Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 40 of 187
Found at i:12447432 original size:17 final size:17
Alignment explanation
Indices: 12447410--12447461 Score: 95
Period size: 17 Copynumber: 3.1 Consensus size: 17
12447400 TTTTCTCTAT
12447410 TAATATTACATTATTAC
1 TAATATTACATTATTAC
*
12447427 TAATATTATATTATTAC
1 TAATATTACATTATTAC
12447444 TAATATTACATTATTAC
1 TAATATTACATTATTAC
12447461 T
1 T
12447462 TTGGGAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATATTACATTATTAC
Found at i:12447819 original size:19 final size:19
Alignment explanation
Indices: 12447795--12447856 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
12447785 GGAGAAGGAA
12447795 AATAGAGCGAAAATCATTC
1 AATAGAGCGAAAATCATTC
* *
12447814 AATAGAGCGAAACA-GATGC
1 AATAGAGCGAAA-ATCATTC
*
12447833 AAATAGAGCTAAAATCATTC
1 -AATAGAGCGAAAATCATTC
12447853 AATA
1 AATA
12447857 ATTCAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 20 0.57
20 15 0.43
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19
Consensus pattern (19 bp):
AATAGAGCGAAAATCATTC
Found at i:12448011 original size:13 final size:13
Alignment explanation
Indices: 12447993--12448019 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12447983 TTTATTTTAA
12447993 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
12448006 GAAGAAGAAGAAG
1 GAAGAAGAAGAAG
12448019 G
1 G
12448020 GTATTTTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGAAG
Found at i:12448358 original size:14 final size:15
Alignment explanation
Indices: 12448282--12448358 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
12448272 GATTGCCAGT
* *
12448282 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
12448296 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
12448310 AAAATATTGTACTTTTCTGT
1 -AAA-A-TG-A-TTTTCTGG
*
12448330 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
12448345 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
12448359 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 18 0.36
15 15 0.30
16 2 0.04
17 4 0.08
18 2 0.04
19 3 0.06
20 6 0.12
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:12450730 original size:27 final size:27
Alignment explanation
Indices: 12450692--12450745 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
12450682 AATTAAAGTG
12450692 ATAGAATTTCAATGTCCAGTTCATGTC
1 ATAGAATTTCAATGTCCAGTTCATGTC
12450719 ATAGAATTTCAATGTCCAGTTCATGTC
1 ATAGAATTTCAATGTCCAGTTCATGTC
12450746 GTTGTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (27 bp):
ATAGAATTTCAATGTCCAGTTCATGTC
Found at i:12452364 original size:2 final size:2
Alignment explanation
Indices: 12452357--12452393 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12452347 TTATTGAAGT
12452357 TA TA TA 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 TA TA TA T
12452394 TCTTAATTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12459049 original size:46 final size:46
Alignment explanation
Indices: 12458982--12459158 Score: 291
Period size: 46 Copynumber: 3.8 Consensus size: 46
12458972 AGTGTGGAAC
*
12458982 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTCAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* * *
12459028 GTAGGTATGGTATTTCAGTAAAGAAAATCATATTGAGTTGTGAGAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* *
12459074 GTAGGTATGATATTTCAGTAACGAAAACCATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
*
12459120 GTAGGTATAGTATTTCAGTAAAGAAAACCATACTGAGTT
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
12459159 ATAGCATTGT
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 119 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (46 bp):
GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
Found at i:12463009 original size:5 final size:5
Alignment explanation
Indices: 12462993--12463042 Score: 93
Period size: 5 Copynumber: 10.2 Consensus size: 5
12462983 TTAAAAGTTA
12462993 ATTAT A-TAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
12463042 A
1 A
12463043 AAAGAAACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.09
5 40 0.91
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:12466712 original size:23 final size:23
Alignment explanation
Indices: 12466686--12466738 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
12466676 TATGGAAGGG
*
12466686 TTCTTTCATTATGGTATTACTTT
1 TTCTTTCATTATGGTATTAATTT
*
12466709 TTCTTTCATTTTGGTATTAATTT
1 TTCTTTCATTATGGTATTAATTT
12466732 TTCTTTC
1 TTCTTTC
12466739 CTCCATCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.15, C:0.13, G:0.08, T:0.64
Consensus pattern (23 bp):
TTCTTTCATTATGGTATTAATTT
Found at i:12473535 original size:293 final size:293
Alignment explanation
Indices: 12473006--12473592 Score: 1138
Period size: 293 Copynumber: 2.0 Consensus size: 293
12472996 CCCCTCTTAT
*
12473006 TGTGTTGTTAAGGACATCCAAACACAGTAAATTTTACTGCGAGGCCAAGTTCGTGATGGTCTCTA
1 TGTGTTGTTAAGGACATCCAAACACAGGAAATTTTACTGCGAGGCCAAGTTCGTGATGGTCTCTA
*
12473071 TCAATTTTCGGCTGGTTCGTCTATTGTTTCTGATCCAAGTCCCTCTGTTCACAACACTGGGGTTA
66 TCAATTTTCGGCTGGTTCGTCTATTGTTTCTGATCCAAGTCCCTCTGTTCACAACACTGAGGTTA
12473136 CAGATTGTCGAGTGAATGATGCTAATGTATTCTCCATATGGCATAAAAGGCTTGTTCATCCTTCT
131 CAGATTGTCGAGTGAATGATGCTAATGTATTCTCCATATGGCATAAAAGGCTTGTTCATCCTTCT
*
12473201 TTTGAAATTGTTAAACTTGTACTTACCAAGTGTATAATTGTTTCAAATAAAAAATGTCTTGATAA
196 TTTGAAATTGTTAAACTTGTACTTACCAAGTGTAGAATTGTTTCAAATAAAAAATGTCTTGATAA
12473266 TGTTTGTGTTGCTTGTCAAAAAAGGAAACCACA
261 TGTTTGTGTTGCTTGTCAAAAAAGGAAACCACA
12473299 TGTGTTGTTAAGGACATCCAAACACAGGAAATTTTACTGCGAGGCCAAGTTCGTGATGGTCTCTA
1 TGTGTTGTTAAGGACATCCAAACACAGGAAATTTTACTGCGAGGCCAAGTTCGTGATGGTCTCTA
*
12473364 TCAATTTTCGGCTGGTTCGTCTGTTGTTTCTGATCCAAGTCCCTCTGTTCACAACACTGAGGTTA
66 TCAATTTTCGGCTGGTTCGTCTATTGTTTCTGATCCAAGTCCCTCTGTTCACAACACTGAGGTTA
12473429 CAGATTGTCGAGTGAATGATGCTAATGTATTCTCCATATGGCATAAAAGGCTTGTTCATCCTTCT
131 CAGATTGTCGAGTGAATGATGCTAATGTATTCTCCATATGGCATAAAAGGCTTGTTCATCCTTCT
12473494 TTTGAAATTGTTAAACTTGTACTTACCAAGTGTAGAATTGTTTCAAATAAAAAATGTCTTGATAA
196 TTTGAAATTGTTAAACTTGTACTTACCAAGTGTAGAATTGTTTCAAATAAAAAATGTCTTGATAA
12473559 TGTTTGTGTTGCTTGTCAAAAAAGGAAACCACA
261 TGTTTGTGTTGCTTGTCAAAAAAGGAAACCACA
12473592 T
1 T
12473593 AGGTTGCCCT
Statistics
Matches: 290, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
293 290 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (293 bp):
TGTGTTGTTAAGGACATCCAAACACAGGAAATTTTACTGCGAGGCCAAGTTCGTGATGGTCTCTA
TCAATTTTCGGCTGGTTCGTCTATTGTTTCTGATCCAAGTCCCTCTGTTCACAACACTGAGGTTA
CAGATTGTCGAGTGAATGATGCTAATGTATTCTCCATATGGCATAAAAGGCTTGTTCATCCTTCT
TTTGAAATTGTTAAACTTGTACTTACCAAGTGTAGAATTGTTTCAAATAAAAAATGTCTTGATAA
TGTTTGTGTTGCTTGTCAAAAAAGGAAACCACA
Found at i:12478976 original size:17 final size:18
Alignment explanation
Indices: 12478954--12478987 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12478944 TAAATGTTAC
12478954 TATTAAACTTTG-AATTT
1 TATTAAACTTTGTAATTT
*
12478971 TATTAAATTTTGTAATT
1 TATTAAACTTTGTAATT
12478988 AAATTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (18 bp):
TATTAAACTTTGTAATTT
Found at i:12478989 original size:30 final size:30
Alignment explanation
Indices: 12478955--12479011 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
12478945 AAATGTTACT
12478955 ATTAAACTTTGAA-TTTT-ATTAAATTTTGTA
1 ATTAAA-TTT-AATTTTTAATTAAATTTTGTA
12478985 ATTAAATTTAATTTTTAATTAAATTTT
1 ATTAAATTTAATTTTTAATTAAATTTT
12479012 ACCACTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 2 0.08
29 7 0.28
30 16 0.64
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (30 bp):
ATTAAATTTAATTTTTAATTAAATTTTGTA
Found at i:12479012 original size:18 final size:18
Alignment explanation
Indices: 12478976--12479010 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
12478966 AATTTTATTA
12478976 AATTTTGTAATTAAATTT
1 AATTTTGTAATTAAATTT
12478994 AATTTT-TAATTAAATTT
1 AATTTTGTAATTAAATTT
12479011 TACCACTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
AATTTTGTAATTAAATTT
Found at i:12479785 original size:6 final size:6
Alignment explanation
Indices: 12479774--12479816 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
12479764 TTAAAAAATT
12479774 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA A
12479817 ATAAAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
ATATTA
Found at i:12479824 original size:18 final size:18
Alignment explanation
Indices: 12479774--12479821 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
12479764 TTAAAAAATT
*
12479774 ATATTAATATTAATATTA
1 ATATTAATATAAATATTA
*
12479792 ATATTAATATTAATATTA
1 ATATTAATATAAATATTA
12479810 ATATTAA-ATAAA
1 ATATTAATATAAA
12479822 ATAAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 4 0.14
18 25 0.86
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATTAATATAAATATTA
Found at i:12480251 original size:71 final size:72
Alignment explanation
Indices: 12480167--12480310 Score: 245
Period size: 72 Copynumber: 2.0 Consensus size: 72
12480157 TTATTTTAGA
* * *
12480167 TACTAAAAATAAAAAAAAATT-ATAATTTAAGCATTCACGTGACGATAGATAGTTATGTTATTTT
1 TACTAAAAATAAAAAAAAATTCATAATTTAAGCACTCACGTCACGATAGATAGTTAAGTTATTTT
12480231 CGTCACT
66 CGTCACT
*
12480238 TACTAAAAATAAAAAAAAATTCATAATTTAAGCACTCACGTCACGTTAGATAGTTAAGTTATTTT
1 TACTAAAAATAAAAAAAAATTCATAATTTAAGCACTCACGTCACGATAGATAGTTAAGTTATTTT
12480303 CGTCACT
66 CGTCACT
12480310 T
1 T
12480311 CCTTCAAATT
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
71 21 0.31
72 47 0.69
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (72 bp):
TACTAAAAATAAAAAAAAATTCATAATTTAAGCACTCACGTCACGATAGATAGTTAAGTTATTTT
CGTCACT
Found at i:12486611 original size:21 final size:21
Alignment explanation
Indices: 12486587--12486626 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12486577 AAATATGGAC
*
12486587 AAATTGAGATTGTAAAAATTG
1 AAATTGAAATTGTAAAAATTG
12486608 AAATTGAAATTGTAAAAAT
1 AAATTGAAATTGTAAAAAT
12486627 AAACAGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.33
Consensus pattern (21 bp):
AAATTGAAATTGTAAAAATTG
Found at i:12491037 original size:17 final size:17
Alignment explanation
Indices: 12491011--12491052 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
12491001 TTTTCATATT
12491011 TTAAATAAAAACATAAAA
1 TTAAA-AAAAACATAAAA
*
12491029 TTAAAAAAAATATAAAA
1 TTAAAAAAAACATAAAA
12491046 TATAAAA
1 T-TAAAA
12491053 TTATGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (17 bp):
TTAAAAAAAACATAAAA
Found at i:12491050 original size:24 final size:24
Alignment explanation
Indices: 12491013--12491066 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
12491003 TTCATATTTT
12491013 AAATAAAAACATAAAATTA-AAAA
1 AAATAAAAACATAAAATTATAAAA
* *
12491036 AAATATAAAATATAAAATTATGAAA
1 AAATA-AAAACATAAAATTATAAAA
12491061 AAATAA
1 AAATAA
12491067 TAATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 5 0.19
24 14 0.52
25 8 0.30
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (24 bp):
AAATAAAAACATAAAATTATAAAA
Found at i:12491328 original size:22 final size:22
Alignment explanation
Indices: 12491301--12491348 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12491291 TTTTTATATA
*
12491301 ATATTTTGATTTTTTAAAATTT
1 ATATTTTGATATTTTAAAATTT
* *
12491323 ATATTTTTATATTTTAGAATTT
1 ATATTTTGATATTTTAAAATTT
12491345 -TATT
1 ATATT
12491349 AAAAATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (22 bp):
ATATTTTGATATTTTAAAATTT
Found at i:12491381 original size:33 final size:33
Alignment explanation
Indices: 12491290--12491381 Score: 91
Period size: 33 Copynumber: 2.8 Consensus size: 33
12491280 AAAAATGAAA
* * * *
12491290 ATTTTTATATAATATTTTGATTTTTTAAAATTT
1 ATTTTTATATAATTTTTTGAATTATTAAAAATT
*
12491323 ATATTTT-TAT-A-TTTTAGAATTTTATTAAAAATT
1 AT-TTTTATATAATTTTTTGAA--TTATTAAAAATT
12491356 ATTTTTATATAATTTTTTGAATTATT
1 ATTTTTATATAATTTTTTGAATTATT
12491382 TATATATTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
31 5 0.11
32 5 0.11
33 25 0.53
34 5 0.11
35 7 0.15
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (33 bp):
ATTTTTATATAATTTTTTGAATTATTAAAAATT
Found at i:12492275 original size:10 final size:10
Alignment explanation
Indices: 12492256--12492301 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
12492246 TTAAAAAATT
*
12492256 AAAAATTAGA
1 AAAAAATAGA
12492266 AAAAAATAGA
1 AAAAAATAGA
12492276 AAAAAAT--A
1 AAAAAATAGA
12492284 AAAAAATAGTA
1 AAAAAATAG-A
12492295 AAAAAAT
1 AAAAAAT
12492302 GTAAAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
8 8 0.25
10 16 0.50
11 8 0.25
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (10 bp):
AAAAAATAGA
Found at i:12492305 original size:10 final size:11
Alignment explanation
Indices: 12492256--12492307 Score: 53
Period size: 10 Copynumber: 5.3 Consensus size: 11
12492246 TTAAAAAATT
*
12492256 AAAAATTAG-A
1 AAAAAATAGTA
12492266 AAAAAATAG--
1 AAAAAATAGTA
12492275 AAAAAA-A-TA
1 AAAAAATAGTA
12492284 AAAAAATAGTA
1 AAAAAATAGTA
12492295 AAAAAAT-GTA
1 AAAAAATAGTA
12492305 AAA
1 AAA
12492308 TTTTATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
8 1 0.03
9 12 0.32
10 15 0.41
11 9 0.24
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAAAATAGTA
Found at i:12492307 original size:29 final size:29
Alignment explanation
Indices: 12492248--12492336 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
12492238 AATTTTAATT
* *
12492248 AAAAAATTAAAAATTAG-AAAAAAATAG-A
1 AAAAAATAAAAAAATAGTAAAAAAAT-GTA
12492276 AAAAAATAAAAAAATAGTAAAAAAATGTA
1 AAAAAATAAAAAAATAGTAAAAAAATGTA
*** * * *
12492305 AAATTTTATAAAAATCGTAAAAAAATATA
1 AAAAAATAAAAAAATAGTAAAAAAATGTA
12492334 AAA
1 AAA
12492337 TATATAGAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
28 16 0.31
29 35 0.69
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.21
Consensus pattern (29 bp):
AAAAAATAAAAAAATAGTAAAAAAATGTA
Found at i:12492308 original size:18 final size:18
Alignment explanation
Indices: 12492265--12492301 Score: 65
Period size: 18 Copynumber: 2.0 Consensus size: 18
12492255 TAAAAATTAG
12492265 AAAAAAATAGAAAAAAAT
1 AAAAAAATAGAAAAAAAT
12492283 AAAAAAATAGTAAAAAAAT
1 AAAAAAATAG-AAAAAAAT
12492302 GTAAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (18 bp):
AAAAAAATAGAAAAAAAT
Found at i:12492317 original size:19 final size:19
Alignment explanation
Indices: 12492276--12492373 Score: 58
Period size: 19 Copynumber: 5.2 Consensus size: 19
12492266 AAAAAATAGA
* *
12492276 AAAAAATAAAAAAATAGTA-
1 AAAAAATATAAAATTA-TAT
* *
12492295 AAAAAATGTAAAATTTTAT
1 AAAAAATATAAAATTATAT
* **
12492314 -AAAAATCGTAAAAAAATAT
1 AAAAAAT-ATAAAATTATAT
* *
12492333 AAAATATATAGAATTATA-
1 AAAAAATATAAAATTATAT
*
12492351 AAAAAATTATAAAATTTTAT
1 AAAAAA-TATAAAATTATAT
12492371 AAA
1 AAA
12492374 GTCATAAGAA
Statistics
Matches: 59, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
18 13 0.22
19 38 0.64
20 8 0.14
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (19 bp):
AAAAAATATAAAATTATAT
Found at i:12492380 original size:29 final size:27
Alignment explanation
Indices: 12492293--12492386 Score: 91
Period size: 29 Copynumber: 3.3 Consensus size: 27
12492283 AAAAAAATAG
* *
12492293 TAAAAAAATGTAAAATTTTATAAAAATCG
1 TAAAAAAATATAAAATTTTAT--AAATCA
* *
12492322 TAAAAAAATATAAAA-TATATAGAATTA
1 TAAAAAAATATAAAATTTTATA-AATCA
12492349 TAAAAAAATTATAAAATTTTATAAAGTCA
1 TAAAAAAA-TATAAAATTTTATAAA-TCA
*
12492378 TAAGAAAAT
1 TAAAAAAAT
12492387 TATACAAAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
26 1 0.02
27 11 0.20
28 14 0.26
29 28 0.52
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (27 bp):
TAAAAAAATATAAAATTTTATAAATCA
Found at i:12497095 original size:14 final size:15
Alignment explanation
Indices: 12497069--12497098 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12497059 ATCATTATTA
12497069 AATTATATTTAAATT
1 AATTATATTTAAATT
12497084 AATTAT-TTTAAATT
1 AATTATATTTAAATT
12497098 A
1 A
12497099 TATAAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTATATTTAAATT
Found at i:12497148 original size:90 final size:91
Alignment explanation
Indices: 12497011--12497246 Score: 429
Period size: 91 Copynumber: 2.6 Consensus size: 91
12497001 ATGATTTTAG
* * *
12497011 TAAATTCATACAAGAATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
12497076 TTTAA-ATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
12497101 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
12497166 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
*
12497192 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTA
12497247 NNNNNNNNNN
Statistics
Matches: 141, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
90 67 0.48
91 74 0.52
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATATTAATTATTTTAAATTATA
Found at i:12497227 original size:44 final size:44
Alignment explanation
Indices: 12497088--12497228 Score: 153
Period size: 44 Copynumber: 3.1 Consensus size: 44
12497078 TAAATTAATT
12497088 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGA
1 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGA
* * * * **
12497132 ATTTTATGAAATTATATATCATT-AT-TAA-ATTATATTTAATATTAATT
1 A-TTT-T-AAATTATATA-AATTCATATAAGA--AAATTTATTATCAAGA
12497179 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGA
1 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGA
12497223 ATTTTA
1 ATTTTA
12497229 TGAAATTATA
Statistics
Matches: 76, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
43 3 0.04
44 30 0.39
45 8 0.11
46 8 0.11
47 24 0.32
48 3 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (44 bp):
ATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGA
Found at i:12497840 original size:15 final size:15
Alignment explanation
Indices: 12497805--12497846 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12497795 TTAAGAATTT
*
12497805 TATTAAATTAT-ATA
1 TATTTAATTATAATA
12497819 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
12497833 TATTTAATAATAAT
1 TATTTAATTATAAT
12497847 TATGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:12498343 original size:18 final size:19
Alignment explanation
Indices: 12498289--12498344 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 19
12498279 TAATAACTTT
* *
12498289 TAAATTTTTTATATTTTTAT
1 TAAAATTTTT-TATTTTTAC
** *
12498309 TAAAATTTAATAATTTT-C
1 TAAAATTTTTTATTTTTAC
12498327 TAAAATTTTTTATTTTTA
1 TAAAATTTTTTATTTTTA
12498345 TTTTTATAAT
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
18 14 0.52
19 6 0.22
20 7 0.26
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TAAAATTTTTTATTTTTAC
Found at i:12498370 original size:22 final size:23
Alignment explanation
Indices: 12498319--12498375 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 23
12498309 TAAAATTTAA
* * *
12498319 TAATTTTCTAAAATTTTTTATTT
1 TAATTTTTTATAATTTTTTATTC
*
12498342 TTA-TTTTTATAATTTTTT-TTC
1 TAATTTTTTATAATTTTTTATTC
*
12498363 TAATTTTTAATAA
1 TAATTTTTTATAA
12498376 GAGTAGGGGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 4 0.15
22 21 0.78
23 2 0.07
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (23 bp):
TAATTTTTTATAATTTTTTATTC
Found at i:12498547 original size:86 final size:86
Alignment explanation
Indices: 12498380--12498551 Score: 197
Period size: 86 Copynumber: 2.0 Consensus size: 86
12498370 TAATAAGAGT
* * * * * *
12498380 AGGGGCTTAATTGCTTTTTTGAAAAATTTTGAGTGTCTTTTTGAAGCATTTTGAAAGTTTAAGTA
1 AGGGGCTTAATT-CTTTTTTGAAAAAGTTTGAGAGCCTTTTTGAAACATTCTGAAAATTTAAGTA
*
12498445 CCCAATTAAGTGAAAAAAAAAC
65 CCCAATTAAATGAAAAAAAAAC
12498467 AGGGGCTTAATT-TTCTTTTGAAAAAGTTTGAGAGCCTTTTT-AATACATTCT-AAAATTTAAGT
1 AGGGGCTTAATTCTT-TTTTGAAAAAGTTTGAGAGCCTTTTTGAA-ACATTCTGAAAATTTAAGT
* * *
12498529 GCTCACTTAAATGCAAAAAAAAA
64 ACCCAATTAAATG-AAAAAAAAA
12498552 AAAACCTTAA
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
85 23 0.32
86 37 0.51
87 12 0.17
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (86 bp):
AGGGGCTTAATTCTTTTTTGAAAAAGTTTGAGAGCCTTTTTGAAACATTCTGAAAATTTAAGTAC
CCAATTAAATGAAAAAAAAAC
Found at i:12501144 original size:33 final size:33
Alignment explanation
Indices: 12501102--12501184 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
12501092 AATATGCTTG
* *
12501102 ATTTCCAACAACAGATACAACAACAAACTGTTA
1 ATTTCCAACAACAAATACAACAACAAACTCTTA
* ** *
12501135 ATTTCCAACAGCAAATACAACGGCAAACTCTTT
1 ATTTCCAACAACAAATACAACAACAAACTCTTA
* *
12501168 ATTTCCAAAAAGAAATA
1 ATTTCCAACAACAAATA
12501185 AATAATTTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.47, C:0.23, G:0.07, T:0.23
Consensus pattern (33 bp):
ATTTCCAACAACAAATACAACAACAAACTCTTA
Found at i:12503820 original size:18 final size:17
Alignment explanation
Indices: 12503780--12503834 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
12503770 TTTGGTTAAA
*
12503780 AATTAACCGAATTAACC
1 AATTACCCGAATTAACC
*
12503797 ATATTACCCGAATTAATCG
1 A-ATTACCCGAATTAA-CC
* *
12503816 AATTACCTGAATTACCC
1 AATTACCCGAATTAACC
12503833 AA
1 AA
12503835 ATTGAATCAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 4 0.13
18 25 0.81
19 2 0.06
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (17 bp):
AATTACCCGAATTAACC
Found at i:12503837 original size:9 final size:9
Alignment explanation
Indices: 12503780--12503829 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
12503770 TTTGGTTAAA
12503780 AATTAACCG
1 AATTAACCG
12503789 AATTAACC-
1 AATTAACCG
*
12503797 ATATTACCCG
1 A-ATTAACCG
*
12503807 AATTAATCG
1 AATTAACCG
12503816 AATT-ACCTG
1 AATTAACC-G
12503825 AATTA
1 AATTA
12503830 CCCAAATTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
8 3 0.09
9 29 0.88
10 1 0.03
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTAACCG
Found at i:12503982 original size:18 final size:18
Alignment explanation
Indices: 12503959--12504012 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
12503949 AATTTTTATG
12503959 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
*
12503977 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGGTA
* *
12503995 CTTGGGTTTGGATTGGGT
1 ATTGGG-TTGGGTTGGGT
12504013 TTAGGTGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 22 0.71
19 9 0.29
ACGTcount: A:0.11, C:0.02, G:0.46, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Found at i:12504531 original size:114 final size:114
Alignment explanation
Indices: 12504385--12504593 Score: 328
Period size: 114 Copynumber: 1.8 Consensus size: 114
12504375 CAAAAATTTT
* * * * * *
12504385 TTAGGAATGTGTTGGGCTGAGTACCCGGGGTGGGGTGTTTGGTTGTCATCTCTCTTCGCGTCAAA
1 TTAGGAATGCGTTGGGCTGAGTAACCGAGGTGGGGTGCTTGGTTGTCATCTCTATTCGCGTAAAA
*
12504450 AGGTTGAATATATTCTAAAGAAAAGAAAAACATATATAAATATAATAAA
66 AGGTTCAATATATTCTAAAGAAAAGAAAAACATATATAAATATAATAAA
*
12504499 TTAGGAGTGCGTTGGGCTGAGTAACCGAGGTGGGGTGCTTGGTTGTCATCTCTATTCGCGTAAAA
1 TTAGGAATGCGTTGGGCTGAGTAACCGAGGTGGGGTGCTTGGTTGTCATCTCTATTCGCGTAAAA
* *
12504564 ATGTTCAATATATTCTTAAGAAAAGAAAAA
66 AGGTTCAATATATTCTAAAGAAAAGAAAAA
12504594 AAAAGAGAAG
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 85 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.31
Consensus pattern (114 bp):
TTAGGAATGCGTTGGGCTGAGTAACCGAGGTGGGGTGCTTGGTTGTCATCTCTATTCGCGTAAAA
AGGTTCAATATATTCTAAAGAAAAGAAAAACATATATAAATATAATAAA
Found at i:12505423 original size:16 final size:17
Alignment explanation
Indices: 12505402--12505435 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12505392 ACATAATTAT
*
12505402 TAGTAA-AAGGTTAATA
1 TAGTAATAAGGTAAATA
12505418 TAGTAATAAGGTAAATA
1 TAGTAATAAGGTAAATA
12505435 T
1 T
12505436 TAACTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (17 bp):
TAGTAATAAGGTAAATA
Found at i:12506360 original size:42 final size:42
Alignment explanation
Indices: 12506304--12506400 Score: 167
Period size: 42 Copynumber: 2.3 Consensus size: 42
12506294 CTATATGAAC
** *
12506304 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGGTAATG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACG
12506346 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACG
12506388 GGCACTAAGTGTG
1 GGCACTAAGTGTG
12506401 TGATACCGAG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.27
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACG
Found at i:12510901 original size:23 final size:22
Alignment explanation
Indices: 12510873--12510916 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
12510863 ATGTGACTTT
*
12510873 AGTACATACATGCATCTTAGATA
1 AGTACATACATACATC-TAGATA
*
12510896 AGTACATTCATACATCTAGAT
1 AGTACATACATACATCTAGAT
12510917 TTCTTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (22 bp):
AGTACATACATACATCTAGATA
Found at i:12517251 original size:2 final size:2
Alignment explanation
Indices: 12517244--12517281 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
12517234 NNNNNNGATT
*
12517244 TA TA TA TA TC 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 TA TA
12517282 AATGTGTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12517547 original size:41 final size:41
Alignment explanation
Indices: 12517502--12517651 Score: 246
Period size: 41 Copynumber: 3.6 Consensus size: 41
12517492 GACTATACGT
*
12517502 CTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
12517543 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
12517584 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
12517625 CTAACAGGCTAAGTGCTGGTGAATCTG
1 CTAGCAGGCTAAGTGCCGGTG-ATCTG
12517652 TTAAATTAAG
Statistics
Matches: 103, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
41 98 0.95
42 5 0.05
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:12521300 original size:44 final size:44
Alignment explanation
Indices: 12521241--12521330 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
12521231 GTTGAAACAA
* * * *
12521241 AATAAAAGTTTTGATAGTTTTACATTTAAAAATAATTATAATTT
1 AATAAAAGTTGTGATAATTATACATTTAAAAATAATTAGAATTT
* *
12521285 AATAGAAGTTGTGATAATTATACATTTAAAAATAGTTAGAATTT
1 AATAAAAGTTGTGATAATTATACATTTAAAAATAATTAGAATTT
12521329 AA
1 AA
12521331 ATTATTAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (44 bp):
AATAAAAGTTGTGATAATTATACATTTAAAAATAATTAGAATTT
Found at i:12521643 original size:27 final size:28
Alignment explanation
Indices: 12521612--12521664 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
12521602 ACCAAAAATT
12521612 TATTTTAAAAAT-AAAAAATAAAAAAAG
1 TATTTTAAAAATAAAAAAATAAAAAAAG
*
12521639 TATTTTAAAATTAAAAAAATAAAAAA
1 TATTTTAAAAATAAAAAAATAAAAAA
12521665 TATATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (28 bp):
TATTTTAAAAATAAAAAAATAAAAAAAG
Found at i:12523461 original size:26 final size:26
Alignment explanation
Indices: 12523430--12523479 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
12523420 AAACATAATT
12523430 TCAAATG-AGAGACTTTTGAGTTTTCA
1 TCAAATGAAG-GACTTTTGAGTTTTCA
*
12523456 TCAAATGAAGGATTTTTGAGTTTT
1 TCAAATGAAGGACTTTTGAGTTTT
12523480 AGGTGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (26 bp):
TCAAATGAAGGACTTTTGAGTTTTCA
Found at i:12538964 original size:18 final size:20
Alignment explanation
Indices: 12538931--12538967 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
12538921 TAGAAAAATC
12538931 TTATTATGTATAAATTATAA
1 TTATTATGTATAAATTATAA
12538951 TTATTA-GT-TAAATTATA
1 TTATTATGTATAAATTATA
12538968 GTTTCCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
TTATTATGTATAAATTATAA
Found at i:12539776 original size:18 final size:17
Alignment explanation
Indices: 12539744--12539777 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12539734 AACTTTATTT
*
12539744 AATTAAATTATTTCTTC
1 AATTAAATTACTTCTTC
12539761 AATTAATATTACTTCTT
1 AATTAA-ATTACTTCTT
12539778 GTTAATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTAAATTACTTCTTC
Found at i:12544893 original size:12 final size:11
Alignment explanation
Indices: 12544855--12544899 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
12544845 ACGTTAGCGA
*
12544855 AAAAAATAAAT
1 AAAATATAAAT
*
12544866 TAAATATAAA-
1 AAAATATAAAT
12544876 AAAATATGAAAT
1 AAAATAT-AAAT
12544888 AAAATATAAAT
1 AAAATATAAAT
12544899 A
1 A
12544900 GAATGATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 6 0.21
11 16 0.55
12 7 0.24
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (11 bp):
AAAATATAAAT
Found at i:12547390 original size:17 final size:17
Alignment explanation
Indices: 12547368--12547414 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
12547358 CACATTTTAT
12547368 ATTGTTTATATTATTGA
1 ATTGTTTATATTATTGA
12547385 ATTGTTTAGTCA-TATTGA
1 ATTGTTTA-T-ATTATTGA
*
12547403 A-TATTTATATTA
1 ATTGTTTATATTA
12547415 AAATTGAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 1 0.04
16 3 0.12
17 13 0.50
18 8 0.31
19 1 0.04
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (17 bp):
ATTGTTTATATTATTGA
Found at i:12555711 original size:11 final size:11
Alignment explanation
Indices: 12555695--12555719 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12555685 GTCAAAAAAA
12555695 ATTATTTTAAT
1 ATTATTTTAAT
12555706 ATTATTTTAAT
1 ATTATTTTAAT
12555717 ATT
1 ATT
12555720 TACAGTATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATTTTAAT
Found at i:12560347 original size:82 final size:82
Alignment explanation
Indices: 12560255--12560488 Score: 271
Period size: 82 Copynumber: 2.9 Consensus size: 82
12560245 TACATATTTG
* * * *
12560255 TTTGGAAACAAAA-CAATATCAAATAAAATCTTGTTAAACGGTGAGAATAAATCCCGAAACATAT
1 TTTGGCAACAAAATCAA-ATCAAATAAAATCTTGTTAAATGGTGGGAATAAATCCCGAAACAGAT
*
12560319 TTTATTTTATTTCTTGTT
65 TTTATTTTATTTCTTATT
* * *
12560337 TTTGGCAACAAAATCAAATCAAATAAATAT-TTATTAAGTGGTGGGAATAAATCCTGAAACAGAT
1 TTTGGCAACAAAATCAAATCAAATAAA-ATCTTGTTAAATGGTGGGAATAAATCCCGAAACAGAT
* *
12560401 TTAATTTAATTTCTTATT
65 TTTATTTTATTTCTTATT
** * * *
12560419 TTT-GCAACAAAATCAAAATGTAAT-AAATC-CGTTGAATGGTGGGAATCAATCCCGAAACAGAT
1 TTTGGCAACAAAATC-AAATCAAATAAAATCTTGTTAAATGGTGGGAATAAATCCCGAAACAGAT
12560481 TTTATTTT
65 TTTATTTT
12560489 TTTGTTTTTT
Statistics
Matches: 128, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
80 35 0.27
81 13 0.10
82 75 0.59
83 5 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (82 bp):
TTTGGCAACAAAATCAAATCAAATAAAATCTTGTTAAATGGTGGGAATAAATCCCGAAACAGATT
TTATTTTATTTCTTATT
Found at i:12560548 original size:78 final size:77
Alignment explanation
Indices: 12560443--12560643 Score: 233
Period size: 78 Copynumber: 2.6 Consensus size: 77
12560433 AAAATGTAAT
* * * *
12560443 AAATCCGTTGAATGGTGGGAATCAATCCCGAAACAGATTTTATTTT-TTTGTTTTTTTAAATAAA
1 AAAT-CGTTGAATGGTGGGAATCAATCCCGAAACAGATTTTATTTTACTCG-TTTTTGAAAAAAA
* *
12560507 ACATATTTTGGAATG
64 ACA-AATTTGGAATA
* * *
12560522 AAATCGTTGAATGGCGGGAATAAATCCCGAAACAAATTTTATTTTACTCGTTTTTGAAAAAAAAC
1 AAATCGTTGAATGGTGGGAATCAATCCCGAAACAGATTTTATTTTACTCGTTTTTGAAAAAAAAC
*
12560587 AAATTTGTAATA
66 AAATTTGGAATA
* * * * *
12560599 AAATCATTAAACGATGGGAATCAATCCAGAAACAGATTTTATTTT
1 AAATCGTTGAATGGTGGGAATCAATCCCGAAACAGATTTTATTTT
12560644 CCTTTAATTT
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
77 45 0.44
78 52 0.50
79 6 0.06
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (77 bp):
AAATCGTTGAATGGTGGGAATCAATCCCGAAACAGATTTTATTTTACTCGTTTTTGAAAAAAAAC
AAATTTGGAATA
Found at i:12560632 original size:77 final size:78
Alignment explanation
Indices: 12560458--12560644 Score: 216
Period size: 77 Copynumber: 2.4 Consensus size: 78
12560448 CGTTGAATGG
* * * * * *
12560458 TGGGAATCAATCCCGAAACAGATTTTATTTTTTTGTTTTTTTAAATAAAACATATTTTGGAATGA
1 TGGGAATCAATCCCGAAACAGATTTTATTTTCTCGTTTTTTGAAAAAAAACATAATTTGGAATAA
* * * *
12560523 AATCGTTGAATGG
66 AATCATTAAACGA
* * * *
12560536 CGGGAATAAATCCCGAAACAAATTTTATTTTACTCG-TTTTTGAAAAAAAACA-AATTTGTAATA
1 TGGGAATCAATCCCGAAACAGATTTTATTTT-CTCGTTTTTTGAAAAAAAACATAATTTGGAATA
12560599 AAATCATTAAACGA
65 AAATCATTAAACGA
*
12560613 TGGGAATCAATCCAGAAACAGATTTTATTTTC
1 TGGGAATCAATCCCGAAACAGATTTTATTTTC
12560645 CTTTAATTTC
Statistics
Matches: 90, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
76 1 0.01
77 45 0.50
78 42 0.47
79 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (78 bp):
TGGGAATCAATCCCGAAACAGATTTTATTTTCTCGTTTTTTGAAAAAAAACATAATTTGGAATAA
AATCATTAAACGA
Found at i:12565979 original size:22 final size:22
Alignment explanation
Indices: 12565954--12565999 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
12565944 TTTCTTCTTC
* *
12565954 TTCTTTTTCCTTTTATTTAATT
1 TTCTTTCTCATTTTATTTAATT
* *
12565976 TTCTTTCTCATTTTCTTTATTT
1 TTCTTTCTCATTTTATTTAATT
12565998 TT
1 TT
12566000 TATTCTTCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (22 bp):
TTCTTTCTCATTTTATTTAATT
Found at i:12572349 original size:7 final size:7
Alignment explanation
Indices: 12572339--12572365 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
12572329 AAAAAAGGAA
12572339 AAAGAAC
1 AAAGAAC
12572346 AAAGAAC
1 AAAGAAC
12572353 AAAGAAC
1 AAAGAAC
12572360 AAAGAA
1 AAAGAA
12572366 GATAACGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.11, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAGAAC
Found at i:12573021 original size:17 final size:18
Alignment explanation
Indices: 12572999--12573032 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
12572989 CGACCGCAAC
12572999 AAACGCGA-CGCGACCGA
1 AAACGCGACCGCGACCGA
12573016 AAACGCGACCGCGACCG
1 AAACGCGACCGCGACCG
12573033 TAATTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.32, C:0.38, G:0.29, T:0.00
Consensus pattern (18 bp):
AAACGCGACCGCGACCGA
Found at i:12573606 original size:15 final size:15
Alignment explanation
Indices: 12573574--12573622 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
12573564 TACTTTAATC
12573574 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
12573589 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
* *
12573604 ATGGTAATGTATATAT
1 ATGGTTA-GTATTTAT
12573620 ATG
1 ATG
12573623 TGCATGGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 9 0.30
15 11 0.37
16 10 0.33
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:12573914 original size:47 final size:47
Alignment explanation
Indices: 12573863--12574297 Score: 634
Period size: 47 Copynumber: 9.4 Consensus size: 47
12573853 TAAATGAATA
12573863 TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATG
1 TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATG
*
12573910 TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAAATATATATG
1 TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATG
* *
12573957 TATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAATTATATATG
1 TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATG
* * *
12574004 TATATGCTGTCAATTTTTGATGTA-TAAGGCAGTCCAATTATATATG
1 TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATG
** *
12574050 TATATGCTGTC-AATTTT--TG-ACGTAT-AAGTCCAATTATATATG
1 TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATG
*
12574092 TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAAATATATATG
1 TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATG
*
12574139 TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAAATATATATG
1 TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATG
* *
12574186 TATATGCTGTCAATTTTTGATGTATAAATGCAGTCCAATTATATATG
1 TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATG
** * * * *
12574233 TATATGCTGTCATTTTTTTATGTATAAATGCAGTCCAATT-T-TGTA
1 TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATG
12574278 TATATGCTGTCCAAATTTTG
1 TATATGCTGT-CAAATTTTG
12574298 GTGTGAAAAT
Statistics
Matches: 356, Mismatches: 25, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
42 28 0.08
43 9 0.03
45 19 0.05
46 42 0.12
47 258 0.72
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (47 bp):
TATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAATTATATATG
Found at i:12574091 original size:182 final size:183
Alignment explanation
Indices: 12573894--12574259 Score: 662
Period size: 182 Copynumber: 2.0 Consensus size: 183
12573884 GTACAAATGC
12573894 AGTCCAATTATATATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAAATATATATGTA
1 AGTCCAATTATATATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAAATATATATGTA
* * *
12573959 TATGCTGTCAATTTTTGATGTATAAATGCAGTCCAATTATATATGTATATGCTGTCAATTTTTGA
66 TATGCTGTCAAATTTTGATGTACAAATGCAGTCCAAATATATATGTATATGCTGTCAATTTTTGA
12574024 TGTAT-AAGGCAGTCCAATTATATATGTATATGCTGTCAATTTTTGACGTATA
131 TGTATAAAGGCAGTCCAATTATATATGTATATGCTGTCAATTTTTGACGTATA
12574076 AGTCCAATTATATATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAAATATATATGTA
1 AGTCCAATTATATATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAAATATATATGTA
12574141 TATGCTGTCAAATTTTGATGTACAAATGCAGTCCAAATATATATGTATATGCTGTCAATTTTTGA
66 TATGCTGTCAAATTTTGATGTACAAATGCAGTCCAAATATATATGTATATGCTGTCAATTTTTGA
* * * *
12574206 TGTATAAATGCAGTCCAATTATATATGTATATGCTGTCATTTTTTTATGTATA
131 TGTATAAAGGCAGTCCAATTATATATGTATATGCTGTCAATTTTTGACGTATA
12574259 A
1 A
12574260 ATGCAGTCCA
Statistics
Matches: 176, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
182 132 0.75
183 44 0.25
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (183 bp):
AGTCCAATTATATATGTATATGCTGTCAAATTTTGATGTACAAATGCAGTCCAAATATATATGTA
TATGCTGTCAAATTTTGATGTACAAATGCAGTCCAAATATATATGTATATGCTGTCAATTTTTGA
TGTATAAAGGCAGTCCAATTATATATGTATATGCTGTCAATTTTTGACGTATA
Found at i:12574094 original size:20 final size:20
Alignment explanation
Indices: 12574034--12574095 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
12574024 TGTATAAGGC
12574034 AGTCCAATTATATATGTATA
1 AGTCCAATTATATATGTATA
* * * *
12574054 TGCTGTCAATT-TTTGACGTATA
1 AG-T-CCAATTATAT-ATGTATA
12574076 AGTCCAATTATATATGTATA
1 AGTCCAATTATATATGTATA
12574096 TGCTGTCAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
20 12 0.40
21 6 0.20
22 12 0.40
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (20 bp):
AGTCCAATTATATATGTATA
Found at i:12574279 original size:21 final size:22
Alignment explanation
Indices: 12574253--12574297 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
12574243 CATTTTTTTA
12574253 TGTATAAATGCAGTCC-AATTT
1 TGTATAAATGCAGTCCAAATTT
* *
12574274 TGTATATATGCTGTCCAAATTT
1 TGTATAAATGCAGTCCAAATTT
12574296 TG
1 TG
12574298 GTGTGAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (22 bp):
TGTATAAATGCAGTCCAAATTT
Found at i:12574622 original size:2 final size:2
Alignment explanation
Indices: 12574615--12574665 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
12574605 GTTATGTGTT
*
12574615 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12574657 TA TA TA TA T
1 TA TA TA TA T
12574666 GTGGAATGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12582157 original size:42 final size:41
Alignment explanation
Indices: 12582126--12582256 Score: 190
Period size: 42 Copynumber: 3.1 Consensus size: 41
12582116 ACTCATATAA
12582126 GTTTTCGTTCAGCTCTTTTGAGCTTCCGTTTAACCCTTATG
1 GTTTTCGTTCAGCTCTTTTGAGCTTCCGTTTAACCCTTATG
* * *
12582167 GGTTTCTGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTTTTG
1 GTTTTC-GTTCAGCTCTTTTGAGCTTCCGTTTAACCC-TTATG
* *
12582210 GTTTTCGTTCAGCTCTTATGAGCTTCCGTTCAACCCTTATG
1 GTTTTCGTTCAGCTCTTTTGAGCTTCCGTTTAACCCTTATG
*
12582251 GGTTTC
1 GTTTTC
12582257 TATTTAACGC
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
41 14 0.18
42 56 0.71
43 9 0.11
ACGTcount: A:0.11, C:0.24, G:0.18, T:0.47
Consensus pattern (41 bp):
GTTTTCGTTCAGCTCTTTTGAGCTTCCGTTTAACCCTTATG
Found at i:12582196 original size:21 final size:21
Alignment explanation
Indices: 12582132--12582241 Score: 71
Period size: 21 Copynumber: 5.2 Consensus size: 21
12582122 ATAAGTTTTC
*
12582132 GTTCAGCTCTTTTGAGCTTCC
1 GTTCAGCTCTTTTGAGCTTCT
* * * * * *
12582153 GTTTAACCCTTATGGGTTTCT
1 GTTCAGCTCTTTTGAGCTTCT
12582174 GTTCAGCTCTTTTGAGCTTCT
1 GTTCAGCTCTTTTGAGCTTCT
* * * *
12582195 GTTTAACCCTTTTTG-G-TTTT
1 GTTCAGCTC-TTTTGAGCTTCT
* *
12582215 CGTTCAGCTCTTATGAGCTTCC
1 -GTTCAGCTCTTTTGAGCTTCT
12582237 GTTCA
1 GTTCA
12582242 ACCCTTATGG
Statistics
Matches: 62, Mismatches: 23, Indels: 8
0.67 0.25 0.09
Matches are distributed among these distances:
20 7 0.11
21 48 0.77
22 7 0.11
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (21 bp):
GTTCAGCTCTTTTGAGCTTCT
Found at i:12582248 original size:21 final size:21
Alignment explanation
Indices: 12582144--12582250 Score: 72
Period size: 21 Copynumber: 5.1 Consensus size: 21
12582134 TCAGCTCTTT
*
12582144 TGAGCTTCCGTTTAACCCTTA
1 TGAGCTTCCGTTCAACCCTTA
* * * * * *
12582165 TGGGTTTCTGTTCAGCTCTTT
1 TGAGCTTCCGTTCAACCCTTA
* * *
12582186 TGAGCTTCTGTTTAACCCTTTT
1 TGAGCTTCCGTTCAACCC-TTA
* * * *
12582208 TG-GTTTTCGTTCAGCTCTTA
1 TGAGCTTCCGTTCAACCCTTA
12582228 TGAGCTTCCGTTCAACCCTTA
1 TGAGCTTCCGTTCAACCCTTA
12582249 TG
1 TG
12582251 GGTTTCTATT
Statistics
Matches: 61, Mismatches: 23, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
20 4 0.07
21 52 0.85
22 5 0.08
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (21 bp):
TGAGCTTCCGTTCAACCCTTA
Found at i:12589339 original size:42 final size:41
Alignment explanation
Indices: 12589292--12589391 Score: 98
Period size: 42 Copynumber: 2.4 Consensus size: 41
12589282 TAGCTCTCAC
*
12589292 GAGCTTCTGTTTAACTCATATA-AGTTT-TCGTTTAGCTATTTT
1 GAGCTTCTGTTTAAC-CAT-TACAGTTTCT-GTTCAGCTATTTT
*
12589334 GAGCTT-TCGTTTAACCATTACGAGTTTCTGTTCAGCTCTTTT
1 GAGCTTCT-GTTTAACCATTAC-AGTTTCTGTTCAGCTATTTT
* *
12589376 AAGCTTCTCTTTAACC
1 GAGCTTCTGTTTAACC
12589392 CTTTTTGGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
40 2 0.04
41 4 0.08
42 41 0.84
43 2 0.04
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (41 bp):
GAGCTTCTGTTTAACCATTACAGTTTCTGTTCAGCTATTTT
Found at i:12589444 original size:42 final size:42
Alignment explanation
Indices: 12589310--12589475 Score: 111
Period size: 42 Copynumber: 4.0 Consensus size: 42
12589300 GTTTAACTCA
* * * * * * *
12589310 TATAAGTTTTCGTTTAGCTATTTTGAGCTTTCGTTTAACCAT
1 TATAGGTTTTCGTTCAGCTCTTATGAGCTTCCCTTCAACCAT
* * * * * *
12589352 TA-CGAG-TTTCTGTTCAGCTCTTTTAAGCTTCTCTTTAACCCT
1 TATAG-GTTTTC-GTTCAGCTCTTATGAGCTTCCCTTCAACCAT
* *
12589394 TTTTGGTTTTCGTTCAGCTCTTATGAGCTTCCCTTCAACCAT
1 TATAGGTTTTCGTTCAGCTCTTATGAGCTTCCCTTCAACCAT
* * * * * *
12589436 TATAGGTTTTTGTTTAGCACTTATGTGCTTTCGTTCAACC
1 TATAGGTTTTCGTTCAGCTCTTATGAGCTTCCCTTCAACC
12589476 TTCGGGCTTT
Statistics
Matches: 96, Mismatches: 24, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
41 4 0.04
42 87 0.91
43 5 0.05
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.47
Consensus pattern (42 bp):
TATAGGTTTTCGTTCAGCTCTTATGAGCTTCCCTTCAACCAT
Found at i:12591728 original size:27 final size:27
Alignment explanation
Indices: 12591671--12591733 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
12591661 CCATCTCGAT
* * *
12591671 GGACCATCTTGTGTTTAGTGTCCCGTT
1 GGACTATCTCGTGTTTAGTGTCCCGTC
* *
12591698 GGACTATCTCGTGTTTATTGTCCTGTC
1 GGACTATCTCGTGTTTAGTGTCCCGTC
12591725 GGACTATCT
1 GGACTATCT
12591734 ATGATGTCGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.13, C:0.22, G:0.24, T:0.41
Consensus pattern (27 bp):
GGACTATCTCGTGTTTAGTGTCCCGTC
Found at i:12591900 original size:45 final size:45
Alignment explanation
Indices: 12591831--12591917 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
12591821 GTCTTTCAGC
* * *
12591831 TATCATGATGCCATAGCGTATTTCAGTTATGGCCTTACTCATCGT
1 TATCATGATGCCATAACATATTTCAATTATGGCCTTACTCATCGT
* * **
12591876 TATCATGATGTCATAACATCTTTCAATTATGGTTTTACTCAT
1 TATCATGATGCCATAACATATTTCAATTATGGCCTTACTCAT
12591918 TTTAGGCATA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (45 bp):
TATCATGATGCCATAACATATTTCAATTATGGCCTTACTCATCGT
Found at i:12601261 original size:21 final size:21
Alignment explanation
Indices: 12601222--12601263 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12601212 TTTTCTTAGG
*
12601222 ATGTGAATTGGATGGAATTGA
1 ATGTGAATTGGATGAAATTGA
* *
12601243 ATGTGAATTGTATTAAATTGA
1 ATGTGAATTGGATGAAATTGA
12601264 GTTAAATTCA
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:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (21 bp):
ATGTGAATTGGATGAAATTGA
Found at i:12601777 original size:25 final size:24
Alignment explanation
Indices: 12601741--12601793 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
12601731 ACATACCGCA
12601741 GCTCTTCATGAGCGTCCAGATATAG
1 GCTCTTCATGAGCGTCCAGATAT-G
* * *
12601766 GCTCTTCGTGAGCTTCCTGATATG
1 GCTCTTCATGAGCGTCCAGATATG
12601790 GCTC
1 GCTC
12601794 ACTTGAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (24 bp):
GCTCTTCATGAGCGTCCAGATATG
Found at i:12602433 original size:15 final size:15
Alignment explanation
Indices: 12602408--12602442 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12602398 GACTCTATTT
*
12602408 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
12602422 TAATTAATATTAAGA
1 TAATTAATATTAAGA
12602437 TAATTA
1 TAATTA
12602443 TTAATGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:12608549 original size:4 final size:4
Alignment explanation
Indices: 12608540--12608604 Score: 62
Period size: 4 Copynumber: 15.5 Consensus size: 4
12608530 CAACCCAATT
*
12608540 TTTA TTTA TTTA TTTA TTTA TTTTC TTTA CTTTA TTTA -TTA CTTTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA TTTA TTTA -TTTA -TTTA
12608591 TTT- TATTA TTTA TT
1 TTTA T-TTA TTTA TT
12608605 ACTTATTTGG
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
3 4 0.08
4 33 0.63
5 15 0.29
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:12610253 original size:15 final size:15
Alignment explanation
Indices: 12610228--12610262 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12610218 GACTCTATTT
*
12610228 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
12610242 TAATTAATATTAAGA
1 TAATTAATATTAAGA
12610257 TAATTA
1 TAATTA
12610263 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:12611308 original size:23 final size:22
Alignment explanation
Indices: 12611276--12611337 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
12611266 CCCGGCCCGT
* *
12611276 TTTTTAATTAAAATTATAATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
12611300 TTTTTATTAAAATTAAAACTAA
1 TTTTTATTAAAATTAAAACTAA
*
12611322 TTGTTATTAAAATTAA
1 TTTTTATTAAAATTAA
12611338 TTGTTATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 16 0.46
23 14 0.40
24 5 0.14
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:12611332 original size:16 final size:16
Alignment explanation
Indices: 12611311--12611368 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
12611301 TTTTATTAAA
*
12611311 ATTAAAACTAATTGTT
1 ATTAAAATTAATTGTT
12611327 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
*
12611343 ATCAAAATTAATTGTT
1 ATTAAAATTAATTGTT
12611359 ATTAAAATTA
1 ATTAAAATTA
12611369 TATCAATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:12611518 original size:93 final size:93
Alignment explanation
Indices: 12611412--12611595 Score: 341
Period size: 93 Copynumber: 2.0 Consensus size: 93
12611402 TTTATAAAAT
*
12611412 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTTTTAATTGTTAATAAAATTATCAAATT
1 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAATAAAATTATCAAATT
12611477 ATATCAAATTATTAATTATTAATTGTTA
66 ATATCAAATTATTAATTATTAATTGTTA
*
12611505 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
1 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAATAAAATTATCAAATT
*
12611570 ATATCAAATTATTAATTGTTAATTGT
66 ATATCAAATTATTAATTATTAATTGT
12611596 ATTAATTGTT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (93 bp):
CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAATAAAATTATCAAATT
ATATCAAATTATTAATTATTAATTGTTA
Found at i:12611652 original size:10 final size:10
Alignment explanation
Indices: 12611637--12611662 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
12611627 TTAGTAAAAT
12611637 TATCAAATTA
1 TATCAAATTA
12611647 TATCAAATTA
1 TATCAAATTA
12611657 TATCAA
1 TATCAA
12611663 GTTTACCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (10 bp):
TATCAAATTA
Found at i:12614042 original size:43 final size:43
Alignment explanation
Indices: 12613941--12614249 Score: 253
Period size: 43 Copynumber: 7.1 Consensus size: 43
12613931 TATAAATAAG
* * * * *
12613941 CGCCGCTAAAGGTTAGGATCTTTAGCGGCG-CTTTTCCAAAAA
1 CGCCGCTAAAGATCATGACCTTTAGCGGCGCCTTTTCCACAAA
* * *
12613983 CGCCACTAAAGGTCATGACCTTTAGCGGCGCCTTTCCCACAAA
1 CGCCGCTAAAGATCATGACCTTTAGCGGCGCCTTTTCCACAAA
* * *
12614026 CGCCGCTAAAGATCATGATCTTCAGCGGCGTTGCGCCTTTCCCACAAA
1 CGCCGCTAAAGATCATGACCTTTA---GCG--GCGCCTTTTCCACAAA
* * * * * * *
12614074 CGCCACTGAAGATCAAGACCTTTAGCAGCGCC-TATCAAAAAAA
1 CGCCGCTAAAGATCATGACCTTTAGCGGCGCCTTTTC-CACAAA
* * ** *
12614117 CGTCGCTATAGATCATGAATTTTAGCGGCGCTTTTTCCACAAA
1 CGCCGCTAAAGATCATGACCTTTAGCGGCGCCTTTTCCACAAA
* * * **
12614160 CGCCGCTATAGATCTTGACCTTTAGCGGCGCTTTTTGAACAAA
1 CGCCGCTAAAGATCATGACCTTTAGCGGCGCCTTTTCCACAAA
* * * * *
12614203 CGCCGCTACAGATCATGACTTTTAGTGGCGCTTTTTTCACAAA
1 CGCCGCTAAAGATCATGACCTTTAGCGGCGCCTTTTCCACAAA
12614246 CGCC
1 CGCC
12614250 TCTGAAACAT
Statistics
Matches: 215, Mismatches: 44, Indels: 15
0.78 0.16 0.05
Matches are distributed among these distances:
42 28 0.13
43 144 0.67
44 3 0.01
45 2 0.01
46 3 0.01
48 35 0.16
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (43 bp):
CGCCGCTAAAGATCATGACCTTTAGCGGCGCCTTTTCCACAAA
Found at i:12614204 original size:86 final size:85
Alignment explanation
Indices: 12613961--12614249 Score: 287
Period size: 86 Copynumber: 3.3 Consensus size: 85
12613951 GGTTAGGATC
* * **
12613961 TTTAGCGGCGC-TTTTCCAAAAACGCCACTAAAGGTCATGACCTTTAGCGGCGCCTTTCCCACAA
1 TTTAGCGGCGCTTTTTCCACAAACGCCACT-AAGATCATGACCTTTAGCGGCGCCTTTCAAACAA
12614025 ACGCCGCTAAAGATCATG-AT
65 ACGCCGCTAAAGATCATGAAT
* * * *
12614045 CTTCAGCGGCG-TTGCGCCTTTCCCACAAACGCCACTGAAGATCAAGACCTTTAGCAGCGCCTAT
1 -TTTAGCGGCGCTT-----TTT-CCACAAACGCCACT-AAGATCATGACCTTTAGCGGCGCCTTT
* * *
12614109 CAAAAAAACGTCGCTATAGATCATGAAT
58 CAAACAAACGCCGCTAAAGATCATGAAT
* * * **
12614137 TTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGATCTTGACCTTTAGCGGCGCTTTTTGAACAA
1 TTTAGCGGCGCTTTTTCCACAAACGCCACTA-AGATCATGACCTTTAGCGGCGCCTTTCAAACAA
* *
12614202 ACGCCGCTACAGATCATGACT
65 ACGCCGCTAAAGATCATGAAT
* *
12614223 TTTAGTGGCGCTTTTTTCACAAACGCC
1 TTTAGCGGCGCTTTTTCCACAAACGCC
12614250 TCTGAAACAT
Statistics
Matches: 167, Mismatches: 27, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
85 11 0.07
86 81 0.49
87 3 0.02
90 3 0.02
91 65 0.39
92 4 0.02
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (85 bp):
TTTAGCGGCGCTTTTTCCACAAACGCCACTAAGATCATGACCTTTAGCGGCGCCTTTCAAACAAA
CGCCGCTAAAGATCATGAAT
Found at i:12622402 original size:31 final size:31
Alignment explanation
Indices: 12622335--12622403 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
12622325 ATTTAACTAA
* *
12622335 TAGTGACCAAAATAGAAATGATTTAAAACAT
1 TAGTGATCAAAATAGAAATGATCTAAAACAT
* **
12622366 GAGTGATCAAAATAGAAATGATCTAAAATGT
1 TAGTGATCAAAATAGAAATGATCTAAAACAT
12622397 TAGTGAT
1 TAGTGAT
12622404 TAAATTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (31 bp):
TAGTGATCAAAATAGAAATGATCTAAAACAT
Found at i:12629348 original size:32 final size:32
Alignment explanation
Indices: 12629307--12629376 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
12629297 GGGTTGTTTG
* * *
12629307 TTTGTTATTTATTGTTTGAATGTGTTGGGTTA
1 TTTGTTATTTATTCTTTGAATGTGCTGAGTTA
* *
12629339 TTTGTTATTTGTTCTTTGATTGTGCTGAGTTA
1 TTTGTTATTTATTCTTTGAATGTGCTGAGTTA
12629371 TTTGTT
1 TTTGTT
12629377 TTTTTTAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.13, C:0.03, G:0.23, T:0.61
Consensus pattern (32 bp):
TTTGTTATTTATTCTTTGAATGTGCTGAGTTA
Found at i:12631392 original size:61 final size:60
Alignment explanation
Indices: 12631297--12631424 Score: 177
Period size: 61 Copynumber: 2.1 Consensus size: 60
12631287 CACGACATCT
* * *
12631297 ATGGATGTCAAGTTTATTGTCTACTACATGTTGAAATGACAACTCAATGAACTT-GACACCC
1 ATGGATGTCAAGTTCATTGTCTACTACATATTGAAATGA-AACTCAATGAA-TTCGACACAC
** *
12631358 ATGGATGTTGAGTTCATTGTCTACTACATATTGAAATGAAACTCAATGAATTCGACATAC
1 ATGGATGTCAAGTTCATTGTCTACTACATATTGAAATGAAACTCAATGAATTCGACACAC
12631418 ATGGATG
1 ATGGATG
12631425 CTAAATTCAC
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
59 2 0.03
60 23 0.38
61 35 0.58
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (60 bp):
ATGGATGTCAAGTTCATTGTCTACTACATATTGAAATGAAACTCAATGAATTCGACACAC
Found at i:12632125 original size:3 final size:3
Alignment explanation
Indices: 12632117--12632199 Score: 157
Period size: 3 Copynumber: 27.7 Consensus size: 3
12632107 TCAACCATTG
*
12632117 TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12632165 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
12632200 GTGTTAGAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:12634837 original size:42 final size:42
Alignment explanation
Indices: 12634691--12634985 Score: 341
Period size: 42 Copynumber: 7.0 Consensus size: 42
12634681 CGCTTATAGA
* *
12634691 AAAAAACGCCGCTAAAGCTCATGTTCTTTAGCGGCGC-TACCGA
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA--GG
* *
12634734 AAAAAACGCCGTTAAAGATCATGTTCTTTAGCGGCACTTAGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
*
12634776 AAAAAAACGCCGCTAAAGATCAT-TATCTGTAGCGGCGCTTAGG
1 -AAAAAACGCCGCTAAAGATCATGT-TCTTTAGCGGCGCTTAGG
* * *
12634819 GAAAAACGCCGTTAAAGATCATGTTCTTTAGCGGCGCTTAAG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
*
12634861 AAAAAACGCCTCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
* * *
12634903 AAGAAAACGCCGCTAAA-AGTAATGTTCTATAGCAGCGCTT-GG
1 AA-AAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTAGG
* *
12634945 TAAAAAGCGCCGCTAAA-AGT-AGTGTTCTTTCGCGGCGCTTA
1 -AAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
12634986 TTTCACAAAC
Statistics
Matches: 220, Mismatches: 23, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
41 1 0.00
42 112 0.51
43 105 0.48
44 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
Found at i:12634844 original size:85 final size:85
Alignment explanation
Indices: 12634689--12634985 Score: 356
Period size: 85 Copynumber: 3.5 Consensus size: 85
12634679 GTCGCTTATA
* *
12634689 GAAAAAAACGCCGCTAAAGCTCATGTTCTTTAGCGGCGC-TACCGAAAAAAACGCCGTTAAAGAT
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA--GGAAAAAACGCCGTTAAAGAT
*
12634753 CATGTTCTTTAGCGGCACTTAG
64 CATGTTCTTTAGCGGCGCTTAG
* *
12634775 GAAAAAAACGCCGCTAAAGATCAT-TATCTGTAGCGGCGCTTAGGGAAAAACGCCGTTAAAGATC
1 GAAAAAAACGCCGCTAAAGATCATGT-TCTTTAGCGGCGCTTAGGAAAAAACGCCGTTAAAGATC
*
12634839 ATGTTCTTTAGCGGCGCTTAA
65 ATGTTCTTTAGCGGCGCTTAG
* *
12634860 G-AAAAAACGCCTCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAGAAAACGCCGCTAAA-AGT
1 GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAA-AAAACGCCGTTAAAGA-T
* * *
12634923 AATGTTCTATAGCAGCGCTT-G
64 CATGTTCTTTAGCGGCGCTTAG
* * *
12634944 GTAAAAAGCGCCGCTAAA-AGT-AGTGTTCTTTCGCGGCGCTTA
1 GAAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
12634986 TTTCACAAAC
Statistics
Matches: 186, Mismatches: 17, Indels: 17
0.85 0.08 0.08
Matches are distributed among these distances:
84 43 0.23
85 106 0.57
86 35 0.19
87 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (85 bp):
GAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGTTAAAGATCA
TGTTCTTTAGCGGCGCTTAG
Found at i:12635458 original size:21 final size:21
Alignment explanation
Indices: 12635434--12635498 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
12635424 CTTCTCTCGA
* *
12635434 TGCTTCTCTTGCTGCGGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
12635455 TGCTTCTCTCGCTGCAGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
* *
12635476 TGCTTCCCTCGCTGCCGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
12635497 TG
1 TG
12635499 TTTTAAGTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.02, C:0.43, G:0.22, T:0.34
Consensus pattern (21 bp):
TGCTTCTCTCGCTGCAGCCTC
Found at i:12637008 original size:15 final size:15
Alignment explanation
Indices: 12636975--12637014 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
12636965 CCTAAACCCC
*
12636975 AAACCCCAAA-TCTT
1 AAACCCCAAACTCAT
12636989 AAACCCCAAACTCAT
1 AAACCCCAAACTCAT
*
12637004 AAACCCTAAAC
1 AAACCCCAAAC
12637015 CCAAAACACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.15
Consensus pattern (15 bp):
AAACCCCAAACTCAT
Found at i:12637030 original size:22 final size:21
Alignment explanation
Indices: 12636965--12637031 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
12636955 ACTAAAGTAG
*
12636965 CCTAAACCCCAAACCCCA-AAT
1 CCTAAACCCCAAA-CCCATAAC
* *
12636986 CTTAAACCCCAAACTCATAAAC
1 CCTAAACCCCAAACCCAT-AAC
*
12637008 CCTAAACCCAAAACACCATAAC
1 CCTAAACCCCAAAC-CCATAAC
12637030 CC
1 CC
12637032 ATATCATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
20 3 0.08
21 12 0.32
22 19 0.51
23 3 0.08
ACGTcount: A:0.45, C:0.43, G:0.00, T:0.12
Consensus pattern (21 bp):
CCTAAACCCCAAACCCATAAC
Found at i:12637740 original size:207 final size:205
Alignment explanation
Indices: 12637365--12637868 Score: 564
Period size: 207 Copynumber: 2.4 Consensus size: 205
12637355 TTGTTAACCG
* ** *
12637365 CCGCTAATAATATGCTTTAGCGGCGATTTATCGTGAACGCCACTAATTCCAGTATACATCAAGAT
1 CCGCTAATAATATGCTTTAGCGGCG-TTTTTCGT-AACGCCACTAATTATAGTATACATCAAGAC
** * * * * * *
12637430 TTAAACGCGGCGTTTCGGTTAATATATTTTGCGGCGCATTAGTATACTTTAGCGGCGTTTTCCAA
64 CAAAACGCTGCGTTTTGGTTAAGAAATTTAGCGGCGCATTAG---ACTTTAGCGGCGTTTTACAA
* * ** *
12637495 TCAGCGCCACTAATTCTAATATACCTCAAGACCAAACTCTGTGTTTTGGTGTGCATATATTGCGG
126 TAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTACGTTTTGGTCTGCATATATTGCGG
* *
12637560 CGCTTAACT-CAAAGCA
191 CGATT--CTAAAAAGCA
* **
12637576 CCGCTAATACTATTATTTAGCGGCGTTTTCTCGTAAGCGCCACTAATTATAGTATACATCAAGAC
1 CCGCTAATAATATGCTTTAGCGGCGTTTT-TCGTAA-CGCCACTAATTATAGTATACATCAAGAC
* * *
12637641 CAAAACGTTGAGTTTTGGTTAAGAAATTTAGCGGCGC-TTACG-CTTTAGCGGCGTTTTACAGTA
64 CAAAACGCTGCGTTTTGGTTAAGAAATTTAGCGGCGCATTA-GACTTTAGCGGCGTTTTACAATA
*
12637704 AGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTACGTTTTGGTCTGCATATCTTGCGGCG
128 AGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTACGTTTTGGTCTGCATATATTGCGGCG
* *
12637769 ATTCTAGAAAATCG
193 ATTCTA-AAAAGCA
** * * * *
12637783 CCGCTAATGTTATGCTTTAGCGGCGTTTTTCCCTAACGCCACTAATTGTATTATACATCGAGACC
1 CCGCTAATAATATGCTTTAGCGGCGTTTTT-CGTAACGCCACTAATTATAGTATACATCAAGACC
*
12637848 AAACCGCTGCGTTTTGGTTAA
65 AAAACGCTGCGTTTTGGTTAA
12637869 CATTTTTTGC
Statistics
Matches: 248, Mismatches: 39, Indels: 17
0.82 0.13 0.06
Matches are distributed among these distances:
205 2 0.01
206 45 0.18
207 113 0.46
210 8 0.03
211 80 0.32
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (205 bp):
CCGCTAATAATATGCTTTAGCGGCGTTTTTCGTAACGCCACTAATTATAGTATACATCAAGACCA
AAACGCTGCGTTTTGGTTAAGAAATTTAGCGGCGCATTAGACTTTAGCGGCGTTTTACAATAAGC
GCCACTAATCCTAATATACCTCAAGACCAAACTCTACGTTTTGGTCTGCATATATTGCGGCGATT
CTAAAAAGCA
Found at i:12637918 original size:55 final size:55
Alignment explanation
Indices: 12637834--12637941 Score: 153
Period size: 55 Copynumber: 2.0 Consensus size: 55
12637824 CTAATTGTAT
* * *
12637834 TATACATCGAGACCAAACCGCTGCGTTTTGGTTAACATTTTTTGCAGCGCTTTAA
1 TATACATCAAGACCAAAACGCTGCGTTTTGGTTAACATATTTTGCAGCGCTTTAA
* * * *
12637889 TATACATCAAGATCAAAACTCTGCGTTTTGGTTATCATATTTTGCGGCGCTTT
1 TATACATCAAGACCAAAACGCTGCGTTTTGGTTAACATATTTTGCAGCGCTTT
12637942 CCGTAAGCGC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (55 bp):
TATACATCAAGACCAAAACGCTGCGTTTTGGTTAACATATTTTGCAGCGCTTTAA
Found at i:12638104 original size:113 final size:113
Alignment explanation
Indices: 12637886--12638143 Score: 286
Period size: 113 Copynumber: 2.3 Consensus size: 113
12637876 TGCAGCGCTT
* ** * * * *
12637886 TAATATACATCAAGATCAAAACTCTGCGTTTTGGTTATCATATTTTGCGGCGCTTTCCGTAAGCG
1 TAATATACATCAAGACCAAAACGATGCGTTTTCGTTAACATATTTTGCGGCGCTTCCCGCAAGCG
* * ** *
12637951 CCGCTAAGACTTGTTTTACTGGCATTTTTTTGTAAACGCCACTAATTC
66 CCGCTAAGACTTGCTTTACTGGCATTTTATCATAAACGCCACTAATTA
* * *
12637999 TAATATACATCGATACCAAAACGATGCGTTTTCGTTAAGAT-TTTTGCGGCGCTTCCCGCAATGC
1 TAATATACATCAAGACCAAAACGATGCGTTTTCGTTAACATATTTTGCGGCGCTTCCCGCAA-GC
* * *
12638063 GCCGCTAATACTTGCTTTAGC-GGCGTTTTATCATAATCGCCACTAATTA
65 GCCGCTAAGACTTGCTTTA-CTGGCATTTTATCATAAACGCCACTAATTA
** * *
12638112 TTGTATACATCAAGACAAAAAAGATGCGTTTT
1 TAATATACATCAAGACCAAAACGATGCGTTTT
12638144 GGTCTTGAGA
Statistics
Matches: 119, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
112 18 0.15
113 100 0.84
114 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (113 bp):
TAATATACATCAAGACCAAAACGATGCGTTTTCGTTAACATATTTTGCGGCGCTTCCCGCAAGCG
CCGCTAAGACTTGCTTTACTGGCATTTTATCATAAACGCCACTAATTA
Found at i:12638753 original size:19 final size:20
Alignment explanation
Indices: 12638731--12638768 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12638721 AAAAAAAATT
12638731 AAAATT-CAAAATATTTATA
1 AAAATTCCAAAATATTTATA
*
12638750 AAAATTCCAAAATTTTTAT
1 AAAATTCCAAAATATTTAT
12638769 TTTTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATTCCAAAATATTTATA
Found at i:12638787 original size:26 final size:27
Alignment explanation
Indices: 12638744--12638794 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
12638734 ATTCAAAATA
* *
12638744 TTTATAAAAATT-CCAAAATTTTTATT
1 TTTAAAAAAATTACAAAAATTTTTATT
*
12638770 TTTAAAAAAATTATAAAAATTTTTA
1 TTTAAAAAAATTACAAAAATTTTTA
12638795 AAAAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
TTTAAAAAAATTACAAAAATTTTTATT
Found at i:12638793 original size:21 final size:20
Alignment explanation
Indices: 12638767--12638809 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
12638757 CAAAATTTTT
12638767 ATTTTTAAAAAAATTATAAAA
1 ATTTTTAAAAAAA-TATAAAA
*
12638788 ATTTTTAAAAAAATCTAAAA
1 ATTTTTAAAAAAATATAAAA
12638808 AT
1 AT
12638810 ATATATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
ATTTTTAAAAAAATATAAAA
Found at i:12638797 original size:20 final size:21
Alignment explanation
Indices: 12638767--12638809 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
12638757 CAAAATTTTT
*
12638767 ATTTTTAAAAAAATTATAAAA
1 ATTTTTAAAAAAAATATAAAA
*
12638788 ATTTTT-AAAAAAATCTAAAA
1 ATTTTTAAAAAAAATATAAAA
12638808 AT
1 AT
12638810 ATATATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
ATTTTTAAAAAAAATATAAAA
Found at i:12644789 original size:18 final size:20
Alignment explanation
Indices: 12644752--12644790 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
12644742 ATTACAAAAT
*
12644752 AATTCAAAATCATTTTTAAA
1 AATTCAAAATCATTTATAAA
12644772 AATT-AAAAT-ATTTATAAA
1 AATTCAAAATCATTTATAAA
12644790 A
1 A
12644791 TTTATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 5 0.28
20 4 0.22
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTCAAAATCATTTATAAA
Found at i:12647444 original size:13 final size:13
Alignment explanation
Indices: 12647422--12647484 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
12647412 TCTTCATTGT
*
12647422 TTTTGGAAAGTGC
1 TTTTGAAAAGTGC
*
12647435 TTTTAAAAAGTGC
1 TTTTGAAAAGTGC
* *
12647448 TGTGGAAAAGTGC
1 TTTTGAAAAGTGC
* * *
12647461 TTTTTAGAAGTGA
1 TTTTGAAAAGTGC
12647474 TTTTGAAAAGT
1 TTTTGAAAAGT
12647485 TTAATTTAAA
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.32, C:0.05, G:0.25, T:0.38
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:12647481 original size:26 final size:26
Alignment explanation
Indices: 12647422--12647484 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
12647412 TCTTCATTGT
* *
12647422 TTTTGGAAAGTGCTTTTAAAAAGTGC
1 TTTTGAAAAGTGCTTTTAAAAAGTGA
* * * *
12647448 TGTGGAAAAGTGCTTTTTAGAAGTGA
1 TTTTGAAAAGTGCTTTTAAAAAGTGA
12647474 TTTTGAAAAGT
1 TTTTGAAAAGT
12647485 TTAATTTAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.32, C:0.05, G:0.25, T:0.38
Consensus pattern (26 bp):
TTTTGAAAAGTGCTTTTAAAAAGTGA
Found at i:12654727 original size:16 final size:17
Alignment explanation
Indices: 12654683--12654734 Score: 70
Period size: 18 Copynumber: 3.1 Consensus size: 17
12654673 GAAGGGAAAA
12654683 TTCCAAAAATGAAAAGT
1 TTCCAAAAATGAAAAGT
*
12654700 TTACCAAAAATGACAA-T
1 TT-CCAAAAATGAAAAGT
*
12654717 TTCCTAAAATGAAAAGT
1 TTCCAAAAATGAAAAGT
12654734 T
1 T
12654735 ATCAAGAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 11 0.37
17 7 0.23
18 12 0.40
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (17 bp):
TTCCAAAAATGAAAAGT
Found at i:12655530 original size:43 final size:43
Alignment explanation
Indices: 12655480--12655707 Score: 287
Period size: 43 Copynumber: 5.3 Consensus size: 43
12655470 GCGTTTTTTA
* *
12655480 CACAAACGCCGCTATAGGCCATGACCTTTAGCGGCGCTTTTCC
1 CACAAACGCCGCTATAGACCACGACCTTTAGCGGCGCTTTTCC
* * *
12655523 CATAAACGCCGCTATAGAACACGACCTTTAGCGGCGCTTTTTC
1 CACAAACGCCGCTATAGACCACGACCTTTAGCGGCGCTTTTCC
* **
12655566 CACAAAAGCTACTATAGACCACGACCTTTAGCGGCGCTTTTCC
1 CACAAACGCCGCTATAGACCACGACCTTTAGCGGCGCTTTTCC
* *
12655609 CACAAACGCCGCTATAGACCATGAACTTTAGCGGCGCTTTTCC
1 CACAAACGCCGCTATAGACCACGACCTTTAGCGGCGCTTTTCC
* * * * * *
12655652 CACAAACGCCGCTAAAGAACA-AACCTTTAGCGACGCTTCTCT
1 CACAAACGCCGCTATAGACCACGACCTTTAGCGGCGCTTTTCC
* *
12655694 TAAAAACGCCGCTA
1 CACAAACGCCGCTA
12655708 AAAACATAAC
Statistics
Matches: 160, Mismatches: 25, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 28 0.17
43 132 0.82
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (43 bp):
CACAAACGCCGCTATAGACCACGACCTTTAGCGGCGCTTTTCC
Found at i:12655843 original size:85 final size:85
Alignment explanation
Indices: 12655674--12655840 Score: 255
Period size: 85 Copynumber: 2.0 Consensus size: 85
12655664 TAAAGAACAA
* ** *
12655674 ACCTTTAGCGACGCTTCTCTTAAAAACGCCGCTAAAAACATAACATTTAAAAAAAATTATTTTAA
1 ACCTTTAGCGACACTTCTCGCAAAAACACCGCTAAAAACATAACATTTAAAAAAAATTATTTTAA
12655739 TCAAATAATATTTATTTTAT
66 TCAAATAATATTTATTTTAT
* * *
12655759 ACCTTTAGCGGCACTTCTCGCAAAAACACCGCTAAAAACATAACCTTT-AAAAAAATTATTTTAG
1 ACCTTTAGCGACACTTCTCGCAAAAACACCGCTAAAAACATAACATTTAAAAAAAATTATTTTAA
*
12655823 TTAAATAATATTTATTTT
66 TCAAATAATATTTATTTT
12655841 TATGATAAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
84 32 0.43
85 42 0.57
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.35
Consensus pattern (85 bp):
ACCTTTAGCGACACTTCTCGCAAAAACACCGCTAAAAACATAACATTTAAAAAAAATTATTTTAA
TCAAATAATATTTATTTTAT
Found at i:12655865 original size:24 final size:22
Alignment explanation
Indices: 12655824--12655867 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
12655814 TTATTTTAGT
12655824 TAAATAATATTTATTTTTATGA
1 TAAATAATATTTATTTTTATGA
*
12655846 TAAATATTATATTATGTTTTAT
1 TAAATAATAT-TTAT-TTTTAT
12655868 TTTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TAAATAATATTTATTTTTATGA
Found at i:12658424 original size:3 final size:3
Alignment explanation
Indices: 12658416--12658440 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12658406 TACCTCAATA
12658416 ACT ACT ACT ACT ACT ACT ACT ACT A
1 ACT ACT ACT ACT ACT ACT ACT ACT A
12658441 GTAGAATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ACT
Found at i:12658876 original size:3 final size:3
Alignment explanation
Indices: 12658868--12658894 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12658858 TCGATTTTTT
12658868 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
12658895 GCAAAATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12660884 original size:41 final size:41
Alignment explanation
Indices: 12660839--12660928 Score: 126
Period size: 41 Copynumber: 2.2 Consensus size: 41
12660829 CTAAAAATAG
** ** *
12660839 AGCATTAGTGGCGCTTTTTTAAAAACGCCGCTAAAGACTCA
1 AGCATTAGTGGCGCTACTCCAAAAACGCCGCTAAAGACCCA
*
12660880 AGCATTAGTGGCGCTACTCCAAAAACGCCGCTAAAGACCCG
1 AGCATTAGTGGCGCTACTCCAAAAACGCCGCTAAAGACCCA
12660921 AGCATTAG
1 AGCATTAG
12660929 AAGCGCCGCT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (41 bp):
AGCATTAGTGGCGCTACTCCAAAAACGCCGCTAAAGACCCA
Found at i:12660980 original size:68 final size:68
Alignment explanation
Indices: 12660864--12660996 Score: 169
Period size: 68 Copynumber: 2.0 Consensus size: 68
12660854 TTTTTAAAAA
* *
12660864 CGCCGCTAAAGACTCAAGCATTAGTGGCGCTACTCCAAAAACGCCGCTAAAGACCCGAGCATTAG
1 CGCCGCTAAAGACTCAAGCATTAGCGGCGCTACCCCAAAAACGCCGCTAAAGACCCGAGCATTAG
12660929 AAG
66 AAG
* * * * * * *
12660932 CGCCGCTAAAGAC-CAGAGTATTAGCGGTGCTTCCCCAGAAGCGTCGCTAAAGACCCGGGCATTA
1 CGCCGCTAAAGACTCA-AGCATTAGCGGCGCTACCCCAAAAACGCCGCTAAAGACCCGAGCATTA
12660996 G
65 G
12660997 CGGCGCTTCT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
67 2 0.04
68 53 0.96
ACGTcount: A:0.30, C:0.29, G:0.25, T:0.16
Consensus pattern (68 bp):
CGCCGCTAAAGACTCAAGCATTAGCGGCGCTACCCCAAAAACGCCGCTAAAGACCCGAGCATTAG
AAG
Found at i:12661054 original size:41 final size:41
Alignment explanation
Indices: 12660932--12661068 Score: 168
Period size: 41 Copynumber: 3.3 Consensus size: 41
12660922 GCATTAGAAG
* * * * * *
12660932 CGCCGCTAAAGACCAGAGTATTAGCGGTGCTTCCCCAGAAG
1 CGCCGCTAAAGCCCAGAGCATTAGCGGCGCTTCTCCAAAAA
* *
12660973 CGTCGCTAAAGACCC-GGGCATTAGCGGCGCTTCTCCAAAAA
1 CGCCGCTAAAG-CCCAGAGCATTAGCGGCGCTTCTCCAAAAA
* *
12661014 CGCCGCTAAAGCCCAGAGCATTAGCGGCGCTTTTCTAAAAA
1 CGCCGCTAAAGCCCAGAGCATTAGCGGCGCTTCTCCAAAAA
12661055 CGCCGCTAAAGCCC
1 CGCCGCTAAAGCCC
12661069 CGAAAACTCA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 3 0.04
41 77 0.94
42 2 0.02
ACGTcount: A:0.27, C:0.32, G:0.24, T:0.17
Consensus pattern (41 bp):
CGCCGCTAAAGCCCAGAGCATTAGCGGCGCTTCTCCAAAAA
Found at i:12666265 original size:41 final size:41
Alignment explanation
Indices: 12666212--12666450 Score: 236
Period size: 41 Copynumber: 5.9 Consensus size: 41
12666202 TTAAACCTTT
* * *
12666212 AGCGCCGCTAATGGTCCGATCTTTAGCGGCGTTTTTATCTG
1 AGCGCCACTAATGCTCTGATCTTTAGCGGCGTTTTTATCTG
* ** * *
12666253 AGTGCCACTAATGCTCTGGCCTTTAGCGGCGTTTTTCTCTA
1 AGCGCCACTAATGCTCTGATCTTTAGCGGCGTTTTTATCTG
* **
12666294 AGCGCCGCTAATGCTC-GTATCTTTAATGGCGTTTTTATCTG
1 AGCGCCACTAATGCTCTG-ATCTTTAGCGGCGTTTTTATCTG
* ** *
12666335 AGCGCCACTAATTCTCTGGCCTTTAGCGGCGTTTTT-TCTA
1 AGCGCCACTAATGCTCTGATCTTTAGCGGCGTTTTTATCTG
* * *
12666375 AGCGCCGCAAATG-T-TAGTATCTTTAGTGGCGTTTTTATCTG
1 AGCGCCACTAATGCTCT-G-ATCTTTAGCGGCGTTTTTATCTG
*
12666416 AGCGCCACTAATGCTCTG-GCTTTTAGCGGCGTTTT
1 AGCGCCACTAATGCTCTGATC-TTTAGCGGCGTTTT
12666451 ATAGGTAAGC
Statistics
Matches: 156, Mismatches: 34, Indels: 16
0.76 0.17 0.08
Matches are distributed among these distances:
38 1 0.01
39 2 0.01
40 30 0.19
41 119 0.76
42 3 0.02
43 1 0.01
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (41 bp):
AGCGCCACTAATGCTCTGATCTTTAGCGGCGTTTTTATCTG
Found at i:12666352 original size:82 final size:81
Alignment explanation
Indices: 12666212--12666450 Score: 372
Period size: 81 Copynumber: 2.9 Consensus size: 81
12666202 TTAAACCTTT
* * *
12666212 AGCGCCGCTAATGGTCCG-ATCTTTAGCGGCGTTTTTATCTGAGTGCCACTAATGCTCTGGCCTT
1 AGCGCCGCTAATGCT-CGTATCTTTAGTGGCGTTTTTATCTGAGCGCCACTAATGCTCTGGCCTT
12666276 TAGCGGCGTTTTTCTCTA
65 TAGCGGCGTTTTT-TCTA
* *
12666294 AGCGCCGCTAATGCTCGTATCTTTAATGGCGTTTTTATCTGAGCGCCACTAATTCTCTGGCCTTT
1 AGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAGCGCCACTAATGCTCTGGCCTTT
12666359 AGCGGCGTTTTTTCTA
66 AGCGGCGTTTTTTCTA
* * * *
12666375 AGCGCCGCAAATGTTAGTATCTTTAGTGGCGTTTTTATCTGAGCGCCACTAATGCTCTGGCTTTT
1 AGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAGCGCCACTAATGCTCTGGCCTTT
12666440 AGCGGCGTTTT
66 AGCGGCGTTTT
12666451 ATAGGTAAGC
Statistics
Matches: 145, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
81 76 0.52
82 69 0.48
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (81 bp):
AGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAGCGCCACTAATGCTCTGGCCTTT
AGCGGCGTTTTTTCTA
Found at i:12666399 original size:40 final size:40
Alignment explanation
Indices: 12666212--12666493 Score: 180
Period size: 41 Copynumber: 6.9 Consensus size: 40
12666202 TTAAACCTTT
* *
12666212 AGCGCCGCTAATGGTCCG-ATCTTTAGCGGCGTTTTTATCTG
1 AGCGCCGCTAAT-GT-TGTATCTTTAGCGGCGTTTTTATCTA
* * ** *
12666253 AGTGCCACTAATGCTCTG-GCCTTTAGCGGCGTTTTTCTCTA
1 AGCGCCGCTAATG-T-TGTATCTTTAGCGGCGTTTTTATCTA
* ** *
12666294 AGCGCCGCTAATGCTCGTATCTTTAATGGCGTTTTTATCTG
1 AGCGCCGCTAATG-TTGTATCTTTAGCGGCGTTTTTATCTA
* * **
12666335 AGCGCCACTAAT-TCTCTGGCCTTTAGCGGCGTTTTT-TCTA
1 AGCGCCGCTAATGT-TGT-ATCTTTAGCGGCGTTTTTATCTA
* * *
12666375 AGCGCCGCAAATGTTAGTATCTTTAGTGGCGTTTTTATCTG
1 AGCGCCGCTAATGTT-GTATCTTTAGCGGCGTTTTTATCTA
* ** **
12666416 AGCGCCACTAATGCTCTGGCT-TTTAGCGGCGTTTTATAGGTA
1 AGCGCCGCTAATG-T-TGTATCTTTAGCGGCGTTTT-TATCTA
* *
12666458 AGCGCCGCGAATGCATT-TACCTTTAGCGGCGTTTTT
1 AGCGCCGCTAATG--TTGTATCTTTAGCGGCGTTTTT
12666494 GCCGAAGCGC
Statistics
Matches: 184, Mismatches: 45, Indels: 24
0.73 0.18 0.09
Matches are distributed among these distances:
39 1 0.01
40 32 0.17
41 117 0.64
42 32 0.17
43 2 0.01
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (40 bp):
AGCGCCGCTAATGTTGTATCTTTAGCGGCGTTTTTATCTA
Found at i:12668945 original size:8 final size:10
Alignment explanation
Indices: 12668923--12668959 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
12668913 TATTTTTACT
12668923 TATATATGGA
1 TATATATGGA
*
12668933 TATATATGAA
1 TATATATGGA
12668943 TATATATGGA
1 TATATATGGA
12668953 TATATAT
1 TATATAT
12668960 ATATAGTTAN
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (10 bp):
TATATATGGA
Found at i:12669643 original size:8 final size:10
Alignment explanation
Indices: 12669621--12669657 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
12669611 TATTTTTACT
12669621 TATATATGGA
1 TATATATGGA
*
12669631 TATATATGAA
1 TATATATGGA
12669641 TATATATGGA
1 TATATATGGA
12669651 TATATAT
1 TATATAT
12669658 ATAGTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (10 bp):
TATATATGGA
Found at i:12669766 original size:27 final size:27
Alignment explanation
Indices: 12669725--12669776 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
12669715 AATAAACAAA
* *
12669725 TAAATAAGTTAGTAATTATTTATTTGT
1 TAAATAAATTAGTAATTAATTATTTGT
*
12669752 TAAATAAATTGGTAATTAATTATTT
1 TAAATAAATTAGTAATTAATTATTT
12669777 AAAAGTAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (27 bp):
TAAATAAATTAGTAATTAATTATTTGT
Found at i:12671005 original size:11 final size:11
Alignment explanation
Indices: 12670989--12671025 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
12670979 TTATATTTTC
12670989 TAATTTGATTA
1 TAATTTGATTA
12671000 TAATTTGATTA
1 TAATTTGATTA
12671011 TAATTTGATTA
1 TAATTTGATTA
12671022 TAAT
1 TAAT
12671026 GTTTACTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (11 bp):
TAATTTGATTA
Found at i:12672662 original size:34 final size:34
Alignment explanation
Indices: 12672616--12672794 Score: 141
Period size: 34 Copynumber: 5.0 Consensus size: 34
12672606 TAGTTTGATT
*
12672616 ATAATTAGTATTATACATAAATTACATAACTTAA
1 ATAATTAATATTATACATAAATTACATAACTTAA
* *
12672650 ATAATTAATATTATACATAACTTACATTAATATTATA
1 ATAATTAATATTATACATAAATTACA-TAA-CTTA-A
12672687 CATAAATTACATAACTTAATTA-ATTAATATTATACATAACTT--
1 -AT-AATTA-AT-A-TT-A-TACA-TAA-A-T-TACATAACTTAA
* *
12672729 A-CATTAATATTATACATAAATTACATAACTTAG
1 ATAATTAATATTATACATAAATTACATAACTTAA
* *
12672762 TTAATTAATATTATACATAACTTACATAACTTA
1 ATAATTAATATTATACATAAATTACATAACTTA
12672795 CTTAATTTGC
Statistics
Matches: 118, Mismatches: 9, Indels: 36
0.72 0.06 0.22
Matches are distributed among these distances:
31 10 0.08
32 1 0.01
33 1 0.01
34 58 0.49
35 5 0.04
36 5 0.04
37 2 0.02
38 4 0.03
39 9 0.08
40 2 0.02
41 2 0.02
42 2 0.02
43 2 0.02
44 5 0.04
45 2 0.02
46 4 0.03
47 4 0.03
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.40
Consensus pattern (34 bp):
ATAATTAATATTATACATAAATTACATAACTTAA
Found at i:12672681 original size:22 final size:22
Alignment explanation
Indices: 12672653--12672698 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
12672643 AACTTAAATA
*
12672653 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTAC
12672675 ATTAATATTATACATAAATTAC
1 ATTAATATTATACATAAATTAC
12672697 AT
1 AT
12672699 AACTTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAATATTATACATAAATTAC
Found at i:12672684 original size:56 final size:56
Alignment explanation
Indices: 12672619--12672788 Score: 313
Period size: 56 Copynumber: 3.0 Consensus size: 56
12672609 TTTGATTATA
* *
12672619 ATTAGTATTATACATAAATTACATAACTTAAATAATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
12672675 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
*
12672731 ATTAATATTATACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
12672787 AT
1 AT
12672789 AACTTACTTA
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 111 1.00
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.41
Consensus pattern (56 bp):
ATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTAC
Done.