Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, whole genome shotgun sequence
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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 2 of 125
Found at i:164674 original size:33 final size:33
Alignment explanation
Indices: 164622--164751 Score: 93
Period size: 33 Copynumber: 3.9 Consensus size: 33
164612 TGAAAAATTT
* * * *
164622 CTCTAACTAAAAGTAATGGTATTTAAAATATCC
1 CTCTAACCAAAGGTCATGGTATTTAAAAGATCC
* * *
164655 CTCTAACCAGAGGTCATGGT-TTATGAAAGATTC
1 CTCTAACCAAAGGTCATGGTATT-TAAAAGATCC
* * * **
164688 TTCTAACTAAAGGTCATGATATTTAAAAGATTT
1 CTCTAACCAAAGGTCATGGTATTTAAAAGATCC
* * *
164721 TTCTAACCCAAGG-CAATAGTATTTAAAAGAT
1 CTCTAACCAAAGGTC-ATGGTATTTAAAAGAT
164752 TCTTCTAGCT
Statistics
Matches: 77, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
32 3 0.04
33 72 0.94
34 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (33 bp):
CTCTAACCAAAGGTCATGGTATTTAAAAGATCC
Found at i:164726 original size:66 final size:66
Alignment explanation
Indices: 164602--164767 Score: 153
Period size: 66 Copynumber: 2.5 Consensus size: 66
164592 TAACTAGAGA
* * * *
164602 CAATACTATTTGAAAA-ATT-TCTCTAACTAAAAGTAATGGTATTTAAAATATCCCTCTAA-CCA
1 CAATAGTATTT-AAAAGATTCT-TCTAACTAAAGGTAATGATATTTAAAAGATCCCTCTAACCCA
164664 GAGG
64 -AGG
* * * ***
164668 TC-ATGGT-TTATGAAAGATTCTTCTAACTAAAGGTCATGATATTTAAAAGATTTTTCTAACCCA
1 -CAATAGTATT-TAAAAGATTCTTCTAACTAAAGGTAATGATATTTAAAAGATCCCTCTAACCCA
164731 AGG
64 AGG
*
164734 CAATAGTATTTAAAAGATTCTTCTAGCTAAAGGT
1 CAATAGTATTTAAAAGATTCTTCTAACTAAAGGT
164768 GGTGAATTTT
Statistics
Matches: 80, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
65 6 0.08
66 67 0.84
67 7 0.09
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.34
Consensus pattern (66 bp):
CAATAGTATTTAAAAGATTCTTCTAACTAAAGGTAATGATATTTAAAAGATCCCTCTAACCCAAG
G
Found at i:166886 original size:17 final size:15
Alignment explanation
Indices: 166848--166879 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
166838 TTGAGTGTTG
*
166848 TTAATATTTGATATA
1 TTAATATTTGACATA
166863 TTAATATTTGACATA
1 TTAATATTTGACATA
166878 TT
1 TT
166880 GTAATATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (15 bp):
TTAATATTTGACATA
Found at i:171352 original size:17 final size:17
Alignment explanation
Indices: 171330--171370 Score: 75
Period size: 16 Copynumber: 2.5 Consensus size: 17
171320 TTTATGATAA
171330 TGGGGCCATCAAGTGCC
1 TGGGGCCATCAAGTGCC
171347 TGGGG-CATCAAGTGCC
1 TGGGGCCATCAAGTGCC
171363 TGGGGCCA
1 TGGGGCCA
171371 CCAAATGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.17, C:0.27, G:0.39, T:0.17
Consensus pattern (17 bp):
TGGGGCCATCAAGTGCC
Found at i:176862 original size:21 final size:20
Alignment explanation
Indices: 176836--176891 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 20
176826 ATAATAATAT
176836 AAAAATATAAAAAATTAAGCA
1 AAAAATATAAAAAATTAAG-A
*
176857 AAAAATGA-AAAAAATTATGA
1 AAAAAT-ATAAAAAATTAAGA
176877 AGAAAATACTAAAAA
1 A-AAAATA-TAAAAA
176892 TGCCCTTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.10
21 21 0.70
22 6 0.20
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (20 bp):
AAAAATATAAAAAATTAAGA
Found at i:177501 original size:2 final size:2
Alignment explanation
Indices: 177496--177529 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
177486 TATATATATA
177496 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
177530 GAGGGTAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:177943 original size:17 final size:17
Alignment explanation
Indices: 177899--177933 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
177889 AAGATGGCAA
177899 AAAGAACAA-AAGAAAAG
1 AAAGAA-AATAAGAAAAG
177916 AAAGAAAATAAGAAAAG
1 AAAGAAAATAAGAAAAG
177933 A
1 A
177934 CAAGGAATAA
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:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (17 bp):
AAAGAAAATAAGAAAAG
Found at i:179825 original size:10 final size:10
Alignment explanation
Indices: 179810--179840 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
179800 AAATTAAATA
179810 TAAAAATTTT
1 TAAAAATTTT
179820 TAAAAATTTT
1 TAAAAATTTT
179830 TAATAAATTTT
1 TAA-AAATTTT
179841 GATATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.65
11 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TAAAAATTTT
Found at i:179865 original size:14 final size:13
Alignment explanation
Indices: 179846--179877 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
179836 ATTTTGATAT
179846 ATTTTTATATAAAA
1 ATTTTTA-ATAAAA
179860 ATTTTTAATAAAA
1 ATTTTTAATAAAA
179873 ATTTT
1 ATTTT
179878 GAAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTTTTAATAAAA
Found at i:180224 original size:4 final size:4
Alignment explanation
Indices: 180215--180242 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
180205 TTATGACATC
180215 AATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT
180243 GTTAATTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:181105 original size:17 final size:17
Alignment explanation
Indices: 181065--181110 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
181055 TTGAAATGTT
*
181065 TAAAAATATATATAAATA
1 TAAAAATAT-TAAAAATA
181083 -ATAAAATATTAAAAATA
1 TA-AAAATATTAAAAATA
181100 TAAAAATATTA
1 TAAAAATATTA
181111 TTAAATTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAAATATTAAAAATA
Found at i:184019 original size:15 final size:15
Alignment explanation
Indices: 183999--184036 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
183989 ATATATTAAT
*
183999 AAGGAAAGGAAAGTA
1 AAGGAAAGGAAAGAA
184014 AAGGAAAGGAAAGAA
1 AAGGAAAGGAAAGAA
*
184029 AAAGAAAG
1 AAGGAAAG
184037 TTTTTTTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.03
Consensus pattern (15 bp):
AAGGAAAGGAAAGAA
Found at i:184483 original size:104 final size:104
Alignment explanation
Indices: 184303--184504 Score: 377
Period size: 104 Copynumber: 1.9 Consensus size: 104
184293 GTACCTAGGG
*
184303 AGGAGAGTTGACAGAAGAGGAGTGAGTTGAGAAAAGAGACATGGCTTTTTTAAGTAATGTTAAAT
1 AGGAGAGTTGACAGAAGAGGAGTGAGTTGAGAAAAGAGACATGGCTTTTTTAAGCAATGTTAAAT
*
184368 AAAAATATGGATATTATAGTCCTTTCTTAAAAAAAAATT
66 AAAAATATGGATATGATAGTCCTTTCTTAAAAAAAAATT
184407 AGGAGAGTTGACAGAAGAGGAGTGAGTTGAGAAAAGAGACATGGCTTTTTTAAGCAATGTTAAAT
1 AGGAGAGTTGACAGAAGAGGAGTGAGTTGAGAAAAGAGACATGGCTTTTTTAAGCAATGTTAAAT
*
184472 AAAAATATGGATATGATAGTCTTTTCTTAAAAA
66 AAAAATATGGATATGATAGTCCTTTCTTAAAAA
184505 TAATTTTTTT
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 95 1.00
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (104 bp):
AGGAGAGTTGACAGAAGAGGAGTGAGTTGAGAAAAGAGACATGGCTTTTTTAAGCAATGTTAAAT
AAAAATATGGATATGATAGTCCTTTCTTAAAAAAAAATT
Found at i:186074 original size:42 final size:41
Alignment explanation
Indices: 185988--186133 Score: 158
Period size: 40 Copynumber: 3.6 Consensus size: 41
185978 TTTGATAGCA
* *
185988 TGATTCAACGAAGAATCTTTCACTGCTTTTTTT-TTTTGCT
1 TGATTCAACAAAGAATCTTTCACTGCTTTTTTTCTGTTGCT
186028 TGATTCAACAAAGAATCTTTCACTGCTTCTTTTTCTGTTGCT
1 TGATTCAACAAAGAATCTTTCACTGCTT-TTTTTCTGTTGCT
* * *
186070 TGATTCAA-AGAAAAATCTTTCAGT-C-TTTTTTCTGTTGGT
1 TGATTCAACA-AAGAATCTTTCACTGCTTTTTTTCTGTTGCT
* * *
186109 CGAGTCAACAGAGAAAT-TTTCACTG
1 TGATTCAACAAAG-AATCTTTCACTG
186134 TCACAAAATT
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
39 25 0.28
40 32 0.36
41 7 0.08
42 26 0.29
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (41 bp):
TGATTCAACAAAGAATCTTTCACTGCTTTTTTTCTGTTGCT
Found at i:187027 original size:4 final size:4
Alignment explanation
Indices: 187018--187101 Score: 51
Period size: 4 Copynumber: 20.5 Consensus size: 4
187008 TAAGTAGGAT
* * * * * * *
187018 ATAC ATAC ATAT ATGC ATTC ATAC ACAC ATAC ATAG ATAGAC ATAA ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT--AC ATAC ATAC
* * * *
187068 ATAC ATAT ATAC AGAC ATGC ATGC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
187102 GCAAGCACAG
Statistics
Matches: 59, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
4 56 0.95
6 3 0.05
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:188121 original size:2 final size:2
Alignment explanation
Indices: 188114--188147 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
188104 TCTGTTAGTT
188114 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
188148 ATTAGTGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:188347 original size:23 final size:23
Alignment explanation
Indices: 188307--188355 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
188297 TTTTCTAATC
*
188307 TTTGGGGTGTCCATTG-AAAAAT
1 TTTGGGGTGTCCAATGAAAAAAT
*
188329 TTTGGGGATGTCTAATGAAAAAAT
1 TTTGGGG-TGTCCAATGAAAAAAT
188353 TTT
1 TTT
188356 CCTTCAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 7 0.30
23 7 0.30
24 9 0.39
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.39
Consensus pattern (23 bp):
TTTGGGGTGTCCAATGAAAAAAT
Found at i:192194 original size:2 final size:2
Alignment explanation
Indices: 192189--192218 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
192179 ACACACACAC
*
192189 GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
192219 ATATACAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:197171 original size:21 final size:21
Alignment explanation
Indices: 197131--197172 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
197121 AATAAATTTT
* *
197131 TTTATTAAATTAAGATATATA
1 TTTATTAAAATAAGACATATA
*
197152 TTTATTAAAATAATACATATA
1 TTTATTAAAATAAGACATATA
197173 CAAATATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTATTAAAATAAGACATATA
Found at i:200364 original size:2 final size:2
Alignment explanation
Indices: 200357--200383 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
200347 ACTTTAAACA
200357 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
200384 AACCAAAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:201253 original size:14 final size:15
Alignment explanation
Indices: 201234--201269 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
201224 AAAAAATGTT
*
201234 AAAAAATATA-TGAA
1 AAAAAATAAATTGAA
201248 AAAAAATAAATTGAA
1 AAAAAATAAATTGAA
201263 AAAAAAT
1 AAAAAAT
201270 TATTTTCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (15 bp):
AAAAAATAAATTGAA
Found at i:201357 original size:51 final size:52
Alignment explanation
Indices: 201297--201398 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 52
201287 AAACTTTAAT
* *
201297 AATAATAATAAAATATATCTTAGAAAAAATTTA-TAAACAAA-AAAAAATTGC
1 AATAATAATAAAATATACCTTA-AAAAAAGTTATTAAACAAATAAAAAATTGC
* * * *
201348 AATAGTAATAGAATATACCTTAAAAAAAGTTATTGAACAAATAAAATATTG
1 AATAATAATAAAATATACCTTAAAAAAAGTTATTAAACAAATAAAAAATTG
201399 ATATATAACA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
50 9 0.21
51 26 0.60
52 8 0.19
ACGTcount: A:0.59, C:0.06, G:0.07, T:0.28
Consensus pattern (52 bp):
AATAATAATAAAATATACCTTAAAAAAAGTTATTAAACAAATAAAAAATTGC
Found at i:202832 original size:22 final size:21
Alignment explanation
Indices: 202807--202847 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
202797 GTGAAAACAA
202807 AAAAATATTATAATTTTTAATG
1 AAAAAT-TTATAATTTTTAATG
* *
202829 AAAAATTTTTTATTTTTAA
1 AAAAATTTATAATTTTTAA
202848 ATATAATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
AAAAATTTATAATTTTTAATG
Found at i:202902 original size:26 final size:26
Alignment explanation
Indices: 202853--202903 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
202843 TTTAAATATA
* * * *
202853 ATACTTCACAAATATATAATAAAATT
1 ATACCTCACAAATAAAAAAAAAAATT
202879 ATACCTCACAAATAAAAAAAAAAAT
1 ATACCTCACAAATAAAAAAAAAAAT
202904 CTCATTTTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (26 bp):
ATACCTCACAAATAAAAAAAAAAATT
Found at i:206206 original size:34 final size:33
Alignment explanation
Indices: 206163--206227 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
206153 AAATCCTGAC
* *
206163 TTTCTAAAAATTCATTTCTTGAAAAGTTTATAACT
1 TTTCTAAAAATCCATTT-TAGAAAAG-TTATAACT
206198 TTTC-AAAAATCCATTTTAGAAAAGTTATAA
1 TTTCTAAAAATCCATTTTAGAAAAGTTATAA
206228 GATTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 6 0.21
33 7 0.25
34 11 0.39
35 4 0.14
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.42
Consensus pattern (33 bp):
TTTCTAAAAATCCATTTTAGAAAAGTTATAACT
Found at i:207905 original size:13 final size:13
Alignment explanation
Indices: 207872--207910 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
207862 CTATTTTTCA
207872 TTTAATTGTTATTT
1 TTTAATT-TTATTT
207886 TTT-ATTTTATTT
1 TTTAATTTTATTT
207898 TTTAATTTT-TTT
1 TTTAATTTTATTT
207910 T
1 T
207911 CAAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 13 0.54
13 8 0.33
14 3 0.12
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTAATTTTATTT
Found at i:208032 original size:21 final size:20
Alignment explanation
Indices: 208007--208086 Score: 56
Period size: 21 Copynumber: 3.8 Consensus size: 20
207997 CCACTGTTTG
208007 TTTTTATTTATTGTTATTATT
1 TTTTTATTTATT-TTATTATT
**
208028 TTTTTAAATATATTTATT-TCT
1 TTTTTATTTAT-TTTATTAT-T
*
208049 ATTTTATTTATTCCATTTATTATT
1 TTTTTATTTA-T---TTTATTATT
208073 TTTTTATTT-TTTTA
1 TTTTTATTTATTTTA
208087 AGATTTATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
19 4 0.09
20 1 0.02
21 22 0.47
22 3 0.06
24 16 0.34
25 1 0.02
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (20 bp):
TTTTTATTTATTTTATTATT
Found at i:208841 original size:99 final size:99
Alignment explanation
Indices: 208659--208848 Score: 249
Period size: 99 Copynumber: 1.9 Consensus size: 99
208649 AAAAAAATTG
* * * * * *
208659 AAAAGGTTCAATCTGAAAGGCTTCTAAATTATTCCTCACTTTCATCTATGCTGGACTAGTAAGAC
1 AAAAGATTCAATCTGAAAAGCTCCTAAATTATTCCTCACTATCATCCATACTGGACTAGTAAGAC
* *
208724 ACTTCGATCCTCATCCATTATAAGTTGTAAACGA
66 ACTTCGATCATCACCCATTATAAGTTGTAAACGA
* * *
208758 AAAAGATTCAATCTGAAAAGCTCCTAGATTATTCCTTACTATCATCCATACTGGACTTA-TAAGG
1 AAAAGATTCAATCTGAAAAGCTCCTAAATTATTCCTCACTATCATCCATACTGGAC-TAGTAAGA
208822 CAC-TCTGATCATCACCCATTATAAGTT
65 CACTTC-GATCATCACCCATTATAAGTT
208849 ACAAACAAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
98 2 0.03
99 74 0.95
100 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (99 bp):
AAAAGATTCAATCTGAAAAGCTCCTAAATTATTCCTCACTATCATCCATACTGGACTAGTAAGAC
ACTTCGATCATCACCCATTATAAGTTGTAAACGA
Found at i:208870 original size:99 final size:98
Alignment explanation
Indices: 208659--208870 Score: 239
Period size: 99 Copynumber: 2.1 Consensus size: 98
208649 AAAAAAATTG
* * * * * *
208659 AAAAGGTTCAATCTGAAAGGCTTCTAAATTATTCCTCACTTTCATCTATGCTGGACTAGTAAGAC
1 AAAAAGTTCAATCTGAAAAGCTCCTAAATTATTCCTCACTATCATCCATACTGGACTAGTAAGAC
* * ** *
208724 ACTTCGATCCTCATCCATTATAAGTTGTAAACG
66 ACTTCGATCATCACCCATTATAAGTTACAAACA
* *
208757 AAAAAGATTCAATCTGAAAAGCTCCTAGATTATTCCTTACTATCATCCATACTGGACTTA-TAAG
1 AAAAAG-TTCAATCTGAAAAGCTCCTAAATTATTCCTCACTATCATCCATACTGGAC-TAGTAAG
*
208821 GCAC-TCTGATCATCACCCATTATAAGTTACAAACAA
64 ACACTTC-GATCATCACCCATTATAAGTTACAAAC-A
*
208857 AAAAAGTTTAATCT
1 AAAAAGTTCAATCT
208871 AAGTGAAAGT
Statistics
Matches: 95, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
98 7 0.07
99 80 0.84
100 8 0.08
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (98 bp):
AAAAAGTTCAATCTGAAAAGCTCCTAAATTATTCCTCACTATCATCCATACTGGACTAGTAAGAC
ACTTCGATCATCACCCATTATAAGTTACAAACA
Found at i:210525 original size:15 final size:15
Alignment explanation
Indices: 210507--210536 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
210497 TTTAAAAATA
*
210507 TATTTATTTCTTTTT
1 TATTTATTCCTTTTT
210522 TATTTATTCCTTTTT
1 TATTTATTCCTTTTT
210537 ATCATTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (15 bp):
TATTTATTCCTTTTT
Found at i:210623 original size:5 final size:5
Alignment explanation
Indices: 210615--210641 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
210605 TTTTATTAAA
210615 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
210642 TTATAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:211456 original size:19 final size:19
Alignment explanation
Indices: 211434--211515 Score: 78
Period size: 22 Copynumber: 4.3 Consensus size: 19
211424 TTTTGCAATT
211434 TTTTTTTGTTGGCAAAAAC
1 TTTTTTTGTTGGCAAAAAC
*
211453 TTTTTTTTTTGCTGGCAAAAAC
1 ---TTTTTTTGTTGGCAAAAAC
*
211475 TTTTTTT-TT-GCAAAATC
1 TTTTTTTGTTGGCAAAAAC
* * *
211492 TTTTTTTTTTGGTAGAAAC
1 TTTTTTTGTTGGCAAAAAC
211511 TTTTT
1 TTTTT
211516 CTGAGAGTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
17 14 0.27
18 3 0.06
19 17 0.33
22 18 0.35
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.56
Consensus pattern (19 bp):
TTTTTTTGTTGGCAAAAAC
Found at i:211485 original size:21 final size:22
Alignment explanation
Indices: 211432--211483 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
211422 TTTTTTGCAA
*
211432 TTTTTTTTTGTTGGCAAAAACT
1 TTTTTTTTTGCTGGCAAAAACT
211454 TTTTTTTTTGCTGGCAAAAACT
1 TTTTTTTTTGCTGGCAAAAACT
211476 TTTTTTTT
1 TTTTTTTT
211484 GCAAAATCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.19, C:0.10, G:0.12, T:0.60
Consensus pattern (22 bp):
TTTTTTTTTGCTGGCAAAAACT
Found at i:218482 original size:18 final size:16
Alignment explanation
Indices: 218443--218482 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
218433 ATACATAAAA
218443 ATATAATTTTTAATAT
1 ATATAATTTTTAATAT
*
218459 AAATAATATTTTAATTAT
1 ATATAAT-TTTTAA-TAT
218477 ATATAA
1 ATATAA
218483 ATATAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 6 0.30
18 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATAATTTTTAATAT
Found at i:219222 original size:23 final size:22
Alignment explanation
Indices: 219185--219242 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
219175 AGAATAAAAG
* *
219185 AGAAAAAAAAAAAAAAGA-AATA
1 AGAAAGAAAAGAAAAAGACAA-A
*
219207 AGAAAGGAAAAGAAAAGGACAAA
1 AGAAA-GAAAAGAAAAAGACAAA
219230 AGAAAG-AAAGAAA
1 AGAAAGAAAAGAAA
219243 GTGACATTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 7 0.23
22 6 0.19
23 16 0.52
24 2 0.06
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (22 bp):
AGAAAGAAAAGAAAAAGACAAA
Found at i:219559 original size:30 final size:29
Alignment explanation
Indices: 219419--219559 Score: 155
Period size: 30 Copynumber: 4.8 Consensus size: 29
219409 AATTGACTAC
*
219419 TTTAT-TTAAATAAAATTTTATATTTTT-A
1 TTTATATTAAATAAATTTTTA-ATTTTTAA
*
219447 -TTATATTCAAAT-AATTTTTGAAATTTTAA
1 TTTATATT-AAATAAATTTTT-AATTTTTAA
*
219476 CTTATATTTAAATAAATTTTTAATTTTTAA
1 TTTATA-TTAAATAAATTTTTAATTTTTAA
* *
219506 TTTATATCTAAATAAACTCTTAATTTTTAA
1 TTTATAT-TAAATAAATTTTTAATTTTTAA
219536 TTTATACTTAAATAAATTTTTAAT
1 TTTATA-TTAAATAAATTTTTAAT
219560 ATAAATCAAT
Statistics
Matches: 96, Mismatches: 8, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
27 4 0.04
28 13 0.14
29 7 0.07
30 62 0.65
31 10 0.10
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (29 bp):
TTTATATTAAATAAATTTTTAATTTTTAA
Found at i:219628 original size:29 final size:29
Alignment explanation
Indices: 219595--219650 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
219585 AAGACTTATA
219595 TATTTGGA-TACAGATAAAAA-ATAAAAAAT
1 TATTT-GATTACA-ATAAAAATATAAAAAAT
219624 TATTTGATTACAATAAAAATATAAAAA
1 TATTTGATTACAATAAAAATATAAAAA
219651 TTTAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (29 bp):
TATTTGATTACAATAAAAATATAAAAAAT
Found at i:219932 original size:13 final size:13
Alignment explanation
Indices: 219914--219939 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
219904 GTATATACTA
219914 AAAACATGAGTTT
1 AAAACATGAGTTT
219927 AAAACATGAGTTT
1 AAAACATGAGTTT
219940 TTTCCCACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
AAAACATGAGTTT
Found at i:222885 original size:18 final size:18
Alignment explanation
Indices: 222864--222898 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
222854 TAAAAATTTA
222864 ATAAAAAATAAAAAATAG
1 ATAAAAAATAAAAAATAG
* *
222882 ATAATATATAAAAAATA
1 ATAAAAAATAAAAAATA
222899 TTAATATTTT
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:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
ATAAAAAATAAAAAATAG
Found at i:227827 original size:21 final size:21
Alignment explanation
Indices: 227803--227872 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
227793 ACAATAATCG
227803 TAAAAAGATATTATTATAATA
1 TAAAAAGATATTATTATAATA
* * *
227824 TAAATA-AT-TAAGTTGAGAATA
1 TAAAAAGATATTA-TT-ATAATA
*
227845 TAAAAAAATTATTATTATAA-A
1 TAAAAAGA-TATTATTATAATA
227866 TAAAAAG
1 TAAAAAG
227873 TGATTCTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
19 2 0.05
20 4 0.11
21 22 0.59
22 4 0.11
23 3 0.08
24 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (21 bp):
TAAAAAGATATTATTATAATA
Found at i:228651 original size:211 final size:211
Alignment explanation
Indices: 228060--228858 Score: 614
Period size: 211 Copynumber: 3.7 Consensus size: 211
228050 AGTTATTCTA
* * * *
228060 AATT-TAAACATAAT-AAATAGTAAGAACAAGTGTACAAA-A-ATTATTGTAATATAAATAATAT
1 AATTCTAAACATAATAAAATA-TAAAAATAAGTGTAAAAAGATATTATTG-AACATAAATAA-A-
** * * * * * *
228121 TTTTGATAACGTAAAAGAATTAATATTACAAATAATTAATAACTTTAAACTAAAAAAATAAGTGT
62 --TTGATAATATAAAAAAATTATTATTATAAATAA-AAATAA--TTCAA-T-AAAAAATAAGTAT
* * * *
228186 TAATATAAAAAGAGTGAGAATAATCATAAAATTAGTATTATTTCACGTAAAATAGTTAGAAGCAT
120 TAACATAAAAAG-GTGAGAATAATCATAAAATTAGTATTATTTAATGTAAAATAGTTAGAAGTAT
* * * * *
228251 CATAACACCTTTAAGATAAAAGTTATAA-
184 CGTAATACC-TTAAAAAAAAAGTTGTAAT
* * * *
228279 AACTTCTAAATAGAATAAAAGATAAGAATAAGTGTAAAAAGATATTATTAGAACATAAATAAATT
1 AA-TTCTAAACATAATAAAATATAAAAATAAGTGTAAAAAGATATTATT-GAACATAAATAAATT
* * * *
228344 AAGTTGACA-ATAAGAAAGAACTATTATTATAAATAAAAAATAATTTTAAATAAAAAGTTAAG-A
64 --GAT-A-ATATAA-AAA-AATTATTATTATAAAT-AAAAATAA--TTCAATAAAAA-ATAAGTA
* * *
228407 GTTAACATAAAACGGTGAGAATAATCGTAAAATTGGTATTATTTAATGTAAAATAGTTAGAAGTA
119 -TTAACATAAAAAGGTGAGAATAATCATAAAATTAGTATTATTTAATGTAAAATAGTTAGAAGTA
* *
228472 TTGTTATACCTTAAAAAAAAAGTTGTAAT
183 TCGTAATACCTTAAAAAAAAAGTTGTAAT
* * * *
228501 AATTCTAAACATAATGAAATATAATAATAAATG-AAAAAGATATTATTGAA-ATGTAATAAATTG
1 AATTCTAAACATAATAAAATATAAAAATAAGTGTAAAAAGATATTATTGAACAT-AAATAAATTG
* * * *
228564 GTAATGTAAAAAAATTAGTATTATAAATAAGAAATAATTCAATAAAAAATAAGTATTAACGTAAA
65 ATAATATAAAAAAATTATTATTATAAATAA-AAATAATTCAATAAAAAATAAGTATTAACATAAA
* * * * * *
228629 AAGGTGAGAATAATCATAAAATTAGTATCATTTGACT-TAAAATATATTAAAATTGTCGTAATAC
129 AAGGTGAGAATAATCATAAAATTAGTATTATTT-AATGTAAAATA-GTTAGAAGTATCGTAATAC
* * * *
228693 CTT-AAGAAAGACTTGTGAT
192 CTTAAAAAAAAAGTTGTAAT
* * *
228712 AATTTTAAACATAATAAAATATAAAAATAAGCGTAAAAA-ATTTTATTGTAACATAAATATAAGT
1 AATTCTAAACATAATAAAATATAAAAATAAGTGTAAAAAGATATTATTG-AACATAAATA-AA-T
* * * * *
228776 TGACAATATAAAAAAATTATTAATATAAATAAATAATAATTACAAACAAAAAAATACGTGTTAAC
63 TGATAATATAAAAAAATTATTATTATAAATAAA-AATAATT-C-AA-TAAAAAATAAGTATTAAC
* **
228841 GTAAAAATATGAGAATAA
124 ATAAAAAGGTGAGAATAA
228859 CTGAAAATTT
Statistics
Matches: 473, Mismatches: 76, Indels: 64
0.77 0.12 0.10
Matches are distributed among these distances:
211 97 0.21
212 40 0.08
213 7 0.01
214 55 0.12
215 5 0.01
216 6 0.01
217 33 0.07
218 2 0.00
219 15 0.03
220 16 0.03
221 66 0.14
222 69 0.15
223 35 0.07
224 25 0.05
225 2 0.00
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.31
Consensus pattern (211 bp):
AATTCTAAACATAATAAAATATAAAAATAAGTGTAAAAAGATATTATTGAACATAAATAAATTGA
TAATATAAAAAAATTATTATTATAAATAAAAATAATTCAATAAAAAATAAGTATTAACATAAAAA
GGTGAGAATAATCATAAAATTAGTATTATTTAATGTAAAATAGTTAGAAGTATCGTAATACCTTA
AAAAAAAAGTTGTAAT
Found at i:228827 original size:38 final size:40
Alignment explanation
Indices: 228746--228830 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
228736 AAATAAGCGT
* * *
228746 AAAAAATTTTATTGTAACATAAATATAAGTTGACAATATA
1 AAAAAATTTTAATATAACATAAATATAAGTTGACAATACA
228786 AAAAAATTATTAATATAA-ATAAATAATAA-TT-ACAA-ACA
1 AAAAAATT-TTAATATAACATAAAT-ATAAGTTGACAATACA
228824 AAAAAAT
1 AAAAAAT
228831 ACGTGTTAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
38 9 0.22
39 4 0.10
40 16 0.40
41 11 0.28
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.31
Consensus pattern (40 bp):
AAAAAATTTTAATATAACATAAATATAAGTTGACAATACA
Found at i:229129 original size:936 final size:935
Alignment explanation
Indices: 227361--229539 Score: 2323
Period size: 942 Copynumber: 2.3 Consensus size: 935
227351 CCAATAGATA
* * * * *
227361 TAAAAAGATATTATTGTTGTAACAAAAATAATTAAGTTGATAATGTAAAATAAATATTATTACAA
1 TAAAAAGATATTA-T-TAG-AACATAAATAATTAAGTTGACAAT-AAAAAAAAATATTATTACAA
* ** ** *
227426 ATAAAAATAATAATTTTAAACCAAAAAATAAAAATTAATGTAAAAAAGTGAGAATGATCGTAAAA
62 AT-AAAA-AATAATTTTAAA-CAAAAAATAAGAATTAACATAAAACGGTGAGAATAATCGTAAAA
* * * * * *
227491 TTAGTATTATTTGACGTAAAATAGTTACAAATATTGTTATACCTTAATAAAATATTGTACTAATT
124 TTAGTATTATTTAACGTAAAATAGTTAGAAGTATTGTTATACCTTAAAAAAAAATTGTAATAATT
* * *
227556 TTAAAAGTAAT-AAAA-AGTAATAAGTATAAAAAATACTATT-AAATTGTAAATAATTAAATTGG
189 CTAAAA-TAATGAAAATAATAATAA--ATAAAAAATATTATTGAAA-TG----TAA-TAAATTGG
* * * *
227618 TAGTGTTAAAAAAATTAGTATTATAAATAAAAAATAATCCTACACCAAAAAATAGGTGTTAACGT
245 TAATG-TAAAAAAATTAGTATTATAAAT-AAAAATAAT--TACAACAAAAAATAAGTATTAACGT
* * ** * * *
227683 AAAAAAAATAAGAATAATCGTAAAATTTGTATTTTTTGAAGTAAAATTGTTAGAAGTGTTGTAAC
306 AAAAAAAATAAGAATAATCATAAAATTAGTATCATTTGAAGTAAAATTATTAAAAGTGTCGTAAC
* * *
227748 ACCTTTAAGAAAAAATAATGATAATTCTAAACGTAAAAAAAGATAACAATAATCGTAAAAAGATA
371 ACCTTTAAGAAAAAATAATGATAATTCTAAACATAAAAAAAGATAAAAATAAGCGTAAAAAGATA
* * * *
227813 TTATTATAATATAAATAATTAAGTTGAGAATATAAAAAAATTATTATTATAAATAAAAAGTGATT
436 TTATTATAACATAAATAATTAAGTTGACAATATAAAAAAATTATTAATATAAATAAAAAGTAATT
* * * *
227878 CTAAACAAAAAAAAAAGGTGTTAATGTACAAAAAGTGAAAGTAATTGTAAAATTGGAATCATTTA
501 CTAAACAAAAAAAAAACGTGTTAACGTACAAAAAGTGAAAGTAACTGTAAAATTGAAATCATTTA
* * * *
227943 GCGTAAAGTGTATTAGAAGTATTGTGACGTAAAAATGTAAGAATAGTTGTAAAATTGATGTCATT
566 GCGTAAAATATATTACAAGTATTGTAACGTAAAAATGTAAGAATAGTTGTAAAATTGATGTCATT
* * * * * **
228008 TGACATAAATTTGATTAAAATTGTGGTAATACCCTAACAAAGAGTTATTCTAAATTTAAACATAA
631 TGACATAAATTGGATTAAAAGTATGGTAACACCCTAACAAAAAGTTATGATAAATTTAAACATAA
* * * * * *
228073 TAAATAGTAAGAACAAGTGTACAAAAATTATTGTAATATAAATAATATTTTTGATAACGTAAAAG
696 TAAAAAATAAGAACAAGTATAAAAAAATTATTGTAATATAAATAATATTTTTGACAACATAAAAG
* *
228138 AATTAATATTACAAATAATTAATAACTTTAAACTAAAAAAATAAGTGTTAATATAAAA-AGAGTG
761 AATTAATATTACAAATAAATAATAACTTTAAACTAAAAAAATAAGTGTTAATATAAAATAAAGTG
* * *
228202 AGAATAATCATAAAATTAGTATTATTTCACGTAAAATAGTTAGAAGCATCATAACACCTTTAAGA
826 AGAATAATCATAAAATTAATATCATTTCACGTAAAATAGTTAGAAGCATCATAACA-CTTTAAAA
* * *
228267 TAAAAGTTAT-AAAACTTCTAAATAGAATAAAAGATAAGAATAAGTG
890 AAAAAGTTATGAAAA-TTCTAAACAGAATAAAAGATAAGAATAAATG
* * *
228313 TAAAAAGATATTATTAGAACATAAATAAATTAAGTTGACAATAAGAAAGAACTATTATTATAAAT
1 TAAAAAGATATTATTAGAACATAAAT-AATTAAGTTGACAATAA-AAAAAAATATTATTACAAAT
* * * *
228378 AAAAAATAATTTTAAATAAAAAGTTAAGAGTTAACATAAAACGGTGAGAATAATCGTAAAATTGG
64 AAAAAATAATTTTAAACAAAAA-ATAAGAATTAACATAAAACGGTGAGAATAATCGTAAAATTAG
*
228443 TATTATTTAATGTAAAATAGTTAGAAGTATTGTTATACCTTAAAAAAAAAGTTGTAATAATTCTA
128 TATTATTTAACGTAAAATAGTTAGAAGTATTGTTATACCTTAAAAAAAAA-TTGTAATAATTCTA
228508 AACATAATGAAATATAATAATAAATGAAAAAGATATTATTGAAATGTAATAAATTGGTAATGTAA
192 AA-ATAATGAAA-ATAATAATAAAT-AAAAA-ATATTATTGAAATGTAATAAATTGGTAATGTAA
* ** *
228573 AAAAATTAGTATTATAAATAAGAAATAATT-CAATAAAAAATAAGTATTAACGT-AAAAAGGTGA
253 AAAAATTAGTATTATAAATAA-AAATAATTACAACAAAAAATAAGTATTAACGTAAAAAAAATAA
** * *
228636 GAATAATCATAAAATTAGTATCATTTGACTTAAAATATATTAAAATTGTCGTAATACC-TTAAGA
317 GAATAATCATAAAATTAGTATCATTTGAAGTAAAAT-TATTAAAAGTGTCGTAACACCTTTAAGA
* * ** * * * * *
228700 AAGACTTGTGATAATTTTAAACATAATAAAATATAAAAATAAGCGTAAAAA-ATTTTATTGTAAC
381 AAAAATAATGATAATTCTAAACATAAAAAAAGATAAAAATAAGCGTAAAAAGATATTATTATAAC
228764 ATAAAT-A-TAAGTTGACAATATAAAAAAATTATTAATATAAATAAATAA-TAATTAC-AAAC-A
446 ATAAATAATTAAGTTGACAATATAAAAAAATTATTAATATAAATAAA-AAGTAATT-CTAAACAA
* * * *
228824 AAAAAATACGTGTTAACGTA-AAAATA-TGAGAA-TAACTG-AAAATTTGAAATTATTTGGTGTA
509 AAAAAAAACGTGTTAACGTACAAAA-AGTGA-AAGTAACTGTAAAA-TTGAAATCATTTAGCGTA
* * * *
228885 AAATATTTTACAA-TGTTGTAATGT-AAAATGATAAGAATAGTTGTAAAATTTG-TGTTATTT-A
571 AAATATATTACAAGTATTGTAACGTAAAAATG-TAAGAATAGTTGTAAAA-TTGATGTCATTTGA
* * ** * * **
228946 GCATAAATTGGATTAGAAGTATTGTAACACTTTAATAAAAAGTTATGATAATTTTAAATGTAATA
634 -CATAAATTGGATTAAAAGTATGGTAACACCCTAACAAAAAGTTATGATAAATTTAAACATAATA
* * *
229011 AAAAATAGGAATAAGTATAAAAAAAATTATTGTAATATAAATAATATTTTTGGCAACATAAAAGA
698 AAAAATAAGAACAAGTAT-AAAAAAATTATTGTAATATAAATAATATTTTTGACAACATAAAAGA
* ** *
229076 ATTATTATTGTAAATAAATAATAA-TTATAAACT-GAAAAATAAGTGTTAATATAAAATAAAGTG
762 ATTAATATTACAAATAAATAATAACTT-TAAACTAAAAAAATAAGTGTTAATATAAAATAAAGTG
* * * * * *
229139 AGAGTAATCGTAAAATTAATATCATTTGACGTAAAATTGTTAGAAGTATCGTAACACTTTAAAAA
826 AGAATAATCATAAAATTAATATCATTTCACGTAAAATAGTTAGAAGCATCATAACACTTTAAAAA
* * * *
229204 AAAAGTTATGATAATTTTAAACATAATAAAAGATAATAATAAATG
891 AAAAGTTATGAAAATTCTAAACAGAATAAAAGATAAGAATAAATG
* * * ** * *
229249 TAAATATATATATATTATTATTATAACTTAAATAATTAAGTTGGTGATGTAAAAAAAATTATTAT
1 T--A-A-A-A-AGA-TATTATTAGAACATAAATAATTAAGTT-GACA-ATAAAAAAAAATATTAT
* *
229314 TACAAATAAAAAATAATTTTAAACAAAAAATAAGAATAAACATAAAACGGTGAGAATAATTGTAA
57 TACAAATAAAAAATAATTTTAAACAAAAAATAAGAATTAACATAAAACGGTGAGAATAATCGTAA
* * * * *
229379 AATTTGTATTATTTTACGTAAAATAGTTTGAAGTAATGTTACACCTTAATAAAAAAAATTGTAAT
122 AATTAGTATTATTTAACGTAAAATAGTTAGAAGTATTGTTATACCTT-A-AAAAAAAATTGTAAT
*
229444 AA--CGTAATGAA-AA-GTAACAATAA-ACATAAA-AAAAAA-ATTATTGAAATGTAATAAATTT
185 AATTC-TAA--AATAATG-AA-AATAATA-ATAAATAAAAAATATTATTGAAATGTAATAAATTG
* * *
229502 ATAATGTATAAAAATTAATATTATAAATAAAAATAATT
244 GTAATGTAAAAAAATTAGTATTATAAATAAAAATAATT
229540 TTAAATAAAA
Statistics
Matches: 1037, Mismatches: 148, Indels: 99
0.81 0.12 0.08
Matches are distributed among these distances:
935 7 0.01
936 165 0.16
937 170 0.16
938 70 0.07
939 46 0.04
940 10 0.01
941 20 0.02
942 184 0.18
943 103 0.10
944 13 0.01
945 2 0.00
946 29 0.03
947 17 0.02
948 92 0.09
949 31 0.03
950 39 0.04
951 7 0.01
952 29 0.03
953 3 0.00
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (935 bp):
TAAAAAGATATTATTAGAACATAAATAATTAAGTTGACAATAAAAAAAAATATTATTACAAATAA
AAAATAATTTTAAACAAAAAATAAGAATTAACATAAAACGGTGAGAATAATCGTAAAATTAGTAT
TATTTAACGTAAAATAGTTAGAAGTATTGTTATACCTTAAAAAAAAATTGTAATAATTCTAAAAT
AATGAAAATAATAATAAATAAAAAATATTATTGAAATGTAATAAATTGGTAATGTAAAAAAATTA
GTATTATAAATAAAAATAATTACAACAAAAAATAAGTATTAACGTAAAAAAAATAAGAATAATCA
TAAAATTAGTATCATTTGAAGTAAAATTATTAAAAGTGTCGTAACACCTTTAAGAAAAAATAATG
ATAATTCTAAACATAAAAAAAGATAAAAATAAGCGTAAAAAGATATTATTATAACATAAATAATT
AAGTTGACAATATAAAAAAATTATTAATATAAATAAAAAGTAATTCTAAACAAAAAAAAAACGTG
TTAACGTACAAAAAGTGAAAGTAACTGTAAAATTGAAATCATTTAGCGTAAAATATATTACAAGT
ATTGTAACGTAAAAATGTAAGAATAGTTGTAAAATTGATGTCATTTGACATAAATTGGATTAAAA
GTATGGTAACACCCTAACAAAAAGTTATGATAAATTTAAACATAATAAAAAATAAGAACAAGTAT
AAAAAAATTATTGTAATATAAATAATATTTTTGACAACATAAAAGAATTAATATTACAAATAAAT
AATAACTTTAAACTAAAAAAATAAGTGTTAATATAAAATAAAGTGAGAATAATCATAAAATTAAT
ATCATTTCACGTAAAATAGTTAGAAGCATCATAACACTTTAAAAAAAAAGTTATGAAAATTCTAA
ACAGAATAAAAGATAAGAATAAATG
Found at i:229546 original size:16 final size:19
Alignment explanation
Indices: 229509--229550 Score: 63
Period size: 16 Copynumber: 2.4 Consensus size: 19
229499 TTTATAATGT
229509 ATAAAAATTAATATTATAA
1 ATAAAAATTAATATTATAA
229528 ATAAAAA-TAAT-TT-TAA
1 ATAAAAATTAATATTATAA
229544 ATAAAAA
1 ATAAAAA
229551 AAATAAGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.43
17 2 0.09
18 4 0.17
19 7 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAAAATTAATATTATAA
Found at i:229591 original size:75 final size:76
Alignment explanation
Indices: 229512--229668 Score: 194
Period size: 76 Copynumber: 2.1 Consensus size: 76
229502 ATAATGTATA
* *
229512 AAAATTAATATTATAAATAAAAA-TAATTTTAAATAAAAAAAATAAGTGTGAAAAT--AAAAAGA
1 AAAATTAATATTATAAATAAAAAGTAATTCTAAACAAAAAAAA-AAGTGTGAAAATACAAAAAG-
229574 TGAAAATAATTGT
64 TGAAAATAATTGT
* * * * **
229587 AAAATTATTATTATAAATAAAAAGTGATTCTAAACAAAAAAAAAGGTGTTAATGTACAAAAAGTG
1 AAAATTAATATTATAAATAAAAAGTAATTCTAAACAAAAAAAAAAGTGTGAAAATACAAAAAGTG
*
229652 AAAGTAATTGT
66 AAAATAATTGT
229663 AAAATT
1 AAAATT
229669 GGAATCATTT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
75 30 0.43
76 34 0.49
77 6 0.09
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29
Consensus pattern (76 bp):
AAAATTAATATTATAAATAAAAAGTAATTCTAAACAAAAAAAAAAGTGTGAAAATACAAAAAGTG
AAAATAATTGT
Found at i:230401 original size:212 final size:214
Alignment explanation
Indices: 229910--230402 Score: 490
Period size: 212 Copynumber: 2.3 Consensus size: 214
229900 CTTTAAACTA
* * *
229910 AAAAAATAAGTGTTAATA-TAAAAAGAGTGAGAATAATCATAAAATTAGTATTATTTCACGTAAA
1 AAAAAATAAGT-TTAA-AGTAAAAAG-GTGAGAATAATCGTAAAATTGGTATTATTTAACGTAAA
* * * *
229974 ATAGTTAGAAGCATCATAACACCTTTAAGATAAAAGTTATAAAACTTCTAAATAGAATAAAAGAT
63 ATAGTTAGAAGCATCATAACACCTTTAAAAAAAAAATTATAAAACTTCTAAACAGAATAAAAGAT
* * * *
230039 AAGAATAAGTGTAAAAAGATATTATTAGAACATAAATAATTAAGTTGACAATAAGAAAGAACTAT
128 AAGAATAAATGTAAAAAGATATTATTAGAACATAAATAATT-AGGTAACAATAAGAAAGAACTAG
*
230104 TATTATAAATAAAAAATAATTTT
192 TATTATAAATAAAAAATAATTAT
* * * * *
230127 AAATAAA-ACG-TTAAGAGT-TAACGGTGAGAATAATCGTAAAATTGATATTATTTAATGTAAAA
1 AAA-AAATAAGTTTAA-AGTAAAAAGGTGAGAATAATCGTAAAATTGGTATTATTTAACGTAAAA
* ** * * * * *
230189 TAGTTAGAAGTATTGTTACACC-TTAAAAAAAAAATTGTAATAA-TTCTAAACATAATGAAATAT
64 TAGTTAGAAGCATCATAACACCTTTAAAAAAAAAATTATAA-AACTTCTAAACAGAATAAAAGAT
* * * *
230252 AATAATAAATG-AAAAAGATATTATT-GAA-ATGTAATAAATT-GGTAAC-GTAA-AAA-AATTA
128 AAGAATAAATGTAAAAAGATATTATTAGAACAT-AAAT-AATTAGGTAACAATAAGAAAGAACTA
230310 GTATTATAAATAAAAAAATAATTCAAT
191 GTATTATAAAT-AAAAAATAATT--AT
* * *
230337 AAAAAATAAGTATTAACGTAAAAAGGTGAGAATAATCGTAAAATTGGTATCATTTGACGTAAAAT
1 AAAAAATAAGT-TTAAAGTAAAAAGGTGAGAATAATCGTAAAATTGGTATTATTTAACGTAAAAT
230402 A
65 A
230403 TATTAAAAAT
Statistics
Matches: 226, Mismatches: 38, Indels: 29
0.77 0.13 0.10
Matches are distributed among these distances:
207 14 0.06
208 14 0.06
209 6 0.03
210 12 0.05
211 8 0.04
212 62 0.27
213 39 0.17
214 54 0.24
215 8 0.04
216 1 0.00
217 5 0.02
218 3 0.01
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.30
Consensus pattern (214 bp):
AAAAAATAAGTTTAAAGTAAAAAGGTGAGAATAATCGTAAAATTGGTATTATTTAACGTAAAATA
GTTAGAAGCATCATAACACCTTTAAAAAAAAAATTATAAAACTTCTAAACAGAATAAAAGATAAG
AATAAATGTAAAAAGATATTATTAGAACATAAATAATTAGGTAACAATAAGAAAGAACTAGTATT
ATAAATAAAAAATAATTAT
Found at i:230557 original size:38 final size:40
Alignment explanation
Indices: 230476--230560 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
230466 AAATAAGCGT
* * *
230476 AAAAAATTTTATTGTAACATAAATATAAGTTGACAATATA
1 AAAAAATTTTAATATAACATAAATATAAGTTGACAATACA
230516 AAAAAATTATTAATATAA-ATAAATAATAA-TT-ACAA-ACA
1 AAAAAATT-TTAATATAACATAAAT-ATAAGTTGACAATACA
230554 AAAAAAT
1 AAAAAAT
230561 ACGTGTTAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
38 9 0.22
39 4 0.10
40 16 0.40
41 11 0.28
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.31
Consensus pattern (40 bp):
AAAAAATTTTAATATAACATAAATATAAGTTGACAATACA
Found at i:231734 original size:3 final size:3
Alignment explanation
Indices: 231728--231763 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
231718 ATATAAAAAA
231728 ATT ATT ATT ATT ATT ATT ATT ATT AATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
231764 CTTACAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:233761 original size:10 final size:10
Alignment explanation
Indices: 233746--233784 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
233736 AGTGGCAAGT
233746 TTGATAGAAC
1 TTGATAGAAC
233756 TTGATAGAAC
1 TTGATAGAAC
* *
233766 AT-AAAGAAC
1 TTGATAGAAC
233775 TTGATAGAAC
1 TTGATAGAAC
233785 ATCATAGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (10 bp):
TTGATAGAAC
Found at i:233791 original size:10 final size:10
Alignment explanation
Indices: 233747--233793 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
233737 GTGGCAAGTT
*
233747 TGATAGAACT
1 TGATAGAACA
233757 TGATAGAACA
1 TGATAGAACA
* *
233767 T-AAAGAACT
1 TGATAGAACA
233776 TGATAGAACA
1 TGATAGAACA
*
233786 TCATAGAA
1 TGATAGAA
233794 TGAATACAGG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
9 7 0.23
10 23 0.77
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (10 bp):
TGATAGAACA
Found at i:237869 original size:10 final size:10
Alignment explanation
Indices: 237854--237883 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
237844 ATTAAATTTT
237854 TATATTTTAA
1 TATATTTTAA
237864 TATATTTTAA
1 TATATTTTAA
237874 T-TATTTTAA
1 TATATTTTAA
237883 T
1 T
237884 TAATTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:237880 original size:9 final size:9
Alignment explanation
Indices: 237856--237885 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
237846 TAAATTTTTA
237856 TATTTTAAT
1 TATTTTAAT
237865 ATATTTTAAT
1 -TATTTTAAT
237875 TATTTTAAT
1 TATTTTAAT
237884 TA
1 TA
237886 ATTAAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:238442 original size:16 final size:16
Alignment explanation
Indices: 238402--238442 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
238392 TATCTTTATT
*
238402 TTATTA-TTAATATAA
1 TTATTATTTAAAATAA
238417 TTAATT-TTTAAAATAA
1 TT-ATTATTTAAAATAA
238433 TTATTATTTA
1 TTATTATTTA
238443 TTTTATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATTATTTAAAATAA
Found at i:238443 original size:43 final size:43
Alignment explanation
Indices: 238348--238452 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 43
238338 ATTAATGCAA
* *
238348 AATTATTA-TTATTTT-TAATTTTAAAATTAATATTTTAAAAT
1 AATTATTATTTATTTTATTATTATAAAATTAATATTTTAAAAT
* * *
238389 AACTA-TCTTTATTTTATTATTAATATAATTAAT-TTTTAAAAT
1 AATTATTATTTATTTTATTATT-ATAAAATTAATATTTTAAAAT
238431 AATTATTATTTATTTTATTATT
1 AATTATTATTTATTTTATTATT
238453 TATCAAATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
40 1 0.02
41 11 0.21
42 17 0.32
43 24 0.45
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (43 bp):
AATTATTATTTATTTTATTATTATAAAATTAATATTTTAAAAT
Found at i:240069 original size:2 final size:2
Alignment explanation
Indices: 240023--240053 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
240013 CTTGTAATTA
*
240023 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
240054 AATTTCTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:240211 original size:37 final size:39
Alignment explanation
Indices: 240146--240220 Score: 111
Period size: 37 Copynumber: 2.0 Consensus size: 39
240136 ACACTGTTTA
*
240146 AAAAATATTTATTTAATTTGTTTTAATTTATTTTTGGTT
1 AAAAATATTTATTTAATTTGTTTAAATTTATTTTTGGTT
240185 AAAAATATATT-TTT-ATTT-TTTAAATTTATTTTTGGT
1 AAAAATAT-TTATTTAATTTGTTTAAATTTATTTTTGGT
240221 ATATATGAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
37 17 0.50
38 4 0.12
39 11 0.32
40 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (39 bp):
AAAAATATTTATTTAATTTGTTTAAATTTATTTTTGGTT
Found at i:242074 original size:19 final size:19
Alignment explanation
Indices: 242052--242095 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
242042 TTAAAGGCTA
*
242052 GGTTTAGGGTCTAGGGTTT
1 GGTTTAGGGTCTAGGGTTG
* * *
242071 GGTTTATGGTTTGGGGTTG
1 GGTTTAGGGTCTAGGGTTG
242090 GGTTTA
1 GGTTTA
242096 AGGTTTTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.09, C:0.02, G:0.43, T:0.45
Consensus pattern (19 bp):
GGTTTAGGGTCTAGGGTTG
Found at i:242100 original size:19 final size:19
Alignment explanation
Indices: 242065--242101 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
242055 TTAGGGTCTA
* *
242065 GGGTTTGGTTTATGGTTTG
1 GGGTTGGGTTTAAGGTTTG
242084 GGGTTGGGTTTAAGGTTT
1 GGGTTGGGTTTAAGGTTT
242102 TTAGTTTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.43, T:0.49
Consensus pattern (19 bp):
GGGTTGGGTTTAAGGTTTG
Found at i:242342 original size:19 final size:19
Alignment explanation
Indices: 242320--242362 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
242310 CTGGGTTTAT
*
242320 GGGTTAGATTTAGGGTTTG
1 GGGTTAGATTTAGGATTTG
* *
242339 GGGTTTGTTTTAGGATTTG
1 GGGTTAGATTTAGGATTTG
*
242358 AGGTT
1 GGGTT
242363 TGTTTGAGGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.40, T:0.47
Consensus pattern (19 bp):
GGGTTAGATTTAGGATTTG
Found at i:242363 original size:19 final size:19
Alignment explanation
Indices: 242328--242367 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
242318 ATGGGTTAGA
* *
242328 TTTAGGGTTTGGGGTTTGT
1 TTTAGGATTTGAGGTTTGT
242347 TTTAGGATTTGAGGTTTGT
1 TTTAGGATTTGAGGTTTGT
242366 TT
1 TT
242368 GAGGGGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.35, T:0.55
Consensus pattern (19 bp):
TTTAGGATTTGAGGTTTGT
Found at i:242971 original size:17 final size:16
Alignment explanation
Indices: 242949--242982 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
242939 CAAGAACTAC
242949 TTGTATGAAAAATAAAA
1 TTGTATGAAAAA-AAAA
*
242966 TTGTATGATAAAAAAA
1 TTGTATGAAAAAAAAA
242982 T
1 T
242983 GAAGAATGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (16 bp):
TTGTATGAAAAAAAAA
Found at i:246383 original size:23 final size:24
Alignment explanation
Indices: 246339--246383 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
246329 GCGAAAAAGG
246339 AAGGGAAAAGATAAGAAAAGAAAT
1 AAGGGAAAAGATAAGAAAAGAAAT
*
246363 AAGGGAAAAG-TAGGAAAAGAA
1 AAGGGAAAAGATAAGAAAAGAA
246384 GAGGGATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (24 bp):
AAGGGAAAAGATAAGAAAAGAAAT
Found at i:247639 original size:2 final size:2
Alignment explanation
Indices: 247632--247674 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
247622 GCTTGGAATT
247632 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
247674 A
1 A
247675 AGGTAAAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:247883 original size:21 final size:22
Alignment explanation
Indices: 247846--247890 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
247836 TCCCTTTTTC
* *
247846 TTTTTTTTTTCTTAATTTTTAA
1 TTTTTTTTTTCTAAATTTTCAA
247868 TTTTTTTTTTC-AAATTTTCAA
1 TTTTTTTTTTCTAAATTTTCAA
247889 TT
1 TT
247891 ACTAGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTTTTTTTCTAAATTTTCAA
Found at i:248131 original size:20 final size:20
Alignment explanation
Indices: 248093--248130 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
248083 AATAAATATA
*
248093 AAATTAGAATATTTAAAAAC
1 AAATTAAAATATTTAAAAAC
248113 AAATTAAAAT-TTTAAAAA
1 AAATTAAAATATTTAAAAA
248131 ATATTTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (20 bp):
AAATTAAAATATTTAAAAAC
Found at i:248660 original size:18 final size:19
Alignment explanation
Indices: 248626--248665 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
248616 TTTAAAATTG
*
248626 AAATATTAAAAGC-AAAAT
1 AAATATTAAAAACAAAAAT
*
248644 AAATATTAAAAATAAAAAT
1 AAATATTAAAAACAAAAAT
248663 AAA
1 AAA
248666 ACTTTACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (19 bp):
AAATATTAAAAACAAAAAT
Found at i:248661 original size:19 final size:18
Alignment explanation
Indices: 248626--248665 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
248616 TTTAAAATTG
*
248626 AAATATTAAAAGCAAAAT
1 AAATATTAAAAGAAAAAT
*
248644 AAATATTAAAAATAAAAAT
1 AAATATT-AAAAGAAAAAT
248663 AAA
1 AAA
248666 ACTTTACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (18 bp):
AAATATTAAAAGAAAAAT
Found at i:257486 original size:272 final size:272
Alignment explanation
Indices: 256882--257698 Score: 1580
Period size: 272 Copynumber: 3.0 Consensus size: 272
256872 GCAATGTAAC
*
256882 CAAAGATTATAATTTGCAGAACATGACAAATTATTTTTTATTGTTTATGTTCACTTTTTCTTACT
1 CAAAGATTATAATTTGCAGAACATGACAAATTATTTTTTATTGTTGATGTTCACTTTTTCTTACT
256947 AATGTAGTTATCATTATTGTACAACCTACAAAGCATACTTAAATACTGTTCTTGTGGACAGTGCT
66 AATGTAGTTATCATTATTGTACAACCTACAAAGCATACTTAAATACTGTTCTTGTGGACAGTGCT
257012 ATTGTCATCGTTATCAAAGTTCTATTAATGGATGAGCACCATTACCTGGTTTAAAGTTAAAATTT
131 ATTGTCATCGTTATCAAAGTTCTATTAATGGATGAGCACCATTACCTGGTTTAAAGTT-AAATTT
257077 CACCCCAGCCCAATGGTTCGATCTTGAGACTTTGAGGTCTTAAGTTCAAACTGATAGGAGCAAAC
195 CACCCCAGCCCAATGGTTCGATCTTGAGACTTTGAGGTCTTAAGTTCAAACTGATAGGAGCAAAC
257142 AAGAGCAAGGGGG
260 AAGAGCAAGGGGG
257155 CAAAGATTATAATTTGCAGAACATGACAAATTATTTTTTATTGTTGATGTTCACTTTTTCTTACT
1 CAAAGATTATAATTTGCAGAACATGACAAATTATTTTTTATTGTTGATGTTCACTTTTTCTTACT
*
257220 AATGTAGTTATCATTATTGTACAACCTACAAAGCATACTTAAATACTGTTCTTGTGGACGGTGCT
66 AATGTAGTTATCATTATTGTACAACCTACAAAGCATACTTAAATACTGTTCTTGTGGACAGTGCT
*
257285 ATTGTCATCATTATCAAAGTTCTATTAATGGATGAGCACCATTACCTGGTTTAAAGTTAAATTTC
131 ATTGTCATCGTTATCAAAGTTCTATTAATGGATGAGCACCATTACCTGGTTTAAAGTTAAATTTC
*
257350 ACCCCAGCCCAATTGTTCGATCTTGAGACTTTGAGGTCTTAAGTTCAAACTGATAGGAGCAAACA
196 ACCCCAGCCCAATGGTTCGATCTTGAGACTTTGAGGTCTTAAGTTCAAACTGATAGGAGCAAACA
257415 AGAGCAAGGGGG
261 AGAGCAAGGGGG
257427 CAAAGATTATAATTTGCAGAACATGACAAATTATTTTTTATTGTTGATGTTCACTTTTTCTTACT
1 CAAAGATTATAATTTGCAGAACATGACAAATTATTTTTTATTGTTGATGTTCACTTTTTCTTACT
*
257492 AATGTAGTTATCATTTTTGTACAACCTACAAAGCATACTTAAATACTGTTCTTGTGGACAGTGCT
66 AATGTAGTTATCATTATTGTACAACCTACAAAGCATACTTAAATACTGTTCTTGTGGACAGTGCT
257557 ATTGTCATCGTTATCAAAGTTCTATTAATGGATGAGCACCATTACCTGGTTTAAAGTTAAATTTC
131 ATTGTCATCGTTATCAAAGTTCTATTAATGGATGAGCACCATTACCTGGTTTAAAGTTAAATTTC
257622 ACCCCAGCCCAATGGTTCGATCTTGAGACTTTGAGGTCTTAAGTTCAAACTGATAGGAGCAAACA
196 ACCCCAGCCCAATGGTTCGATCTTGAGACTTTGAGGTCTTAAGTTCAAACTGATAGGAGCAAACA
257687 AGAGCAAGGGGG
261 AGAGCAAGGGGG
257699 GAGTTATGAA
Statistics
Matches: 536, Mismatches: 8, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
272 351 0.65
273 185 0.35
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (272 bp):
CAAAGATTATAATTTGCAGAACATGACAAATTATTTTTTATTGTTGATGTTCACTTTTTCTTACT
AATGTAGTTATCATTATTGTACAACCTACAAAGCATACTTAAATACTGTTCTTGTGGACAGTGCT
ATTGTCATCGTTATCAAAGTTCTATTAATGGATGAGCACCATTACCTGGTTTAAAGTTAAATTTC
ACCCCAGCCCAATGGTTCGATCTTGAGACTTTGAGGTCTTAAGTTCAAACTGATAGGAGCAAACA
AGAGCAAGGGGG
Found at i:260519 original size:19 final size:21
Alignment explanation
Indices: 260487--260525 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
260477 TTTTTTGGTT
*
260487 AATTAATTGTAATAA-ATTGC
1 AATTAATTGAAATAAGATTGC
260507 AATT-ATTGAAATAAGATTG
1 AATTAATTGAAATAAGATTG
260526 AAGTAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.38
Consensus pattern (21 bp):
AATTAATTGAAATAAGATTGC
Found at i:265707 original size:3 final size:3
Alignment explanation
Indices: 265699--265726 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
265689 TAATATGGCT
265699 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
265727 ACTAAGTCTT
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:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:266008 original size:14 final size:14
Alignment explanation
Indices: 265989--266017 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
265979 TTCATATATC
265989 CAAACCATCTCAAA
1 CAAACCATCTCAAA
266003 CAAACCATCTCAAA
1 CAAACCATCTCAAA
266017 C
1 C
266018 GGCCTTCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.38, G:0.00, T:0.14
Consensus pattern (14 bp):
CAAACCATCTCAAA
Found at i:267871 original size:3 final size:3
Alignment explanation
Indices: 267863--267888 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
267853 CAAATCTTCA
267863 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
267889 AGCAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:272347 original size:22 final size:23
Alignment explanation
Indices: 272321--272370 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
272311 TATGTTCAAT
* *
272321 TTTATTAA-GTTAAATGAATTTA
1 TTTATTAATATTAAATGAATATA
*
272343 TTTATTAATATTAATTGAATATA
1 TTTATTAATATTAAATGAATATA
272366 TTTAT
1 TTTAT
272371 AAAGATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (23 bp):
TTTATTAATATTAAATGAATATA
Found at i:272426 original size:25 final size:25
Alignment explanation
Indices: 272396--272471 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 25
272386 TTATGAATAA
272396 TAAATAAATTATAATTAAATAAATT
1 TAAATAAATTATAATTAAATAAATT
272421 TAAATAAA-TA-AATATAAATAAAATT
1 TAAATAAATTATAAT-TAAAT-AAATT
* *
272446 AAAATAAATGATAA--AAATATAATT
1 TAAATAAATTATAATTAAATA-AATT
272470 TA
1 TA
272472 TTATTATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
23 4 0.09
24 16 0.37
25 20 0.47
26 1 0.02
27 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (25 bp):
TAAATAAATTATAATTAAATAAATT
Found at i:272428 original size:14 final size:14
Alignment explanation
Indices: 272394--272442 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
272384 GTTTATGAAT
272394 AATAAATAAATTATA
1 AATAAATAAATT-TA
*
272409 ATTAAATAAATTTA
1 AATAAATAAATTTA
*
272423 AATAAATAAATATA
1 AATAAATAAATTTA
272437 AATAAA
1 AATAAA
272443 ATTAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAAATAAATTTA
Found at i:272453 original size:29 final size:29
Alignment explanation
Indices: 272394--272467 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 29
272384 GTTTATGAAT
* *
272394 AATAAATAAAT-TATAATTAAATAAATTTA
1 AATAAATAAATATA-AATAAAATAAATATA
272423 AATAAATAAATATAAATAAAATTAAA-ATA
1 AATAAATAAATATAAATAAAA-TAAATATA
272452 AATGATAA-AAATATAA
1 AAT-A-AATAAATATAA
272468 TTTATTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 22 0.56
30 15 0.38
31 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (29 bp):
AATAAATAAATATAAATAAAATAAATATA
Found at i:272817 original size:13 final size:13
Alignment explanation
Indices: 272785--272828 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
272775 TTAAAATTTT
272785 AATTCAAATATAACAA
1 AATTCAAATAT---AA
272801 AATTCAAATATAA
1 AATTCAAATATAA
*
272814 AATTTAAATATAA
1 AATTCAAATATAA
272827 AA
1 AA
272829 ATAGATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 16 0.59
16 11 0.41
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
AATTCAAATATAA
Found at i:272982 original size:14 final size:14
Alignment explanation
Indices: 272965--272998 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
272955 AATAAAAAAT
272965 AATTAAA-TCAATC
1 AATTAAATTCAATC
272978 AAATTAAATTCAATC
1 -AATTAAATTCAATC
272993 AATTAA
1 AATTAA
272999 TTTTTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (14 bp):
AATTAAATTCAATC
Found at i:273624 original size:24 final size:21
Alignment explanation
Indices: 273591--273639 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
273581 AATTTTTAAT
*
273591 TATAACATTTTTAATTAAATAACA
1 TATAACA--TTTAAATAAA-AACA
*
273615 TATAATATTTAAATAAAAACA
1 TATAACATTTAAATAAAAACA
273636 TATA
1 TATA
273640 GCATCAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 9 0.39
24 6 0.26
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (21 bp):
TATAACATTTAAATAAAAACA
Found at i:275533 original size:15 final size:14
Alignment explanation
Indices: 275515--275562 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
275505 TTTAATTTAA
275515 TATATTTTAATAATT
1 TATA-TTTAATAATT
275530 TATATTTAAT-A--
1 TATATTTAATAATT
275541 TAT-TTTAATAATT
1 TATATTTAATAATT
275554 TATAATTTA
1 TAT-ATTTA
275563 TTATGTTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
10 6 0.21
11 4 0.14
13 4 0.14
14 6 0.21
15 8 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATATTTAATAATT
Found at i:275537 original size:24 final size:24
Alignment explanation
Indices: 275504--275562 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
275494 AAAAGACAGG
275504 ATTTA-ATTTAATATATTTTAATA
1 ATTTATATTTAATATATTTTAATA
275527 ATTTATATTTAATATATTTTAATA
1 ATTTATATTTAATATATTTTAATA
275551 ATTTATAATTTA
1 ATTTAT-ATTTA
275563 TTATGTTGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 5 0.15
24 24 0.71
25 5 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTTATATTTAATATATTTTAATA
Found at i:279523 original size:17 final size:18
Alignment explanation
Indices: 279498--279532 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
279488 TTCTAAAACC
279498 CCTAGAAATTCAAAATCT
1 CCTAGAAATTCAAAATCT
279516 CCTA-AAATTCAAAATCT
1 CCTAGAAATTCAAAATCT
279533 TTTAAAATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.29
Consensus pattern (18 bp):
CCTAGAAATTCAAAATCT
Found at i:279538 original size:17 final size:17
Alignment explanation
Indices: 279503--279550 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
279493 AAACCCCTAG
*
279503 AAATTCAAAATCTCCTA
1 AAATTCAAAATCTTCTA
*
279520 AAATTCAAAATCTTTTA
1 AAATTCAAAATCTTCTA
* *
279537 AAATCCAAAGTCTT
1 AAATTCAAAATCTT
279551 AAAAATCCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (17 bp):
AAATTCAAAATCTTCTA
Found at i:290889 original size:9 final size:9
Alignment explanation
Indices: 290849--290899 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
290839 TATTTTGCTT
290849 AAAAAAATG
1 AAAAAAATG
*
290858 AAAAGAA-G
1 AAAAAAATG
290866 AAAAAATAT-
1 AAAAAA-ATG
290875 ACAAAAAATG
1 A-AAAAAATG
290885 AAAAAAATG
1 AAAAAAATG
290894 AAAAAA
1 AAAAAA
290900 TGAGAAAGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 6 0.17
9 24 0.67
10 6 0.17
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAAAAATG
Found at i:292172 original size:105 final size:105
Alignment explanation
Indices: 292044--293061 Score: 1446
Period size: 105 Copynumber: 9.7 Consensus size: 105
292034 CTAGTCATCT
* *
292044 TTATCCTT-TGATTCACGGTTTAATCCCGATCTTTTTATTTTTTGATTCGA-GGTTCAATCTCGA
1 TTAT-CTTCTGATTCACGGTTTAATCCCGATCTTTTTATTCTCTGATTC-ACGGTTCAATCTCGA
*
292107 TCTCTTTAATTTAAAATCGCAGTTTAATCTCGATTGTTATTG
64 TCTCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTATTG
* ** * * *
292149 TTATCTTCTGATTCACGATTTAATCCTAATCTTTTTATTCTCTAATTCGCGGTTCAATCCCGATC
1 TTATCTTCTGATTCACGGTTTAATCCCGATCTTTTTATTCTCTGATTCACGGTTCAATCTCGATC
* * *
292214 TCTTTAATTCAAAGTCACAGTTTAATCTCGATTGTTGTTG
66 TCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTATTG
* * * * *
292254 TTATTTTTTGATTCACGATTTAATCGCGATCTTTTTATTCTCTGATTCACGGTTCAATCCCGATC
1 TTATCTTCTGATTCACGGTTTAATCCCGATCTTTTTATTCTCTGATTCACGGTTCAATCTCGATC
* *
292319 TCTTTAATTTAAAATTACAGTTTAATCTCAATTGTTATTG
66 TCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTATTG
* *
292359 TTATCTTCTGATTCGCGGTTTAATCCCAATCTTTTTATTCTCTGATTCACGGTTCAATCTCGATC
1 TTATCTTCTGATTCACGGTTTAATCCCGATCTTTTTATTCTCTGATTCACGGTTCAATCTCGATC
292424 TCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTATTG
66 TCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTATTG
* * * * *
292464 TTATCTTCTTATTCGCGATTTAATCTCGATCTTTTTATTCTCTGATTCACGGTTCAATCTCGATT
1 TTATCTTCTGATTCACGGTTTAATCCCGATCTTTTTATTCTCTGATTCACGGTTCAATCTCGATC
*
292529 TTTTTAATTTAAAATCACAGTTTAATCTCGATTGTTATTG
66 TCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTATTG
** * *
292569 TTATCTTCTGATTCGTGGTTTAATCCCGATCTTTTTATTCTCTGATTCGCGGTTCAATATCGATC
1 TTATCTTCTGATTCACGGTTTAATCCCGATCTTTTTATTCTCTGATTCACGGTTCAATCTCGATC
* * * *
292634 TCTTTAATTCAAAGTCACAGTTTAATCTCGATTATTGTTG
66 TCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTATTG
* * * *
292674 TTATCTTTTGATTCGCGGTTTAATCCTGATCTTTTTATTCTCTGATTCGCGGTTCAATCTCGATC
1 TTATCTTCTGATTCACGGTTTAATCCCGATCTTTTTATTCTCTGATTCACGGTTCAATCTCGATC
* * * *
292739 TCTTTAATTCAAAGTCACAGTTTAATCTCGATTATTGTTG
66 TCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTATTG
* * *
292779 TTATCTTCTGATTCGCGGTTTAATCTCGATCTTTTTATTCTCTGATTCACGGTTCAATCCCGATC
1 TTATCTTCTGATTCACGGTTTAATCCCGATCTTTTTATTCTCTGATTCACGGTTCAATCTCGATC
*
292844 TCTTTAATTTAAAATTACAGTTTAATCTCGATTGTTATTG
66 TCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTATTG
* * * *
292884 TTATCTTCTGATTCATGATTTAATCCCAATCTTTTTATTCTCTGATTCACGGTTCAATCCCGATC
1 TTATCTTCTGATTCACGGTTTAATCCCGATCTTTTTATTCTCTGATTCACGGTTCAATCTCGATC
** * *
292949 TCTTTAATTTAAAATCGTAATTTAATCTCGATTGTTATTA
66 TCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTATTG
* * *** *
292989 TTATCTTCTGATTCACGGTTTAATCCCAATCTTTTTATTCTTTGATTTGTGGTTCGATCTCGATC
1 TTATCTTCTGATTCACGGTTTAATCCCGATCTTTTTATTCTCTGATTCACGGTTCAATCTCGATC
*
293054 TTTTTAAT
66 TCTTTAAT
293062 CTCAATTATT
Statistics
Matches: 827, Mismatches: 84, Indels: 4
0.90 0.09 0.00
Matches are distributed among these distances:
104 3 0.00
105 824 1.00
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (105 bp):
TTATCTTCTGATTCACGGTTTAATCCCGATCTTTTTATTCTCTGATTCACGGTTCAATCTCGATC
TCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTATTG
Found at i:292556 original size:33 final size:34
Alignment explanation
Indices: 292405--292561 Score: 97
Period size: 33 Copynumber: 4.6 Consensus size: 34
292395 ATTCTCTGAT
* * * *
292405 TCACGGTTCAATCTCGATCTCTTTAATTT-AAAA
1 TCACAGTTTAATCTCGATTTTTTTAATTTCAAAA
* ** *
292438 TCACAGTTTAATCTCGATTGTTATTGTTATCTTCTTAT
1 TCACAGTTTAATCTCGATT-TT-TT-TAAT-TTCAAAA
* * ** *
292476 TCGC-GATTTAATCTCGATCTTTTT-ATTCTCTGAT
1 TCACAG-TTTAATCTCGATTTTTTTAATT-TCAAAA
* *
292510 TCACGGTTCAATCTCGATTTTTTTAATTT-AAAA
1 TCACAGTTTAATCTCGATTTTTTTAATTTCAAAA
292543 TCACAGTTTAATCTCGATT
1 TCACAGTTTAATCTCGATT
292562 GTTATTGTTA
Statistics
Matches: 96, Mismatches: 19, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
33 35 0.36
34 28 0.29
35 7 0.07
36 5 0.05
37 5 0.05
38 16 0.17
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.46
Consensus pattern (34 bp):
TCACAGTTTAATCTCGATTTTTTTAATTTCAAAA
Found at i:294605 original size:22 final size:23
Alignment explanation
Indices: 294577--294621 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
294567 ATTTATGCAT
*
294577 GATAAATGTTTAAAT-TTATTAA
1 GATAAATATTTAAATGTTATTAA
*
294599 GATAAATATTTAATTGTTATTAA
1 GATAAATATTTAAATGTTATTAA
294622 TAATAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (23 bp):
GATAAATATTTAAATGTTATTAA
Found at i:295011 original size:17 final size:17
Alignment explanation
Indices: 294976--295023 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
294966 AAACCCTTAG
*
294976 AAATTCAAAATCTCCTA
1 AAATTCAAAATCTTCTA
*
294993 AAATTCAAAATCTTTTA
1 AAATTCAAAATCTTCTA
* *
295010 AAATCCAAAGTCTT
1 AAATTCAAAATCTT
295024 AAAAATCCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (17 bp):
AAATTCAAAATCTTCTA
Found at i:298885 original size:78 final size:78
Alignment explanation
Indices: 298792--298939 Score: 296
Period size: 78 Copynumber: 1.9 Consensus size: 78
298782 TTTAAAGTAG
298792 TTTTTTTTTTCTTTCATTTCATATTAACTTATTGTTATGACCCAATTTTAATTGGAATTTTGGTA
1 TTTTTTTTTTCTTTCATTTCATATTAACTTATTGTTATGACCCAATTTTAATTGGAATTTTGGTA
298857 TCCCTAAGTAGTT
66 TCCCTAAGTAGTT
298870 TTTTTTTTTTCTTTCATTTCATATTAACTTATTGTTATGACCCAATTTTAATTGGAATTTTGGTA
1 TTTTTTTTTTCTTTCATTTCATATTAACTTATTGTTATGACCCAATTTTAATTGGAATTTTGGTA
298935 TCCCT
66 TCCCT
298940 TGCACCTAAC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.22, C:0.14, G:0.09, T:0.55
Consensus pattern (78 bp):
TTTTTTTTTTCTTTCATTTCATATTAACTTATTGTTATGACCCAATTTTAATTGGAATTTTGGTA
TCCCTAAGTAGTT
Found at i:303787 original size:21 final size:21
Alignment explanation
Indices: 303763--303806 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
303753 TTGGATATAC
*
303763 AATCAAATATGAATTTGTTTA
1 AATCAAATATGAACTTGTTTA
303784 AATCAAATATGAACTTGTTTA
1 AATCAAATATGAACTTGTTTA
303805 AA
1 AA
303807 ACTTCTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (21 bp):
AATCAAATATGAACTTGTTTA
Found at i:308911 original size:2 final size:2
Alignment explanation
Indices: 308906--308938 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
308896 CACACTCCGA
*
308906 AT AT AT AT AT AT AT AT AT AT GT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
308939 GTCCTGAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:323643 original size:30 final size:30
Alignment explanation
Indices: 323587--323648 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
323577 ACTTATCTTG
* **
323587 ATCATTTAAATGTAGCTCATGTTTACCTGAA
1 ATCATTTAAATATAGCTCATAATTACCT-AA
323618 ATCA-TTAAATATAGCTCATAATTACCTAA
1 ATCATTTAAATATAGCTCATAATTACCTAA
323647 AT
1 AT
323649 GACCCTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 4 0.14
30 20 0.71
31 4 0.14
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (30 bp):
ATCATTTAAATATAGCTCATAATTACCTAA
Found at i:326601 original size:86 final size:86
Alignment explanation
Indices: 326456--326626 Score: 288
Period size: 86 Copynumber: 2.0 Consensus size: 86
326446 CATCATTTAT
* *
326456 ATAGCAAAAACATAAAATAATCACATGTTTGATCATATTTTCATATATCAAAAATAAAGAAATAA
1 ATAGCAAAAACACAAAATAATCACATGCTTGATCATATTTTCATATATCAAAAATAAAGAAATAA
326521 AACATTTACTAATTTAGAAAC
66 AACATTTACTAATTTAGAAAC
* * *
326542 ATAGCAAAAACACAAAATAATCATATGCTTGATCTTATTTTTATATATCAAAAATAAAGAAATAA
1 ATAGCAAAAACACAAAATAATCACATGCTTGATCATATTTTCATATATCAAAAATAAAGAAATAA
*
326607 AATATTTACTAATTTAGAAA
66 AACATTTACTAATTTAGAAA
326627 TATACATATA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.32
Consensus pattern (86 bp):
ATAGCAAAAACACAAAATAATCACATGCTTGATCATATTTTCATATATCAAAAATAAAGAAATAA
AACATTTACTAATTTAGAAAC
Found at i:330011 original size:43 final size:43
Alignment explanation
Indices: 329956--330042 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
329946 GGTCCAACAC
*
329956 ATTGCATTTTTAGGGATGGTGCTTTTGATGATTAAGAGTCCAG
1 ATTGCATTTTTAGGGATGGTGCTTCTGATGATTAAGAGTCCAG
*
329999 ATTGCATTTTTAGGGATGGTGCTTCTGATGCTTAAGAGTCCAG
1 ATTGCATTTTTAGGGATGGTGCTTCTGATGATTAAGAGTCCAG
330042 A
1 A
330043 AAAAATTGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.23, C:0.11, G:0.28, T:0.38
Consensus pattern (43 bp):
ATTGCATTTTTAGGGATGGTGCTTCTGATGATTAAGAGTCCAG
Found at i:332916 original size:89 final size:89
Alignment explanation
Indices: 332777--332943 Score: 273
Period size: 89 Copynumber: 1.9 Consensus size: 89
332767 TGACTTCAAT
** *
332777 AAGGGGAAGGTTTTGCACTTTCCCCTCCTTTCCTTTCTTTTCCCTCCCATCTTC-CTCAATCCAA
1 AAGGGGAAGGTTTCCCACTTTCCCCTCATTTCCTTTCTTTTCCCTCCCATCTTCTC-CAATCCAA
332841 ATACACTGTAAGGTCTGACCCAAAC
65 ATACACTGTAAGGTCTGACCCAAAC
* *
332866 AAGGGGAAGGTTTCCCACTTTCCCCTCATTTCCTTTCTTTTCCCTTCCATCTTCTCCAATCCAGA
1 AAGGGGAAGGTTTCCCACTTTCCCCTCATTTCCTTTCTTTTCCCTCCCATCTTCTCCAATCCAAA
332931 TACACTGTAAGGT
66 TACACTGTAAGGT
332944 TCTCTAATTA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
89 71 0.99
90 1 0.01
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (89 bp):
AAGGGGAAGGTTTCCCACTTTCCCCTCATTTCCTTTCTTTTCCCTCCCATCTTCTCCAATCCAAA
TACACTGTAAGGTCTGACCCAAAC
Found at i:337189 original size:29 final size:28
Alignment explanation
Indices: 337152--337212 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
337142 AGTTAACATA
*
337152 TTTATAGTTCATA-TATTATATTAGAAAAT
1 TTTAAAGTTCA-AGTATTATATTA-AAAAT
* *
337181 TTTAAAGTTTAAGTATTATATTAAATAT
1 TTTAAAGTTCAAGTATTATATTAAAAAT
337209 TTTA
1 TTTA
337213 TTATAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.51
Consensus pattern (28 bp):
TTTAAAGTTCAAGTATTATATTAAAAAT
Found at i:342485 original size:66 final size:66
Alignment explanation
Indices: 342381--342509 Score: 231
Period size: 66 Copynumber: 2.0 Consensus size: 66
342371 TTCCATTAAG
*
342381 AAGAACATTTCCAGTCATGACAACATTTCCAGAGAGTCTACCTGCATAAATTTCAAAGATTATTT
1 AAGAACATTTCCAATCATGACAACATTTCCAGAGAGTCTACCTGCATAAATTTCAAAGATTATTT
342446 T
66 T
* *
342447 AAGAACATTTCCAATCATGACAACATTTCTAGAGAGTCTACCTGCCTAAATTTCAAAGATTAT
1 AAGAACATTTCCAATCATGACAACATTTCCAGAGAGTCTACCTGCATAAATTTCAAAGATTAT
342510 CTTGATGTCC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (66 bp):
AAGAACATTTCCAATCATGACAACATTTCCAGAGAGTCTACCTGCATAAATTTCAAAGATTATTT
T
Found at i:343040 original size:40 final size:38
Alignment explanation
Indices: 342989--343066 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 38
342979 TTGGTATCTC
* *
342989 TCTCTCAAGTGGATCAGAGGTGACTTCTAAACTAATTA
1 TCTCTCAAGTGGATCAGAGGTGACCTCTAAACCAATTA
* *
343027 TCTCTCGAGAGTGGATTAGAGGTGACCTCTGAACCAATTA
1 TCTCTC-A-AGTGGATCAGAGGTGACCTCTAAACCAATTA
343067 CTGCTCTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 6 0.18
39 1 0.03
40 27 0.79
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (38 bp):
TCTCTCAAGTGGATCAGAGGTGACCTCTAAACCAATTA
Found at i:347662 original size:15 final size:15
Alignment explanation
Indices: 347632--347668 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
347622 TTGACTAAGT
*
347632 AAATTCTTTGTTAGCC
1 AAATT-TTTGTCAGCC
347648 AAATTTTTGTCAGCC
1 AAATTTTTGTCAGCC
347663 AAATTT
1 AAATTT
347669 ATTGCTGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (15 bp):
AAATTTTTGTCAGCC
Found at i:350248 original size:14 final size:14
Alignment explanation
Indices: 350228--350260 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
350218 TAAATACTAA
350228 TTTTAATA-AAATT
1 TTTTAATATAAATT
350241 TATTTAATATAAATT
1 T-TTTAATATAAATT
350256 TTTTA
1 TTTTA
350261 TTTATAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 11 0.61
15 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTAATATAAATT
Found at i:351781 original size:60 final size:59
Alignment explanation
Indices: 351655--352046 Score: 555
Period size: 59 Copynumber: 6.6 Consensus size: 59
351645 TCGTGTAGGT
351655 AAAATTGATACTTTCAACTTTTT-TCCAAAAATA--TTTTTTGAAAATTTCGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTTCT-CAAAAATATTTTTTTTGAAAATTT--ATTTTCAAGG
*
351714 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTTGAAATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTTGAAAATTT-ATTTTCAAGG
* ***
351774 AAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTA-TTTCTAAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTTGAAAATTTATTTTC-AAGG
* * *
351833 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTTGAAAATTTATTTTCAAGG
*
351892 AAAATTGATACTTTCAACTTTTTCCCAAAAATA-TTTTTTTGAAAATTTA-TTTCTAAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTTGAAAATTTATTTTC-AAGG
* * *
351950 AAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAAT-ATTTTTTTTGAAAATTTATTTTCAAGG
*
352010 AAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTT
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTT
352047 CTGAATTTAT
Statistics
Matches: 304, Mismatches: 20, Indels: 19
0.89 0.06 0.06
Matches are distributed among these distances:
57 3 0.01
58 59 0.19
59 129 0.42
60 97 0.32
61 16 0.05
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTTGAAAATTTATTTTCAAGG
Found at i:351931 original size:118 final size:116
Alignment explanation
Indices: 351655--352062 Score: 619
Period size: 119 Copynumber: 3.5 Consensus size: 116
351645 TCGTGTAGGT
*
351655 AAAATTGATACTTTCAACTTTTTTCCAAAAATA-TTTTTTGAAAATTTCGATTT-TCAAGGAAAA
1 AAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTTGAAAATTT--ATTTCT-AAGGAAAA
* * *
351718 TTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTTGAAATTTTGATTTTCAAGG
62 TTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTT-ATTTTTAAGG
**
351774 AAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTATTTCTAAGGAAAATT
1 AAAATTGATACTTTCAACTTTTCC-CAAAAA-TATTTTTTTGAAAATTTATTTCTAAGGAAAATT
*
351839 GATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTTTAAGG
64 GATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTATTTTTAAGG
351892 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAAATTTATTTCTAAGGAAAATTG
1 AAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTTGAAAATTTATTTCTAAGGAAAATTG
*
351957 ATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTTGAAAATTTATTTTTAAGG
65 ATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTTTGAAAATTTATTTTTAAGG
*
352010 AAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTCTG--AATTTATTT-TAAG
1 AAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAAATTTATTTCTAAG
352063 AAGACAAAAA
Statistics
Matches: 271, Mismatches: 12, Indels: 17
0.90 0.04 0.06
Matches are distributed among these distances:
114 4 0.01
115 9 0.03
117 77 0.28
118 82 0.30
119 84 0.31
120 1 0.00
121 14 0.05
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (116 bp):
AAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGAAAATTTATTTCTAAGGAAAATTGA
TACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTATTTTTAAGG
Found at i:352088 original size:6 final size:6
Alignment explanation
Indices: 352070--352143 Score: 75
Period size: 6 Copynumber: 12.8 Consensus size: 6
352060 AAGAAGACAA
* *
352070 AAAAAT AAAAA- AAATAA- AAAAAT AAGAAT AAAAAT AAAAAT AAAGAT
1 AAAAAT AAAAAT AAA-AAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* *
352117 AAAGAT AAAAAT -AGAAT -AAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
352144 AGTACTAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
5 13 0.22
6 46 0.78
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:352109 original size:35 final size:34
Alignment explanation
Indices: 352070--352143 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 34
352060 AAGAAGACAA
*
352070 AAAAATAAA-AAAAATAAAAAAATAAGAATAAAAAT
1 AAAAATAAAGAAAAAGAAAAAAAT-AGAAT-AAAAT
* *
352105 AAAAATAAAGATAAAGATAAAAATAGAATAAAAT
1 AAAAATAAAGAAAAAGAAAAAAATAGAATAAAAT
352139 AAAAA
1 AAAAA
352144 AGTACTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
34 10 0.29
35 14 0.40
36 11 0.31
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (34 bp):
AAAAATAAAGAAAAAGAAAAAAATAGAATAAAAT
Found at i:352144 original size:18 final size:18
Alignment explanation
Indices: 352068--352144 Score: 74
Period size: 17 Copynumber: 4.3 Consensus size: 18
352058 TTAAGAAGAC
*
352068 AAAAAAATA-AAAAAAAT
1 AAAAAAATAGAATAAAAT
352085 AAAAAAATAAGAATAAAAAT
1 AAAAAAAT-AGAAT-AAAAT
352105 AAAAATAA-AG-ATAAAGAT
1 AAAAA-AATAGAATAAA-AT
352123 --AAAAATAGAATAAAAT
1 AAAAAAATAGAATAAAAT
352139 AAAAAA
1 AAAAAA
352145 GTACTAAATA
Statistics
Matches: 50, Mismatches: 1, Indels: 17
0.74 0.01 0.25
Matches are distributed among these distances:
15 2 0.04
16 7 0.14
17 16 0.32
18 9 0.18
19 4 0.08
20 10 0.20
21 2 0.04
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (18 bp):
AAAAAAATAGAATAAAAT
Found at i:352183 original size:3 final size:3
Alignment explanation
Indices: 352170--352217 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
352160 AGATATAGTC
352170 AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
352216 AA
1 AA
352218 ATAAATAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:354385 original size:22 final size:22
Alignment explanation
Indices: 354358--354410 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
354348 TCCCTTTTTT
*
354358 TTCTTC-CCGTCTCCTATTCGGA
1 TTCTTCTCC-TCTCCTATTCCGA
*
354380 TTCTTCTTCTCTCCTATTCCGA
1 TTCTTCTCCTCTCCTATTCCGA
354402 -T-TTCTCCTC
1 TTCTTCTCCTC
354411 CATCTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 7 0.26
21 1 0.04
22 18 0.67
23 1 0.04
ACGTcount: A:0.08, C:0.38, G:0.08, T:0.47
Consensus pattern (22 bp):
TTCTTCTCCTCTCCTATTCCGA
Found at i:354959 original size:105 final size:105
Alignment explanation
Indices: 354777--354986 Score: 375
Period size: 105 Copynumber: 2.0 Consensus size: 105
354767 AAATATTTTA
* *
354777 GGTTTTTCTTAGAATAGTTTAGTAAGTATTTGACATACTGCAGGTGAAATAAATTTGTGAAGGAA
1 GGTTTTTCTTAGAATAGTTTAGTAAGCATCTGACATACTGCAGGTGAAATAAATTTGTGAAGGAA
*
354842 TATTAATTCTTGCAGTCATGAGTCACTTATCACCAACTCC
66 TATTAATTCTTGCAGTCATGAGTCACTCATCACCAACTCC
* *
354882 GGTTTTTCTTGGAATAGTTTAGTAAGCATCTGACATACTGCAGGTGAAATAAATTTGTGCAGGAA
1 GGTTTTTCTTAGAATAGTTTAGTAAGCATCTGACATACTGCAGGTGAAATAAATTTGTGAAGGAA
354947 TATTAATTCTTGCAGTCATGAGTCACTCATCACCAACTCC
66 TATTAATTCTTGCAGTCATGAGTCACTCATCACCAACTCC
354987 TCGAGCCAAC
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 100 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (105 bp):
GGTTTTTCTTAGAATAGTTTAGTAAGCATCTGACATACTGCAGGTGAAATAAATTTGTGAAGGAA
TATTAATTCTTGCAGTCATGAGTCACTCATCACCAACTCC
Found at i:355623 original size:24 final size:25
Alignment explanation
Indices: 355595--355650 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
355585 TTTTTTATTA
355595 AATTTTTTTAAAT-ATAATTATAAT
1 AATTTTTTTAAATCATAATTATAAT
* *
355619 AATTTTTTTTAATCGTAATTATAAT
1 AATTTTTTTAAATCATAATTATAAT
355644 AATTTTT
1 AATTTTT
355651 ATTATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
AATTTTTTTAAATCATAATTATAAT
Found at i:355624 original size:22 final size:24
Alignment explanation
Indices: 355598--355650 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
355588 TTTATTAAAT
355598 TTTTTTAAAT-ATAATTATAATAA
1 TTTTTTAAATCATAATTATAATAA
* *
355621 TTTTTTTTAATCGTAATTATAATAA
1 -TTTTTTAAATCATAATTATAATAA
355646 TTTTT
1 TTTTT
355651 ATTATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
TTTTTTAAATCATAATTATAATAA
Found at i:355794 original size:15 final size:15
Alignment explanation
Indices: 355774--355818 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
355764 AATAATAAAC
*
355774 AAATTTTACACAAAT
1 AAATTTTAAACAAAT
355789 AAA-TTTAAACAAAT
1 AAATTTTAAACAAAT
* *
355803 GAATTTTAAATAAAT
1 AAATTTTAAACAAAT
355818 A
1 A
355819 TAAATAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (15 bp):
AAATTTTAAACAAAT
Found at i:355838 original size:31 final size:32
Alignment explanation
Indices: 355785--355853 Score: 88
Period size: 35 Copynumber: 2.1 Consensus size: 32
355775 AATTTTACAC
355785 AAATAAATTTAAACAAATGAATTTT-AAATAAATAT
1 AAATAAATTTAAAC--A-GAATTTTAAAATAAA-AT
355820 AAATAAATTTAAAC-GAATTTTAAAATAAAAT
1 AAATAAATTTAAACAGAATTTTAAAATAAAAT
355851 AAA
1 AAA
355854 ACTAAAACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
31 12 0.36
32 7 0.21
35 14 0.42
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (32 bp):
AAATAAATTTAAACAGAATTTTAAAATAAAAT
Found at i:361904 original size:28 final size:28
Alignment explanation
Indices: 361871--361958 Score: 106
Period size: 28 Copynumber: 3.1 Consensus size: 28
361861 CCCAAGCCTG
* *
361871 ATTTTGATTCGACTGGGC-TCTAAGCCCA
1 ATTTTGACTCAACTGGGCTTC-AAGCCCA
* * *
361899 ATTTTGGCTCAACTGGGCTTCGAGCCCG
1 ATTTTGACTCAACTGGGCTTCAAGCCCA
*
361927 ATTTTGACTCAATTGGGCTTCAAGCCCA
1 ATTTTGACTCAACTGGGCTTCAAGCCCA
361955 ATTT
1 ATTT
361959 GATCCAACCA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
28 48 0.96
29 2 0.04
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (28 bp):
ATTTTGACTCAACTGGGCTTCAAGCCCA
Found at i:363076 original size:23 final size:23
Alignment explanation
Indices: 363043--363091 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
363033 GGTTCAAGTT
* * *
363043 TTTTTTTTTTTAAATTTTTTTTA
1 TTTTTTGTTTTAAATATTATTTA
*
363066 TTTTTTGTTTTATATATTATTTA
1 TTTTTTGTTTTAAATATTATTTA
363089 TTT
1 TTT
363092 ATATCATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (23 bp):
TTTTTTGTTTTAAATATTATTTA
Found at i:363580 original size:16 final size:14
Alignment explanation
Indices: 363559--363628 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 14
363549 TCTGAAATTG
363559 AAACCCTAAATCCTTC
1 AAACCCTAAA-CC-TC
*
363575 AAACCCTAAAAC-C
1 AAACCCTAAACCTC
* *
363588 AAACTCTAAAACTCTT
1 AAACCCT-AAAC-CTC
363604 AAACCCTAAACCTC
1 AAACCCTAAACCTC
363618 TAAACCCTAAA
1 -AAACCCTAAA
363629 ATTAAATCCC
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
13 7 0.16
14 5 0.11
15 16 0.36
16 16 0.36
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACCCTAAACCTC
Found at i:363596 original size:13 final size:13
Alignment explanation
Indices: 363574--363659 Score: 55
Period size: 15 Copynumber: 5.9 Consensus size: 13
363564 CTAAATCCTT
363574 CAAACCCTAAAAC
1 CAAACCCTAAAAC
*
363587 CAAACTCTAAAAC
1 CAAACCCTAAAAC
*
363600 TCTTAAACCCTAAACC
1 -C--AAACCCTAAAAC
*
363616 TCTAAACCCTAAAAT
1 -C-AAACCCTAAAAC
*
363631 TAAATCCCTAAAACATC
1 CAAA-CCCT-AAA-A-C
363648 CAAACCCTAAAA
1 CAAACCCTAAAA
363660 TTAAAACCCT
Statistics
Matches: 58, Mismatches: 8, Indels: 13
0.73 0.10 0.16
Matches are distributed among these distances:
13 15 0.26
14 6 0.10
15 17 0.29
16 17 0.29
17 3 0.05
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.19
Consensus pattern (13 bp):
CAAACCCTAAAAC
Found at i:363615 original size:7 final size:7
Alignment explanation
Indices: 363559--363628 Score: 52
Period size: 8 Copynumber: 9.4 Consensus size: 7
363549 TCTGAAATTG
363559 AAACCCT
1 AAACCCT
*
363566 AAATCCTT
1 AAA-CCCT
363574 CAAACCCT
1 -AAACCCT
*
363582 AAAACC-
1 AAACCCT
*
363588 AAACTCT
1 AAACCCT
*
363595 AAAACTCTT
1 -AAAC-CCT
363604 AAACCCT
1 AAACCCT
363611 AAACCTCT
1 AAACC-CT
363619 AAACCCT
1 AAACCCT
363626 AAA
1 AAA
363629 ATTAAATCCC
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
6 4 0.08
7 20 0.41
8 21 0.43
9 4 0.08
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (7 bp):
AAACCCT
Found at i:363639 original size:29 final size:29
Alignment explanation
Indices: 363602--363820 Score: 115
Period size: 30 Copynumber: 7.8 Consensus size: 29
363592 TCTAAAACTC
363602 TTAAA-CCCTAAACCTCTAAACCCTAAAA
1 TTAAATCCCTAAACCTCTAAACCCTAAAA
* *
363630 TTAAATCCCTAAAACATCCAAACCCTAAAA
1 TTAAATCCCT-AAACCTCTAAACCCTAAAA
* * * *
363660 TTAAAACCCTAAA-TTCAAAAACC--AAA
1 TTAAATCCCTAAACCTCTAAACCCTAAAA
* *
363686 --AAAT-CCAAAATCTC-AAACCCT-AAA
1 TTAAATCCCTAAACCTCTAAACCCTAAAA
* * *
363710 TTCCAGTCTCTAAACACTCTAAACCCT-AAA
1 TT-AAATCCCTAAAC-CTCTAAACCCTAAAA
* * * *
363740 TTAAA-ACTTAAACCCTCCAAATCCTAAAA
1 TTAAATCCCTAAA-CCTCTAAACCCTAAAA
* *
363769 TCAAA-CCCTAAATCCTCTAGACCCTAAAA
1 TTAAATCCCTAAA-CCTCTAAACCCTAAAA
* *
363798 CTAAAATCCC-AAACTTC-AAACCC
1 -TTAAATCCCTAAACCTCTAAACCC
363821 CAAACACGAA
Statistics
Matches: 145, Mismatches: 32, Indels: 28
0.71 0.16 0.14
Matches are distributed among these distances:
23 10 0.07
24 8 0.06
26 3 0.02
27 2 0.01
28 34 0.23
29 40 0.28
30 45 0.31
31 3 0.02
ACGTcount: A:0.47, C:0.31, G:0.01, T:0.21
Consensus pattern (29 bp):
TTAAATCCCTAAACCTCTAAACCCTAAAA
Found at i:363642 original size:45 final size:45
Alignment explanation
Indices: 363559--363658 Score: 116
Period size: 45 Copynumber: 2.2 Consensus size: 45
363549 TCTGAAATTG
* *
363559 AAACCCTAAATCCTTCAAACCCTAAAACCAAACTCTAAAAC-TCTT
1 AAACCCTAAATCCTTCAAACCCTAAAACCAAACCCTAAAACATC-C
**
363604 AAACCCTAAA-CC-TCTAAACCCTAAAATTAAATCCCTAAAACATCC
1 AAACCCTAAATCCTTC-AAACCCTAAAACCAAA-CCCTAAAACATCC
363649 AAACCCTAAA
1 AAACCCTAAA
363659 ATTAAAACCC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
43 2 0.04
44 16 0.33
45 28 0.58
46 2 0.04
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (45 bp):
AAACCCTAAATCCTTCAAACCCTAAAACCAAACCCTAAAACATCC
Found at i:363657 original size:16 final size:16
Alignment explanation
Indices: 363559--363659 Score: 56
Period size: 16 Copynumber: 6.7 Consensus size: 16
363549 TCTGAAATTG
* * *
363559 AAACCCTAAATCCTTC
1 AAACCCTAAAACATCC
363575 AAACCCT-AAA-A-CC
1 AAACCCTAAAACATCC
* *
363588 AAACTCTAAAAC-TCTT
1 AAACCCTAAAACATC-C
* *
363604 AAACCCT-AAACCTCT
1 AAACCCTAAAACATCC
*
363619 AAACCCT-AAA-AT-T
1 AAACCCTAAAACATCC
363632 AAATCCCTAAAACATCC
1 AAA-CCCTAAAACATCC
363649 AAACCCTAAAA
1 AAACCCTAAAA
363660 TTAAAACCCT
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
13 11 0.16
14 8 0.12
15 21 0.31
16 25 0.37
17 3 0.04
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.20
Consensus pattern (16 bp):
AAACCCTAAAACATCC
Done.