Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 105 of 345
Found at i:28297108 original size:29 final size:30
Alignment explanation
Indices: 28297047--28297108 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
28297037 ATTTCAAAAT
* **
28297047 TTTAAAAATATAAGGACTAAAATTGACTAA
1 TTTAAAAATATAAGAACTAAAATCCACTAA
28297077 TTTAAAAAGTATAAGAACT-AAATCCAC-AA
1 TTTAAAAA-TATAAGAACTAAAATCCACTAA
28297106 TTT
1 TTT
28297109 TTTATAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.18
30 14 0.50
31 9 0.32
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.31
Consensus pattern (30 bp):
TTTAAAAATATAAGAACTAAAATCCACTAA
Found at i:28303779 original size:3 final size:3
Alignment explanation
Indices: 28303773--28303847 Score: 54
Period size: 3 Copynumber: 26.3 Consensus size: 3
28303763 ATTTTTTTAA
*
28303773 TAT TAT T-T T-T TAT TATT TAT TATT TAT T-T TGT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TA-T TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* * *
28303816 TAT TA- TGT TCT TAT TAT T-T TAT TGT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
28303848 TAGATATTGT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
2 11 0.19
3 42 0.71
4 6 0.10
ACGTcount: A:0.23, C:0.01, G:0.04, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:28303843 original size:11 final size:11
Alignment explanation
Indices: 28303767--28303844 Score: 88
Period size: 11 Copynumber: 7.2 Consensus size: 11
28303757 ATGATAATTT
*
28303767 TTTTAATATTA
1 TTTTATTATTA
28303778 TTTT-TTATTA
1 TTTTATTATTA
28303788 -TTTATTATTTA
1 TTTTATTA-TTA
*
28303799 TTTTGTTATTA
1 TTTTATTATTA
28303810 TTTTATTATTA
1 TTTTATTATTA
* *
28303821 TGTTCTTATTA
1 TTTTATTATTA
*
28303832 TTTTATTGTTA
1 TTTTATTATTA
28303843 TT
1 TT
28303845 ATTTAGATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
9 3 0.05
10 8 0.14
11 39 0.70
12 6 0.11
ACGTcount: A:0.23, C:0.01, G:0.04, T:0.72
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:28304078 original size:12 final size:12
Alignment explanation
Indices: 28304057--28304091 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
28304047 TATATATTTT
*
28304057 AAAATTATATAA
1 AAAATAATATAA
28304069 AAAATAATATAA
1 AAAATAATATAA
*
28304081 AAATTAATATA
1 AAAATAATATA
28304092 GGCGGGCCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:28313197 original size:3 final size:3
Alignment explanation
Indices: 28313182--28313221 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
28313172 AACACCCAAC
*
28313182 ATG ATG GTG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
28313222 AGTGACTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:28315350 original size:13 final size:14
Alignment explanation
Indices: 28315326--28315370 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
28315316 TAAAATTAAG
28315326 TATTAAATTTTTAT
1 TATTAAATTTTTAT
*
28315340 TATTAAATTTTATAA
1 TATTAAATTTT-TAT
* *
28315355 AATTAAATTTATAT
1 TATTAAATTTTTAT
28315369 TA
1 TA
28315371 GAAAATTGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTAAATTTTTAT
Found at i:28316026 original size:2 final size:2
Alignment explanation
Indices: 28316019--28316044 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28316009 ATAATAATTC
28316019 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
28316045 GTATGTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28316791 original size:21 final size:21
Alignment explanation
Indices: 28316750--28316791 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28316740 TCAGCTAATA
* *
28316750 ATATATTATTTATTTATATTT
1 ATATAGTATTTAATTATATTT
28316771 ATATAGTATTTTAATTA-ATTT
1 ATATAGTA-TTTAATTATATTT
28316792 TATTTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
ATATAGTATTTAATTATATTT
Found at i:28321885 original size:2 final size:2
Alignment explanation
Indices: 28321880--28321919 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
28321870 ACAAGCTAGC
28321880 TA TA TA TA TA TA 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
28321920 CAAAACTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28327096 original size:17 final size:17
Alignment explanation
Indices: 28327071--28327113 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
28327061 ATTACATATT
*
28327071 AATTGAAAAATAATT-AA
1 AATTTAAAAA-AATTAAA
*
28327088 AATTTAAAAAATTTAAA
1 AATTTAAAAAAATTAAA
28327105 AATTTAAAA
1 AATTTAAAA
28327114 TTAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AATTTAAAAAAATTAAA
Found at i:28331956 original size:49 final size:49
Alignment explanation
Indices: 28331854--28331957 Score: 126
Period size: 48 Copynumber: 2.1 Consensus size: 49
28331844 CACGGGTAGT
* *
28331854 TCACACGTCCGTGTCTATTTAACAGATTGCAACACGGCCTAAGCCACAC
1 TCACACGTCCGTGTCTATTTAACAGATTGAAACACGGCCTAAACCACAC
*
28331903 -CACACAG-CCGTGTCTATTTAGCAGACTCT-AAACACGGCCTAAACCAC-C
1 TCACAC-GTCCGTGTCTATTTAACAGA-T-TGAAACACGGCCTAAACCACAC
28331951 TCACACG
1 TCACACG
28331958 GGCATGTCCC
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
48 24 0.50
49 23 0.48
50 1 0.02
ACGTcount: A:0.30, C:0.35, G:0.15, T:0.20
Consensus pattern (49 bp):
TCACACGTCCGTGTCTATTTAACAGATTGAAACACGGCCTAAACCACAC
Found at i:28333396 original size:10 final size:11
Alignment explanation
Indices: 28333357--28333398 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
28333347 TATTTACAAA
*
28333357 GTTAATTGAGTG
1 GTTAATT-AGAG
28333369 GTTAATTAGAG
1 GTTAATTAGAG
*
28333380 TTTAATTA-AG
1 GTTAATTAGAG
28333390 GTTAATTAG
1 GTTAATTAG
28333399 GTATAAGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 9 0.35
11 10 0.38
12 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (11 bp):
GTTAATTAGAG
Found at i:28334040 original size:16 final size:16
Alignment explanation
Indices: 28334019--28334065 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
28334009 ATGAATTAAA
28334019 TATTATTATATTATAT
1 TATTATTATATTATAT
* *
28334035 TATTATTATAATGTAT
1 TATTATTATATTATAT
*
28334051 CATTATTAATATTAT
1 TATTATT-ATATTAT
28334066 TAACTAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (16 bp):
TATTATTATATTATAT
Found at i:28334043 original size:19 final size:21
Alignment explanation
Indices: 28334019--28334065 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
28334009 ATGAATTAAA
28334019 TATTATTATAT-TAT-ATTAT
1 TATTATTATATGTATCATTAT
28334038 TATTA-TA-ATGTATCATTAT
1 TATTATTATATGTATCATTAT
*
28334057 TAATATTAT
1 TATTATTAT
28334066 TAACTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 2 0.09
18 5 0.22
19 14 0.61
20 2 0.09
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TATTATTATATGTATCATTAT
Found at i:28334079 original size:2 final size:2
Alignment explanation
Indices: 28334072--28334097 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28334062 TTATTAACTA
28334072 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
28334098 GAAATAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28335268 original size:44 final size:44
Alignment explanation
Indices: 28335219--28335305 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
28335209 TCAGGGATAC
* * *
28335219 TTCGACCTTGAGTCAATGAGGCACTATAAGTGTCGTACTGTTAG
1 TTCGACCTTGAGTCAATGAGACACCATAAGTGTCATACTGTTAG
* * **
28335263 TTCGACTTTGAGTCGATGAGACACCATGTGTGTCATACTGTTA
1 TTCGACCTTGAGTCAATGAGACACCATAAGTGTCATACTGTTA
28335306 CTGTTACTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (44 bp):
TTCGACCTTGAGTCAATGAGACACCATAAGTGTCATACTGTTAG
Found at i:28336832 original size:3 final size:3
Alignment explanation
Indices: 28336824--28336862 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
28336814 TAAATATGTA
28336824 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28336863 GGTTTTATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:28337304 original size:2 final size:2
Alignment explanation
Indices: 28337297--28337338 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
28337287 GTTAACTTAT
28337297 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28337339 AAGTAAAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28337436 original size:17 final size:17
Alignment explanation
Indices: 28337414--28337446 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28337404 GCAAGGGAGA
28337414 AAAAGAAAGAAAGAAAG
1 AAAAGAAAGAAAGAAAG
*
28337431 AAAAGAAAGGAAGAAA
1 AAAAGAAAGAAAGAAA
28337447 AGAGAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAAGAAAGAAAGAAAG
Found at i:28337437 original size:13 final size:13
Alignment explanation
Indices: 28337415--28337449 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
28337405 CAAGGGAGAA
28337415 AAAG-AAAGAAAG
1 AAAGAAAAGAAAG
28337427 AAAGAAAAGAAAG
1 AAAGAAAAGAAAG
*
28337440 GAAGAAAAGA
1 AAAGAAAAGA
28337450 GAAAATTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AAAGAAAAGAAAG
Found at i:28338181 original size:28 final size:27
Alignment explanation
Indices: 28338101--28338181 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
28338091 ATCATAATGT
28338101 TGAATTGAATGTGTGATT-AT-TGGAAA
1 TGAATTGAATGTG-GATTGATATGGAAA
** *
28338127 TGAATTGAAATGTATATTG-TATTGAAA
1 TGAATTG-AATGTGGATTGATATGGAAA
*
28338154 GTGAATTGCATGTGGATTGATATGGAAA
1 -TGAATTGAATGTGGATTGATATGGAAA
28338182 AATGTACTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
26 11 0.26
27 18 0.42
28 14 0.33
ACGTcount: A:0.36, C:0.01, G:0.26, T:0.37
Consensus pattern (27 bp):
TGAATTGAATGTGGATTGATATGGAAA
Found at i:28338216 original size:23 final size:25
Alignment explanation
Indices: 28338181--28338226 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
28338171 TGATATGGAA
28338181 AAATGTACTAAATTG-AATTGAAATT
1 AAATGTACTAAA-TGAAATTGAAATT
28338206 AAAT-TAC-AAATGAAATTGAAA
1 AAATGTACTAAATGAAATTGAAA
28338227 ATTTGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 2 0.10
23 11 0.55
24 3 0.15
25 4 0.20
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.30
Consensus pattern (25 bp):
AAATGTACTAAATGAAATTGAAATT
Found at i:28338900 original size:40 final size:40
Alignment explanation
Indices: 28338853--28338932 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
28338843 ATGAAAAAGT
28338853 TAATCAAGTTATTAGATGATGAAGGTTAAATGAGTTGCAA
1 TAATCAAGTTATTAGATGATGAAGGTTAAATGAGTTGCAA
28338893 TAATCAAGTTATTAGATGATGAAGGTTAAATGAGTTGCAA
1 TAATCAAGTTATTAGATGATGAAGGTTAAATGAGTTGCAA
28338933 AGAAATTACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.33
Consensus pattern (40 bp):
TAATCAAGTTATTAGATGATGAAGGTTAAATGAGTTGCAA
Found at i:28345467 original size:6 final size:6
Alignment explanation
Indices: 28345456--28345481 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28345446 ACACCGTAGG
28345456 GTAACA GTAACA GTAACA GTAACA GT
1 GTAACA GTAACA GTAACA GTAACA GT
28345482 CATAGTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:28346428 original size:21 final size:21
Alignment explanation
Indices: 28346390--28346433 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28346380 TTGTCTGTTC
* *
28346390 TTTCTTTCTTTTTCTATTTTA
1 TTTCTTTATTTTTCTATTATA
28346411 TTTCTTTATTCTTT-TATTATA
1 TTTCTTTATT-TTTCTATTATA
28346432 TT
1 TT
28346434 AATATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTCTTTATTTTTCTATTATA
Found at i:28346669 original size:19 final size:20
Alignment explanation
Indices: 28346635--28346672 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
28346625 AATCCTTACA
28346635 CTAAATTAACCTTAATTAAG
1 CTAAATTAACCTTAATTAAG
*
28346655 CTAAATTTA-CTTAATTAA
1 CTAAATTAACCTTAATTAA
28346673 AATCTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (20 bp):
CTAAATTAACCTTAATTAAG
Found at i:28353656 original size:21 final size:21
Alignment explanation
Indices: 28353618--28353661 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28353608 TTGTCTGTTC
* *
28353618 TTTCTTTCTTTTTCTATTTTA
1 TTTCTTTATTTTTCTATTATA
28353639 TTTCTTTATTCTTT-TATTATA
1 TTTCTTTATT-TTTCTATTATA
28353660 TT
1 TT
28353662 AATATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTCTTTATTTTTCTATTATA
Found at i:28353669 original size:13 final size:11
Alignment explanation
Indices: 28353652--28353717 Score: 64
Period size: 13 Copynumber: 5.8 Consensus size: 11
28353642 CTTTATTCTT
28353652 TTATTATATTAA
1 TTATTATATT-A
28353664 TATATTATATTA
1 T-TATTATATTA
28353676 TTATTATATT-
1 TTATTATATTA
*
28353686 TTAGTA-ATTA
1 TTATTATATTA
28353696 TTATTATTATTA
1 TTATTA-TATTA
*
28353708 CTTATAATAT
1 -TTATTATAT
28353718 AAGCAAACAT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
9 3 0.07
10 10 0.22
11 9 0.20
12 10 0.22
13 14 0.30
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (11 bp):
TTATTATATTA
Found at i:28353676 original size:29 final size:29
Alignment explanation
Indices: 28353644--28353718 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
28353634 TTTTATTTCT
* * *
28353644 TTATTCTTTTATTATATTAATATATTA-TA
1 TTATTATTATATTATAGTAAT-TATTATTA
*
28353673 TTATTATTATATTTTAGTAATTATTATTA
1 TTATTATTATATTATAGTAATTATTATTA
*
28353702 TTATTACTTATAATATA
1 TTATTA-TTATATTATA
28353719 AGCAAACATA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 5 0.13
29 25 0.66
30 8 0.21
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (29 bp):
TTATTATTATATTATAGTAATTATTATTA
Found at i:28353677 original size:3 final size:3
Alignment explanation
Indices: 28353652--28353712 Score: 51
Period size: 3 Copynumber: 21.3 Consensus size: 3
28353642 CTTTATTCTT
* *
28353652 TTA TTA -TA TTA ATA -TA TTA -TA TTA TTA TTA -TA TT- TTA GTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
28353693 TTA TTA TTA TTA TTA CTTA T
1 TTA TTA TTA TTA TTA -TTA T
28353713 AATATAAGCA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
2 10 0.21
3 33 0.69
4 5 0.10
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:28354675 original size:43 final size:43
Alignment explanation
Indices: 28354516--28354676 Score: 170
Period size: 43 Copynumber: 3.7 Consensus size: 43
28354506 AATGCGAACA
* * * *
28354516 TCCCAGACGTGGTCTTACATGAAATCACATGTCAATGCCACTA
1 TCCCAGACGTGGTCTTACATGAAATCACATATCGATGCCAATG
* *
28354559 TCCCAGACAG-GGTCTTACACG-AATCACA-ATTACGATGCCGATG
1 TCCCAGAC-GTGGTCTTACATGAAATCACATA-T-CGATGCCAATG
* *
28354602 TCCCAGGCATGGTCTTAC-TCGAAATCACATATCGATGCCAATG
1 TCCCAGACGTGGTCTTACAT-GAAATCACATATCGATGCCAATG
28354645 TCCCAGACGTGGTCTTACATGAGAA-CACATAT
1 TCCCAGACGTGGTCTTACATGA-AATCACATAT
28354677 TGGAAATCCT
Statistics
Matches: 97, Mismatches: 12, Indels: 18
0.76 0.09 0.14
Matches are distributed among these distances:
42 8 0.08
43 76 0.78
44 12 0.12
45 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (43 bp):
TCCCAGACGTGGTCTTACATGAAATCACATATCGATGCCAATG
Found at i:28361083 original size:18 final size:17
Alignment explanation
Indices: 28361056--28361091 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
28361046 ACATCTCTAT
28361056 TTTTTCTATTCTTCTTC
1 TTTTTCTATTCTTCTTC
*
28361073 TTTTTCTTATTCTTTTTC
1 TTTTTC-TATTCTTCTTC
28361091 T
1 T
28361092 ACTGCCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTCTATTCTTCTTC
Found at i:28361419 original size:12 final size:12
Alignment explanation
Indices: 28361402--28361430 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
28361392 ACTAAGTTTT
28361402 TATATTTATTTA
1 TATATTTATTTA
28361414 TATATTTATTTA
1 TATATTTATTTA
28361426 TATAT
1 TATAT
28361431 ATAAATTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TATATTTATTTA
Found at i:28361891 original size:24 final size:24
Alignment explanation
Indices: 28361863--28361933 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
28361853 GAATTTACTA
28361863 TTAGATTTTAATTTAA-AATAAAT
1 TTAGATTTTAATTTAATAATAAAT
**
28361886 TCTAGA--AAAATTTAATAATAAAT
1 T-TAGATTTTAATTTAATAATAAAT
* * *
28361909 TAATATTTTAATATAATAATAAAT
1 TTAGATTTTAATTTAATAATAAAT
28361933 T
1 T
28361934 AATATTAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
22 9 0.24
23 9 0.24
24 19 0.51
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (24 bp):
TTAGATTTTAATTTAATAATAAAT
Found at i:28361951 original size:24 final size:23
Alignment explanation
Indices: 28361898--28361943 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
28361888 TAGAAAAATT
28361898 TAATAATAAATTAATATTTTAATA
1 TAATAATAAATTAATA-TTTAATA
28361922 TAATAATAAATTAATA-TTAATA
1 TAATAATAAATTAATATTTAATA
28361944 ATCAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 6 0.27
24 16 0.73
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATAATAAATTAATATTTAATA
Found at i:28361956 original size:13 final size:13
Alignment explanation
Indices: 28361940--28361966 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28361930 AATTAATATT
28361940 AATAATCAATAAA
1 AATAATCAATAAA
28361953 AATAATCAATAAA
1 AATAATCAATAAA
28361966 A
1 A
28361967 TTAGTAAACT
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:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (13 bp):
AATAATCAATAAA
Found at i:28365560 original size:9 final size:9
Alignment explanation
Indices: 28365548--28365573 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28365538 ATAAATACAA
28365548 TAATAATAG
1 TAATAATAG
28365557 TAATAATAG
1 TAATAATAG
28365566 TAATAATA
1 TAATAATA
28365574 ATAAAATGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (9 bp):
TAATAATAG
Found at i:28367265 original size:44 final size:44
Alignment explanation
Indices: 28367212--28367830 Score: 304
Period size: 44 Copynumber: 13.7 Consensus size: 44
28367202 TGTTGTTTCC
* * *
28367212 ATCTACTCCACTACAACTTCAGAGAGATAAGATTAGTAGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCA
* * * * *
28367256 ATCTGCTCCACTACAACTTCGGGGAGATAAAATTCACTATCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-AGTAGCTTCA
** * * * *
28367301 ATCTGCTCCACTATAACTTTAGGGAGATTAGACTT-CTAGCTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTAGCTTCA
* * *
28367345 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAG-TAGCTTCA
* * * * *
28367390 ATCTACTCCACTGTAACTTTAAGGAGATAAGACTT-GTAACTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTAGCTTCA
* * * *
28367434 ACCTACTCCACTGCAACTTCAGGGAGATAAGGTTAGTGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCA
* * * *
28367478 ATCTGCTCCACTGCAATTTCAAGGAGATAATATTCGCCATAATTTGTAGCTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGAT-A-A---G-----ATTAGTAGCTTCA
* * * * * * *
28367532 ATCAGTTCCACTGTAACTTTAGGGAAATAAGATTCGCTATCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAG-TAGCTTCA
* * * * ** *
28367577 GTTTGCTCCACTGTAACTTTAGGGAGATAAGACTT-GTAATTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTAGCTTCA
* * * * * * * * *
28367621 ACCTGTTTCACTGCAACCTCCA-GAAGACAAGATTTGTTTA-TTATTA
1 ATCTGCTCCACTGCAA-CTTCAGGGAGATAAGATTAG--TAGCT-TCA
* * * * * *
28367667 A-CTTACTCCGCTGCAAATTCAGGGAGATAAGGTTTA-TAGGTTTA
1 ATC-TGCTCCACTGCAACTTCAGGGAGATAA-GATTAGTAGCTTCA
* * * ** * *
28367711 ATATGCTCTACTGCAACTTTAGATAGATAAGATT-TTCCATCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGT--AGCTTCA
* * *
28367756 GTCTGCTCCACTGCAACTTTAGGGAGATAAGACTT-GTAACTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTAGCTTCA
*
28367800 ACCTGCTCCACTGCAAC-TCTAGGGAGATAAG
1 ATCTGCTCCACTGCAACTTC-AGGGAGATAAG
28367831 GTTCAAAGCT
Statistics
Matches: 439, Mismatches: 103, Indels: 66
0.72 0.17 0.11
Matches are distributed among these distances:
43 11 0.03
44 215 0.49
45 145 0.33
46 31 0.07
47 3 0.01
49 2 0.00
52 1 0.00
53 1 0.00
54 30 0.07
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCA
Found at i:28367341 original size:89 final size:88
Alignment explanation
Indices: 28367212--28367830 Score: 350
Period size: 89 Copynumber: 6.9 Consensus size: 88
28367202 TGTTGTTTCC
* * * *
28367212 ATCTACTCCACTACAACTTCAGAGAGATAAGA-TTAGTAGCTTCAATCTGCTCCACTACAACTTC
1 ATCTACTCCACTATAACTTTAGGGAGATAAGACTT-GTAGCTTCAATCTGCTCCACTGCAACTTC
* *
28367276 GGGGAGATAAAATTCACTATCTTCA
65 AGGGAGATAAGATT-ACTATCTTCA
* * * *
28367301 ATCTGCTCCACTATAACTTTAGGGAGATTAGACTTCTAGCTTTAATCTGCTCCACTGCAACTTCA
1 ATCTACTCCACTATAACTTTAGGGAGATAAGACTTGTAGCTTCAATCTGCTCCACTGCAACTTCA
* *
28367366 GGGAGATAAGATTTGCTATCTTCG
66 GGGAGATAAGA-TTACTATCTTCA
* * * * *
28367390 ATCTACTCCACTGTAACTTTAAGGAGATAAGACTTGTAACTTCAACCTACTCCACTGCAACTTCA
1 ATCTACTCCACTATAACTTTAGGGAGATAAGACTTGTAGCTTCAATCTGCTCCACTGCAACTTCA
* * **
28367455 GGGAGATAAGGTTAGTGGCTTCA
66 GGGAGATAAGATTACTATCTTCA
* ** * * * * *
28367478 ATCTGCTCCACTGCAA-TTTCAAGGAGATAATATTCGCCATAATTTGTAGCTTTAATCAGTTCCA
1 ATCTACTCCACTATAACTTT-AGGGAGAT-A-A---G-----ACTTGTAGCTTCAATCTGCTCCA
* * * *
28367542 CTGTAACTTTAGGGAAATAAGATTCGCTATCTTCA
55 CTGCAACTTCAGGGAGATAAGATT-ACTATCTTCA
* * * * ** * * * * *
28367577 GTTTGCTCCACTGTAACTTTAGGGAGATAAGACTTGTAATTTTAACCTGTTTCACTGCAACCTCC
1 ATCTACTCCACTATAACTTTAGGGAGATAAGACTTGTAGCTTCAATCTGCTCCACTGCAA-CTTC
* * ** *
28367642 A-GAAGACAAGATTTGTTTAT-TATTA
65 AGGGAGATAAGA-TT-ACTATCT-TCA
* ** * * ** * * * * * *
28367667 A-CTTACTCCGCTGCAAATTCAGGGAGATAAGGTTTATAGGTTTAATATGCTCTACTGCAACTTT
1 ATC-TACTCCACTATAACTTTAGGGAGATAAGACTTGTAGCTTCAATCTGCTCCACTGCAACTTC
** * *
28367731 AGATAGATAAGATTTTCCATCTTCA
65 AGGGAGATAAGA-TTACTATCTTCA
* * ** * *
28367756 GTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAAC-TCT
1 ATCTACTCCACTATAACTTTAGGGAGATAAGACTTGTAGCTTCAATCTGCTCCACTGCAACTTC-
28367820 AGGGAGATAAG
65 AGGGAGATAAG
28367831 GTTCAAAGCT
Statistics
Matches: 401, Mismatches: 106, Indels: 46
0.73 0.19 0.08
Matches are distributed among these distances:
87 3 0.01
88 30 0.07
89 230 0.57
90 69 0.17
93 1 0.00
94 1 0.00
97 1 0.00
98 37 0.09
99 26 0.06
100 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (88 bp):
ATCTACTCCACTATAACTTTAGGGAGATAAGACTTGTAGCTTCAATCTGCTCCACTGCAACTTCA
GGGAGATAAGATTACTATCTTCA
Found at i:28367433 original size:133 final size:132
Alignment explanation
Indices: 28367212--28367507 Score: 299
Period size: 133 Copynumber: 2.2 Consensus size: 132
28367202 TGTTGTTTCC
* * * * *
28367212 ATCTACTCCACTACAACTTCAGAGAGATAAGATTAGTAGCTTCAATCTGCTCCACTACAACTTCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAATCTACTCCACTACAACTTCA
* * * * * * *
28367277 GGGAGATAAAATTCACTATCTTCAATCTGCTCCACTATAACTTTAGGGAGATTAGACTT-CTAGC
66 AGGAGATAAAATT-ACTAACTTCAACCTACTCCACTACAACTTCAGGGAGATAAG-CTTACTAGC
*
28367341 TTTA
129 TTCA
* * * ** *
28367345 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCGATCTACTCCACTGTAACTTT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAG-TAGCTTCAATCTACTCCACTACAACTTC
* * * * * *
28367410 AAGGAGATAAGACTT-GTAACTTCAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTAGTGGC
65 AAGGAGATAA-AATTACTAACTTCAACCTACTCCACTACAACTTCAGGGAGATAAGCTTACTAGC
28367474 TTCA
129 TTCA
* *
28367478 ATCTGCTCCACTGCAATTTCAAGGAGATAA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAA
28367508 TATTCGCCAT
Statistics
Matches: 133, Mismatches: 27, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
132 2 0.02
133 98 0.74
134 30 0.23
135 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (132 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAATCTACTCCACTACAACTTCA
AGGAGATAAAATTACTAACTTCAACCTACTCCACTACAACTTCAGGGAGATAAGCTTACTAGCTT
CA
Found at i:28369113 original size:18 final size:18
Alignment explanation
Indices: 28369090--28369134 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
28369080 GTCAATCATT
28369090 TATTCAGTAACAGTCAAG
1 TATTCAGTAACAGTCAAG
* *
28369108 TATTCAGTAGCAGTCAAT
1 TATTCAGTAACAGTCAAG
*
28369126 TCTTCAGTA
1 TATTCAGTA
28369135 CCTTTATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (18 bp):
TATTCAGTAACAGTCAAG
Found at i:28371131 original size:96 final size:96
Alignment explanation
Indices: 28370951--28371124 Score: 231
Period size: 96 Copynumber: 1.8 Consensus size: 96
28370941 GGTCGTTACA
* * * * *
28370951 AATCTGCTCTACTGCATCTTCAGAGAGACAAGATTTGCTATTTTAAATCTACTCCGCTGTAACTT
1 AATCTGCTCCACTGCAACTTCAGAGAGACAAGATTTGCTATCTTAAATCTACTCCACTGCAACTT
**
28371016 TGGGGAGATAAGATATGTAATTTGTAGCTTT
66 CAGGGAGATAAGATATGTAATTTGTAGCTTT
* * * * * *
28371047 AATCTGTTCCACTGCAACTTTAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTT
1 AATCTGCTCCACTGCAACTTCAGAGAGACAAGATTTGCTATCTTAAATCTACTCCACTGCAACTT
28371112 CAGGGAGATAAGA
66 CAGGGAGATAAGA
28371125 CTTGTAACTT
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
96 65 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (96 bp):
AATCTGCTCCACTGCAACTTCAGAGAGACAAGATTTGCTATCTTAAATCTACTCCACTGCAACTT
CAGGGAGATAAGATATGTAATTTGTAGCTTT
Found at i:28371325 original size:96 final size:96
Alignment explanation
Indices: 28371176--28371354 Score: 229
Period size: 96 Copynumber: 1.9 Consensus size: 96
28371166 AGGTTCATAA
* * * *
28371176 CTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATATTCTATTTTAAATCTACTCCACTGCA
1 CTTTAATCTGCTCCACTGCAACTTCAGAGAAATAAGATATTCTATCTTAAATCTACTCCACTACA
28371241 ACTTCAGGGAGATAAGATATGTAATTTGTAG
66 ACTTCAGGGAGATAAGATATGTAATTTGTAG
* * *
28371272 CTTTAATCTGTTCCACTGCAACTTCAG-GAAAATAA-A-ATTCGCTATCTTCAATCTGCTCCACT
1 CTTTAATCTGCTCCACTGCAACTTCAGAG-AAATAAGATATT--CTATCTTAAATCTACTCCACT
* *
28371334 ACAACTTTATGGAGATAAGAT
63 ACAACTTCAGGGAGATAAGAT
28371355 TTGTGTCTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
94 3 0.04
95 2 0.03
96 66 0.93
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (96 bp):
CTTTAATCTGCTCCACTGCAACTTCAGAGAAATAAGATATTCTATCTTAAATCTACTCCACTACA
ACTTCAGGGAGATAAGATATGTAATTTGTAG
Found at i:28371392 original size:44 final size:44
Alignment explanation
Indices: 28371035--28371399 Score: 311
Period size: 44 Copynumber: 8.1 Consensus size: 44
28371025 AAGATATGTA
* * * *
28371035 ATTTGTAGCTTTAATCTGTTCCACTGCAACTTTAGAGAGATAAG
1 ATTTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
* *
28371079 ATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
1 ATTTG-TATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
* * * * * *
28371124 ACTTGTAACTTCAACCTGCTCCACTACAAC-ACTAGGGAGATAAG
1 ATTTGTATCTTTAATCTGCTCCACTGCAACTTC-AGGGAGATAAG
* ** * * *
28371168 GTTCATAACTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAG
1 ATTTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
* *
28371212 ATATTCTAT-TTTAAATCTACTCCACTGCAACTTCAGGGAGATAAGATATG
1 AT-TTGTATCTTT-AATCTGCTCCACTGCAACTTCAGGGAGAT---A-A-G
* * * * *
28371262 TAATTTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGAAAATAAA
1 --ATTTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
* * * * *
28371308 ATTCGCTATCTTCAATCTGCTCCACTACAACTTTATGGAGATAAG
1 ATTTG-TATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
* * *
28371353 ATTTGTGTCTTTGATCTGCTTCACTGCAACTTCAGGGAGATAAG
1 ATTTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
28371397 ATT
1 ATT
28371400 CGCCACGATG
Statistics
Matches: 253, Mismatches: 54, Indels: 28
0.76 0.16 0.08
Matches are distributed among these distances:
43 1 0.00
44 112 0.44
45 101 0.40
47 1 0.00
48 2 0.01
49 1 0.00
50 1 0.00
51 29 0.11
52 5 0.02
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (44 bp):
ATTTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
Found at i:28379141 original size:29 final size:29
Alignment explanation
Indices: 28379084--28379141 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
28379074 CGAGTGAAGT
* * *
28379084 CCCACAATTCTGATACTTACCGTTTCGTC
1 CCCACAATTCTGATACGTACCCTTCCGTC
28379113 CCCACAATTCTGATACGTACCCTTCCGTC
1 CCCACAATTCTGATACGTACCCTTCCGTC
28379142 AGACTATCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.38, G:0.10, T:0.31
Consensus pattern (29 bp):
CCCACAATTCTGATACGTACCCTTCCGTC
Found at i:28380996 original size:31 final size:31
Alignment explanation
Indices: 28380944--28381005 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
28380934 CACTAATAGT
*
28380944 AATAATAATAAAATGTGTAAATA-AAGGAATA
1 AATAATAATAAAATGTCTAAATACAA-GAATA
*
28380975 AATAATCATATAAAT-TCTAAATACAAGAATA
1 AATAATAATA-AAATGTCTAAATACAAGAATA
28381006 GTAAAAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 21 0.78
32 6 0.22
ACGTcount: A:0.60, C:0.05, G:0.08, T:0.27
Consensus pattern (31 bp):
AATAATAATAAAATGTCTAAATACAAGAATA
Found at i:28386115 original size:43 final size:43
Alignment explanation
Indices: 28386067--28386153 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
28386057 TTTTCTATCC
28386067 GTATTGATTTTATTTTTGAAATTTTATTTTGTTCTGCACTTTA
1 GTATTGATTTTATTTTTGAAATTTTATTTTGTTCTGCACTTTA
28386110 GTATTGATTTTATTTTTGAAATTTTATTTTGTTCTGCACTTTA
1 GTATTGATTTTATTTTTGAAATTTTATTTTGTTCTGCACTTTA
28386153 G
1 G
28386154 GCTAACCTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.21, C:0.07, G:0.13, T:0.60
Consensus pattern (43 bp):
GTATTGATTTTATTTTTGAAATTTTATTTTGTTCTGCACTTTA
Found at i:28392072 original size:30 final size:30
Alignment explanation
Indices: 28392036--28392096 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
28392026 CTCCCAAAGG
28392036 TAAGATTATTAATCTAAACTAAGTAAACAA
1 TAAGATTATTAATCTAAACTAAGTAAACAA
28392066 TAAGATTATTAATCTAAACTAAGTAAACAA
1 TAAGATTATTAATCTAAACTAAGTAAACAA
28392096 T
1 T
28392097 CTTTGATCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (30 bp):
TAAGATTATTAATCTAAACTAAGTAAACAA
Found at i:28394865 original size:22 final size:20
Alignment explanation
Indices: 28394829--28394872 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
28394819 AAATGGTAGT
* *
28394829 AAAATAGTGAGAAAATAACAAG
1 AAAATAGT-A-AAAAAAAAAAG
28394851 AAAATAGTAAAAAAAAAAAG
1 AAAATAGTAAAAAAAAAAAG
28394871 AA
1 AA
28394873 TAGGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 1 0.05
22 8 0.40
ACGTcount: A:0.73, C:0.02, G:0.14, T:0.11
Consensus pattern (20 bp):
AAAATAGTAAAAAAAAAAAG
Found at i:28396451 original size:16 final size:16
Alignment explanation
Indices: 28396432--28396463 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28396422 TAATTTAATT
*
28396432 AATTAATAAAAATTAA
1 AATTAAAAAAAATTAA
28396448 AATTAAAAAAAATTAA
1 AATTAAAAAAAATTAA
28396464 CTCCAAATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AATTAAAAAAAATTAA
Found at i:28396989 original size:4 final size:4
Alignment explanation
Indices: 28396980--28397016 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
28396970 ATATATGCAT
28396980 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
28397017 CATATATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:28407761 original size:16 final size:16
Alignment explanation
Indices: 28407740--28407770 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28407730 CCAGAATAGG
28407740 AATGAAGTTAATTTTA
1 AATGAAGTTAATTTTA
28407756 AATGAAGTTAATTTT
1 AATGAAGTTAATTTT
28407771 GTCTTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (16 bp):
AATGAAGTTAATTTTA
Found at i:28409584 original size:16 final size:17
Alignment explanation
Indices: 28409546--28409587 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
28409536 GGCTCAAATG
* *
28409546 AAATTTAATTTTCTATT
1 AAATTTAAATTTCTATA
28409563 AAATTTAAATTT-TATA
1 AAATTTAAATTTCTATA
28409579 AAATTTAAA
1 AAATTTAAA
28409588 GGGCCAAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTTAAATTTCTATA
Found at i:28413287 original size:34 final size:34
Alignment explanation
Indices: 28413249--28413315 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
28413239 ATGTCTTAGA
28413249 ATGTCGTTTTCGATCTATTTTCTATTGTTTGAGT
1 ATGTCGTTTTCGATCTATTTTCTATTGTTTGAGT
28413283 ATGTCGTTTTCGATCTATTTTCTATTGTTTGAG
1 ATGTCGTTTTCGATCTATTTTCTATTGTTTGAG
28413316 ATACTTGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.15, C:0.12, G:0.18, T:0.55
Consensus pattern (34 bp):
ATGTCGTTTTCGATCTATTTTCTATTGTTTGAGT
Found at i:28415545 original size:19 final size:19
Alignment explanation
Indices: 28415503--28415539 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
28415493 CGAAGTTTTA
28415503 AAATAGATAAAAAAATAAG
1 AAATAGATAAAAAAATAAG
28415522 AAATAGA-AATAAAAATAA
1 AAATAGATAA-AAAAATAA
28415540 ATAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (19 bp):
AAATAGATAAAAAAATAAG
Found at i:28415765 original size:24 final size:23
Alignment explanation
Indices: 28415737--28415790 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
28415727 ATATACTTTA
* *
28415737 AAAAGATAAATTATATATAAATTT
1 AAAAGATAAA-CATATATAAATAT
28415761 AAAAGA-AAACATATATAAATAT
1 AAAAGATAAACATATATAAATAT
28415783 AAATAGAT
1 AAA-AGAT
28415791 TTAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 14 0.54
23 6 0.23
24 6 0.23
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (23 bp):
AAAAGATAAACATATATAAATAT
Found at i:28417671 original size:56 final size:56
Alignment explanation
Indices: 28417585--28417696 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 56
28417575 GTATTCTGTC
* * *
28417585 ACATTGGTCGGTGGTACCTTTCTACTAACATTGTTAGTTTGTGTTGGTGTGACACT
1 ACATTGGTCGGTGGTACCTCTCCACTAACATTGTTAGCTTGTGTTGGTGTGACACT
*
28417641 ACATTGGTTGGTGGTACCTCTCCACTAACATTGTTAGCTTGTGTTGGTGTGACACT
1 ACATTGGTCGGTGGTACCTCTCCACTAACATTGTTAGCTTGTGTTGGTGTGACACT
28417697 GATATTCAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (56 bp):
ACATTGGTCGGTGGTACCTCTCCACTAACATTGTTAGCTTGTGTTGGTGTGACACT
Found at i:28418408 original size:21 final size:23
Alignment explanation
Indices: 28418383--28418430 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
28418373 GAATATGATT
*
28418383 TAAATTGAAAG-TTTTTGATAGA
1 TAAATTGAAAGATTATTGATAGA
28418405 -AAA-TGAAAGATTATTGATAGA
1 TAAATTGAAAGATTATTGATAGA
28418426 TAAAT
1 TAAAT
28418431 CACTTTTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 6 0.27
21 13 0.59
22 3 0.14
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.35
Consensus pattern (23 bp):
TAAATTGAAAGATTATTGATAGA
Found at i:28419611 original size:25 final size:23
Alignment explanation
Indices: 28419559--28419613 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
28419549 TATAAATAGT
28419559 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
28419582 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
28419607 AATAGTG
1 AATAGTG
28419614 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:28419719 original size:76 final size:73
Alignment explanation
Indices: 28419639--28419807 Score: 167
Period size: 76 Copynumber: 2.2 Consensus size: 73
28419629 ATGTTAAGAT
* * * * *
28419639 ATATATAATATATACATATGTATAAAATAGATATAAAAAAATATGTACATAATATAGTGTAAAAA
1 ATATATAATATATACATAAG-ATAAAAT-G-TAGAAAAAAA-ATATAAATAATATAGTATAAAAA
28419704 ATACATACATAA
62 ATACATACATAA
* * * *
28419716 TATAATTAAAATATATACATAAGATAACATGTAGAAAAAAAATATAAATAATATAGTATTAAAGA
1 -AT-A-TATAATATATACATAAGATAAAATGTAGAAAAAAAATATAAATAATATAGTATAAAAAA
*
28419781 TATATACATAAA
63 TACATACAT-AA
28419793 ATAGTATAATATATA
1 ATA-TATAATATATA
28419808 TACGTAATAT
Statistics
Matches: 76, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
75 11 0.14
76 29 0.38
77 11 0.14
78 3 0.04
79 7 0.09
80 15 0.20
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (73 bp):
ATATATAATATATACATAAGATAAAATGTAGAAAAAAAATATAAATAATATAGTATAAAAAATAC
ATACATAA
Found at i:28419785 original size:25 final size:25
Alignment explanation
Indices: 28419679--28419885 Score: 105
Period size: 23 Copynumber: 8.6 Consensus size: 25
28419669 ATATAAAAAA
* * * *
28419679 ATATGTACATAATATAGTGTAAAAA
1 ATATATACATAATATAGTATTAAAG
*
28419704 ATACATACATAATATA--ATTAAA-
1 ATATATACATAATATAGTATTAAAG
* ** *
28419726 ATATATACATAAGATAACATGTAGAAAAA
1 ATATATACAT-A-AT-ATA-GTATTAAAG
* *
28419755 AAATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAGTATTAAAG
* *
28419780 ATATATACATAAAATAGTA-T-AAT
1 ATATATACATAATATAGTATTAAAG
* * *
28419803 ATATATACGTAATATAGAATT-TAG
1 ATATATACATAATATAGTATTAAAG
* *
28419827 A-ATATACCTAATATA-T-TAAAAG
1 ATATATACATAATATAGTATTAAAG
* *
28419849 AATATATATATAATATAATATTAAA-
1 -ATATATACATAATATAGTATTAAAG
28419874 A-ATATA-ATAATA
1 ATATATACATAATA
28419886 ACAAAAAAAG
Statistics
Matches: 139, Mismatches: 30, Indels: 29
0.70 0.15 0.15
Matches are distributed among these distances:
21 1 0.01
22 17 0.12
23 42 0.30
24 19 0.14
25 39 0.28
26 6 0.04
27 2 0.01
28 5 0.04
29 8 0.06
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (25 bp):
ATATATACATAATATAGTATTAAAG
Found at i:28419791 original size:29 final size:28
Alignment explanation
Indices: 28419687--28419792 Score: 77
Period size: 25 Copynumber: 4.0 Consensus size: 28
28419677 AAATATGTAC
* *
28419687 ATAATATAGT-GTAAAA-A-ATACATAC
1 ATAATATAGTATTAAAATATATACATAA
28419712 ATAATATA--ATTAAAATATATACATAA
1 ATAATATAGTATTAAAATATATACATAA
* * * *
28419738 GATAACAT-GTA-GAAAA-A-AAATATAA
1 -ATAATATAGTATTAAAATATATACATAA
28419763 ATAATATAGTATTAAAGATATATACATAA
1 ATAATATAGTATTAAA-ATATATACATAA
28419792 A
1 A
28419793 ATAGTATAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 18
0.68 0.11 0.20
Matches are distributed among these distances:
24 11 0.18
25 18 0.30
26 11 0.18
27 11 0.18
28 2 0.03
29 7 0.12
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (28 bp):
ATAATATAGTATTAAAATATATACATAA
Found at i:28420200 original size:16 final size:16
Alignment explanation
Indices: 28420162--28420200 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28420152 ATCTCCAAAA
*
28420162 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
28420178 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
28420194 AATAACT
1 AAAAACT
28420201 CTTCTCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:28420392 original size:30 final size:30
Alignment explanation
Indices: 28420356--28420453 Score: 178
Period size: 30 Copynumber: 3.3 Consensus size: 30
28420346 AGGTACAAGT
*
28420356 GGTGGTGGAGCAAGTGTGGCTAATGGAGTA
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
28420386 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
*
28420416 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTT
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
28420446 GGTGGTGG
1 GGTGGTGG
28420454 CAAAGGCTAG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.18, C:0.06, G:0.51, T:0.24
Consensus pattern (30 bp):
GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
Found at i:28420413 original size:18 final size:18
Alignment explanation
Indices: 28420390--28420443 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
28420380 GGAGTAGGTG
28420390 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
*
28420408 GTGGAG-TAG-GT-G---
1 GTGGAGCAAGTGTGGCTA
28420420 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
28420438 GTGGAG
1 GTGGAG
28420444 TTGGTGGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 6 0.21
13 2 0.07
14 2 0.07
15 2 0.07
16 2 0.07
17 2 0.07
18 12 0.43
ACGTcount: A:0.20, C:0.07, G:0.50, T:0.22
Consensus pattern (18 bp):
GTGGAGCAAGTGTGGCTA
Found at i:28421357 original size:91 final size:89
Alignment explanation
Indices: 28421144--28421654 Score: 426
Period size: 91 Copynumber: 5.7 Consensus size: 89
28421134 AAAAACAGAA
* ** * *
28421144 ATTGAAAATAGCTCAGCACGTGAGCC-AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
1 ATTGAAAATACCTCAGCGTGTGA-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
* * *
28421208 --AAAACAAAATTTGTAAAACAGAT
65 GCAAAACAAAATTTGAAAAAAAAAT
* * ** * *
28421231 TTTGAAAATACCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTG
1 ATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
*
28421296 CAAAGCATAAA-TTGAAAAAAAAAT
66 CAAAACA-AAATTTGAAAAAAAAAT
* *
28421320 CAATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 --ATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TT
*
28421385 TTTG-ACAAACATAAA-TTGAAAAAAAAAGAA
62 TTTGCA-AAACA-AAATTTG-AAAAAAAA-AT
* *
28421415 ATTGAAAATATCTCAGCGTGT--CCTGAGGCTGAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 ATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTT
* *
28421478 GGAAAAACAAAATTTGAAAAACAGAAT
65 -GCAAAACAAAATTTGAAAAA-AAAAT
* * * *
28421505 -TTGAAAATACCTCAGCGTGTGA-GTCAAGGCTCAACTCACCACTCGCAATATGAGCTGATTTTT
1 ATTGAAAATACCTCAGCGTGTGACCT-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTT
* *
28421568 TTG-AAACACAGAAA-TTGAAGAACAGAA-
63 TTGCAAA-ACA-AAATTTGAA-AAAAAAAT
* * * * * *
28421595 ATGGAAAACACCTCAGC-T-T--CTTGAGGTTCAACTCACTTCTCGCAATATGAGCTGATTTTT
1 ATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
28421655 TTTGAAAGAC
Statistics
Matches: 360, Mismatches: 40, Indels: 50
0.80 0.09 0.11
Matches are distributed among these distances:
85 5 0.01
86 2 0.01
87 82 0.23
88 1 0.00
89 35 0.10
90 23 0.06
91 154 0.43
92 13 0.04
93 36 0.10
94 8 0.02
95 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (89 bp):
ATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
CAAAACAAAATTTGAAAAAAAAAT
Found at i:28421511 original size:13 final size:14
Alignment explanation
Indices: 28421479--28421511 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
28421469 TGATTTTTTG
28421479 GAAAAACAAAATTT
1 GAAAAACAAAATTT
*
28421493 GAAAAACAGAATTT
1 GAAAAACAAAATTT
28421507 GAAAA
1 GAAAA
28421512 TACCTCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.64, C:0.06, G:0.12, T:0.18
Consensus pattern (14 bp):
GAAAAACAAAATTT
Found at i:28421511 original size:182 final size:172
Alignment explanation
Indices: 28421134--28422046 Score: 642
Period size: 147 Copynumber: 5.5 Consensus size: 172
28421124 ACTAGACATT
* ** * * *
28421134 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGATCTAAGGCTCAACTCACCTCTCGCAATATGAG
* ** * * * *
28421199 TTGATTTTT-AAAACAAAATTTGTAAAACAGATTTTGAAAATACCTCGGTATGTGACCCGAGGCT
66 TTGATTTTTGAAAACAAAA-TTGAAAAACAGAAATTGAAAATACCTCAG--CGTGTCCTGAGGCT
*
28421263 CAACTCACCTCTCGTAATATGAGTTGATTTTTGCAAAGCATAAA-TTG
128 CAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAA-CA-AAATTTG
* * * *
28421310 AAAAAAAAATCAATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATG
1 AAAAACAGA--AATTGAAAATACCTCAGCGTGTGATCTAAGGCTCAACTCACCTCTCGCAATATG
* *
28421375 AGTTGATTTTTTTGACAAACATAAATTGAAAAAAAAAGAAATTGAAAATATCTCAGCGTGTCCTG
64 AGTTGA--TTTTTGA-AAACA-AAATTG--AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTG
*
28421440 AGGCTGAACTCACCTCTCGCAATATGAGTTGATTTTTTGGAAAAACAAAATTTG
123 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTT-G--AAACAAAATTTG
* *
28421494 AAAAACAGAATTTGAAAATACCTCAGCGTGTGAGTC-AAGGCTCAACTCACCACTCGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGA-TCTAAGGCTCAACTCACCTCTCGCAATATGA
* * * * *
28421558 GCTGATTTTTTTGAAACACAGAAATTGAAGAACAGAAATGGAAAACACCTCAGC-T-TCTTGAGG
65 GTTGA--TTTTTGAAA-ACA-AAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGG
* * *
28421621 TTCAACTCACTTCTCGCAATATGAGCTGATTTTT---------TTTG
126 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACAAAATTTG
* * * *
28421659 AAAGACAGAAATTGAAAATACCTCAACGTGT-CT-TGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGATCTAAGGCTCAACTCACCTCTCGCAATATGAG
* * * *
28421722 TTGATTTTTG---AC---------AAACAAAAATTGAAATTACCTCAGC--GTCTTGAGGTTCAA
66 TTGATTTTTGAAAACAAAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAA
*
28421773 CTCACCTATCGCAATATGAGTTGATTTTT---------TTTG
131 CTCACCTCTCGCAATATGAGTTGATTTTTGAAACAAAATTTG
* * * *
28421806 AAAAACAGAAATTGAAAATACCTCAACGTGT-CT-TGAGGTTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGATCTAAGGCTCAACTCACCTCTCGCAATATGAG
* * * * *
28421869 CTGATTTTT----------TTTAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAA
66 TTGATTTTTGAAAACAAAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAA
28421924 CTCACCTCTCGCAATATGAGTTGATTTTTG--AC--------
131 CTCACCTCTCGCAATATGAGTTGATTTTTGAAACAAAATTTG
* * * * *
28421956 --AAACAAAAATTGAAATTACCTCAGCGTGT--CCTGAGGCTCAACTCACCTATCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGATCTAAGGCTCAACTCACCTCTCGCAATATGAG
28422017 TTGATTTTTTTGAAAAACAGAAATTGAAAA
66 TTGA--TTTTTG-AAAACA-AAATTGAAAA
28422047 TACTTTGAGG
Statistics
Matches: 622, Mismatches: 73, Indels: 98
0.78 0.09 0.12
Matches are distributed among these distances:
147 132 0.21
148 57 0.09
149 21 0.03
150 5 0.01
151 41 0.07
157 2 0.00
161 6 0.01
162 5 0.01
163 31 0.05
165 32 0.05
176 7 0.01
177 5 0.01
178 84 0.14
179 1 0.00
180 27 0.04
181 3 0.00
182 114 0.18
183 13 0.02
184 33 0.05
185 3 0.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (172 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGTGATCTAAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTGAAAACAAAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAA
CTCACCTCTCGCAATATGAGTTGATTTTTGAAACAAAATTTG
Found at i:28421803 original size:73 final size:73
Alignment explanation
Indices: 28421588--28422183 Score: 668
Period size: 73 Copynumber: 8.2 Consensus size: 73
28421578 GAAATTGAAG
* * * * * *
28421588 AACAGAAATGGAAAACACCTCAGCTTCTTGAGGTTCAACTCACTTCTCGCAATATGAGCTGATTT
1 AACAGAAATTGAAAATACCTCAGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TT
28421653 TTTTTGA-A
65 TTTTTGACA
*
28421661 AGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 A-ACAGAAATTGAAAATACCTC-A-GCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
28421726 --TTTTTGACA
63 TTTTTTTGACA
* * * *
28421735 AACAAAAATTGAAATTACCTCAGCGTCTTGAGGTTCAACTCACCTATCGCAATATGAGTTGATTT
1 AACAGAAATTGAAAATACCTCAGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TT
*
28421800 TTTTTGAAA
65 TTTTTGACA
* * *
28421809 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGAT
1 AACAGAAATTGAAAATACCTC-A-GCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
28421874 TTTTTTTA-A
64 TTTTTTGACA
*
28421883 AGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 A-ACAGAAATTGAAAATACCTC-A-GCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
28421948 --TTTTTGACA
63 TTTTTTTGACA
* * * *
28421957 AACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGC--GTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
28422022 TTTTTTGAAA
64 TTTTTTGACA
* *
28422032 AACAGAAATTG-AAA-A--T-A-C-T-TTGAGGCTCAACTCACCTCTTGCAATATGAGTTGA--G
1 AACAGAAATTGAAAATACCTCAGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
28422087 TTTTGACA
66 TTTTGACA
* * * *
28422095 AACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGC--GTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
28422160 TTTTTT-AGA
64 TTTTTTGACA
* *
28422169 AACATAAATTAAAAA
1 AACAGAAATTGAAAA
28422184 AAGAAAATTG
Statistics
Matches: 451, Mismatches: 45, Indels: 53
0.82 0.08 0.10
Matches are distributed among these distances:
63 17 0.04
64 2 0.00
65 33 0.07
66 1 0.00
67 1 0.00
68 1 0.00
69 2 0.00
70 1 0.00
71 39 0.09
72 3 0.01
73 119 0.26
74 67 0.15
75 93 0.21
76 72 0.16
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Consensus pattern (73 bp):
AACAGAAATTGAAAATACCTCAGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
TTTTGACA
Found at i:28421874 original size:147 final size:143
Alignment explanation
Indices: 28421582--28422178 Score: 706
Period size: 147 Copynumber: 4.1 Consensus size: 143
28421572 AACACAGAAA
* * * * * *
28421582 TTGAAGAACAGAAATGGAAAACACCTCAGCTTCTTGAGGTTCAACTCACTTCTCGCAATATGAGC
1 TTGAA-AACAGAAATTG-AAATACCTCAGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
* * *
28421647 TGATTTTTTTTGAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTC
64 TGA---TTTTTGAAAAACAAAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTC
28421712 GCAATATGAGTTGA-TTT
126 GCAATATGAGTTGATTTT
* * *
28421729 TTGACAAACAAAAATTGAAATTACCTCAGCGTCTTGAGGTTCAACTCACCTATCGCAATATGAGT
1 TTGA-AAACAGAAATTGAAA-TACCTCAGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
* * *
28421794 TGATTTTTTTTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTC
64 TGA---TTTTTGAAAAACAAAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTC
*
28421859 GCAATATGAGCTGATTTTT
126 GCAATATGAGTTGA-TTTT
* *
28421878 TTTAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAA-ACAGAAATTG-AAATACCTC-A-GCGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
* * * *
28421943 GTTGATTTTTGACAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTATCG
62 GTTGATTTTTGAAAAACAAAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCG
28422008 CAATATGAGTTGATTTTT
127 CAATATGAGTTGA-TTTT
*
28422026 TTGAAAAACAGAAATTGAAA-A--T-A-C-T-TTGAGGCTCAACTCACCTCTTGCAATATGAGTT
1 TTG-AAAACAGAAATTGAAATACCTCAGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* * * * *
28422084 GAGTTTTGACAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAA
65 GATTTTTGAAAAACAAAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAA
28422149 TATGAGTTGATTTT
130 TATGAGTTGATTTT
* *
28422163 TTTAGAAACATAAATT
1 TTGA-AAACAGAAATT
28422179 AAAAAAAGAA
Statistics
Matches: 409, Mismatches: 31, Indels: 30
0.87 0.07 0.06
Matches are distributed among these distances:
136 1 0.00
137 16 0.04
138 104 0.25
139 1 0.00
142 1 0.00
144 1 0.00
146 4 0.01
147 131 0.32
148 85 0.21
149 24 0.06
150 4 0.01
151 37 0.09
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (143 bp):
TTGAAAACAGAAATTGAAATACCTCAGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTGAAAAACAAAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
ATGAGTTGATTTT
Found at i:28422387 original size:14 final size:13
Alignment explanation
Indices: 28422352--28422396 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
28422342 TTGATTTTTG
28422352 AAAAACAGAAATT
1 AAAAACAGAAATT
*
28422365 AAAAGCAGAAATT
1 AAAAACAGAAATT
28422378 GAAAAACAGAAATT
1 -AAAAACAGAAATT
28422392 AAAAA
1 AAAAA
28422397 TACCTCGGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.69, C:0.07, G:0.11, T:0.13
Consensus pattern (13 bp):
AAAAACAGAAATT
Found at i:28422417 original size:100 final size:101
Alignment explanation
Indices: 28422174--28422540 Score: 453
Period size: 100 Copynumber: 3.8 Consensus size: 101
28422164 TTAGAAACAT
* *
28422174 AAATT-AAAAAAAGAAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
1 AAATTGAAAAACAG-AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAAT
* * * *
28422238 ATGAGTTGA--TTTGAAAAGCAGAATTTGTAAGGCAA
65 ATGAGTTGATTTTTGAAAAGCAGAAATTGAAAAGCAG
28422273 AAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATA
1 AAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATA
*
28422338 TGAGTTGATTTTTGAAAAACAGAAATT-AAAAGCAG
66 TGAGTTGATTTTTGAAAAGCAGAAATTGAAAAGCAG
* * * *
28422373 AAATTGAAAAACAGAAATTAAAAATACCTCGGCGTGCCCCGAGGCTCAGCTCACCTCTCGCAATA
1 AAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATA
*
28422438 TGAGTTGATTTTTGAAAAGCATAAATT--------G
66 TGAGTTGATTTTTGAAAAGCAGAAATTGAAAAGCAG
* * *
28422466 --A---AAAAACGGAAATTGAAAATACCTCAGCGTGTGACCTGAGGCCCAACTCACCTCTCGCAA
1 AAATTGAAAAACAGAAATTGAAAATACCTCAGC--GTGCCCTGAGGCTCAACTCACCTCTCGCAA
28422526 TATGAGTTGATTTTT
64 TATGAGTTGATTTTT
28422541 TTGAAAGATA
Statistics
Matches: 243, Mismatches: 20, Indels: 19
0.86 0.07 0.07
Matches are distributed among these distances:
88 24 0.10
90 41 0.17
91 1 0.00
93 1 0.00
99 63 0.26
100 98 0.40
101 15 0.06
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (101 bp):
AAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATA
TGAGTTGATTTTTGAAAAGCAGAAATTGAAAAGCAG
Found at i:28422533 original size:90 final size:87
Alignment explanation
Indices: 28422365--28422540 Score: 253
Period size: 90 Copynumber: 2.0 Consensus size: 87
28422355 AACAGAAATT
* * *
28422365 AAAAGCAGAAATTGAAAAACAGAAATTAAAAATACCTCGGCGTGCCCCGAGGCTCAGCTCACCTC
1 AAAAGCAGAAATTGAAAAACAGAAATTAAAAATACCTCGGCGTGACCCGAGGCCCAACTCACCTC
28422430 TCGCAATATGAGTTGATTTTTG
66 TCGCAATATGAGTTGATTTTTG
* * * * *
28422452 AAAAGCATAAATTGAAAAAACGGAAATTGAAAATACCTCAGCGTGTGACCTGAGGCCCAACTCAC
1 AAAAGCAGAAATTG-AAAAACAGAAATTAAAAATACCTC-G-GCGTGACCCGAGGCCCAACTCAC
28422517 CTCTCGCAATATGAGTTGATTTTT
63 CTCTCGCAATATGAGTTGATTTTT
28422541 TTGAAAGATA
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
87 13 0.17
88 22 0.28
89 1 0.01
90 42 0.54
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (87 bp):
AAAAGCAGAAATTGAAAAACAGAAATTAAAAATACCTCGGCGTGACCCGAGGCCCAACTCACCTC
TCGCAATATGAGTTGATTTTTG
Found at i:28433561 original size:26 final size:25
Alignment explanation
Indices: 28433480--28433561 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 25
28433470 CATAATAAAG
28433480 ATATTAAGAGTATGTACGTAAAATA
1 ATATTAAGAGTATGTACGTAAAATA
* ** * * *
28433505 AAAACAACGAATATATACATAATAA-A
1 ATATTAA-GAGTATGTACGTAA-AATA
28433531 GATATTAAGAGTATGTACGTAAAATA
1 -ATATTAAGAGTATGTACGTAAAATA
28433557 TATAT
1 -ATAT
28433562 ATATTTATAA
Statistics
Matches: 40, Mismatches: 13, Indels: 7
0.67 0.22 0.12
Matches are distributed among these distances:
25 6 0.15
26 28 0.70
27 6 0.15
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (25 bp):
ATATTAAGAGTATGTACGTAAAATA
Found at i:28433629 original size:25 final size:23
Alignment explanation
Indices: 28433577--28433631 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
28433567 TATAAATAGT
28433577 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
28433600 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
28433625 AATAGTG
1 AATAGTG
28433632 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:28433808 original size:29 final size:28
Alignment explanation
Indices: 28433704--28433809 Score: 86
Period size: 25 Copynumber: 4.0 Consensus size: 28
28433694 AAAAATGTAC
* *
28433704 ATAATATAGT-GTAAAA-A-ATACATAC
1 ATAATATAGTATTAAAATATATACATAA
28433729 ATAATATA--ATTAAAATATATACATAA
1 ATAATATAGTATTAAAATATATACATAA
* * *
28433755 GATAACAT-GTA-GAAAA-A-ATATATAA
1 -ATAATATAGTATTAAAATATATACATAA
28433780 ATAATATAGTATTAAAGATATATACATAA
1 ATAATATAGTATTAAA-ATATATACATAA
28433809 A
1 A
28433810 ATAGTATAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
24 11 0.18
25 19 0.31
26 11 0.18
27 11 0.18
28 2 0.03
29 8 0.13
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.30
Consensus pattern (28 bp):
ATAATATAGTATTAAAATATATACATAA
Found at i:28433823 original size:23 final size:25
Alignment explanation
Indices: 28433701--28433905 Score: 104
Period size: 23 Copynumber: 8.4 Consensus size: 25
28433691 AAAAAAAATG
* * * *
28433701 TACATAATATAGTGTAAAAAATACA
1 TACATAATATAGTATTAAAGATATA
28433726 TACATAATATA--ATTAAA-ATATA
1 TACATAATATAGTATTAAAGATATA
* ** *
28433748 TACATAAGATAACATGTAGAAAAAATATA
1 TACAT-A-AT-ATA-GTATTAAAGATATA
*
28433777 TAAATAATATAGTATTAAAGATATA
1 TACATAATATAGTATTAAAGATATA
* *
28433802 TACATAAAATAGTA-T-AATATATA
1 TACATAATATAGTATTAAAGATATA
* * *
28433825 TACGTAATATAGAATT-TAGA-ATA
1 TACATAATATAGTATTAAAGATATA
* * ** *
28433848 TACCTAATATATTAAAAGAATATATA
1 TACATAATATAGTATTA-AAGATATA
* * *
28433874 TATATAATATAATATT-AAGAAATA
1 TACATAATATAGTATTAAAGATATA
28433898 TA-ATAATA
1 TACATAATA
28433906 ACAAAAAAAA
Statistics
Matches: 136, Mismatches: 33, Indels: 24
0.70 0.17 0.12
Matches are distributed among these distances:
22 9 0.07
23 43 0.32
24 14 0.10
25 38 0.28
26 16 0.12
27 2 0.01
28 5 0.04
29 9 0.07
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.33
Consensus pattern (25 bp):
TACATAATATAGTATTAAAGATATA
Found at i:28434226 original size:16 final size:16
Alignment explanation
Indices: 28434188--28434226 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
28434178 ATCTCCAAAA
*
28434188 AAAAACTAGCCTTTCC
1 AAAAACTAGCCTTTAC
28434204 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTTTAC
*
28434220 AATAACT
1 AAAAACT
28434227 CTTCTCCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.26
Consensus pattern (16 bp):
AAAAACTAGCCTTTAC
Found at i:28434422 original size:30 final size:30
Alignment explanation
Indices: 28434386--28434483 Score: 160
Period size: 30 Copynumber: 3.3 Consensus size: 30
28434376 AGGTACAAGT
*
28434386 GGTGGTGGAGCAAGTGTGGCTAATGGAGTA
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
*
28434416 GGTGGTGGAGTAAGTGTGGCTAGTGGAGTA
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
* *
28434446 GGTGGTAGAGCAAGTGTGGCTAGTGGAGTT
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
28434476 GGTGGTGG
1 GGTGGTGG
28434484 CAAAGGCTAG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.19, C:0.05, G:0.50, T:0.26
Consensus pattern (30 bp):
GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
Found at i:28434443 original size:18 final size:18
Alignment explanation
Indices: 28434420--28434474 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
28434410 GGAGTAGGTG
28434420 GTGGAGTAAGTGTGGCTA
1 GTGGAGTAAGTGTGGCTA
28434438 GTGGAGT-AG-GTGG-TA
1 GTGGAGTAAGTGTGGCTA
*
28434453 ---GAGCAAGTGTGGCTA
1 GTGGAGTAAGTGTGGCTA
28434468 GTGGAGT
1 GTGGAGT
28434475 TGGTGGTGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
12 3 0.10
13 2 0.07
14 4 0.14
15 4 0.14
16 4 0.14
17 2 0.07
18 10 0.34
ACGTcount: A:0.22, C:0.05, G:0.47, T:0.25
Consensus pattern (18 bp):
GTGGAGTAAGTGTGGCTA
Found at i:28435142 original size:32 final size:32
Alignment explanation
Indices: 28435106--28435293 Score: 135
Period size: 33 Copynumber: 5.8 Consensus size: 32
28435096 GGTTATGTAC
* *
28435106 ACTTTGTGTGTATACTTGGAAAGGAAAGGTAT
1 ACTTTGTGTGTACACTTGAAAAGGAAAGGTAT
*
28435138 ACTTTGTGTATAC-CATATGAAAAGGAAAGGTAT
1 ACTTTGTGTGTACAC-T-TGAAAAGGAAAGGTAT
* * *
28435171 ATTTTGTGTATACCACTTGAAAAGGAAAGGTAC
1 ACTTTGTGTGTA-CACTTGAAAAGGAAAGGTAT
* * * ** * **
28435204 ACTATATGTGTACACTTGAAAATGTTATGTGC
1 ACTTTGTGTGTACACTTGAAAAGGAAAGGTAT
* * ** * *
28435236 ACTTTGAGTGTACAAATTGAAAAGGGTATGTAC
1 ACTTTGTGTGTAC-ACTTGAAAAGGAAAGGTAT
*
28435269 ACTTTGTATGTACCACTTGAAAAGG
1 ACTTTGTGTGTA-CACTTGAAAAGG
28435294 GAATGTGCAC
Statistics
Matches: 126, Mismatches: 24, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
31 1 0.01
32 37 0.29
33 84 0.67
34 3 0.02
35 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (32 bp):
ACTTTGTGTGTACACTTGAAAAGGAAAGGTAT
Found at i:28435166 original size:33 final size:33
Alignment explanation
Indices: 28435106--28435225 Score: 138
Period size: 33 Copynumber: 3.7 Consensus size: 33
28435096 GGTTATGTAC
* * *
28435106 ACTTTGTGTGTA-TACTTGGAAAGGAAAGGTAT
1 ACTTTGTGTATACCACTTGAAAAGGAAAGGTAT
28435138 ACTTTGTGTATACCA-TATGAAAAGGAAAGGTAT
1 ACTTTGTGTATACCACT-TGAAAAGGAAAGGTAT
* *
28435171 ATTTTGTGTATACCACTTGAAAAGGAAAGGTAC
1 ACTTTGTGTATACCACTTGAAAAGGAAAGGTAT
* * *
28435204 ACTATATGTGTA-CACTTGAAAA
1 ACTTTGTGTATACCACTTGAAAA
28435226 TGTTATGTGC
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
32 22 0.29
33 53 0.70
34 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (33 bp):
ACTTTGTGTATACCACTTGAAAAGGAAAGGTAT
Found at i:28435258 original size:33 final size:33
Alignment explanation
Indices: 28435211--28435325 Score: 126
Period size: 33 Copynumber: 3.5 Consensus size: 33
28435201 TACACTATAT
* *
28435211 GTGTAC-ACTTGAAAATGTTATGTGCACTTTGA
1 GTGTACAACTTGAAAAGGGTATGTGCACTTTGA
* *
28435243 GTGTACAAATTGAAAAGGGTATGTACACTTTGTA
1 GTGTACAACTTGAAAAGGGTATGTGCACTTTG-A
* * * *
28435277 -TGTACCACTTGAAAAGGGAATGTGCACCTCGA
1 GTGTACAACTTGAAAAGGGTATGTGCACTTTGA
*
28435309 GTGTACAACTAGAAAAG
1 GTGTACAACTTGAAAAG
28435326 AAAAAGTCCA
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
32 7 0.10
33 60 0.88
34 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (33 bp):
GTGTACAACTTGAAAAGGGTATGTGCACTTTGA
Found at i:28441114 original size:44 final size:45
Alignment explanation
Indices: 28441061--28441163 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 45
28441051 TGTCTTTGAC
* * *
28441061 ATGGACTTACATGAATTATTCCTGTCTCCAATGCC-ATATATAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCAATATATAAT
** * * *
28441105 ATGGACTTACATGGCTCAATCCTGTCTCTAAAGCCAAATTTCTAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCC-AATATATAAT
28441151 ATGGACTTACATG
1 ATGGACTTACATG
28441164 GCTCATTTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 29 0.59
46 20 0.41
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (45 bp):
ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCAATATATAAT
Found at i:28451152 original size:68 final size:67
Alignment explanation
Indices: 28451080--28451229 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
28451070 CATCATGTGT
* * * *
28451080 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
28451142 ATGTAG
62 ATGTAG
** * *
28451148 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
28451213 AG
66 AG
28451215 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
28451230 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:28451185 original size:64 final size:64
Alignment explanation
Indices: 28451104--28451287 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
28451094 AGACATTATG
* *
28451104 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
28451168 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
28451233 AA
63 AA
* * * *
28451235 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
28451288 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:28452379 original size:2 final size:2
Alignment explanation
Indices: 28452372--28452404 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
28452362 TCATGACATG
28452372 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 T
28452405 GACTAGTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28453287 original size:44 final size:45
Alignment explanation
Indices: 28453234--28453336 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 45
28453224 TGTCTTTGAC
* * * *
28453234 ATGGACTTACATGAATTATTCCTGTCTCCAATGCC-ATATATAAT
1 ATGGACTTACATGAATCAATCCTATCTCCAAAGCCAATATATAAT
** * *
28453278 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCAAATTTCTAAT
1 ATGGACTTACATGAATCAATCCTATCTCCAAAGCC-AATATATAAT
28453324 ATGGACTTACATG
1 ATGGACTTACATG
28453337 GCTCATTTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 29 0.59
46 20 0.41
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (45 bp):
ATGGACTTACATGAATCAATCCTATCTCCAAAGCCAATATATAAT
Found at i:28455785 original size:23 final size:22
Alignment explanation
Indices: 28455713--28455800 Score: 92
Period size: 21 Copynumber: 4.1 Consensus size: 22
28455703 TACCTGATTA
*
28455713 GAATACGACACATAA-GTGCCT
1 GAATACGACACACAAGGTGCCT
*
28455734 GAA-ACGACACACGAGGTGCCT
1 GAATACGACACACAAGGTGCCT
* *
28455755 G-CTGCGACACACAAGGTGCCT
1 GAATACGACACACAAGGTGCCT
* *
28455776 GAAATACGACACATAAAGTGCCT
1 G-AATACGACACACAAGGTGCCT
28455799 GA
1 GA
28455801 TCAGTAAAGC
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
20 9 0.17
21 27 0.50
22 1 0.02
23 17 0.31
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (22 bp):
GAATACGACACACAAGGTGCCT
Found at i:28455797 original size:44 final size:41
Alignment explanation
Indices: 28455718--28455799 Score: 101
Period size: 44 Copynumber: 1.9 Consensus size: 41
28455708 GATTAGAATA
* * *
28455718 CGACACATAAGTGCCTGAAACGACACACGAGGTGCCTGCTG
1 CGACACACAAGTGCCTGAAACGACACACAAAGTGCCTGCTG
*
28455759 CGACACACAAGGTGCCTGAAATACGACACATAAAGTGCCTG
1 CGACACACAA-GTGCCTG-AA-ACGACACACAAAGTGCCTG
28455800 ATCAGTAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 9 0.26
42 7 0.21
43 2 0.06
44 16 0.47
ACGTcount: A:0.33, C:0.28, G:0.24, T:0.15
Consensus pattern (41 bp):
CGACACACAAGTGCCTGAAACGACACACAAAGTGCCTGCTG
Found at i:28456017 original size:23 final size:24
Alignment explanation
Indices: 28455991--28456085 Score: 93
Period size: 28 Copynumber: 3.6 Consensus size: 24
28455981 AAATGTCCAA
28455991 CCAAAACACACCAG-TATAATCCT
1 CCAAAACACACCAGATATAATCCT
28456014 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----ATATAATCCT
*
28456042 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG----ATATAATCC-T
28456071 CCAAAACACACCAGA
1 CCAAAACACACCAGA
28456086 ATAGCACAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
23 14 0.23
25 1 0.02
28 33 0.53
29 14 0.23
ACGTcount: A:0.46, C:0.34, G:0.04, T:0.16
Consensus pattern (24 bp):
CCAAAACACACCAGATATAATCCT
Found at i:28456087 original size:29 final size:28
Alignment explanation
Indices: 28456005--28456088 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
28455995 AACACACCAG
* *
28456005 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
28456033 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
28456061 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
28456089 GCACAAAGTG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:28458476 original size:8 final size:8
Alignment explanation
Indices: 28458463--28458492 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
28458453 TTATTAAGTA
28458463 AATTTTCC
1 AATTTTCC
28458471 AATTTTCC
1 AATTTTCC
28458479 AATTTTCC
1 AATTTTCC
28458487 AATTTT
1 AATTTT
28458493 GCCCTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (8 bp):
AATTTTCC
Found at i:28459417 original size:19 final size:18
Alignment explanation
Indices: 28459373--28459410 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28459363 CTGGCTCGCC
*
28459373 AATATTAATTTTTTATAT
1 AATATTAATTTTTTACAT
*
28459391 TATATTAATTTTTTACAT
1 AATATTAATTTTTTACAT
28459409 AA
1 AA
28459411 ATTTTAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
AATATTAATTTTTTACAT
Found at i:28459448 original size:18 final size:19
Alignment explanation
Indices: 28459416--28459453 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
28459406 CATAAATTTT
* *
28459416 AAATATATAATACA-TAAA
1 AAATATAAAAAACATTAAA
28459434 AAATATAAAAAACATTAAA
1 AAATATAAAAAACATTAAA
28459453 A
1 A
28459454 TAAATATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATATAAAAAACATTAAA
Found at i:28459570 original size:13 final size:13
Alignment explanation
Indices: 28459534--28459594 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 13
28459524 TTGGCAATGT
28459534 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
* *
28459547 TGTGGAAAAGTGC
1 TTTTGAAAAGTGC
* **
28459560 TTTTGAGAAGTAT
1 TTTTGAAAAGTGC
*
28459573 TTTTGAGAAGTGC
1 TTTTGAAAAGTGC
*
28459586 TTTGGAAAA
1 TTTTGAAAA
28459595 ATTTAAGTGT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.36
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:28466193 original size:42 final size:42
Alignment explanation
Indices: 28466121--28466205 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
28466111 TGAGGTAGAA
28466121 ATGTTATCAATTTCATAAAGCGTTGAGTTGAAAGTAATAAAG
1 ATGTTATCAATTTCATAAAGCGTTGAGTTGAAAGTAATAAAG
*
28466163 ATGTTATCAATTTCATAGAAG-GTTGGGTTGAAAGTAATAAAG
1 ATGTTATCAATTTCATA-AAGCGTTGAGTTGAAAGTAATAAAG
28466205 A
1 A
28466206 CAAATCACTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 38 0.93
43 3 0.07
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (42 bp):
ATGTTATCAATTTCATAAAGCGTTGAGTTGAAAGTAATAAAG
Found at i:28472032 original size:24 final size:24
Alignment explanation
Indices: 28471989--28472037 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
28471979 TAGTTTTGTA
* ** *
28471989 TTTTTTAATTTTAATTTTTATATT
1 TTTTTTAAATTTAAAATTTAGATT
28472013 TTTTTTAAATTTAAAATTTAGATT
1 TTTTTTAAATTTAAAATTTAGATT
28472037 T
1 T
28472038 AACTGTTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTTTAAATTTAAAATTTAGATT
Found at i:28483937 original size:14 final size:14
Alignment explanation
Indices: 28483892--28483937 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
28483882 TATAAGGGTA
28483892 TTTTTACATAATTT
1 TTTTTACATAATTT
*
28483906 TTTTATAAAT-ATATT
1 TTTT-TACATAAT-TT
28483921 TTTTTACATAATTT
1 TTTTTACATAATTT
28483935 TTT
1 TTT
28483938 ATCCACATCG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTACATAATTT
Found at i:28483938 original size:12 final size:13
Alignment explanation
Indices: 28483892--28483937 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 13
28483882 TATAAGGGTA
28483892 TTTTTACATAATTT
1 TTTTTACATAA-TT
*
28483906 TTTTATAAATATATT
1 TTTT-TACATA-ATT
28483921 TTTTTACATAATT
1 TTTTTACATAATT
28483934 TTTT
1 TTTT
28483938 ATCCACATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 7 0.25
14 9 0.32
15 11 0.39
16 1 0.04
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTTTACATAATT
Found at i:28494835 original size:6 final size:6
Alignment explanation
Indices: 28494824--28494883 Score: 58
Period size: 6 Copynumber: 10.8 Consensus size: 6
28494814 AGGCAACCCA
*
28494824 ATTTTT ATTTTT ATTTTT A-TTTT A-GTTT A-TTTT ATTTTT A--TTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
* *
28494867 ATTTTT CTTATT ATTTT
1 ATTTTT ATTTTT ATTTT
28494884 CTTATTTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
4 4 0.09
5 13 0.29
6 28 0.62
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (6 bp):
ATTTTT
Found at i:28494858 original size:15 final size:15
Alignment explanation
Indices: 28494826--28494871 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
28494816 GCAACCCAAT
28494826 TTTTATTTTTA--T-
1 TTTTATTTTTATTTA
28494838 TTTTA-TTTTAGTTTA
1 TTTTATTTTTA-TTTA
28494853 TTTTATTTTTATTTA
1 TTTTATTTTTATTTA
28494868 TTTT
1 TTTT
28494872 TCTTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.17
12 5 0.17
14 1 0.03
15 13 0.45
16 5 0.17
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTATTTTTATTTA
Found at i:28494880 original size:16 final size:14
Alignment explanation
Indices: 28494833--28494882 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 14
28494823 AATTTTTATT
28494833 TTTATTTTTATTTTA
1 TTTATTTTT-TTTTA
28494848 GTTTATTTTATTTTTA
1 -TTTATTTT-TTTTTA
28494864 TTTATTTTTCTTATTA
1 TTTATTTTT-TT-TTA
28494880 TTT
1 TTT
28494883 TCTTATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.03
15 10 0.32
16 19 0.61
17 1 0.03
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTATTTTTTTTTA
Found at i:28494880 original size:27 final size:26
Alignment explanation
Indices: 28494826--28494893 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
28494816 GCAACCCAAT
28494826 TTTTATTTTTATTTTTATTTTAGTTTA
1 TTTTATTTTTATTTTTATTTTAG-TTA
*
28494853 TTTTATTTTTATTTATTTTTCTTA-TTA
1 TTTTATTTTTATTT-TTATT-TTAGTTA
*
28494880 TTTTCTTATTTATT
1 TTTTATT-TTTATT
28494894 GTTTTAGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 23 0.64
28 10 0.28
29 3 0.08
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (26 bp):
TTTTATTTTTATTTTTATTTTAGTTA
Found at i:28494892 original size:12 final size:12
Alignment explanation
Indices: 28494861--28494893 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
28494851 TATTTTATTT
28494861 TTATTTATTTTTC
1 TTATTTA-TTTTC
28494874 TTA-TTATTTTC
1 TTATTTATTTTC
28494885 TTATTTATT
1 TTATTTATT
28494894 GTTTTAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.42
12 8 0.42
13 3 0.16
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTTATTTTC
Found at i:28496025 original size:21 final size:21
Alignment explanation
Indices: 28495999--28496039 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
28495989 GAAAACTTAA
28495999 GGTTCTCTTTATTTTTCATAG
1 GGTTCTCTTTATTTTTCATAG
28496020 GGTTCTCTTTATTTTTCATA
1 GGTTCTCTTTATTTTTCATA
28496040 TGCGTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.59
Consensus pattern (21 bp):
GGTTCTCTTTATTTTTCATAG
Found at i:28496451 original size:15 final size:15
Alignment explanation
Indices: 28496431--28496460 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28496421 CATTTTATTT
*
28496431 ATATTAGGATAATTA
1 ATATTAAGATAATTA
28496446 ATATTAAGATAATTA
1 ATATTAAGATAATTA
28496461 TCAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:28497866 original size:17 final size:18
Alignment explanation
Indices: 28497828--28497864 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28497818 AAAAATTTTG
28497828 AATTTATTTCCTAATTTA
1 AATTTATTTCCTAATTTA
28497846 AATTTATTT-CTAATGTTA
1 AATTTATTTCCTAAT-TTA
28497864 A
1 A
28497865 TTAATTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (18 bp):
AATTTATTTCCTAATTTA
Found at i:28498552 original size:73 final size:73
Alignment explanation
Indices: 28498433--28498581 Score: 298
Period size: 73 Copynumber: 2.0 Consensus size: 73
28498423 CTCTGATTTG
28498433 AGCATTTAGCGTTATTCATACGACAATTATTATTGTTGATTAATATGTTGAAGCAAGTAATAGTA
1 AGCATTTAGCGTTATTCATACGACAATTATTATTGTTGATTAATATGTTGAAGCAAGTAATAGTA
28498498 TACTTAGT
66 TACTTAGT
28498506 AGCATTTAGCGTTATTCATACGACAATTATTATTGTTGATTAATATGTTGAAGCAAGTAATAGTA
1 AGCATTTAGCGTTATTCATACGACAATTATTATTGTTGATTAATATGTTGAAGCAAGTAATAGTA
28498571 TACTTAGT
66 TACTTAGT
28498579 AGC
1 AGC
28498582 TTCCAAAAAC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (73 bp):
AGCATTTAGCGTTATTCATACGACAATTATTATTGTTGATTAATATGTTGAAGCAAGTAATAGTA
TACTTAGT
Found at i:28508637 original size:18 final size:18
Alignment explanation
Indices: 28508614--28508650 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28508604 ATTTGGATTA
28508614 AAATGATGCTCATGAACT
1 AAATGATGCTCATGAACT
28508632 AAATGATGCTCATGAACT
1 AAATGATGCTCATGAACT
28508650 A
1 A
28508651 TTGCATTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (18 bp):
AAATGATGCTCATGAACT
Found at i:28513613 original size:20 final size:18
Alignment explanation
Indices: 28513588--28513624 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
28513578 CAATAATTTA
28513588 TCAAATTAATATATTAAATG
1 TCAAA-TAATA-ATTAAATG
28513608 TCAAATAATAATTAAAT
1 TCAAATAATAATTAAAT
28513625 AATCTTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (18 bp):
TCAAATAATAATTAAATG
Found at i:28520767 original size:53 final size:53
Alignment explanation
Indices: 28520687--28520788 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
28520677 CCATGGCAAC
* *
28520687 ATGTGATATGTGATTTCCGTATAAGACCACAACTAGGCTATGGCATCGGAGAG
1 ATGTGATATGTGACTTCCGTATAAGACCACAACTAGGATATGGCATCGGAGAG
* * *
28520740 ATGTGATTATGTG-CTTCCGTATAAGACCATATCTGGGATATGGCATCGG
1 ATGTGA-TATGTGACTTCCGTATAAGACCACAACTAGGATATGGCATCGG
28520789 TGTGATATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 37 0.86
54 6 0.14
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (53 bp):
ATGTGATATGTGACTTCCGTATAAGACCACAACTAGGATATGGCATCGGAGAG
Found at i:28520816 original size:47 final size:47
Alignment explanation
Indices: 28520741--28520846 Score: 151
Period size: 47 Copynumber: 2.2 Consensus size: 47
28520731 ATCGGAGAGA
* * *
28520741 TGTGATTATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATCG-G
1 TGTGA-TATGTGCTACCATATAAAACCATATCTGGGATATGGCAT-GAG
*
28520789 TGTGATATGTGCTACTATATAAAACCATATCTGGGATATGGCATGAG
1 TGTGATATGTGCTACCATATAAAACCATATCTGGGATATGGCATGAG
28520836 TGTGATATGTG
1 TGTGATATGTG
28520847 ATTCGTGTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
46 1 0.02
47 47 0.89
48 5 0.09
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.34
Consensus pattern (47 bp):
TGTGATATGTGCTACCATATAAAACCATATCTGGGATATGGCATGAG
Found at i:28531917 original size:27 final size:29
Alignment explanation
Indices: 28531864--28531918 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
28531854 TTAATACAAT
28531864 TATTGATATAACATCAATTTATATTTATA
1 TATTGATATAACATCAATTTATATTTATA
28531893 TATTG-TATACACAT-AA-TTATATTTAT
1 TATTGATATA-ACATCAATTTATATTTAT
28531919 CTAATATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 10 0.40
28 6 0.24
29 9 0.36
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (29 bp):
TATTGATATAACATCAATTTATATTTATA
Found at i:28532012 original size:30 final size:31
Alignment explanation
Indices: 28531953--28532012 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
28531943 TATTTATTTA
*
28531953 ATGTGTATAATCGAATCAATATTAAAGTTCT
1 ATGTGTATAATCGAATCAATATCAAAGTTCT
*
28531984 ATGTGTATAATCGTA-CTAA-ATCAAAGTTC
1 ATGTGTATAATCGAATC-AATATCAAAGTTC
28532013 ACGTATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (31 bp):
ATGTGTATAATCGAATCAATATCAAAGTTCT
Found at i:28534557 original size:3 final size:3
Alignment explanation
Indices: 28534551--28534584 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
28534541 TGTTGATGAT
28534551 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
28534585 TTGTTGATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:28537370 original size:15 final size:15
Alignment explanation
Indices: 28537328--28537374 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
28537318 AATAATAATT
28537328 TAAGTGACTAAAATA
1 TAAGTGACTAAAATA
* * *
28537343 TAA-TAATTTAAATA
1 TAAGTGACTAAAATA
28537357 TAAGTGACTAAAATA
1 TAAGTGACTAAAATA
28537372 TAA
1 TAA
28537375 TATGAGACAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.55, C:0.04, G:0.09, T:0.32
Consensus pattern (15 bp):
TAAGTGACTAAAATA
Found at i:28537562 original size:5 final size:5
Alignment explanation
Indices: 28537552--28537589 Score: 67
Period size: 5 Copynumber: 7.4 Consensus size: 5
28537542 ATTTATTGTC
28537552 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATTAAT AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT AT
28537590 TTAATGATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:28540109 original size:12 final size:12
Alignment explanation
Indices: 28540092--28540123 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
28540082 TGCTTTCAAC
28540092 AAATAAATATTT
1 AAATAAATATTT
*
28540104 AAATAAAAATTT
1 AAATAAATATTT
28540116 AAATAAAT
1 AAATAAAT
28540124 TAAGTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAATAAATATTT
Found at i:28542478 original size:19 final size:20
Alignment explanation
Indices: 28542439--28542478 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28542429 AAGGGGATGA
**
28542439 AAGACAAATTATATGAGAAG
1 AAGACAAATTATAAAAGAAG
28542459 AAGACAAATT-TAAAAGAAG
1 AAGACAAATTATAAAAGAAG
28542478 A
1 A
28542479 TGATGACAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.60, C:0.05, G:0.17, T:0.17
Consensus pattern (20 bp):
AAGACAAATTATAAAAGAAG
Done.