GGTATTTCGATCATTTTACCTTACAGA
* *
31366844 GGTATTTCGATCATTTTACCTTATAGG
1 GGTATTTCGATCATTTTACCTTACAGA
*
31366871 GGTATTTCGGTCATTTTACCT
1 GGTATTTCGATCATTTTACCT
31366892 ATTTTAGGGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.45
Consensus pattern (27 bp):
GGTATTTCGATCATTTTACCTTACAGA
Found at i:31367162 original size:20 final size:20
Alignment explanation
Indices: 31367139--31367176 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31367129 GCCAATCTCT
*
31367139 GCCCAACATGGCCTATTACG
1 GCCCAACATGGCCCATTACG
31367159 GCCCAACATGGCCCATTA
1 GCCCAACATGGCCCATTA
31367177 TAGCCGAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.37, G:0.18, T:0.18
Consensus pattern (20 bp):
GCCCAACATGGCCCATTACG
Found at i:31368976 original size:151 final size:151
Alignment explanation
Indices: 31368693--31368995 Score: 498
Period size: 151 Copynumber: 2.0 Consensus size: 151
31368683 TTTCTCACTG
* * * *
31368693 AGCTCAGTCCAATACAATGGATTTCTACATTTATGACCATATAGAGCCTCATACGGTGCCATCTT
1 AGCTCAGTACAATACAATGGAGTTCTACATTTACGACCATACAGAGCCTCATACGGTGCCATCTT
*
31368758 AATACTTGACTGATAACTGTTATTATATACGAATTCGACTAAAGACAGGTATTTTTCCCAATTGC
66 AATACTTGACTGATAACTATTATTATATACGAATTCGACTAAAGACAGGTATTTTTCCCAATTGC
31368823 CTTCGAATTCTAACACACAGC
131 CTTCGAATTCTAACACACAGC
*
31368844 AGCTTAGTACAATACAATGGAGTTCTACATTTACGACCATACAGAGCCTCATACGGTGCCATCTT
1 AGCTCAGTACAATACAATGGAGTTCTACATTTACGACCATACAGAGCCTCATACGGTGCCATCTT
* ** *
31368909 AATACTTGACTGATAATTATTATTATATGTGAATTCGACTAAAGGCAGGTATTTTTCCCAATTGC
66 AATACTTGACTGATAACTATTATTATATACGAATTCGACTAAAGACAGGTATTTTTCCCAATTGC
* *
31368974 CTTCGAATTTTAATACACAGC
131 CTTCGAATTCTAACACACAGC
31368995 A
1 A
31368996 CCGAAGCATA
Statistics
Matches: 140, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
151 140 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (151 bp):
AGCTCAGTACAATACAATGGAGTTCTACATTTACGACCATACAGAGCCTCATACGGTGCCATCTT
AATACTTGACTGATAACTATTATTATATACGAATTCGACTAAAGACAGGTATTTTTCCCAATTGC
CTTCGAATTCTAACACACAGC
Found at i:31375247 original size:5 final size:5
Alignment explanation
Indices: 31375216--31375259 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
31375206 TAAATTAAAC
* * *
31375216 TCAAT TTAAT ACAAT TCACAA TCAAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCAAT TCA
31375260 CATCCTAGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.36
Consensus pattern (5 bp):
TCAAT
Found at i:31378437 original size:26 final size:26
Alignment explanation
Indices: 31378408--31378458 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
31378398 AACAGTGTTG
*
31378408 CCCTAGAGGGTAAATGACTATTTTGC
1 CCCTAGAGGGTAAATGACTAATTTGC
*
31378434 CCCTCGAGGGTAAATGACTAATTTG
1 CCCTAGAGGGTAAATGACTAATTTG
31378459 TGCTATAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (26 bp):
CCCTAGAGGGTAAATGACTAATTTGC
Found at i:31385419 original size:22 final size:22
Alignment explanation
Indices: 31385393--31385435 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
31385383 CTGGACTACA
* *
31385393 ATACATCGGATAGGACTCAAGC
1 ATACATCAGATAGGACCCAAGC
31385415 ATACATCAGATAGGACCCAAG
1 ATACATCAGATAGGACCCAAG
31385436 AAAAATAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (22 bp):
ATACATCAGATAGGACCCAAGC
Found at i:31395820 original size:22 final size:22
Alignment explanation
Indices: 31395794--31395838 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
31395784 ATTATATGTA
31395794 TTAATTCATAATATAA-TTAATT
1 TTAATTCAT-ATATAATTTAATT
* *
31395816 TTAATTTATATCTAATTTAATT
1 TTAATTCATATATAATTTAATT
31395838 T
1 T
31395839 GGCTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTCATATATAATTTAATT
Found at i:31403047 original size:41 final size:41
Alignment explanation
Indices: 31403001--31403110 Score: 166
Period size: 41 Copynumber: 2.7 Consensus size: 41
31402991 CATCAAATGT
*
31403001 AAGGGGTTGCTAAGCGCAGATTCCCCGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAA
* * *
31403042 AAGGGGTTGGTAAGTGCAAATTCCCCGAATCACTGATTAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAA
* *
31403083 AAGGGGTTGCTACGTGTAGATTCCCCGA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGA
31403111 GGGGTTGCTA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAA
Found at i:31403113 original size:26 final size:26
Alignment explanation
Indices: 31403084--31403136 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
31403074 CTGATTAAAA
*
31403084 AGGGGTTGCTACGTGTAGATTCCCCG
1 AGGGGTTGCTAAGTGTAGATTCCCCG
*
31403110 AGGGGTTGCTAAGTGTTGATTCCCCG
1 AGGGGTTGCTAAGTGTAGATTCCCCG
31403136 A
1 A
31403137 ATTATTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.17, C:0.21, G:0.34, T:0.28
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGTAGATTCCCCG
Found at i:31403215 original size:43 final size:41
Alignment explanation
Indices: 31403110--31403261 Score: 139
Period size: 42 Copynumber: 3.6 Consensus size: 41
31403100 AGATTCCCCG
* *
31403110 AGGGGTTGCTAAGTGTTGATTCC-CCGAATTATTTATTATAA
1 AGGGGTTGCTAAGTGTTGATTCCACCGTA-TATTGATTATAA
* *
31403151 AGGTGGTTGCTAAGTGCTGATTCCACCGTATACTTGATTGTGAA
1 AGG-GGTTGCTAAGTGTTGATTCCACCGTATA-TTGATTAT-AA
* ** *
31403195 AGGGGTTGCTATGTGTTGATT-CACCGTATCGCTGAATAT-A
1 AGGGGTTGCTAAGTGTTGATTCCACCGTAT-ATTGATTATAA
* *
31403235 AGTTGGTTGCTAAGTGCTGATTCCACC
1 AG-GGGTTGCTAAGTGTTGATTCCACC
31403262 TAGTAACGGT
Statistics
Matches: 91, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
40 3 0.03
41 19 0.21
42 38 0.42
43 26 0.29
44 5 0.05
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.36
Consensus pattern (41 bp):
AGGGGTTGCTAAGTGTTGATTCCACCGTATATTGATTATAA
Found at i:31403256 original size:41 final size:41
Alignment explanation
Indices: 31403146--31403257 Score: 111
Period size: 43 Copynumber: 2.7 Consensus size: 41
31403136 AATTATTTAT
* *
31403146 TATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATACTTGAT
1 TATAAA-GTGGTTGCTAAGTGCTGATT-CACCGTATACCTGAA
* * * *
31403189 TGTGAAAGGGGTTGCTATGTGTTGATTCACCGTAT-CGCTGAA
1 TAT-AAAGTGGTTGCTAAGTGCTGATTCACCGTATAC-CTGAA
31403231 TAT-AAGTTGGTTGCTAAGTGCTGATTC
1 TATAAAG-TGGTTGCTAAGTGCTGATTC
31403258 CACCTAGTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
40 3 0.05
41 18 0.32
42 13 0.23
43 19 0.34
44 3 0.05
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (41 bp):
TATAAAGTGGTTGCTAAGTGCTGATTCACCGTATACCTGAA
Done.