Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 30 of 204
Found at i:11001346 original size:11 final size:10
Alignment explanation
Indices: 11001148--11001356 Score: 52
Period size: 10 Copynumber: 21.6 Consensus size: 10
11001138 ATTAAAAAGT
11001148 TAAAATTATA
1 TAAAATTATA
*
11001158 TAAACTTATA
1 TAAAATTATA
*
11001168 -AATA-T-TA
1 TAAAATTATA
11001175 TAAAA-TAT-
1 TAAAATTATA
*
11001183 TAAAAATATA
1 TAAAATTATA
* *
11001193 AAAAACCTA-A
1 TAAAA-TTATA
*
11001203 T-AAATTCAAA
1 TAAAATT-ATA
11001213 T-AAATTATA
1 TAAAATTATA
* *
11001222 AAAAATTTTA
1 TAAAATTATA
*
11001232 TAACATTA-A
1 TAAAATTATA
** *
11001241 TAAAACACATT
1 TAAAA-TTATA
*
11001252 TAAAA-TATT
1 TAAAATTATA
11001261 TAAAATTTTATA
1 TAAAA--TTATA
**
11001273 TAAACCTAT-
1 TAAAATTATA
*
11001282 TAAAATTCTA
1 TAAAATTATA
*
11001292 TAAAAATCATA
1 T-AAAATTATA
11001303 T-AAATTACT-
1 TAAAATTA-TA
*
11001312 TAAAAATATA
1 TAAAATTATA
* *
11001322 -AAAAGTA-C
1 TAAAATTATA
11001330 TAAAATTGATA
1 TAAAATT-ATA
11001341 TAAAATTATA
1 TAAAATTATA
*
11001351 AAAAAT
1 TAAAAT
11001357 CATAAAAACT
Statistics
Matches: 144, Mismatches: 34, Indels: 42
0.65 0.15 0.19
Matches are distributed among these distances:
7 2 0.01
8 11 0.08
9 49 0.34
10 53 0.37
11 22 0.15
12 7 0.05
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.34
Consensus pattern (10 bp):
TAAAATTATA
Found at i:11005245 original size:32 final size:30
Alignment explanation
Indices: 11005200--11005279 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 30
11005190 TGTTTTATAT
11005200 ATTGCC-AAGTTGATTTATATGTAGATACATAC
1 ATTGCCGAA-TTGATTTATATGT--ATACATAC
* *
11005232 ATTGCCGAATTGATTTCTATATGTATATATAT
1 ATTGCCGAATTGA-TT-TATATGTATACATAC
*
11005264 ATTACCGAATTGATTT
1 ATTGCCGAATTGATTT
11005280 GAGATCCCGT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
30 1 0.02
31 2 0.05
32 28 0.67
33 4 0.10
34 7 0.17
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (30 bp):
ATTGCCGAATTGATTTATATGTATACATAC
Found at i:11005385 original size:42 final size:43
Alignment explanation
Indices: 11005279--11005433 Score: 143
Period size: 42 Copynumber: 3.5 Consensus size: 43
11005269 CGAATTGATT
* * *
11005279 TGAGATCCCGTATAAGACTATATCTGGGATATGACATCGGCATCGATT
1 TGAGATCCCGTATAAGACCATAGCTGGGATAT----T-GGCATCGATA
* *
11005327 TGAGATCCCGTATAAGATCATATCTGGGATA-TGGCATCGATA
1 TGAGATCCCGTATAAGACCATAGCTGGGATATTGGCATCGATA
* * *
11005369 TGAGA-CTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATA
1 TGAGATC-CCGTATAAGACCATAGCTGGGATATTGGCATCGATA
* *
11005412 TGAGATTTCCATATAAGACCAT
1 TGAGA-TCCCGTATAAGACCAT
11005434 GTCTGAGACA
Statistics
Matches: 91, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
41 1 0.01
42 33 0.36
43 17 0.19
44 11 0.12
48 29 0.32
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (43 bp):
TGAGATCCCGTATAAGACCATAGCTGGGATATTGGCATCGATA
Found at i:11014029 original size:6 final size:6
Alignment explanation
Indices: 11014020--11014049 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
11014010 AACAAATAAA
11014020 AATTTG AATTTG AATTTG AATTTG AATTTG
1 AATTTG AATTTG AATTTG AATTTG AATTTG
11014050 GGCAAATCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
AATTTG
Found at i:11016796 original size:3 final size:3
Alignment explanation
Indices: 11016788--11016820 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
11016778 TTGTGTTCTT
*
11016788 TTA TTA TTA TTA TTA TTA TTA TTA TTA TGA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11016821 ATAAGTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:11027282 original size:6 final size:6
Alignment explanation
Indices: 11027271--11027330 Score: 66
Period size: 6 Copynumber: 10.0 Consensus size: 6
11027261 GCCATCATCA
* * * *
11027271 CCACCT CCACCT CCACCT CCACCT CCACCC CCCCCT CCACCG CCTCCT
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT
**
11027319 CTTCCT CCACCT
1 CCACCT CCACCT
11027331 ATCCCTCGTC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.12, C:0.68, G:0.02, T:0.18
Consensus pattern (6 bp):
CCACCT
Found at i:11035357 original size:6 final size:6
Alignment explanation
Indices: 11035348--11035379 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
11035338 TCGCAACCAT
11035348 AGCCGC AGCCGC AGCCGC AGCCGC AGCCGC AG
1 AGCCGC AGCCGC AGCCGC AGCCGC AGCCGC AG
11035380 TAACAGCCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.47, G:0.34, T:0.00
Consensus pattern (6 bp):
AGCCGC
Found at i:11035360 original size:18 final size:18
Alignment explanation
Indices: 11035339--11035378 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
11035329 TCCTCGCAAT
*
11035339 CGCAACCATAGCCGCAGC
1 CGCAACCACAGCCGCAGC
* *
11035357 CGCAGCCGCAGCCGCAGC
1 CGCAACCACAGCCGCAGC
11035375 CGCA
1 CGCA
11035379 GTAACAGCCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.47, G:0.28, T:0.03
Consensus pattern (18 bp):
CGCAACCACAGCCGCAGC
Found at i:11035386 original size:18 final size:18
Alignment explanation
Indices: 11035348--11035389 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
11035338 TCGCAACCAT
**
11035348 AGCCGCAGCCGCAGCCGC
1 AGCCGCAGCCGCAGCAAC
*
11035366 AGCCGCAGCCGCAGTAAC
1 AGCCGCAGCCGCAGCAAC
11035384 AGCCGC
1 AGCCGC
11035390 CGTCGCAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.45, G:0.31, T:0.02
Consensus pattern (18 bp):
AGCCGCAGCCGCAGCAAC
Found at i:11039250 original size:28 final size:28
Alignment explanation
Indices: 11039201--11039260 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
11039191 ATGTAAAGAG
* * *
11039201 ATATATATGTATATTTTAAAATTGTGAA
1 ATATATATGTATATTATAAAATTATAAA
11039229 ATATATATGTATA-TATATAAATTATAAA
1 ATATATATGTATATTATA-AAATTATAAA
11039257 ATAT
1 ATAT
11039261 GTGTGCATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 3 0.11
28 25 0.89
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (28 bp):
ATATATATGTATATTATAAAATTATAAA
Found at i:11041701 original size:5 final size:5
Alignment explanation
Indices: 11041691--11041716 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
11041681 GAACAAATAT
11041691 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
11041717 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:11042034 original size:16 final size:17
Alignment explanation
Indices: 11042007--11042038 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
11041997 AAATTTTTTA
11042007 AGTTTGTGGGCTTGTTT
1 AGTTTGTGGGCTTGTTT
11042024 AGTTT-TGGGCTTGTT
1 AGTTTGTGGGCTTGTT
11042039 GGGTTAGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.06, C:0.06, G:0.34, T:0.53
Consensus pattern (17 bp):
AGTTTGTGGGCTTGTTT
Found at i:11042236 original size:12 final size:12
Alignment explanation
Indices: 11042212--11042261 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
11042202 CCTTACAGAA
11042212 TCATTTCTCATTT
1 TCATTTC-CATTT
*
11042225 TCATTTTCATTT
1 TCATTTCCATTT
* *
11042237 CCATTTCCGTTT
1 TCATTTCCATTT
*
11042249 TAATTTCCATTT
1 TCATTTCCATTT
11042261 T
1 T
11042262 GAGAAAACTA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 24 0.80
13 6 0.20
ACGTcount: A:0.16, C:0.22, G:0.02, T:0.60
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:11042249 original size:18 final size:18
Alignment explanation
Indices: 11042212--11042260 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
11042202 CCTTACAGAA
*
11042212 TCATTTCTCATTTTCATTT
1 TCATTTC-CATTTCCATTT
*
11042231 TCATTTCCATTTCCGTTT
1 TCATTTCCATTTCCATTT
*
11042249 TAATTTCCATTT
1 TCATTTCCATTT
11042261 TGAGAAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.16, C:0.22, G:0.02, T:0.59
Consensus pattern (18 bp):
TCATTTCCATTTCCATTT
Found at i:11043884 original size:23 final size:23
Alignment explanation
Indices: 11043858--11044025 Score: 318
Period size: 23 Copynumber: 7.3 Consensus size: 23
11043848 ATAAGTGCCA
*
11043858 CACTGATATGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
11043881 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
11043904 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
*
11043927 CACTGATATGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
11043950 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
11043973 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
11043996 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
11044019 CACTGAT
1 CACTGAT
11044026 CAATAACACT
Statistics
Matches: 142, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 142 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.19
Consensus pattern (23 bp):
CACTGATACGTAGCCGAAGCTAC
Found at i:11044277 original size:18 final size:17
Alignment explanation
Indices: 11044251--11044289 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
11044241 ATTTTCCTTC
11044251 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
11044268 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
11044286 CACA
1 CACA
11044290 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:11046997 original size:54 final size:54
Alignment explanation
Indices: 11046937--11047060 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 54
11046927 TCGAAATTTG
* *** *
11046937 GGTCACACGGCCTTGTCAAAGACCGTGTGCCTGTCTGTGTGTA-AATCGAAATAA
1 GGTCACACGGCCGTGTCAAAGACCGTGTGCCAACCCGTGTG-AGAATCGAAATAA
* * * * *
11046991 GGTCACATGACCGTGTCACAGATCGTGTGCCAACCCGTGTGAGATTCGAAATAA
1 GGTCACACGGCCGTGTCAAAGACCGTGTGCCAACCCGTGTGAGAATCGAAATAA
*
11047045 GGTTACACGGCCGTGT
1 GGTCACACGGCCGTGT
11047061 TACTAGGCTA
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
53 1 0.02
54 55 0.98
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (54 bp):
GGTCACACGGCCGTGTCAAAGACCGTGTGCCAACCCGTGTGAGAATCGAAATAA
Found at i:11052205 original size:58 final size:60
Alignment explanation
Indices: 11052136--11052251 Score: 166
Period size: 61 Copynumber: 1.9 Consensus size: 60
11052126 ATTACTTTAA
* *
11052136 TATTAAATTAATATAATACTTA-T-CAAGATAAATATTAGATTAAATT-TAATATTAAATC
1 TATTAAATTAATAGAATACTTACTACAAGATAAATATTAAATT-AATTCTAATATTAAATC
*
11052194 TATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAATTCTAATATTAA
1 TATTAAATTAATAGAATACTTA-CTACAAGATAAATATTAAATTAATTCTAATATTAA
11052252 GATAATCACT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
58 20 0.39
60 5 0.10
61 26 0.51
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.41
Consensus pattern (60 bp):
TATTAAATTAATAGAATACTTACTACAAGATAAATATTAAATTAATTCTAATATTAAATC
Found at i:11052316 original size:18 final size:17
Alignment explanation
Indices: 11052293--11052336 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
11052283 GCTATCTAGA
11052293 TAAGTATTAAATTAAATT
1 TAAGTATTAAATT-AATT
**
11052311 TAAGTATTTTATTAATT
1 TAAGTATTAAATTAATT
11052328 TAA-TATTAA
1 TAAGTATTAA
11052337 GTCTATTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 4 0.18
17 7 0.32
18 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
TAAGTATTAAATTAATT
Found at i:11053815 original size:107 final size:108
Alignment explanation
Indices: 11053520--11053917 Score: 520
Period size: 109 Copynumber: 3.7 Consensus size: 108
11053510 ATATTTAACA
* *
11053520 ATTTGGTTAAACGAG-AAATCGGA-ACCCAACACCTTAGGGCACGTTCCTCGAATTTCCAAACGC
1 ATTTGGTTGAACGAGAAAATC-GACACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGC
* *
11053583 AAAACATTGCCTCATTTT-ATAATTTTTG-AAAGGATATTTAGCC
65 AAAACATTGCCTTATTTTGA-AATTTTTGAAAAGGATATTAAGCC
* * * *
11053626 GTTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTATCTCGAATCTCCAAACG
1 ATTTGGTTGAACGAG-AAAATCGACACCCAGCACCTTAGGGCACGTT-CCTCGAATTTCCAAACG
* *
11053691 CAAAACATTGCCATATTTTGAGATTTTTGAAAAGGATATTAAGCC
64 CAAAACATTGCCTTATTTTGAAATTTTTGAAAAGGATATTAAGCC
* *
11053736 ATTTGGTTGAACGAG-AAATCG-CAACCTAGCACCTTAGGGTACGTTCCTCGAATTTCCAAACGC
1 ATTTGGTTGAACGAGAAAATCGAC-ACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGC
* * *
11053799 AGAACATTACCTTATTTTGAAATTTTTGAAAAAGATATTAAGCC
65 AAAACATTGCCTTATTTTGAAATTTTTGAAAAGGATATTAAGCC
* * *
11053843 GTTTGGTTGAACGAGAAAGATCGACACCCAGCACCTTAGGGCATGTTTCTCGAATTTCCAAACGC
1 ATTTGGTTGAACGAGAAA-ATCGACACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGC
* *
11053908 TAAATATTGC
65 AAAACATTGC
11053918 ATCAATTAGA
Statistics
Matches: 252, Mismatches: 30, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
106 13 0.05
107 72 0.29
108 52 0.21
109 85 0.34
110 30 0.12
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (108 bp):
ATTTGGTTGAACGAGAAAATCGACACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCA
AAACATTGCCTTATTTTGAAATTTTTGAAAAGGATATTAAGCC
Found at i:11053896 original size:216 final size:216
Alignment explanation
Indices: 11053520--11053917 Score: 638
Period size: 216 Copynumber: 1.8 Consensus size: 216
11053510 ATATTTAACA
*
11053520 ATTTGGTTAAACGAGAAATCGGAACCCAACACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
1 ATTTGGTTAAACGAGAAATCGCAACCCAACACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
* * *
11053585 AACATTGCCTCATTTTATAATTTTTGAAAGGATATTTAGCCGTTTGGTTGAACGAGAAAAATCGA
66 AACATTACCTCATTTTATAATTTTTGAAAAGATATTAAGCCGTTTGGTTGAACGAGAAAAATCGA
11053650 CACCCAGCACCTTAGGGCATGTTATCTCGAATCTCCAAACGCAAAACATTGCCATATTTTGAGAT
131 CACCCAGCACCTTAGGGCATGTTATCTCGAATCTCCAAACGCAAAACATTGCCATATTTTGAGAT
11053715 TTTTGAAAAGGATATTAAGCC
196 TTTTGAAAAGGATATTAAGCC
* * * * *
11053736 ATTTGGTTGAACGAGAAATCGCAACCTAGCACCTTAGGGTACGTTCCTCGAATTTCCAAACGCAG
1 ATTTGGTTAAACGAGAAATCGCAACCCAACACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
* *
11053801 AACATTACCTTATTTTGA-AATTTTTGAAAAAGATATTAAGCCGTTTGGTTGAACGAGAAAGATC
66 AACATTACCTCATTTT-ATAATTTTTG-AAAAGATATTAAGCCGTTTGGTTGAACGAGAAAAATC
* * *
11053865 GACACCCAGCACCTTAGGGCATGTT-TCTCGAATTTCCAAACGCTAAATATTGC
129 GACACCCAGCACCTTAGGGCATGTTATCTCGAATCTCCAAACGCAAAACATTGC
11053918 ATCAATTAGA
Statistics
Matches: 166, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
216 106 0.64
217 60 0.36
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (216 bp):
ATTTGGTTAAACGAGAAATCGCAACCCAACACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
AACATTACCTCATTTTATAATTTTTGAAAAGATATTAAGCCGTTTGGTTGAACGAGAAAAATCGA
CACCCAGCACCTTAGGGCATGTTATCTCGAATCTCCAAACGCAAAACATTGCCATATTTTGAGAT
TTTTGAAAAGGATATTAAGCC
Found at i:11054566 original size:23 final size:22
Alignment explanation
Indices: 11054530--11054594 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
11054520 TATATAAGGT
*
11054530 AAATGAAAATATAAACAAAACAGA
1 AAAT-AAAAAATAAA-AAAACAGA
* * *
11054554 AATTAATAAATAAAGAAAA-ATA
1 AAATAAAAAATAAA-AAAACAGA
11054576 AAATAAAAAATAAAAAAAC
1 AAATAAAAAATAAAAAAAC
11054595 GGAGGGGATT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
21 4 0.12
22 14 0.42
23 12 0.36
24 3 0.09
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (22 bp):
AAATAAAAAATAAAAAAACAGA
Found at i:11056732 original size:4 final size:4
Alignment explanation
Indices: 11056723--11056752 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
11056713 TGAAATTAAC
*
11056723 TTTA TTTA TTTA TTTA TTTA TTTA TCTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
11056753 CATCATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:11061237 original size:22 final size:20
Alignment explanation
Indices: 11061212--11061270 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
11061202 ATATTTTGTT
11061212 TTAATAGTTAACTATAAGTTAA
1 TTAATAGTTAA-TATAA-TTAA
*
11061234 TTAATAGTATATTAT-ATTAA
1 TTAATAGT-TAATATAATTAA
*
11061254 TTAATTGTTAATATAAT
1 TTAATAGTTAATATAAT
11061271 ATTTTTAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 5 0.16
20 13 0.41
21 1 0.03
22 11 0.34
23 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (20 bp):
TTAATAGTTAATATAATTAA
Found at i:11061272 original size:22 final size:22
Alignment explanation
Indices: 11061212--11061273 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
11061202 ATATTTTGTT
*
11061212 TTAATAGTTAACTATAA-GTTAA
1 TTAATAGTTAA-TATAATATTAA
*
11061234 TTAATAG-T-ATATTATATTAA
1 TTAATAGTTAATATAATATTAA
*
11061254 TTAATTGTTAATATAATATT
1 TTAATAGTTAATATAATATT
11061274 TTTAAGCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 4 0.12
20 11 0.33
21 2 0.06
22 16 0.48
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (22 bp):
TTAATAGTTAATATAATATTAA
Found at i:11069097 original size:27 final size:27
Alignment explanation
Indices: 11069062--11069153 Score: 148
Period size: 27 Copynumber: 3.4 Consensus size: 27
11069052 GTAGTGATTC
* *
11069062 AATTGGGTTAATTTGGGTAATTCGGTT
1 AATTCGGTTAATTCGGGTAATTCGGTT
* *
11069089 AATTCGGTTAATTCGAGTAATCCGGTT
1 AATTCGGTTAATTCGGGTAATTCGGTT
11069116 AATTCGGTTAATTCGGGTAATTCGGTT
1 AATTCGGTTAATTCGGGTAATTCGGTT
11069143 AATTCGGTTAA
1 AATTCGGTTAA
11069154 CCGACCGAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (27 bp):
AATTCGGTTAATTCGGGTAATTCGGTT
Found at i:11069102 original size:9 final size:9
Alignment explanation
Indices: 11069062--11069153 Score: 123
Period size: 9 Copynumber: 10.2 Consensus size: 9
11069052 GTAGTGATTC
*
11069062 AATTGGGTT
1 AATTCGGTT
* *
11069071 AATTTGGGT
1 AATTCGGTT
11069080 AATTCGGTT
1 AATTCGGTT
11069089 AATTCGGTT
1 AATTCGGTT
11069098 AATTCGAG-T
1 AATTCG-GTT
*
11069107 AATCCGGTT
1 AATTCGGTT
11069116 AATTCGGTT
1 AATTCGGTT
*
11069125 AATTCGGGT
1 AATTCGGTT
11069134 AATTCGGTT
1 AATTCGGTT
11069143 AATTCGGTT
1 AATTCGGTT
11069152 AA
1 AA
11069154 CCGACCGAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
8 1 0.01
9 71 0.97
10 1 0.01
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:11090860 original size:12 final size:12
Alignment explanation
Indices: 11090843--11090875 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
11090833 TATAATATTT
11090843 TAAAAAATTATA
1 TAAAAAATTATA
11090855 T-AAAAATTATA
1 TAAAAAATTATA
11090866 TAAAAAATTA
1 TAAAAAATTA
11090876 AGACAGTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAAAAATTATA
Found at i:11091517 original size:2 final size:2
Alignment explanation
Indices: 11091510--11091537 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11091500 ATTATTCCTG
11091510 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11091538 TAACATGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11093460 original size:23 final size:23
Alignment explanation
Indices: 11093430--11093478 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
11093420 AGAATGAATG
11093430 ATAAAATGTGTCCTATTATAGAC
1 ATAAAATGTGTCCTATTATAGAC
11093453 ATAAAATGTGTCCTATTATAGAC
1 ATAAAATGTGTCCTATTATAGAC
11093476 ATA
1 ATA
11093479 CCTCCCATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (23 bp):
ATAAAATGTGTCCTATTATAGAC
Found at i:11096961 original size:19 final size:21
Alignment explanation
Indices: 11096923--11096963 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
11096913 ATTGGGTGGA
*
11096923 TCAGCTTTTACGAGCTTCTGT
1 TCAGCTTTTACGACCTTCTGT
11096944 TCAGC-TTT-CGACCTTCTGT
1 TCAGCTTTTACGACCTTCTGT
11096963 T
1 T
11096964 GGCGTATCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 3 0.16
21 5 0.26
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.44
Consensus pattern (21 bp):
TCAGCTTTTACGACCTTCTGT
Found at i:11097981 original size:121 final size:123
Alignment explanation
Indices: 11097845--11098066 Score: 315
Period size: 123 Copynumber: 1.8 Consensus size: 123
11097835 GTGGGCTCTT
* * * *
11097845 CTCTTGAATAAAAAATGGAGACATT-AA-AGAGAAAT-GAACATGTTAAAAGTATTTGTAAATCC
1 CTCTTGAATAAAAAATGAAGACATTAAAGAGAGAAATGGAA-ATGTTAAAAATATTTGCAAAGCC
* ** * *
11097907 ATGAGAGGCTTCATTGGTGCAATATGAACATGATCCATTAACTATATAGGTTGCCTCCC
65 AGGAGACACTTCATTGGTCCAATATGAAAATGATCCATTAACTATATAGGTTGCCTCCC
*
11097966 CTCTTGAATAAAAAATGAAGACATTAAAGAGAGAAATGGAAATGTTAAAAATATTTGCAAAGCTA
1 CTCTTGAATAAAAAATGAAGACATTAAAGAGAGAAATGGAAATGTTAAAAATATTTGCAAAGCCA
*
11098031 GGAGACACTTTATTGGTCCAATATGAAAATGATCCA
66 GGAGACACTTCATTGGTCCAATATGAAAATGATCCA
11098067 CTAATTGTAT
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
121 24 0.28
122 2 0.02
123 58 0.67
124 3 0.03
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.27
Consensus pattern (123 bp):
CTCTTGAATAAAAAATGAAGACATTAAAGAGAGAAATGGAAATGTTAAAAATATTTGCAAAGCCA
GGAGACACTTCATTGGTCCAATATGAAAATGATCCATTAACTATATAGGTTGCCTCCC
Found at i:11100464 original size:126 final size:126
Alignment explanation
Indices: 11100110--11100472 Score: 541
Period size: 126 Copynumber: 2.9 Consensus size: 126
11100100 ACTTTTATTT
* * *
11100110 TTTTTCTACAGTAGTTTTTGAAAAAATAATTTTGAGAAGACGGTTCT-AA-AAGATAATGTAAAA
1 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGATTCTGAACAA-ATAGTGTAAAA
* * * *
11100173 AACGCTTCAAGCAGGATGCACTGTTAGCAAAATTACTAAAAAATAGCTCCCATGTGGATGCTC
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAA-AGCTCCCACGTGGACGCTC
* *
11100236 TTTTTCTACAGTAGTTTCTAAAAAAAATAATTTTGAGAAGACGATTCGGAACAAATAGTGTAAAA
1 TTTTTCTACAGTAGTTTCT-GAAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGT-AAA
*
11100301 AAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTGCCACGTGGACGCTC
64 AAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
* * *
11100364 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAATACGATTCTGAACAAATAGTGTTAAAA
1 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGTAAAAA
* *
11100429 ACTCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAG
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAG
11100473 TTACATAAGT
Statistics
Matches: 216, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
126 64 0.30
127 63 0.29
128 42 0.19
129 47 0.22
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.28
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGTAAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
Found at i:11103373 original size:9 final size:9
Alignment explanation
Indices: 11103350--11103380 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
11103340 ATTTCTATTT
11103350 TATTAAAAA
1 TATTAAAAA
11103359 TA-TAAAAA
1 TATTAAAAA
11103367 TATTAAAAA
1 TATTAAAAA
11103376 TATTA
1 TATTA
11103381 CCTTATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TATTAAAAA
Found at i:11103457 original size:24 final size:24
Alignment explanation
Indices: 11103401--11103457 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
11103391 AAGAACTTCT
*
11103401 ATTTTATTGAAAATATAAAAATAA
1 ATTTTATTGAAAATATAAAAACAA
*
11103425 ATTACTATT-AAAATATTAAAAACAA
1 ATT-TTATTGAAAATA-TAAAAACAA
*
11103450 CTTTTATT
1 ATTTTATT
11103458 TTATAAATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (24 bp):
ATTTTATTGAAAATATAAAAACAA
Found at i:11103599 original size:93 final size:92
Alignment explanation
Indices: 11103405--11103596 Score: 300
Period size: 93 Copynumber: 2.1 Consensus size: 92
11103395 ACTTCTATTT
* * *
11103405 TATTGAAAATATAAAAATAAATTACTATTAAAATATTAAAAACAACTTTTATTTTATAAATTGAA
1 TATTAAAAATATAAAAATAAATTACTATCAAAATATTAAAAACAAATTTTATTTTATAAATTGAA
*
11103470 ACAATATAAAAATAGTTTGTACAAATA
66 ACAATATAAAAATAGATTGTACAAATA
*
11103497 TATTAAAAATATAAAAAATAAATTACTATCAAAATATTAAAAATAAATTTTATTTTATTAAA-TG
1 TATTAAAAATAT-AAAAATAAATTACTATCAAAATATTAAAAACAAATTTTATTTTA-TAAATTG
11103561 AAACAATATAAAAA-A-ATTGTACAAATA
64 AAACAATATAAAAATAGATTGTACAAATA
11103588 TATTAAAAA
1 TATTAAAAA
11103597 AATCAATGTT
Statistics
Matches: 93, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
91 20 0.22
92 12 0.13
93 57 0.61
94 4 0.04
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (92 bp):
TATTAAAAATATAAAAATAAATTACTATCAAAATATTAAAAACAAATTTTATTTTATAAATTGAA
ACAATATAAAAATAGATTGTACAAATA
Found at i:11105576 original size:24 final size:24
Alignment explanation
Indices: 11105526--11105576 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
11105516 ACTGTTATAA
* * *
11105526 AAAATTATAAAATGAAAATTAATT
1 AAAATTACAAAATGAAAATAAACT
11105550 AAAATTACATAAATGAAAA-AAACT
1 AAAATTACA-AAATGAAAATAAACT
11105574 AAA
1 AAA
11105577 TAATATTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (24 bp):
AAAATTACAAAATGAAAATAAACT
Found at i:11105764 original size:11 final size:11
Alignment explanation
Indices: 11105738--11105777 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
11105728 AGAGAGCTTT
11105738 GAGAAATTTAGA
1 GAGAAATTT-GA
11105750 GAGAAATTTGA
1 GAGAAATTTGA
*
11105761 GAGAAAATTGA
1 GAGAAATTTGA
11105772 -AGAAAT
1 GAGAAAT
11105778 AATGTGTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 5 0.19
11 12 0.46
12 9 0.35
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.23
Consensus pattern (11 bp):
GAGAAATTTGA
Found at i:11111240 original size:5 final size:5
Alignment explanation
Indices: 11111230--11111258 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
11111220 CATTAACACC
11111230 AGTGG AGTGG AGTGG AGTGG AGT-G AGTGG
1 AGTGG AGTGG AGTGG AGTGG AGTGG AGTGG
11111259 GAAAGGTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.59, T:0.21
Consensus pattern (5 bp):
AGTGG
Found at i:11114050 original size:6 final size:7
Alignment explanation
Indices: 11114033--11114060 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
11114023 TCAGAACTAA
11114033 AAAAAAT
1 AAAAAAT
11114040 AAAAAAT
1 AAAAAAT
11114047 AAAAAAT
1 AAAAAAT
11114054 AAAAAAT
1 AAAAAAT
11114061 GCTACAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:11114248 original size:5 final size:5
Alignment explanation
Indices: 11114203--11114233 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
11114193 GCAAATCAGT
11114203 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
11114234 TCGGATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:11115986 original size:3 final size:3
Alignment explanation
Indices: 11115978--11116012 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
11115968 TTATTTGCAA
11115978 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11116013 ATTATGGAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11120408 original size:18 final size:18
Alignment explanation
Indices: 11120347--11120408 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
11120337 AAAGGGTGAG
11120347 AAGTAAAAGTTTATGGGGA
1 AAGTAAAAGTTT-TGGGGA
* *
11120366 AAATAAAAAGTTTTGGGGG
1 AAGT-AAAAGTTTTGGGGA
11120385 AA-TAAAA-TTTTGAGGGA
1 AAGTAAAAGTTTTG-GGGA
11120402 AAGTAAA
1 AAGTAAA
11120409 TAGGTAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.14
17 9 0.24
18 5 0.14
19 10 0.27
20 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.27, T:0.26
Consensus pattern (18 bp):
AAGTAAAAGTTTTGGGGA
Found at i:11121384 original size:21 final size:21
Alignment explanation
Indices: 11121360--11121422 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
11121350 ATAATAGAAT
11121360 ATTTAATTAGGGAACTTAACA
1 ATTTAATTAGGGAACTTAACA
* * *
11121381 ATTT--TT--TGAATTTATA-T
1 ATTTAATTAGGGAACTTA-ACA
11121398 ATTTAATTAGGGAACTTAACA
1 ATTTAATTAGGGAACTTAACA
11121419 ATTT
1 ATTT
11121423 TTTGAATTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
17 10 0.33
18 1 0.03
19 4 0.13
20 1 0.03
21 14 0.47
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.44
Consensus pattern (21 bp):
ATTTAATTAGGGAACTTAACA
Found at i:11121400 original size:38 final size:38
Alignment explanation
Indices: 11121358--11121441 Score: 159
Period size: 38 Copynumber: 2.2 Consensus size: 38
11121348 TCATAATAGA
11121358 ATATTTAATTAGGGAACTTAACAATTTTTTGAATTTAT
1 ATATTTAATTAGGGAACTTAACAATTTTTTGAATTTAT
11121396 ATATTTAATTAGGGAACTTAACAATTTTTTGAATTTAT
1 ATATTTAATTAGGGAACTTAACAATTTTTTGAATTTAT
*
11121434 ATCTTTAA
1 ATATTTAA
11121442 CTCCACTCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.48
Consensus pattern (38 bp):
ATATTTAATTAGGGAACTTAACAATTTTTTGAATTTAT
Found at i:11124243 original size:16 final size:16
Alignment explanation
Indices: 11124222--11124289 Score: 91
Period size: 16 Copynumber: 4.2 Consensus size: 16
11124212 TGGTTCGCTA
*
11124222 TAATGGAATAGAGGTG
1 TAATGGAATAGAGGCG
***
11124238 TAATGGAATAGAGATA
1 TAATGGAATAGAGGCG
*
11124254 TAATGGAATAGATGCG
1 TAATGGAATAGAGGCG
11124270 TAATGGAATAGAGGCG
1 TAATGGAATAGAGGCG
11124286 TAAT
1 TAAT
11124290 AGGTAATTCT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.41, C:0.03, G:0.31, T:0.25
Consensus pattern (16 bp):
TAATGGAATAGAGGCG
Found at i:11124261 original size:32 final size:32
Alignment explanation
Indices: 11124220--11124282 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
11124210 TTTGGTTCGC
*
11124220 TATAATGGAATAGAGGTGTAATGGAATAGAGA
1 TATAATGGAATAGAGGCGTAATGGAATAGAGA
*
11124252 TATAATGGAATAGATGCGTAATGGAATAGAG
1 TATAATGGAATAGAGGCGTAATGGAATAGAG
11124283 GCGTAATAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.43, C:0.02, G:0.30, T:0.25
Consensus pattern (32 bp):
TATAATGGAATAGAGGCGTAATGGAATAGAGA
Found at i:11124358 original size:44 final size:46
Alignment explanation
Indices: 11124271--11124363 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
11124261 ATAGATGCGT
* *
11124271 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGATGAATGG
11124317 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGATGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGATGAATGG
11124361 AAT
1 AAT
11124364 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 23 0.51
45 3 0.07
46 19 0.42
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.35
Consensus pattern (46 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGATGAATGG
Found at i:11124706 original size:49 final size:49
Alignment explanation
Indices: 11124635--11124732 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
11124625 AATTATTATT
* * *
11124635 AAATATAATTTAATATCATGAATCAAAAGGTGAACCCTTTATAAAATTA
1 AAATATAATTTAATATCATGAATCAAAAGCTGAACACTGTATAAAATTA
*
11124684 AAAT-TAATTTCAATATCATGAATCAAAAGCTTAACACTGTATAAAATTA
1 AAATATAATTT-AATATCATGAATCAAAAGCTGAACACTGTATAAAATTA
11124733 TAACACATGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 6 0.14
49 38 0.86
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (49 bp):
AAATATAATTTAATATCATGAATCAAAAGCTGAACACTGTATAAAATTA
Found at i:11128351 original size:28 final size:28
Alignment explanation
Indices: 11128319--11128374 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
11128309 CGTCGTATCA
11128319 GAGTGGTGAGTGTAAACTTAAGGTGTTG
1 GAGTGGTGAGTGTAAACTTAAGGTGTTG
*
11128347 GAGTGGTGAGTGTAAACTTGAGGTGTTG
1 GAGTGGTGAGTGTAAACTTAAGGTGTTG
11128375 TTGGACTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.04, G:0.41, T:0.32
Consensus pattern (28 bp):
GAGTGGTGAGTGTAAACTTAAGGTGTTG
Found at i:11134828 original size:6 final size:6
Alignment explanation
Indices: 11134782--11134827 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
11134772 AACTCATACT
* *
11134782 TTTATA TTTATA TTTATA TTTATA TTTATA ATT-TA TTTATT TTTAT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTAT
11134828 TAATAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
5 4 0.11
6 32 0.89
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTATA
Found at i:11135055 original size:16 final size:16
Alignment explanation
Indices: 11135034--11135066 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
11135024 TTCGCTGTAT
11135034 TGGAATAGAGACGTAA
1 TGGAATAGAGACGTAA
*
11135050 TGGAATAGAGGCGTAA
1 TGGAATAGAGACGTAA
11135066 T
1 T
11135067 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGACGTAA
Found at i:11135318 original size:14 final size:15
Alignment explanation
Indices: 11135279--11135315 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
11135269 AATCATATTG
*
11135279 ATTATTATTAAATAT
1 ATTATAATTAAATAT
11135294 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
11135308 A-TATAATT
1 ATTATAATT
11135316 TAAGAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.33
14 3 0.14
15 11 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:11135404 original size:120 final size:120
Alignment explanation
Indices: 11135279--11135501 Score: 401
Period size: 120 Copynumber: 1.9 Consensus size: 120
11135269 AATCATATTG
*
11135279 ATTATTATTAAATATATTATAATTAAAATATATAATTTAAGAAAATTCTTAATAATCAATATTCT
1 ATTATTATTAAATATATTATAATTAAAATATATAATTTAAGAAAATTCTTAATAATCAAAATTCT
* *
11135344 TATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTTAACATA
66 TATATGAATTTACTAAAATCATAATATATGATAATATAAAATATAATTTAACATA
* *
11135399 ATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAAAATTCT
1 ATTATTATTAAATATATTATAATTAAAATATATAATTTAAGAAAATTCTTAATAATCAAAATTCT
11135464 TATATGAATTTACTAAAATCATAATATATGATAATATA
66 TATATGAATTTACTAAAATCATAATATATGATAATATA
11135502 TAATTTACTA
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 98 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTATTATTAAATATATTATAATTAAAATATATAATTTAAGAAAATTCTTAATAATCAAAATTCT
TATATGAATTTACTAAAATCATAATATATGATAATATAAAATATAATTTAACATA
Found at i:11135431 original size:18 final size:17
Alignment explanation
Indices: 11135410--11135444 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11135400 TTATTATTAA
*
11135410 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
11135428 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
11135445 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:11135461 original size:16 final size:15
Alignment explanation
Indices: 11135436--11135465 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
11135426 ATATATAATT
11135436 TAATAAAATTCTTAA
1 TAATAAAATTCTTAA
11135451 TAATCAAAATTCTTA
1 TAAT-AAAATTCTTA
11135466 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATAAAATTCTTAA
Found at i:11135491 original size:59 final size:59
Alignment explanation
Indices: 11135308--11135491 Score: 144
Period size: 60 Copynumber: 3.1 Consensus size: 59
11135298 TAATTAAAAT
* * *
11135308 ATATAATTTAAGAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAATCAAAATTCTTATATGAATTTACTAAAATCATA
* * * * * * * * * * *
11135367 ATAT-ATGATACTATAAAA-T-ATAATTTAA-CATAATTATTAT-TAAATATATTTTAATTAAAA
1 ATATAAT-TTA--ATAAAATTCTTAA--TAATCAAAATTCTTATATGAATTTA-CTAAAATCATA
11135427 TATATAATTTAATAAAATTCTTAATAATCAAAATTCTTATATGAATTTACTAAAATCATA
1 -ATATAATTTAATAAAATTCTTAATAATCAAAATTCTTATATGAATTTACTAAAATCATA
11135487 ATATA
1 ATATA
11135492 TGATAATATA
Statistics
Matches: 89, Mismatches: 24, Indels: 24
0.65 0.18 0.18
Matches are distributed among these distances:
58 2 0.02
59 29 0.33
60 33 0.37
61 23 0.26
62 2 0.02
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (59 bp):
ATATAATTTAATAAAATTCTTAATAATCAAAATTCTTATATGAATTTACTAAAATCATA
Found at i:11135593 original size:15 final size:15
Alignment explanation
Indices: 11135550--11135603 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
11135540 TATGAATTTG
11135550 TATAATTTAA-AATA
1 TATAATTTAATAATA
* *
11135564 -ATTA-TTATTAA-A
1 TATAATTTAATAATA
11135576 TATAATTTAATAATA
1 TATAATTTAATAATA
*
11135591 TATAATTTCATAA
1 TATAATTTAATAA
11135604 AATTCGTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
12 4 0.13
13 8 0.26
14 6 0.19
15 13 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
TATAATTTAATAATA
Found at i:11135605 original size:91 final size:87
Alignment explanation
Indices: 11135494--11135767 Score: 374
Period size: 91 Copynumber: 3.1 Consensus size: 87
11135484 ATAATATATG
* * *
11135494 ATAATATATAATTT-ACTAAAATAATTATCACTAATAAATTGTCTTATATGAATTTGTATAATTT
1 ATAATATATAATTTCA-TAAAAT--TT-TGA-TAATAAATTTTCTTATATGAATTTATATAATTT
*
11135558 AAAATAATTATTATTAAATATAATTTA
61 AAAATAATTAATATTAAATATAATTTA
*
11135585 ATAATATATAATTTCATAAAATTCGTGAT--TAAATTTTCTTATATGAATTTATATAATTTAAAA
1 ATAATATATAATTTCATAAAATT-TTGATAATAAATTTTCTTATATGAATTTATATAATTTAAAA
*
11135648 TAATTAATGTTAAATATAATTTA
65 TAATTAATATTAAATATAATTTA
*
11135671 ATAATGATATATAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTA
1 AT-A--ATATATAATTTCATAAAATT-TTGATAATAAATTTTCTTATATGAATTTATATAATTTA
11135736 AAATAATTAATATTAAATATAATTTA
62 AAATAATTAATATTAAATATAATTTA
11135762 ATAATA
1 ATAATA
11135768 AAATGTTCTT
Statistics
Matches: 167, Mismatches: 9, Indels: 17
0.87 0.05 0.09
Matches are distributed among these distances:
86 55 0.33
87 1 0.01
88 4 0.02
89 28 0.17
90 1 0.01
91 77 0.46
92 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (87 bp):
ATAATATATAATTTCATAAAATTTTGATAATAAATTTTCTTATATGAATTTATATAATTTAAAAT
AATTAATATTAAATATAATTTA
Found at i:11135634 original size:86 final size:87
Alignment explanation
Indices: 11135527--11135767 Score: 385
Period size: 91 Copynumber: 2.7 Consensus size: 87
11135517 ATTATCACTA
* * *
11135527 ATAAATTGTCTTATATGAATTTGTATAATTTAAAATAATTATTATTAAATATAATTTAATAATAT
1 ATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAATAT
11135592 ATAATTTCATAAAATTCGTGAT
66 ATAATTTCATAAAATTCGTGAT
*
11135614 -TAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATGTTAAATATAATTTAATAATGA
1 ATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAAT-A--A
*
11135678 TATATAATTTCATAAAATTCTTGAT
63 TATATAATTTCATAAAATTCGTGAT
*
11135703 AATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATA
1 -ATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAATA
11135768 AAATGTTCTT
Statistics
Matches: 142, Mismatches: 7, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
86 55 0.39
87 1 0.01
88 3 0.02
89 25 0.18
90 1 0.01
91 57 0.40
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (87 bp):
ATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAATAT
ATAATTTCATAAAATTCGTGAT
Found at i:11135764 original size:17 final size:15
Alignment explanation
Indices: 11135733--11135771 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
11135723 TTTATACAAT
11135733 TTAAAATAATTAATA
1 TTAAAATAATTAATA
11135748 TTAAATATAATTTAATA
1 TTAAA-ATAA-TTAATA
*
11135765 ATAAAAT
1 TTAAAAT
11135772 GTTCTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 6 0.29
17 10 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAAATAATTAATA
Found at i:11135943 original size:19 final size:19
Alignment explanation
Indices: 11135919--11135957 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
11135909 CATCAAAAAG
11135919 TTTGAACATTGATTTTTAA
1 TTTGAACATTGATTTTTAA
11135938 TTTGAACATTGATTTTTAA
1 TTTGAACATTGATTTTTAA
11135957 T
1 T
11135958 GGTCAGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (19 bp):
TTTGAACATTGATTTTTAA
Found at i:11138347 original size:30 final size:30
Alignment explanation
Indices: 11138311--11138377 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
11138301 CGATTAACTC
11138311 AAACAAATAATGCAATACAGGCAAGAACCG
1 AAACAAATAATGCAATACAGGCAAGAACCG
11138341 AAACAAATAATGCAATACAGGCAAGAACCG
1 AAACAAATAATGCAATACAGGCAAGAACCG
11138371 AAACAAA
1 AAACAAA
11138378 CTATTTAGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.57, C:0.19, G:0.15, T:0.09
Consensus pattern (30 bp):
AAACAAATAATGCAATACAGGCAAGAACCG
Found at i:11142736 original size:3 final size:3
Alignment explanation
Indices: 11142728--11142785 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
11142718 AGACGGCAAT
*
11142728 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAG GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
11142776 GAG GAA GAA G
1 GAA GAA GAA G
11142786 GACCTGAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:11155553 original size:19 final size:19
Alignment explanation
Indices: 11155529--11155639 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
11155519 AATCTTCAGG
11155529 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11155548 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
11155567 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11155586 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
***
11155605 GATAAATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11155624 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
11155640 AGATATGATT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 80 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:11155579 original size:38 final size:38
Alignment explanation
Indices: 11155536--11155639 Score: 190
Period size: 38 Copynumber: 2.7 Consensus size: 38
11155526 AGGGATATGC
*
11155536 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATAAAT
*
11155574 AATCTTAGATATGATATGCAATCTTAGATATGATAAAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATAAAT
11155612 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
11155640 AGATATGATT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATAAAT
Found at i:11155665 original size:22 final size:21
Alignment explanation
Indices: 11155529--11155665 Score: 105
Period size: 19 Copynumber: 6.9 Consensus size: 21
11155519 AATCTTCAGG
*
11155529 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
11155548 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
* *
11155567 AATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
11155586 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
**
11155605 GATAAATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
11155624 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
11155646 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
11155666 TTAATTTGTA
Statistics
Matches: 100, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
19 77 0.77
22 12 0.12
23 11 0.11
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:11156309 original size:23 final size:23
Alignment explanation
Indices: 11156282--11156325 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
11156272 TATAATTTTT
*
11156282 TATATGTA-ATTATTTTTTTTATC
1 TATATGTATA-TATTTATTTTATC
11156305 TATATGTATATATTTATTTTA
1 TATATGTATATATTTATTTTA
11156326 GTATACATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (23 bp):
TATATGTATATATTTATTTTATC
Found at i:11158890 original size:20 final size:20
Alignment explanation
Indices: 11158865--11158904 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
11158855 TTTCAAATTA
*
11158865 ATTTTACCAAATATAATATT
1 ATTTTAACAAATATAATATT
**
11158885 ATTTTAATGAATATAATATT
1 ATTTTAACAAATATAATATT
11158905 TATCTAGATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (20 bp):
ATTTTAACAAATATAATATT
Found at i:11163366 original size:27 final size:26
Alignment explanation
Indices: 11163305--11163462 Score: 129
Period size: 27 Copynumber: 5.9 Consensus size: 26
11163295 CACGCCATAC
* *
11163305 AGGCAAT-CATATAGAGTCTGCCACCA
1 AGGCAATCCAT-TAGAGTATGCCACAA
* * *
11163331 AGTCGATCCATTCAGAGTATGCCATAA
1 AGGCAATCCATT-AGAGTATGCCACAA
* *
11163358 AGGCAATCCATTTAAAGTGTGCCACAA
1 AGGCAATCCA-TTAGAGTATGCCACAA
* * * *
11163385 AGGCGAGCCAGTCAGAGTACGCCACAA
1 AGGCAATCCA-TTAGAGTATGCCACAA
*
11163412 AGGCAATCCAATTAGAGTACGCCACAA
1 AGGCAATCC-ATTAGAGTATGCCACAA
* *
11163439 AGGTAATCCAGTTAGAGTTTGCCA
1 AGGCAATCCA-TTAGAGTATGCCA
11163463 TGGCTATGGG
Statistics
Matches: 104, Mismatches: 23, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
26 7 0.07
27 94 0.90
28 3 0.03
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (26 bp):
AGGCAATCCATTAGAGTATGCCACAA
Found at i:11163403 original size:54 final size:54
Alignment explanation
Indices: 11163296--11163441 Score: 168
Period size: 54 Copynumber: 2.7 Consensus size: 54
11163286 CTAACAGGTC
* * * * * * *
11163296 ACGCCATACAGGCAAT-CATATAGAGTCTGCCACCAAGTCGATCCATTCAGAGT
1 ACGCCATAAAGGCAATCCATTTAGAGTATGCCACAAAGGCGAGCCAGTCAGAGT
* * *
11163349 ATGCCATAAAGGCAATCCATTTAAAGTGTGCCACAAAGGCGAGCCAGTCAGAGT
1 ACGCCATAAAGGCAATCCATTTAGAGTATGCCACAAAGGCGAGCCAGTCAGAGT
* * *
11163403 ACGCCACAAAGGCAATCCAATTAGAGTACGCCACAAAGG
1 ACGCCATAAAGGCAATCCATTTAGAGTATGCCACAAAGG
11163442 TAATCCAGTT
Statistics
Matches: 77, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
53 14 0.18
54 63 0.82
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (54 bp):
ACGCCATAAAGGCAATCCATTTAGAGTATGCCACAAAGGCGAGCCAGTCAGAGT
Found at i:11163450 original size:54 final size:54
Alignment explanation
Indices: 11163336--11163456 Score: 143
Period size: 54 Copynumber: 2.2 Consensus size: 54
11163326 CACCAAGTCG
* * * * ** *
11163336 ATCCATTCAGAGTATGCCATAAAGGCAATCCATTTAAAGTGTGCCACAAAGGCG
1 ATCCAGTCAGAGTACGCCACAAAGGCAATCCAATTAAAGTACGCCACAAAGGCA
* * *
11163390 AGCCAGTCAGAGTACGCCACAAAGGCAATCCAATTAGAGTACGCCACAAAGGTA
1 ATCCAGTCAGAGTACGCCACAAAGGCAATCCAATTAAAGTACGCCACAAAGGCA
*
11163444 ATCCAGTTAGAGT
1 ATCCAGTCAGAGT
11163457 TTGCCATGGC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.19
Consensus pattern (54 bp):
ATCCAGTCAGAGTACGCCACAAAGGCAATCCAATTAAAGTACGCCACAAAGGCA
Found at i:11175682 original size:114 final size:113
Alignment explanation
Indices: 11175474--11175778 Score: 384
Period size: 114 Copynumber: 2.7 Consensus size: 113
11175464 AAAATAAGCA
* * * * **
11175474 TTAGCGGCGTTTTTGAGAAAGCGCCAC-AAAAAACCTAAGCCCAACGACGTCGTTTCCCAAGCTT
1 TTAGCGGTGTTTTT-AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * *
11175538 TCGGGGATTTAGCGGTGTTTCTAAGAAAGCGCCGCTAATGCTCCAGGCT
65 TCGGGGATTTAGCGCTGTTTATAAGAAAGCGCCGCTAATGCTCAAGGCT
* *
11175587 TTAGCGGTGTTTTTACAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTATGAGCTT
1 TTAGCGGTGTTTTTA-GAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
*
11175652 TCGGGGATTTAGCAGCT-TTTATAAGGAAGCGCCGCTAATGCTCAAGGCT
65 TCGGGGATTTAGC-GCTGTTTATAAGAAAGCGCCGCTAATGCTCAAGGCT
* * * *
11175701 TTAGCGATGTTTTTGGGAAAGAGCCGCAAAAAAACCTAAGGCCC-ACGACACCGTTTTCTGAGCT
1 TTAGCGGTGTTTTT-AGAAAGCGCCGCAAAAAAACCTAA-GCCCAACGACGCCGTTTTCTGAGCT
*
11175765 TT-AGGGATTTAGCG
64 TTCGGGGATTTAGCG
11175779 GCGTTTTTGG
Statistics
Matches: 168, Mismatches: 19, Indels: 11
0.85 0.10 0.06
Matches are distributed among these distances:
112 2 0.01
113 32 0.19
114 128 0.76
115 6 0.04
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (113 bp):
TTAGCGGTGTTTTTAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
CGGGGATTTAGCGCTGTTTATAAGAAAGCGCCGCTAATGCTCAAGGCT
Found at i:11176070 original size:15 final size:15
Alignment explanation
Indices: 11176050--11176080 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11176040 CATATTTTAA
11176050 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
11176065 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
11176080 G
1 G
11176081 ATTAGGGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:11176338 original size:15 final size:15
Alignment explanation
Indices: 11176318--11176348 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11176308 CATATTTTAA
11176318 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
11176333 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
11176348 G
1 G
11176349 ATTAGGGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:11176890 original size:147 final size:147
Alignment explanation
Indices: 11176623--11176915 Score: 507
Period size: 147 Copynumber: 2.0 Consensus size: 147
11176613 NNNNNNTTTA
*
11176623 TAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGTAAAGAATAAATC
1 TAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAGAATAAATC
* *
11176688 AATTTATTAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAA-
66 AATTTATAAAAAAAATAAAAAAAATTTAGAATAGAAAAACGGCGTCGTTTTGTTCAAAATGAAAT
11176752 AATTTTTGCGGCGTTTTT
131 AA-TTTTGCGGCGTTTTT
* *
11176770 TAAGAAGCGCCGCTAAAGGTAAGTAATAGCGGCGTTTTCTATAAAAATGCCGCAAAGAATAAATC
1 TAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAGAATAAATC
*
11176835 AATTTATAAAAAAAATAAAAAAAATTTAGAATCGAAAAACGGCGTCGTTTTGTTCAAAATGAAAT
66 AATTTATAAAAAAAATAAAAAAAATTTAGAATAGAAAAACGGCGTCGTTTTGTTCAAAATGAAAT
*
11176900 AATTTTGCGGTGTTTT
131 AATTTTGCGGCGTTTT
11176916 CATAACGCCG
Statistics
Matches: 138, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
147 136 0.99
148 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (147 bp):
TAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAGAATAAATC
AATTTATAAAAAAAATAAAAAAAATTTAGAATAGAAAAACGGCGTCGTTTTGTTCAAAATGAAAT
AATTTTGCGGCGTTTTT
Found at i:11179350 original size:23 final size:23
Alignment explanation
Indices: 11179320--11179622 Score: 200
Period size: 23 Copynumber: 13.3 Consensus size: 23
11179310 GAAATTTGAT
11179320 AGTGCTGCAAATTGAAGTGTTTA
1 AGTGCTGCAAATTGAAGTGTTTA
*
11179343 AGTGCTGCAAATTGAAGTATTT-
1 AGTGCTGCAAATTGAAGTGTTTA
* *
11179365 AGTTGCTGGAAATTG-AGATGTTTT
1 AG-TGCTGCAAATTGAAG-TGTTTA
* * *
11179389 A-TCGCTG-TAATTGAGGTGTATA
1 AGT-GCTGCAAATTGAAGTGTTTA
* * **
11179411 AATGTTGTTAATTGATA-TGTTTA
1 AGTGCTGCAAATTGA-AGTGTTTA
*
11179434 AGTGCTGCAAATTGAAGTATTT-
1 AGTGCTGCAAATTGAAGTGTTTA
* *
11179456 AGTTGCTGGAAATTG-AGATGTTTT
1 AG-TGCTGCAAATTGAAG-TGTTTA
* * *
11179480 A-TCGCTG-TAATTGAGGTGTATA
1 AGT-GCTGCAAATTGAAGTGTTTA
* * **
11179502 AATGTTGTTAATTGATA-TGTTTA
1 AGTGCTGCAAATTGA-AGTGTTTA
11179525 AGTGCTGCAAATTGAAGTGTTTA
1 AGTGCTGCAAATTGAAGTGTTTA
*
11179548 AGTGCTGCAAATTGACGTGTTT-
1 AGTGCTGCAAATTGAAGTGTTTA
*
11179570 AGTTGCTGCAAATTG-AGATGTTTT
1 AG-TGCTGCAAATTGAAG-TGTTTA
* *
11179594 A-TCGCTGTAAATTGAAGTGTTAA
1 AGT-GCTGCAAATTGAAGTGTTTA
11179617 AGTGCT
1 AGTGCT
11179623 ACTTTCCATT
Statistics
Matches: 223, Mismatches: 33, Indels: 48
0.73 0.11 0.16
Matches are distributed among these distances:
22 42 0.19
23 175 0.78
24 6 0.03
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.40
Consensus pattern (23 bp):
AGTGCTGCAAATTGAAGTGTTTA
Found at i:11179425 original size:45 final size:45
Alignment explanation
Indices: 11179375--11179523 Score: 165
Period size: 45 Copynumber: 3.3 Consensus size: 45
11179365 AGTTGCTGGA
11179375 AATTGAGATGTTTTATCGCTGTAATTGAGGTGTATAAATGTTGTT
1 AATTGAGATGTTTTATCGCTGTAATTGAGGTGTATAAATGTTGTT
* * * * * * ** * **
11179420 AATTGATATGTTTAAGT-GCTGCAAATTGAAGTATTTAGTTGCTGGA
1 AATTGAGATGTTTTA-TCGCTG-TAATTGAGGTGTATAAATGTTGTT
11179466 AATTGAGATGTTTTATCGCTGTAATTGAGGTGTATAAATGTTGTT
1 AATTGAGATGTTTTATCGCTGTAATTGAGGTGTATAAATGTTGTT
*
11179511 AATTGATATGTTT
1 AATTGAGATGTTT
11179524 AAGTGCTGCA
Statistics
Matches: 78, Mismatches: 23, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
45 45 0.58
46 33 0.42
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.44
Consensus pattern (45 bp):
AATTGAGATGTTTTATCGCTGTAATTGAGGTGTATAAATGTTGTT
Found at i:11179569 original size:91 final size:91
Alignment explanation
Indices: 11179329--11179562 Score: 418
Period size: 91 Copynumber: 2.6 Consensus size: 91
11179319 TAGTGCTGCA
11179329 AATTGA-AGTGTTTAAGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTTTTATCG
1 AATTGATA-TGTTTAAGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTTTTATCG
11179393 CTGTAATTGAGGTGTATAAATGTTGTT
65 CTGTAATTGAGGTGTATAAATGTTGTT
11179420 AATTGATATGTTTAAGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTTTTATCGC
1 AATTGATATGTTTAAGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTTTTATCGC
11179485 TGTAATTGAGGTGTATAAATGTTGTT
66 TGTAATTGAGGTGTATAAATGTTGTT
* *
11179511 AATTGATATGTTTAAGTGCTGCAAATTGAAGTGTTTAAG-TGCTGCAAATTGA
1 AATTGATATGTTTAAGTGCTGCAAATTGAAGTATTT-AGTTGCTGGAAATTGA
11179563 CGTGTTTAGT
Statistics
Matches: 139, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
91 136 0.98
92 3 0.02
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.40
Consensus pattern (91 bp):
AATTGATATGTTTAAGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGATGTTTTATCGC
TGTAATTGAGGTGTATAAATGTTGTT
Found at i:11180674 original size:42 final size:43
Alignment explanation
Indices: 11180533--11180719 Score: 252
Period size: 43 Copynumber: 4.4 Consensus size: 43
11180523 GTTTTTGGAG
* * * * * *
11180533 AAAGCGTCGCTAAAGGTCTTGTTTTTTAGCGGCGCTTCAGGAA
1 AAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGAGGGA
* * *
11180576 AAAGCACCGCTAAAGGTCTTGGTTTTTAGCAGCGTTTGAGGGA
1 AAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGAGGGA
*
11180619 AAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCG-TTGGGGGA
1 AAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGAGGGA
*
11180661 AAAGCGCCGCTAAAGGTCATT-GTCTTTAGCGGCGTTTGTGGGA
1 AAAGCGCCGCTAAAGGTC-TTGGTCTTTAGCGGCGTTTGAGGGA
11180704 AAAGCGCCGCTAAAGG
1 AAAGCGCCGCTAAAGG
11180720 CCTTAAAAAG
Statistics
Matches: 130, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
42 38 0.29
43 92 0.71
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.26
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGAGGGA
Found at i:11180704 original size:85 final size:86
Alignment explanation
Indices: 11180513--11180719 Score: 267
Period size: 85 Copynumber: 2.4 Consensus size: 86
11180503 TTTTTGTGAC
* * * * *
11180513 CTTTAGTGGCGTTT-TTGGAGAAAGCGTCGCTAAAGGTCTTGTTTTTTAGCGGCGCTTCAGGAAA
1 CTTTAGCGGCGTTTGTGGGA-AAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGCTTCAGGAAA
11180577 AAGCACCGCTAAAGGTCTTGGT
65 AAGCACCGCTAAAGGTCTTGGT
* * * ** *
11180599 TTTTAGCAGCGTTTGAGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCG-TTGGGGGAAA
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGCTTCAGGAAAA
*
11180663 AGCGCCGCTAAAGGTCATT-GT
66 AGCACCGCTAAAGGTC-TTGGT
11180684 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGG
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGG
11180720 CCTTAAAAAG
Statistics
Matches: 104, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
85 57 0.55
86 44 0.42
87 3 0.03
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (86 bp):
CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGCTTCAGGAAAA
AGCACCGCTAAAGGTCTTGGT
Found at i:11183231 original size:13 final size:13
Alignment explanation
Indices: 11183197--11183239 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
11183187 GTAGTAGTAA
*
11183197 TTTTTCCTGTTTCC
1 TTTTTCCT-TTTTC
*
11183211 TGTTTCCTTTTTC
1 TTTTTCCTTTTTC
11183224 TTTTTCCTTTTT-
1 TTTTTCCTTTTTC
11183236 TTTT
1 TTTT
11183240 ATTGGTGATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 4 0.15
13 15 0.58
14 7 0.27
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (13 bp):
TTTTTCCTTTTTC
Found at i:11183917 original size:3 final size:3
Alignment explanation
Indices: 11183909--11183943 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
11183899 CTACCACAGT
11183909 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
11183944 GGTCTTCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:11183949 original size:12 final size:12
Alignment explanation
Indices: 11183910--11183955 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
11183900 TACCACAGTT
*
11183910 TCTTCTTCTTCT
1 TCTTCTTCTTCG
*
11183922 TCTTCTTCTTCT
1 TCTTCTTCTTCG
*
11183934 TCTTCTTCTTGG
1 TCTTCTTCTTCG
*
11183946 TCTTCCTCTT
1 TCTTCTTCTT
11183956 GGCCGTCCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.00, C:0.33, G:0.04, T:0.63
Consensus pattern (12 bp):
TCTTCTTCTTCG
Found at i:11201068 original size:14 final size:14
Alignment explanation
Indices: 11201049--11201087 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
11201039 TGTGGAATAT
11201049 TTTTATTGATGAAG
1 TTTTATTGATGAAG
11201063 TTTTATTTG-TGAAG
1 TTTTA-TTGATGAAG
11201077 -TTTATTGATGA
1 TTTTATTGATGA
11201088 GTATTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.13
13 7 0.30
14 10 0.43
15 3 0.13
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.54
Consensus pattern (14 bp):
TTTTATTGATGAAG
Found at i:11213295 original size:20 final size:23
Alignment explanation
Indices: 11213257--11213297 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
11213247 TTAAGCGTTT
11213257 TTTTTGTTTGTTTTAGTTAAATG
1 TTTTTGTTTGTTTTAGTTAAATG
11213280 TTTTT-TTT-TTTT-GTTAAA
1 TTTTTGTTTGTTTTAGTTAAA
11213298 ATTGAGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 3 0.17
23 5 0.28
ACGTcount: A:0.17, C:0.00, G:0.12, T:0.71
Consensus pattern (23 bp):
TTTTTGTTTGTTTTAGTTAAATG
Found at i:11217822 original size:11 final size:11
Alignment explanation
Indices: 11217791--11217831 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
11217781 AATACTTGAT
*
11217791 AATAATAAAAA
1 AATAATAATAA
* *
11217802 AATCAGAATAA
1 AATAATAATAA
11217813 AATAATAATAA
1 AATAATAATAA
11217824 AATAATAA
1 AATAATAA
11217832 GATCTGACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (11 bp):
AATAATAATAA
Found at i:11219837 original size:17 final size:16
Alignment explanation
Indices: 11219815--11219875 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 16
11219805 ATAATGATTC
*
11219815 TTTAATTTTATATATTT
1 TTTAATTTT-TATAATT
11219832 TTTAATTTTTATAATT
1 TTTAATTTTTATAATT
* * *
11219848 TATAATTTATACTTATT
1 TTTAATTTTTA-TAATT
*
11219865 TTTATTTTTTA
1 TTTAATTTTTA
11219876 ATGGTTATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
16 15 0.42
17 21 0.58
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTAATTTTTATAATT
Found at i:11219853 original size:16 final size:17
Alignment explanation
Indices: 11219817--11219855 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
11219807 AATGATTCTT
* *
11219817 TAATTTTATATATTTTT
1 TAATTTTATATAATTTA
11219834 TAATTTT-TATAATTTA
1 TAATTTTATATAATTTA
11219850 TAATTT
1 TAATTT
11219856 ATACTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TAATTTTATATAATTTA
Found at i:11228912 original size:50 final size:50
Alignment explanation
Indices: 11228810--11228998 Score: 225
Period size: 50 Copynumber: 3.7 Consensus size: 50
11228800 ATGAGATCCC
*
11228810 ATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTAAGATTATGAGAGGTCCT
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----CGA-TATGAGAGGTCCT
* *
11228866 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCT
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGGTCCT
** * ** *
11228916 CCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGGTCCT
* *
11228966 ATGTAAGACCATATCTGGGATATGGCATTGGCA
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCA
11228999 GTACAGAAAA
Statistics
Matches: 117, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
50 82 0.70
51 2 0.02
55 1 0.01
56 32 0.27
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (50 bp):
ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAGGTCCT
Found at i:11228991 original size:100 final size:103
Alignment explanation
Indices: 11228812--11228998 Score: 254
Period size: 100 Copynumber: 1.8 Consensus size: 103
11228802 GAGATCCCAT
* ** *
11228812 GTAAGACCATGTCTGGGACATGGCATTGGCATCATTAAGATTATGAGAGGTCCTATGTAAGACCA
1 GTAAGACCATGTCTGGGACATGGCATGGGCATC---AAGATTATGAGAACTCCCATGTAAGACCA
* *
11228877 TGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCTCC
63 TATCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCTCC
*
11228918 GTAAGACCATGTCTGGGACATGGCATGGGCA-C-CGA-TATGAGAACTCCCATGTAAGACCATAT
1 GTAAGACCATGTCTGGGACATGGCATGGGCATCAAGATTATGAGAACTCCCATGTAAGACCATAT
*
11228980 CTGGGATATGGCATTGGCA
66 CTGGGACATGGCATTGGCA
11228999 GTACAGAAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
100 40 0.55
101 2 0.03
105 1 0.01
106 30 0.41
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (103 bp):
GTAAGACCATGTCTGGGACATGGCATGGGCATCAAGATTATGAGAACTCCCATGTAAGACCATAT
CTGGGACATGGCATTGGCACCGAGATGAGAGGTCCTCC
Found at i:11229265 original size:12 final size:12
Alignment explanation
Indices: 11229248--11229286 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
11229238 ATGAGTTATT
11229248 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
11229260 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
11229272 TAAGTGAGTAAG
1 TAAGTAAGCAAG
11229284 TAA
1 TAA
11229287 AGAAGCGAGT
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:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:11230255 original size:19 final size:19
Alignment explanation
Indices: 11230226--11230275 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
11230216 TATATTTTTT
11230226 TATTTTT-AAAT-TTTTAAA
1 TATTTTTAAAATATTTT-AA
**
11230244 TATTTTTAAAATATTTTTT
1 TATTTTTAAAATATTTTAA
11230263 TATTTTTAAAATA
1 TATTTTTAAAATA
11230276 AATTGTTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 7 0.25
19 17 0.61
20 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTTAAAATATTTTAA
Found at i:11231687 original size:31 final size:31
Alignment explanation
Indices: 11231649--11231711 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
11231639 TTATTCGGGA
*
11231649 TACGCAATGTCACTATTAAGGAAGAAGTTAT
1 TACGCAATGTCACCATTAAGGAAGAAGTTAT
11231680 TACGCAATGTCACCATTAAGGAAGAAGTTAT
1 TACGCAATGTCACCATTAAGGAAGAAGTTAT
11231711 T
1 T
11231712 CACGAGTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (31 bp):
TACGCAATGTCACCATTAAGGAAGAAGTTAT
Found at i:11234246 original size:15 final size:15
Alignment explanation
Indices: 11234226--11234277 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
11234216 ATAATAAAAC
11234226 AAAGAAATAGAAGAA
1 AAAGAAATAGAAGAA
11234241 AAAGAAATA-AAGAA
1 AAAGAAATAGAAGAA
**
11234255 AGAA-AAAGGGAAGCAA
1 A-AAGAAATAGAAG-AA
11234271 AAAGAAA
1 AAAGAAA
11234278 CAAAGAAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 9 0.29
15 16 0.52
16 6 0.19
ACGTcount: A:0.73, C:0.02, G:0.21, T:0.04
Consensus pattern (15 bp):
AAAGAAATAGAAGAA
Found at i:11234274 original size:18 final size:17
Alignment explanation
Indices: 11234253--11234316 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
11234243 AGAAATAAAG
*
11234253 AAAGAAAAAGGGAAGCAA
1 AAAGAAAAA-AGAAGCAA
11234271 AAAGAAACAAAGAAGCAA
1 AAAGAAA-AAAGAAGCAA
* * *
11234289 AAACAAAACAGGAG-AA
1 AAAGAAAAAAGAAGCAA
11234305 AAAGTAAAAAAG
1 AAAG-AAAAAAG
11234317 GAGAAAACTA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 5 0.13
17 11 0.29
18 20 0.53
19 2 0.05
ACGTcount: A:0.70, C:0.08, G:0.20, T:0.02
Consensus pattern (17 bp):
AAAGAAAAAAGAAGCAA
Found at i:11235236 original size:41 final size:39
Alignment explanation
Indices: 11235179--11235314 Score: 152
Period size: 40 Copynumber: 3.5 Consensus size: 39
11235169 TGACTTCGAG
11235179 TCGATGAGACACTGGGTGTCAATTTATTACTTCGGATATAT
1 TCGATGAGACACTGGGTGTCAA-TTATTACTTCGGAT-TAT
* * *
11235220 TCGATGAGGCACTGGGTGCCAA-T-TTACTTCGGTTTA-
1 TCGATGAGACACTGGGTGTCAATTATTACTTCGGATTAT
* * *
11235256 GCTGATGAGACACTAGGTGTCAAATTATTACTTCGAATTAT
1 TC-GATGAGACACTGGGTGTC-AATTATTACTTCGGATTAT
*
11235297 TCGATGAGGCACTGGGTG
1 TCGATGAGACACTGGGTG
11235315 CCAAACTGGT
Statistics
Matches: 78, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
36 1 0.01
37 17 0.22
38 12 0.15
39 2 0.03
40 25 0.32
41 21 0.27
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (39 bp):
TCGATGAGACACTGGGTGTCAATTATTACTTCGGATTAT
Found at i:11241547 original size:2 final size:2
Alignment explanation
Indices: 11241540--11241570 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11241530 NNNNNNNNNN
11241540 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11241571 CAAAACATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11243995 original size:6 final size:6
Alignment explanation
Indices: 11243984--11244008 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
11243974 TGTATGTAAT
11243984 ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA A
11244009 ATGATGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:11244099 original size:29 final size:30
Alignment explanation
Indices: 11244056--11244114 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
11244046 GAATTAGATC
11244056 AAATCAAAATTTCATGTATAAAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
*
11244086 AAATCAAAA-TTCATGTATACAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
11244115 TTAAACCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.29
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:11244133 original size:31 final size:29
Alignment explanation
Indices: 11244060--11244135 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
11244050 TAGATCAAAT
*
11244060 CAAAATTTCATGTATAAAATTACACAAAAT
1 CAAAA-TTCATGTATAAAATTACACAAAAC
*
11244090 CAAAATTCATGTATACAATTACACATTAAAC
1 CAAAATTCATGTATAAAATTACACA--AAAC
* *
11244121 CATAGTTCATGTATA
1 CAAAATTCATGTATA
11244136 GTTTTTGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 19 0.47
30 5 0.12
31 16 0.40
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (29 bp):
CAAAATTCATGTATAAAATTACACAAAAC
Found at i:11245376 original size:10 final size:10
Alignment explanation
Indices: 11245361--11245394 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
11245351 AAAATTATAG
11245361 AATTATTTAA
1 AATTATTTAA
11245371 AATTATTTAAA
1 AATTATTT-AA
11245382 AATTATTTAA
1 AATTATTTAA
11245392 AAT
1 AAT
11245395 AAGGTTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AATTATTTAA
Found at i:11245385 original size:11 final size:11
Alignment explanation
Indices: 11245361--11245393 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
11245351 AAAATTATAG
11245361 AATTATTT-AA
1 AATTATTTAAA
11245371 AATTATTTAAA
1 AATTATTTAAA
11245382 AATTATTTAAA
1 AATTATTTAAA
11245393 A
1 A
11245394 TAAGGTTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AATTATTTAAA
Found at i:11260113 original size:14 final size:14
Alignment explanation
Indices: 11260090--11260129 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
11260080 TGAGTTTGTA
11260090 AATA-TTATTAGTT
1 AATATTTATTAGTT
11260103 AATATTTATTAGTT
1 AATATTTATTAGTT
11260117 AATTATATTATTA
1 AA-TAT-TTATTA
11260130 TATTTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.17
14 11 0.46
15 3 0.12
16 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (14 bp):
AATATTTATTAGTT
Found at i:11266176 original size:21 final size:22
Alignment explanation
Indices: 11266150--11266207 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 22
11266140 AAGCATATAT
11266150 ATATAAATATAAAATAATCA-A
1 ATATAAATATAAAATAATCATA
* *
11266171 ATATAAATAT-TAATAATTATA
1 ATATAAATATAAAATAATCATA
*
11266192 TTATAAATA-AAAATAA
1 ATATAAATATAAAATAA
11266208 ACATCCAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 7 0.23
21 24 0.77
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
ATATAAATATAAAATAATCATA
Found at i:11267071 original size:20 final size:21
Alignment explanation
Indices: 11267027--11267079 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 21
11267017 AAAGACATGG
11267027 ATTATGTTTTACTTGAGATTT
1 ATTATGTTTTACTTGAGATTT
*
11267048 -TTATTTTTTACCTT-AG-TTT
1 ATTATGTTTTA-CTTGAGATTT
*
11267067 ATTAT-ATTTACTT
1 ATTATGTTTTACTT
11267080 TAAAGAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 3 0.11
19 7 0.25
20 15 0.54
21 3 0.11
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (21 bp):
ATTATGTTTTACTTGAGATTT
Found at i:11273773 original size:2 final size:2
Alignment explanation
Indices: 11273768--11273806 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
11273758 AAAAATGTAG
*
11273768 TA TA TA AA TA -A TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11273807 GATTTCAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:11274933 original size:21 final size:22
Alignment explanation
Indices: 11274897--11274948 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
11274887 AAATTAAATG
* *
11274897 AAAATAAAAATCTTAAA-ATTC
1 AAAATAAAAATATTAAATATTA
*
11274918 AAAATAAAATTATTAAATTATTA
1 AAAATAAAAATATTAAA-TATTA
11274941 AAAATAAA
1 AAAATAAA
11274949 TATTCATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 15 0.58
23 11 0.42
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATAAAAATATTAAATATTA
Found at i:11278839 original size:30 final size:31
Alignment explanation
Indices: 11278787--11278887 Score: 102
Period size: 30 Copynumber: 3.3 Consensus size: 31
11278777 ATATTTTATG
* *
11278787 TATCATTATATTAAATTATTTAAATATGATT
1 TATCATTATATTAAAATATTTAAATATCATT
11278818 TATCATTATA-TAAAATATTTAAATATCATT
1 TATCATTATATTAAAATATTTAAATATCATT
* * *
11278848 TCTTATTGTATTTAAAAT-TTTAAA-AT-ATT
1 TATCATTATA-TTAAAATATTTAAATATCATT
11278877 TCATCTATTAT
1 T-ATC-ATTAT
11278888 TAAATTTACA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
29 4 0.07
30 28 0.48
31 20 0.34
32 6 0.10
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (31 bp):
TATCATTATATTAAAATATTTAAATATCATT
Found at i:11284955 original size:21 final size:21
Alignment explanation
Indices: 11284931--11284974 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
11284921 TATTGGTTTA
* *
11284931 TTGCGGATCAAGTCAAGTTAC
1 TTGCGGAACAAGTCAAGTCAC
11284952 TTGCGGAACAAGTCAAGTCAC
1 TTGCGGAACAAGTCAAGTCAC
11284973 TT
1 TT
11284975 TCTATAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (21 bp):
TTGCGGAACAAGTCAAGTCAC
Found at i:11292307 original size:24 final size:24
Alignment explanation
Indices: 11292275--11292323 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
11292265 GTCTTTTACC
*
11292275 ACCCTTAAAGGGCTTTCATATACT
1 ACCCGTAAAGGGCTTTCATATACT
*
11292299 ACCCGTAAAGGTCTTTCATATACT
1 ACCCGTAAAGGGCTTTCATATACT
11292323 A
1 A
11292324 GTGTGCAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (24 bp):
ACCCGTAAAGGGCTTTCATATACT
Found at i:11301529 original size:22 final size:22
Alignment explanation
Indices: 11301482--11301531 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
11301472 ATCTATATAT
* **
11301482 ATATGTATATTTTTTTATGTAC
1 ATATTTATATTTTTTTAACTAC
11301504 ATATTTATATTTTTTTCAACTA-
1 ATATTTATATTTTTTT-AACTAC
11301526 ATATTT
1 ATATTT
11301532 TTCTCATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (22 bp):
ATATTTATATTTTTTTAACTAC
Found at i:11301712 original size:2 final size:2
Alignment explanation
Indices: 11301663--11301703 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
11301653 ATTCTTTTAC
11301663 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11301704 CGCATATATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11306783 original size:20 final size:19
Alignment explanation
Indices: 11306760--11306804 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
11306750 AAAATATTTC
11306760 AAAATATAAAAAAAAGAAAG
1 AAAATAT-AAAAAAAGAAAG
*
11306780 AAAAAATAAAAAAAGAAAG
1 AAAATATAAAAAAAGAAAG
11306799 AAAATA
1 AAAATA
11306805 GAGAGGCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (19 bp):
AAAATATAAAAAAAGAAAG
Found at i:11308048 original size:44 final size:43
Alignment explanation
Indices: 11308000--11308222 Score: 132
Period size: 44 Copynumber: 5.1 Consensus size: 43
11307990 GATAACAGAT
*
11308000 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACTAGC
1 CTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACAC-AGC
* * * ** * * *
11308044 CTTGCCTCCCTG-AGTTG-CAGC-AGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTTCCTGCA-CTGACAGCGA-AGCAGATCGAAGACA-CAG-C
11308088 CTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACA-CAGC
* * ** * * ** * * *
11308132 CTTACCTCCCTAG-GTTG-CAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTTCCT-GCACTGACAGCGAAGCAGATCGAAGACA-CAG-C
*
11308176 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACA-CAGC
11308220 CTT
1 CTT
11308223 ACCTCATTGG
Statistics
Matches: 125, Mismatches: 43, Indels: 22
0.66 0.23 0.12
Matches are distributed among these distances:
42 1 0.01
43 36 0.29
44 50 0.40
45 37 0.30
46 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (43 bp):
CTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACAGC
Found at i:11308149 original size:88 final size:88
Alignment explanation
Indices: 11307995--11308462 Score: 602
Period size: 88 Copynumber: 5.3 Consensus size: 88
11307985 GTGAAGATAA
*
11307995 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCT-GAGT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAG-GT
*
11308059 TGCAGCAGAGCAGGTTAAAAATAG
65 TGCAGCGGAGCAGGTTAAAAATAG
* *
11308083 CAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTACCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
11308148 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* ** *
11308171 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTACCTCATTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
* *
11308236 ACGGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * ** *
11308259 TAGATTTTGCCTTTTTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
* * *
11308324 GCAGCGGAACAGATTGAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * * * * *
11308347 CAGATATTGCCTTCCTGTACTGACAACGAAGTAGATCGAA-ATCACAAAGCCTTGCCTCCTTAGG
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGA-CAC-CAGCCTTGCCTCCCTAGG
* * *
11308411 TTGCAGTGGAGCAGGTTGAAAA-CG
64 TTGCAGCGGAGCAGGTTAAAAATAG
* *
11308435 CCAG-TCTTGCCTTCCTGTACTGACAGCG
1 -CAGATCTTGCCTTCCTGCACCGACAGCG
11308463 GGGCAGACTT
Statistics
Matches: 337, Mismatches: 39, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
87 1 0.00
88 298 0.88
89 38 0.11
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTT
GCAGCGGAGCAGGTTAAAAATAG
Found at i:11308623 original size:43 final size:43
Alignment explanation
Indices: 11308572--11308822 Score: 191
Period size: 43 Copynumber: 5.8 Consensus size: 43
11308562 AATTACAGAT
* * *
11308572 CTTATCTCCCTAAGCTGTAGTGGAGCAGATCGAAGTCCCCAGC
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATTGAAGTCCCCAGC
* * * * ** *
11308615 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAT-TACAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATTG-AAGTCCCCAG-C
* * *
11308659 CTTATCTCCCTAAGTAGGAGTGGAACAGATTGAAGTCCCCAGC
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATTGAAGTCCCCAGC
* * * * * * ** *
11308702 CTTATCTCACTGAGCAGCAGTAGAGTAGGTTGAAAAT-TACAGGT
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATTG-AAGTCCCCA-GC
* * * *
11308746 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCCAGA
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATTGAAGTCCCCAGC
* * *
11308789 CTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAA
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATTGAA
11308823 AATTACAGAT
Statistics
Matches: 153, Mismatches: 49, Indels: 12
0.71 0.23 0.06
Matches are distributed among these distances:
43 90 0.59
44 63 0.41
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (43 bp):
CTTATCTCCCTAAGCAGCAGTGGAGCAGATTGAAGTCCCCAGC
Found at i:11308626 original size:87 final size:87
Alignment explanation
Indices: 11308524--11308867 Score: 528
Period size: 87 Copynumber: 4.0 Consensus size: 87
11308514 ATCAAAGAGA
* * * *
11308524 CCAGCC-TATCTCCCTGAGTAGCAGTTGAGTAGGTTGGAAATTACAGATCTTATCTCCCTAAGCT
1 CCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCA
11308588 GTAGTGGAGCAGATCGAAGTCC
66 GTAGTGGAGCAGATCGAAGTCC
*
11308610 CCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGTA
1 CCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCA
* * *
11308675 GGAGTGGAACAGATTGAAGTCC
66 GTAGTGGAGCAGATCGAAGTCC
* * *
11308697 CCAGCCTTATCTCACTGAGCAGCAGTAGAGTAGGTTGAAAATTACAGGTCTTATCTCCCTAAGCA
1 CCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCA
*
11308762 GTAGTGGAGCAGATCGAAGACC
66 GTAGTGGAGCAGATCGAAGTCC
* * * * *
11308784 CCAGACTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTACCTCCCTAAACA
1 CCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCA
11308849 GTAGTGGAGCAGATCGAAG
66 GTAGTGGAGCAGATCGAAG
11308868 ATAGCAAATC
Statistics
Matches: 233, Mismatches: 24, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
86 6 0.03
87 227 0.97
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (87 bp):
CCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCA
GTAGTGGAGCAGATCGAAGTCC
Found at i:11308668 original size:44 final size:44
Alignment explanation
Indices: 11308530--11308857 Score: 252
Period size: 44 Copynumber: 7.5 Consensus size: 44
11308520 GAGACCAGCC
* * * *
11308530 TATCTCCCTGAGTAGCAGTTGAGTAGGTTGGAAATTACAGATCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCT
* * * * * * ** *
11308574 TATCTCCCTAAGCTGTAGTGGAGCAGATCG-AAGTCCCCAG-CCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAAT-TACAGATCT
*
11308617 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCT
* * ** * * ** *
11308661 TATCTCCCTAAGTAGGAGTGGAACAGATTG-AAGTCCCCAG-CCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAAT-TACAGATCT
* * * *
11308704 TATCTCACTGAGCAGCAGTAGAGTAGGTTGAAAATTACAGGTCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCT
* * * * * ***
11308748 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCCAGA-CT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCT
*
11308791 TGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCT
1 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCT
* * *
11308835 TACCTCCCTAAACAGTAGTGGAG
1 TATCTCCCTAAGCAGCAGTGGAG
11308858 CAGATCGAAG
Statistics
Matches: 208, Mismatches: 69, Indels: 14
0.71 0.24 0.05
Matches are distributed among these distances:
43 96 0.46
44 112 0.54
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (44 bp):
TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCT
Found at i:11310308 original size:43 final size:43
Alignment explanation
Indices: 11310257--11310507 Score: 191
Period size: 43 Copynumber: 5.8 Consensus size: 43
11310247 AATTACAGAT
* * *
11310257 CTTATCTCCCTAAGCAGTAGTGGAGGAGATCGAAGTCCCCAGC
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATTGAAGTCCCCAGC
* * * * ** *
11310300 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAAT-TACAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATTG-AAGTCCCCAG-C
* *
11310344 CTTATCTCCCTAAGCAGGAGTGGAACAGATTGAAGTCCCCAGC
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATTGAAGTCCCCAGC
** * * * * * ** *
11310387 CTTATCTCATTGAGCAGCAGTAGAGTAGGTTGAAAAT-TACAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATTG-AAGTCCCCAG-C
* * *
11310431 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACCCCAGA
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATTGAAGTCCCCAGC
* * * *
11310474 CTTGTCTCCCTAAGTAGCAGTGGAGTAGGTTGAA
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATTGAA
11310508 AATTACAGAT
Statistics
Matches: 155, Mismatches: 47, Indels: 12
0.72 0.22 0.06
Matches are distributed among these distances:
43 91 0.59
44 64 0.41
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (43 bp):
CTTATCTCCCTAAGCAGCAGTGGAGCAGATTGAAGTCCCCAGC
Done.