Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 44 of 135
Found at i:17347393 original size:14 final size:13
Alignment explanation
Indices: 17347366--17347391 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17347356 AACTTTAACG
17347366 GTCAATGGTTAAA
1 GTCAATGGTTAAA
17347379 GTCAATGGTTAAA
1 GTCAATGGTTAAA
17347392 AGACATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
GTCAATGGTTAAA
Found at i:17347455 original size:39 final size:39
Alignment explanation
Indices: 17347407--17347488 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
17347397 TTTTTTTATA
*
17347407 TTTTTATGA-TTTTTATAAAATTTTCTAATTTTCTATATT
1 TTTTTATGATTTTTTAT-AAATTTTCTAATTTTCAATATT
** *
17347446 TTTTTATGATTTTTTATATTTTTTCTAATTTTCAATGTT
1 TTTTTATGATTTTTTATAAATTTTCTAATTTTCAATATT
17347485 TTTT
1 TTTT
17347489 ATTAAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 31 0.82
40 7 0.18
ACGTcount: A:0.23, C:0.05, G:0.04, T:0.68
Consensus pattern (39 bp):
TTTTTATGATTTTTTATAAATTTTCTAATTTTCAATATT
Found at i:17347476 original size:10 final size:10
Alignment explanation
Indices: 17347398--17347517 Score: 72
Period size: 10 Copynumber: 12.5 Consensus size: 10
17347388 TAAAAGACAT
17347398 TTTTTTAT-A
1 TTTTTTATAA
*
17347407 -TTTTTATGA
1 TTTTTTATAA
17347416 -TTTTTATAA
1 TTTTTTATAA
** *
17347425 AATTTTCTAA
1 TTTTTTATAA
* *
17347435 TTTTCTATAT
1 TTTTTTATAA
*
17347445 TTTTTTATGA
1 TTTTTTATAA
17347455 TTTTTTAT-A
1 TTTTTTATAA
*
17347464 TTTTTTCTAA
1 TTTTTTATAA
** *
17347474 TTTTCAAT-G
1 TTTTTTATAA
17347483 TTTTTTATTAA
1 TTTTTTA-TAA
**
17347494 AATTTTATAA
1 TTTTTTATAA
17347504 -TTTTTATAA
1 TTTTTTATAA
17347513 TTTTT
1 TTTTT
17347518 ATTGATTTTT
Statistics
Matches: 83, Mismatches: 22, Indels: 11
0.72 0.19 0.09
Matches are distributed among these distances:
8 7 0.08
9 30 0.36
10 41 0.49
11 5 0.06
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:17347500 original size:39 final size:39
Alignment explanation
Indices: 17347417--17347516 Score: 105
Period size: 39 Copynumber: 2.5 Consensus size: 39
17347407 TTTTTATGAT
* * **
17347417 TTTTATAAAATTTTCTAATTTTCTATATTTTTTTATGATT
1 TTTTAT-AATTTTTCTAATTTTCTATATTTTTTTATAAAA
*
17347457 TTTTATATTTTTTCTAATTTTC-A-ATGTTTTTTATTAAAA
1 TTTTATAATTTTTCTAATTTTCTATAT-TTTTTTA-TAAAA
*
17347496 TTTTATAATTTTTATAATTTT
1 TTTTATAATTTTTCTAATTTT
17347517 TATTGATTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
37 2 0.04
38 8 0.16
39 35 0.69
40 6 0.12
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (39 bp):
TTTTATAATTTTTCTAATTTTCTATATTTTTTTATAAAA
Found at i:17347528 original size:10 final size:9
Alignment explanation
Indices: 17347399--17347519 Score: 73
Period size: 9 Copynumber: 12.8 Consensus size: 9
17347389 AAAAGACATT
17347399 TTTTTAT-A
1 TTTTTATAA
*
17347407 TTTTTATGA
1 TTTTTATAA
17347416 TTTTTATAAA
1 TTTTTAT-AA
* *
17347426 ATTTTCTAA
1 TTTTTATAA
*
17347435 TTTTCTATATT
1 TTTT-TATA-A
*
17347446 TTTTTATGAT
1 TTTTTAT-AA
*
17347456 TTTTTATAT
1 TTTTTATAA
*
17347465 TTTTTCTAA
1 TTTTTATAA
* **
17347474 TTTTCAATGT
1 TTTT-TATAA
17347484 TTTTTATTAAA
1 TTTTTA-T-AA
*
17347495 ATTTTATAA
1 TTTTTATAA
17347504 TTTTTATAA
1 TTTTTATAA
17347513 TTTTTAT
1 TTTTTAT
17347520 TGATTTTTAA
Statistics
Matches: 88, Mismatches: 17, Indels: 15
0.73 0.14 0.12
Matches are distributed among these distances:
8 7 0.08
9 44 0.50
10 27 0.31
11 10 0.11
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:17347540 original size:9 final size:9
Alignment explanation
Indices: 17347493--17347542 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
17347483 TTTTTTATTA
17347493 AAATTTTAT
1 AAATTTTAT
*
17347502 AATTTTTAT
1 AAATTTTAT
*
17347511 AATTTTTAT
1 AAATTTTAT
**
17347520 TGATTTT-T
1 AAATTTTAT
17347528 -AATTTTAT
1 AAATTTTAT
17347536 AAATTTT
1 AAATTTT
17347543 TTGCTACATA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
7 5 0.15
8 2 0.06
9 27 0.79
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
AAATTTTAT
Found at i:17347543 original size:17 final size:16
Alignment explanation
Indices: 17347494--17347544 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
17347484 TTTTTATTAA
17347494 AATTTTATAATTTTTAT
1 AATTTTATAATTTTT-T
*
17347511 AATTTT-TATTGATTTTT
1 AATTTTATAAT--TTTTT
17347528 AATTTTATAAATTTTTT
1 AATTTTAT-AATTTTTT
17347545 GCTACATATC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 3 0.11
17 18 0.64
18 5 0.18
19 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
AATTTTATAATTTTTT
Found at i:17347788 original size:91 final size:90
Alignment explanation
Indices: 17347693--17347879 Score: 198
Period size: 91 Copynumber: 2.1 Consensus size: 90
17347683 TCTTAGGGCT
* * * * * ***
17347693 TTTTTAATGTATTTTGATAGTTCAAATACTCAATTAAATGTAAAAAAA-AAAGGCAATGGCTTAA
1 TTTTTAATATATTTTAAAAGTTCAAATACCCAATTAAATGGAAAAAAACAAA--CAAAAACTTAA
**
17347757 TTACTTTT-TTGGAAAAATTTGAAAATC
64 TTACTTTTATTAAAAAAATTTGAAAA-C
* * * *
17347784 TTTTTTATATATTTTAAAATTTCAAATACCCAATTGAGTGGAAAAAAACAAACAAAAACTTAATT
1 TTTTTAATATATTTTAAAAGTTCAAATACCCAATTAAATGGAAAAAAACAAACAAAAACTTAATT
*
17347849 ACTTTTATTAAAAAAATTTGACAAC
66 ACTTTTATTAAAAAAATTTGAAAAC
17347874 TTTTTA
1 TTTTTA
17347880 CCCCTTAAAC
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
90 22 0.28
91 53 0.68
92 3 0.04
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.39
Consensus pattern (90 bp):
TTTTTAATATATTTTAAAAGTTCAAATACCCAATTAAATGGAAAAAAACAAACAAAAACTTAATT
ACTTTTATTAAAAAAATTTGAAAAC
Found at i:17351795 original size:5 final size:6
Alignment explanation
Indices: 17351770--17351794 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17351760 CATTAATAGC
17351770 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
17351795 TCTTTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:17352373 original size:46 final size:45
Alignment explanation
Indices: 17352303--17352421 Score: 193
Period size: 46 Copynumber: 2.6 Consensus size: 45
17352293 AATTTTTTTA
17352303 CTTCAAAATAAAAAATAAAACAATTAAAAAATATAATCTTAATTG
1 CTTCAAAATAAAAAATAAAACAATTAAAAAATATAATCTTAATTG
* * * *
17352348 CTTTAAAATAAAATAATAAAACAATTAACAAATATACTCTTATTTG
1 CTTCAAAATAAAA-AATAAAACAATTAAAAAATATAATCTTAATTG
17352394 CTTCAAAATAAAAAATAAAACAATTAAA
1 CTTCAAAATAAAAAATAAAACAATTAAA
17352422 CTAAATTCAA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 26 0.39
46 41 0.61
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (45 bp):
CTTCAAAATAAAAAATAAAACAATTAAAAAATATAATCTTAATTG
Found at i:17364345 original size:23 final size:22
Alignment explanation
Indices: 17364318--17364367 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 22
17364308 GCTAACTACA
17364318 AAATCAAATC-TCTAAGATTTAT
1 AAATCAAATCTTCTAAGA-TTAT
17364340 AGAATCAAATCTTCTAAGATTAT
1 A-AATCAAATCTTCTAAGATTAT
17364363 AAATC
1 AAATC
17364368 CTCTACGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.19
23 14 0.54
24 7 0.27
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (22 bp):
AAATCAAATCTTCTAAGATTAT
Found at i:17371190 original size:2 final size:2
Alignment explanation
Indices: 17371178--17371208 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17371168 GGGGTCTCTT
*
17371178 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17371209 GTACTCTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:17387714 original size:6 final size:6
Alignment explanation
Indices: 17387703--17387733 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
17387693 TCCTCCTTGA
17387703 CAAACC CAAACC CAAACC CAAACC CAAACC C
1 CAAACC CAAACC CAAACC CAAACC CAAACC C
17387734 TGTCGAGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAACC
Found at i:17388996 original size:3 final size:3
Alignment explanation
Indices: 17388988--17389020 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
17388978 TTTGGGATGC
17388988 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
17389021 GCATAGCGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:17390961 original size:12 final size:12
Alignment explanation
Indices: 17390939--17390971 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17390929 TTAAAAGTTG
17390939 TATAT-AAAAAA
1 TATATAAAAAAA
*
17390950 TATTTAAAAAAA
1 TATATAAAAAAA
17390962 TATATAAAAA
1 TATATAAAAA
17390972 TTATTGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
TATATAAAAAAA
Found at i:17393868 original size:13 final size:13
Alignment explanation
Indices: 17393831--17393868 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
17393821 TTAATTTATA
17393831 AAAAATTAAA-AT
1 AAAAATTAAATAT
17393843 AATTAAATTAAATAT
1 AA--AAATTAAATAT
17393858 AAAAATTAAAT
1 AAAAATTAAAT
17393869 CCACAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.09
13 9 0.39
14 8 0.35
15 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAATTAAATAT
Found at i:17395489 original size:92 final size:91
Alignment explanation
Indices: 17395375--17395560 Score: 329
Period size: 92 Copynumber: 2.0 Consensus size: 91
17395365 TTTAGAATTT
* *
17395375 AAAGATGGCTTTATTAACAAAAAAAATACCATTTATTGTTTGACATTAAAAAT-ATTTATTTTTT
1 AAAGATGGCTTTATTAACAAAAAAAATACCATTTATTGTTTGACATTAAAAATAATTTA-TTATA
17395439 TTACTTATCATTATGTGATAATAAAAA
65 TTACTTATCATTATGTGATAATAAAAA
17395466 AAAGTATGGCTTTATTAACAAAAAAAATACCATTTATTGTTTGACATTAAAAATAATTTATTATA
1 AAAG-ATGGCTTTATTAACAAAAAAAATACCATTTATTGTTTGACATTAAAAATAATTTATTATA
17395531 TTACTTATCATTATGTGATAATAAAAA
65 TTACTTATCATTATGTGATAATAAAAA
17395558 AAA
1 AAA
17395561 AGTAATATTA
Statistics
Matches: 91, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
91 4 0.04
92 82 0.90
93 5 0.05
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (91 bp):
AAAGATGGCTTTATTAACAAAAAAAATACCATTTATTGTTTGACATTAAAAATAATTTATTATAT
TACTTATCATTATGTGATAATAAAAA
Found at i:17400943 original size:19 final size:20
Alignment explanation
Indices: 17400894--17400943 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 20
17400884 ACCTGCAAGC
17400894 AACA-TGAAAAAGAAATAGA
1 AACAGTGAAAAAGAAATAGA
* * * *
17400913 AGCAGCGTAAAAGAGA-AGA
1 AACAGTGAAAAAGAAATAGA
17400932 AACAGTGAAAAA
1 AACAGTGAAAAA
17400944 ATAAAAAAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.62, C:0.08, G:0.22, T:0.08
Consensus pattern (20 bp):
AACAGTGAAAAAGAAATAGA
Found at i:17404009 original size:50 final size:50
Alignment explanation
Indices: 17403879--17404019 Score: 185
Period size: 50 Copynumber: 2.8 Consensus size: 50
17403869 ATACCCGGTT
** * *
17403879 CACATAGTAGCCTGCACATAGTACTACACACGTGATCGAAGTTATTCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCTAGTCATTCAGTA
* * *
17403930 CGCATAGTAGCCTGCACATAGTACTACACATGCGACCTA-TCATTCCAGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCTAGTCATT-CAGTA
*
17403980 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCTAG
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCTAG
17404020 CAACTTCACT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
49 4 0.05
50 41 0.53
51 32 0.42
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.23
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCTAGTCATTCAGTA
Found at i:17404220 original size:15 final size:16
Alignment explanation
Indices: 17404176--17404223 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
17404166 ATCCAGTTCA
*
17404176 AAAATAACATTTTTGC
1 AAAATCACATTTTTGC
17404192 AAAATCACATTTTTGC
1 AAAATCACATTTTTGC
* *
17404208 AAAATTATATTTTTGC
1 AAAATCACATTTTTGC
17404224 CCCTAAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (16 bp):
AAAATCACATTTTTGC
Found at i:17405163 original size:2 final size:2
Alignment explanation
Indices: 17405156--17405201 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
17405146 TTATAACATG
* *
17405156 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC T- TT TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17405196 TA TA TA
1 TA TA TA
17405202 AATACATGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17411560 original size:26 final size:26
Alignment explanation
Indices: 17411531--17411591 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
17411521 CCCGTTATAT
*
17411531 GGCTCTTCGTGAGCTTCTCGATTAAA
1 GGCTCTTCGGGAGCTTCTCGATTAAA
* * * * *
17411557 GGCTATTTGGGAGCTTTTTGATTAAT
1 GGCTCTTCGGGAGCTTCTCGATTAAA
17411583 GGCTCTTCG
1 GGCTCTTCG
17411592 AAGCTTCCTA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.39
Consensus pattern (26 bp):
GGCTCTTCGGGAGCTTCTCGATTAAA
Found at i:17411646 original size:25 final size:25
Alignment explanation
Indices: 17411618--17411683 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 25
17411608 CTTGCTTGAA
17411618 CTTCCCGA-TACATGGCTATCCGAAG
1 CTTCCCGATTA-ATGGCTATCCGAAG
* * *
17411643 CTTCCTGATTAATGGCTCTTCGAAG
1 CTTCCCGATTAATGGCTATCCGAAG
* *
17411668 CTACCCG-TTATTGGCT
1 CTTCCCGATTAATGGCT
17411684 CACATGAGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
24 8 0.24
25 24 0.71
26 2 0.06
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.32
Consensus pattern (25 bp):
CTTCCCGATTAATGGCTATCCGAAG
Found at i:17417512 original size:13 final size:14
Alignment explanation
Indices: 17417496--17417524 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17417486 ATAATTTTAA
17417496 ATAAAAA-TTAAAT
1 ATAAAAATTTAAAT
17417509 ATAAAAATTTAAAT
1 ATAAAAATTTAAAT
17417523 AT
1 AT
17417525 TTGATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAAAATTTAAAT
Found at i:17422119 original size:29 final size:29
Alignment explanation
Indices: 17422084--17422148 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
17422074 CTTAATATCC
17422084 AGCCCAATATTTTAAATCAATTTACGAAT
1 AGCCCAATATTTTAAATCAATTTACGAAT
* *
17422113 AGTCCAATATTTTAAATTAATTTACGAAT
1 AGCCCAATATTTTAAATCAATTTACGAAT
17422142 AGCCCAA
1 AGCCCAA
17422149 AACAGACCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.34
Consensus pattern (29 bp):
AGCCCAATATTTTAAATCAATTTACGAAT
Found at i:17430448 original size:175 final size:175
Alignment explanation
Indices: 17430157--17430500 Score: 688
Period size: 175 Copynumber: 2.0 Consensus size: 175
17430147 GGGGAATAGT
17430157 TCCTTACACTTTCATAGGAAACCTAAATCCTTAAAGAGCCTCAAAGTCCTATAGTTCAATTATTG
1 TCCTTACACTTTCATAGGAAACCTAAATCCTTAAAGAGCCTCAAAGTCCTATAGTTCAATTATTG
17430222 GAATTCAACACCTTGATCAGGATACAAGGCCTTGGTGAAACAAAACAAAGGATCTATCACATGGA
66 GAATTCAACACCTTGATCAGGATACAAGGCCTTGGTGAAACAAAACAAAGGATCTATCACATGGA
17430287 ATGCATCTATAACAGAAACAGGAGACACTTACTCATATGCATCTA
131 ATGCATCTATAACAGAAACAGGAGACACTTACTCATATGCATCTA
17430332 TCCTTACACTTTCATAGGAAACCTAAATCCTTAAAGAGCCTCAAAGTCCTATAGTTCAATTATTG
1 TCCTTACACTTTCATAGGAAACCTAAATCCTTAAAGAGCCTCAAAGTCCTATAGTTCAATTATTG
17430397 GAATTCAACACCTTGATCAGGATACAAGGCCTTGGTGAAACAAAACAAAGGATCTATCACATGGA
66 GAATTCAACACCTTGATCAGGATACAAGGCCTTGGTGAAACAAAACAAAGGATCTATCACATGGA
17430462 ATGCATCTATAACAGAAACAGGAGACACTTACTCATATG
131 ATGCATCTATAACAGAAACAGGAGACACTTACTCATATG
17430501 TATTATCTAC
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
175 169 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.26
Consensus pattern (175 bp):
TCCTTACACTTTCATAGGAAACCTAAATCCTTAAAGAGCCTCAAAGTCCTATAGTTCAATTATTG
GAATTCAACACCTTGATCAGGATACAAGGCCTTGGTGAAACAAAACAAAGGATCTATCACATGGA
ATGCATCTATAACAGAAACAGGAGACACTTACTCATATGCATCTA
Found at i:17430946 original size:64 final size:64
Alignment explanation
Indices: 17430866--17430995 Score: 242
Period size: 64 Copynumber: 2.0 Consensus size: 64
17430856 AAGACAATAC
17430866 TGATAAATAATCTAAAACAGTACACATGATATTCCTGGTCCAAATTATAACACATCATGTGCTT
1 TGATAAATAATCTAAAACAGTACACATGATATTCCTGGTCCAAATTATAACACATCATGTGCTT
* *
17430930 TGATAAATCATCTAAAACAGTACACATGATATTCCTGGTCCAAATTATAACACATTATGTGCTT
1 TGATAAATAATCTAAAACAGTACACATGATATTCCTGGTCCAAATTATAACACATCATGTGCTT
17430994 TG
1 TG
17430996 TTATGCATGT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (64 bp):
TGATAAATAATCTAAAACAGTACACATGATATTCCTGGTCCAAATTATAACACATCATGTGCTT
Found at i:17435628 original size:23 final size:22
Alignment explanation
Indices: 17435600--17435642 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
17435590 AATTATAATA
17435600 TTAAAATTAAAAATTTTAAAAGG
1 TTAAAA-TAAAAATTTTAAAAGG
* *
17435623 TTAAAATGAATATTTTAAAA
1 TTAAAATAAAAATTTTAAAA
17435643 TACAGCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (22 bp):
TTAAAATAAAAATTTTAAAAGG
Found at i:17437063 original size:12 final size:12
Alignment explanation
Indices: 17437030--17437072 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
17437020 TTATTAAAAA
*
17437030 ATAAAAAAAACT
1 ATAAAAAAAATT
* *
17437042 ATAAGCAAAATTT
1 ATAA-AAAAAATT
17437055 ATAAAAAAAATT
1 ATAAAAAAAATT
17437067 ATAAAA
1 ATAAAA
17437073 TTTTTATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (12 bp):
ATAAAAAAAATT
Found at i:17437200 original size:22 final size:21
Alignment explanation
Indices: 17437175--17437243 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
17437165 CAACAATGTT
17437175 ATTTTTTAATAAAATTTTTATA
1 ATTTTTT-ATAAAATTTTTATA
* * * *
17437197 ATTTTTGTTTATAATTTTTCTG
1 ATTTTT-TATAAAATTTTTATA
17437219 A-TTTTTATAATAATTTTTA-A
1 ATTTTTTATAA-AATTTTTATA
17437239 ATTTT
1 ATTTT
17437244 AAAGGGGCTT
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
20 4 0.11
21 14 0.39
22 17 0.47
23 1 0.03
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (21 bp):
ATTTTTTATAAAATTTTTATA
Found at i:17437207 original size:13 final size:13
Alignment explanation
Indices: 17437191--17437215 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17437181 TAATAAAATT
17437191 TTTATAATTTTTG
1 TTTATAATTTTTG
17437204 TTTATAATTTTT
1 TTTATAATTTTT
17437216 CTGATTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTATAATTTTTG
Found at i:17472463 original size:17 final size:17
Alignment explanation
Indices: 17472443--17472486 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
17472433 TTTGTGCAAT
* *
17472443 TATTAATTGATAAATTG
1 TATTAATTAAAAAATTG
*
17472460 TATTAACTCAAAAAATTG
1 TATTAA-TTAAAAAATTG
17472478 TATTAATTA
1 TATTAATTA
17472487 TCTAACATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (17 bp):
TATTAATTAAAAAATTG
Found at i:17472610 original size:39 final size:39
Alignment explanation
Indices: 17472567--17472693 Score: 141
Period size: 38 Copynumber: 3.3 Consensus size: 39
17472557 TATATAAAAT
*
17472567 TATTAATTGTTACTACCAGTCAAAAAATTGTATTAATTG
1 TATTAATAGTTACTACCAGTCAAAAAATTGTATTAATTG
* * * * ** * * *
17472606 TATTAATAGTTAGTA-AAATTATCAAATTATATAAAAT-
1 TATTAATAGTTACTACCAGTCAAAAAATTGTATTAATTG
*
17472643 TATTAATTGTTACTACCAGTCAAAAAATTGTATTAATTG
1 TATTAATAGTTACTACCAGTCAAAAAATTGTATTAATTG
17472682 TATTAATAGTTA
1 TATTAATAGTTA
17472694 GTAAAATTAT
Statistics
Matches: 65, Mismatches: 21, Indels: 4
0.72 0.23 0.04
Matches are distributed among these distances:
37 13 0.20
38 28 0.43
39 24 0.37
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.42
Consensus pattern (39 bp):
TATTAATAGTTACTACCAGTCAAAAAATTGTATTAATTG
Found at i:17472611 original size:76 final size:76
Alignment explanation
Indices: 17472525--17472716 Score: 375
Period size: 76 Copynumber: 2.5 Consensus size: 76
17472515 AACAAGCAAA
*
17472525 AATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTACTACCAGTCAA
1 AATTGTATTAATAGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTACTACCAGTCAA
17472590 AAAATTGTATT
66 AAAATTGTATT
17472601 AATTGTATTAATAGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTACTACCAGTCAA
1 AATTGTATTAATAGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTACTACCAGTCAA
17472666 AAAATTGTATT
66 AAAATTGTATT
17472677 AATTGTATTAATAGTTAGTAAAATTATCAAATTATATAAA
1 AATTGTATTAATAGTTAGTAAAATTATCAAATTATATAAA
17472717 TAGGGTTAGG
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 115 1.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (76 bp):
AATTGTATTAATAGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTACTACCAGTCAA
AAAATTGTATT
Found at i:17472751 original size:29 final size:29
Alignment explanation
Indices: 17472717--17473989 Score: 1478
Period size: 29 Copynumber: 43.6 Consensus size: 29
17472707 ATTATATAAA
*
17472717 TAGGGTTAGGGTTTTTAATTAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
*
17472746 TAGGGTTAGGGTTTTTAATCGAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
*
17472775 TAGGGTTAGGGTTTTTAATGAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
* *
17472804 TAGGGGTAGGGATTTTAATCAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
*
17472833 TAGGGTTAGGGTTTTTAATTAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
*
17472862 TAGGGTTAGGGTTTTTAATTAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
17472891 TAGGGTTAGGGTTTTTAATCAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
* * * *
17472920 TAGGGGTATGGTTTTTACTTAAATTAGGCTAGGGT
1 TAGGGTTAGGGTTTTTAATCAAA-T----TA-GGT
* *
17472955 TAGGGTTAGAGTTTTTAATTAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
* *
17472984 TAGGGTTATGATTTTTAATCAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
* * *
17473013 TAGGGTTAAGATTTTTAATTAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
17473042 TAGGGTTAGGGTTTTTAATCAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
* *
17473071 TAGGGGTAGGGTTTTTAATCAAATTAGTT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
*
17473100 TAGGGTTAGGGTTTTTAATTC-AATTAAGT
1 TAGGGTTAGGGTTTTTAA-TCAAATTAGGT
* *
17473129 TAGAGTTAGGGTTTTTAAT-TAA--A--T
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
17473153 TA-GGTTAGGGTTTTTAATCAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
* *
17473181 TAGGGGTAGGGTTTTTAATCCAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
* *
17473210 TAGGGGTAGGGTTTTTAATCCAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
* *
17473239 TAGGGGTAGGGTTTTTAATTAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
* * * * ** * **
17473268 TAGGGATACGGTTTAGGGGTAGGGTTTTTAATCAAAT
1 TAGGGTTAGGGTTT----TTA----ATCAAATTAGGT
*
17473305 TA-GGTTAGGGATACGGTTTTTAATTAAATTAGGT
1 TAGGGTTA--G----GGTTTTTAATCAAATTAGGT
*
17473339 TAGGGGTA-GGTTTTTAATCAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
* * *
17473367 TAGGGGTACGATTTTTAATCAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
*
17473396 TAGGGTTAGGGTTATTAATCAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
*
17473425 TAGGGTTAGAGTTTTTAATCAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
* * *
17473454 TAGGGTTAGGGTTTTTAATTAAATTCGAT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
17473483 TAGGGTTAGGGTTTTTAATCAAATTCA-GT
1 TAGGGTTAGGGTTTTTAATCAAATT-AGGT
*
17473512 TAGGGTTAAGGTTTTTAATCAAATTAGGTTAGT
1 TAGGGTTAGGGTTTTTAATCAAATTA-G---GT
17473545 TAGGGTTAGGGTTTTTAATCAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
* * *
17473574 TAGGGGTACGGTTTTT-ACCTAAATTAGGT
1 TAGGGTTAGGGTTTTTAATC-AAATTAGGT
* * *
17473603 TAGAGTTAAGGTTTTTAATTAAATTAGGTTAGGGT
1 TAGGGTTAGGGTTTTTAA-TCAA--A--TTA-GGT
*
17473638 TAGGGTTAGGGTTTTTAATTAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
*
17473667 TAGGGTTAGGGTTTTTAATCGAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
*
17473696 TAGGGTTAGGGTTTTTAATGAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
* *
17473725 TAGGGGTAGGGATTTTAATCAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
*
17473754 TAGGGTTAGGGTTTTTAAT-TAA--A--T
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
17473778 TA-GGTTAGGGTTTTTAATCAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
*
17473806 TAGGGTTAGGGTTTTTAAT-TAA--A--T
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
17473830 TA-GGTTAGGGTTTTTAATCAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
17473858 TAGGGTTAGGGTTTTTAATCAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
17473887 TAGGGTTAGGGTTTTTAATCAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
* *
17473916 TAGGGTTAGGGCTTTTAATCAAATTAGTT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
*
17473945 TAGGGTTAAGG-TTTTAATCAAATTAGGT
1 TAGGGTTAGGGTTTTTAATCAAATTAGGT
* *
17473973 TAGGGTTTGGGGTTTTA
1 TAGGGTTAGGGTTTTTA
17473990 GGGTTTATGG
Statistics
Matches: 1083, Mismatches: 104, Indels: 114
0.83 0.08 0.09
Matches are distributed among these distances:
23 47 0.04
24 15 0.01
26 6 0.01
28 71 0.07
29 818 0.76
30 11 0.01
32 3 0.00
33 29 0.03
34 18 0.02
35 45 0.04
36 4 0.00
37 9 0.01
38 2 0.00
42 5 0.00
ACGTcount: A:0.28, C:0.03, G:0.27, T:0.42
Consensus pattern (29 bp):
TAGGGTTAGGGTTTTTAATCAAATTAGGT
Found at i:17473292 original size:71 final size:70
Alignment explanation
Indices: 17473205--17473351 Score: 242
Period size: 71 Copynumber: 2.1 Consensus size: 70
17473195 TTAATCCAAT
* * *
17473205 TAGG-TTAGGGGTAGGGTTTTTAATCCAATTAGGTTAGGGGTAGGGTTTTTAATTAAATTAGGTT
1 TAGGTTTAGGGGTAGGGTTTTTAATCAAATTAGGTTAGGGATACGGTTTTTAATTAAATTAGGTT
17473269 AGGGA
66 AGGGA
17473274 TACGGTTTAGGGGTAGGGTTTTTAATCAAATTAGGTTAGGGATACGGTTTTTAATTAAATTAGGT
1 TA-GGTTTAGGGGTAGGGTTTTTAATCAAATTAGGTTAGGGATACGGTTTTTAATTAAATTAGGT
*
17473339 TAGGGG
65 TAGGGA
17473345 TAGGTTT
1 TAGGTTT
17473352 TTAATCAAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
69 2 0.03
70 7 0.10
71 63 0.88
ACGTcount: A:0.26, C:0.03, G:0.32, T:0.39
Consensus pattern (70 bp):
TAGGTTTAGGGGTAGGGTTTTTAATCAAATTAGGTTAGGGATACGGTTTTTAATTAAATTAGGTT
AGGGA
Found at i:17473297 original size:42 final size:42
Alignment explanation
Indices: 17473238--17473323 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
17473228 TCCAATTAGG
*
17473238 TTAGGGGTAGGGTTTTTAATTAAATTAGGTTAGGGATACGGT
1 TTAGGGGTAGGGTTTTTAATCAAATTAGGTTAGGGATACGGT
17473280 TTAGGGGTAGGGTTTTTAATCAAATTAGGTTAGGGATACGGT
1 TTAGGGGTAGGGTTTTTAATCAAATTAGGTTAGGGATACGGT
17473322 TT
1 TT
17473324 TTAATTAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.03, G:0.33, T:0.38
Consensus pattern (42 bp):
TTAGGGGTAGGGTTTTTAATCAAATTAGGTTAGGGATACGGT
Found at i:17473996 original size:7 final size:7
Alignment explanation
Indices: 17473972--17474011 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
17473962 TCAAATTAGG
17473972 TTAGGGT
1 TTAGGGT
*
17473979 TTGGGGTT
1 TTAGGG-T
17473987 TTAGGGT
1 TTAGGGT
*
17473994 TTATGGT
1 TTAGGGT
17474001 TTAGGGT
1 TTAGGGT
17474008 TTAG
1 TTAG
17474012 AATTCAGTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 22 0.79
8 6 0.21
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.47
Consensus pattern (7 bp):
TTAGGGT
Found at i:17474400 original size:18 final size:18
Alignment explanation
Indices: 17474377--17474411 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17474367 CGGAAAAGGA
*
17474377 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
17474395 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
17474412 AAACGCATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:17476113 original size:18 final size:18
Alignment explanation
Indices: 17476083--17476125 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
17476073 TCTACAGACT
17476083 TTTATAA-AAATAATAAA
1 TTTATAATAAATAATAAA
17476100 TTTATAATAAATAATAAA
1 TTTATAATAAATAATAAA
*
17476118 TTAATAAT
1 TTTATAAT
17476126 TATCTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTATAATAAATAATAAA
Found at i:17476371 original size:29 final size:29
Alignment explanation
Indices: 17476339--17476422 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 29
17476329 AATTGAAATT
*
17476339 AAATATGGATTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGAAAGG
**
17476368 AAAT-T-GA---GAG-GAA-TTTGAAATT
1 AAATATGGATTTGAGAGAATTTTGAAAGG
17476390 AAATATGGATTTGAGAGAATTTTGAAAGG
1 AAATATGGATTTGAGAGAATTTTGAAAGG
17476419 AAAT
1 AAAT
17476423 TGAGAGGAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
22 10 0.23
23 4 0.09
24 5 0.12
27 5 0.12
28 4 0.09
29 15 0.35
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.31
Consensus pattern (29 bp):
AAATATGGATTTGAGAGAATTTTGAAAGG
Found at i:17476384 original size:22 final size:22
Alignment explanation
Indices: 17476349--17476456 Score: 78
Period size: 22 Copynumber: 4.6 Consensus size: 22
17476339 AAATATGGAT
*
17476349 TTGAGA-GAATTTTGGAAGGAAA
1 TTGAGAGGAA-TTTGAAAGGAAA
**
17476371 TTGAGAGGAATTTGAAATTAAA
1 TTGAGAGGAATTTGAAAGGAAA
17476393 TATGGATTTGAGAGAATTTTGAAAGGAAA
1 T-T-GA---GAG-GAA-TTTGAAAGGAAA
*
17476422 TTGAGAGGAA-TTGAGAGGAAA
1 TTGAGAGGAATTTGAAAGGAAA
17476443 TATGAGAGG-ATTTG
1 T-TGAGAGGAATTTG
17476457 TTTGTGAAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
21 12 0.17
22 26 0.37
23 7 0.10
24 5 0.07
27 5 0.07
28 4 0.06
29 11 0.16
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.29
Consensus pattern (22 bp):
TTGAGAGGAATTTGAAAGGAAA
Found at i:17476429 original size:51 final size:51
Alignment explanation
Indices: 17476312--17476433 Score: 217
Period size: 51 Copynumber: 2.4 Consensus size: 51
17476302 TTATTTTAAA
* *
17476312 AAAGGAAATTGAGAGCAAATTGAAATTAAATATGGATTTGAGAGAATTTTG
1 AAAGGAAATTGAGAGGAATTTGAAATTAAATATGGATTTGAGAGAATTTTG
*
17476363 GAAGGAAATTGAGAGGAATTTGAAATTAAATATGGATTTGAGAGAATTTTG
1 AAAGGAAATTGAGAGGAATTTGAAATTAAATATGGATTTGAGAGAATTTTG
17476414 AAAGGAAATTGAGAGGAATT
1 AAAGGAAATTGAGAGGAATT
17476434 GAGAGGAAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 67 1.00
ACGTcount: A:0.44, C:0.01, G:0.26, T:0.29
Consensus pattern (51 bp):
AAAGGAAATTGAGAGGAATTTGAAATTAAATATGGATTTGAGAGAATTTTG
Found at i:17476440 original size:21 final size:22
Alignment explanation
Indices: 17476411--17476452 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
17476401 TGAGAGAATT
17476411 TTGAAAGGAAAT-TGAGAGGAA
1 TTGAAAGGAAATATGAGAGGAA
*
17476432 TTGAGAGGAAATATGAGAGGA
1 TTGAAAGGAAATATGAGAGGA
17476453 TTTGTTTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.19
Consensus pattern (22 bp):
TTGAAAGGAAATATGAGAGGAA
Found at i:17476450 original size:12 final size:11
Alignment explanation
Indices: 17476411--17476452 Score: 59
Period size: 10 Copynumber: 3.8 Consensus size: 11
17476401 TGAGAGAATT
*
17476411 TTGAAAGGAAA
1 TTGAGAGGAAA
17476422 TTGAGAGG-AA
1 TTGAGAGGAAA
17476432 TTGAGAGGAAA
1 TTGAGAGGAAA
17476443 TATGAGAGGA
1 T-TGAGAGGA
17476453 TTTGTTTGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 10 0.36
11 10 0.36
12 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.19
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:17487001 original size:26 final size:25
Alignment explanation
Indices: 17486953--17487027 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 25
17486943 TGACTAATGG
*
17486953 AGGTGCCAACTTGAGAAAAAAAATAGTTT
1 AGGTACCAACTTGAG---AAAAA-AGTTT
17486982 AGGTACACAACTTGAGAAAAAAGTTT
1 AGGTAC-CAACTTGAGAAAAAAGTTT
* *
17487008 AGGTACCAATTTGGGAAAAA
1 AGGTACCAACTTGAGAAAAA
17487028 GAGTATAGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 12 0.29
26 11 0.26
27 5 0.12
29 5 0.12
30 9 0.21
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (25 bp):
AGGTACCAACTTGAGAAAAAAGTTT
Found at i:17491264 original size:236 final size:236
Alignment explanation
Indices: 17490851--17491325 Score: 871
Period size: 236 Copynumber: 2.0 Consensus size: 236
17490841 ACAAAAGCTC
* *
17490851 ATCTATGAGTATTAGCTAGAGTACAGTAACAGATAAAAACTAATTACATAAAAATCAGTCTAAAA
1 ATCTATGAGAATTAGCTAGAGTACAGCAACAGATAAAAACTAATTACATAAAAATCAGTCTAAAA
*
17490916 GAAGAGAGAAAAACAAAAAGGAGTAAAACACACCAGTCAAAATTCTACTTTTCACAAAATATTTT
66 GAAGAGAGAAAAACAAAAAGGAGTAAAACACACCAGTCAAAAGTCTACTTTTCACAAAATATTTT
* *
17490981 TTTTTCTTAAAACTGGGGGAAGGGGAGGACTTCCAGCGATGTGCAGAAAATCTTCAGATGTTGCT
131 ATTTTCTTAAAAATGGGGGAAGGGGAGGACTTCCAGCGATGTGCAGAAAATCTTCAGATGTTGCT
17491046 ACTGCC-AACAAGTTCTTACAATATGTAAATACTAAAATTTA
196 ACTGCCGAA-AAGTTCTTACAATATGTAAATACTAAAATTTA
17491087 ATCTATGAGAATTAGCTAGAGTACAGCAACAGATAAAAACTAATTACATAAAAATCAGTCTAAAA
1 ATCTATGAGAATTAGCTAGAGTACAGCAACAGATAAAAACTAATTACATAAAAATCAGTCTAAAA
* *
17491152 GAAGAGAGAAAAAGAAAAAGGAGTAAAACACACCAGTCAAAAGTCTACTTTTCACTAAATATTTT
66 GAAGAGAGAAAAACAAAAAGGAGTAAAACACACCAGTCAAAAGTCTACTTTTCACAAAATATTTT
17491217 ATTTTCTTAAAAATGGGGGAAGGGGAGGACTTCCAGCGATGTGCAGAAAATCTTCAGATGTTGCT
131 ATTTTCTTAAAAATGGGGGAAGGGGAGGACTTCCAGCGATGTGCAGAAAATCTTCAGATGTTGCT
17491282 ACTGCCGAAAAGTTCTTACAATATGTAAATACTAAAATTTA
196 ACTGCCGAAAAGTTCTTACAATATGTAAATACTAAAATTTA
17491323 ATC
1 ATC
17491326 GTGAAGTATA
Statistics
Matches: 231, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
236 229 0.99
237 2 0.01
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (236 bp):
ATCTATGAGAATTAGCTAGAGTACAGCAACAGATAAAAACTAATTACATAAAAATCAGTCTAAAA
GAAGAGAGAAAAACAAAAAGGAGTAAAACACACCAGTCAAAAGTCTACTTTTCACAAAATATTTT
ATTTTCTTAAAAATGGGGGAAGGGGAGGACTTCCAGCGATGTGCAGAAAATCTTCAGATGTTGCT
ACTGCCGAAAAGTTCTTACAATATGTAAATACTAAAATTTA
Found at i:17495260 original size:19 final size:19
Alignment explanation
Indices: 17495090--17495265 Score: 83
Period size: 19 Copynumber: 9.2 Consensus size: 19
17495080 AAATATGTAT
* *
17495090 AAAATCATAACAACTTATA
1 AAAATTATAAAAACTTATA
* * *
17495109 AATATTATAAAACCCTATA
1 AAAATTATAAAAACTTATA
* *
17495128 AAAATTCTAATAAA-TTAAA
1 AAAATTATAA-AAACTTATA
* *
17495147 AAAATAATAAGAAA-ATATA
1 AAAATTATAA-AAACTTATA
* *
17495166 AAACA-TATAAATAAATATTTA
1 AAA-ATTATAAA-AACT-TATA
* * *
17495187 AAATTTTATATAAACTTACA
1 AAA-ATTATAAAAACTTATA
17495207 AAAATTATAAAAA--TATA
1 AAAATTATAAAAACTTATA
** * **
17495224 AAAAAAATCAAATTTTATA
1 AAAATTATAAAAACTTATA
*
17495243 AATATTATAAAAACTTATA
1 AAAATTATAAAAACTTATA
17495262 AAAA
1 AAAA
17495266 ATCATACTTT
Statistics
Matches: 111, Mismatches: 38, Indels: 16
0.67 0.23 0.10
Matches are distributed among these distances:
17 12 0.11
18 1 0.01
19 76 0.68
20 8 0.07
21 9 0.08
22 5 0.05
ACGTcount: A:0.62, C:0.07, G:0.01, T:0.31
Consensus pattern (19 bp):
AAAATTATAAAAACTTATA
Found at i:17495262 original size:10 final size:9
Alignment explanation
Indices: 17495090--17495265 Score: 68
Period size: 10 Copynumber: 18.4 Consensus size: 9
17495080 AAATATGTAT
*
17495090 AAAATCATA
1 AAAATTATA
*
17495099 ACAACTTATA
1 A-AAATTATA
*
17495109 AATATTATA
1 AAAATTATA
**
17495118 AAACCCTATA
1 AAA-ATTATA
*
17495128 AAAATTCTA
1 AAAATTATA
*
17495137 ATAAATTAAA
1 A-AAATTATA
*
17495147 AAAATAATA
1 AAAATTATA
*
17495156 AGAAAATATA
1 A-AAATTATA
17495166 AAACA-TATAA
1 AAA-ATTAT-A
*
17495176 ATAAATATTTA
1 A-AAAT-TATA
*
17495187 AAATTTTATA
1 AAA-ATTATA
* *
17495197 TAAACTTACA
1 -AAAATTATA
17495207 AAAATTATA
1 AAAATTATA
17495216 AAAA-TATA
1 AAAATTATA
**
17495224 AAAAAAATCA
1 AAAATTAT-A
**
17495234 AATTTTATA
1 AAAATTATA
*
17495243 AATATTATA
1 AAAATTATA
17495252 AAAACTTATA
1 AAAA-TTATA
17495262 AAAA
1 AAAA
17495266 ATCATACTTT
Statistics
Matches: 123, Mismatches: 30, Indels: 27
0.68 0.17 0.15
Matches are distributed among these distances:
8 8 0.07
9 50 0.41
10 55 0.45
11 8 0.07
12 2 0.02
ACGTcount: A:0.62, C:0.07, G:0.01, T:0.31
Consensus pattern (9 bp):
AAAATTATA
Found at i:17501826 original size:13 final size:13
Alignment explanation
Indices: 17501808--17501834 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17501798 ACAAGCAATC
17501808 TGTAAGTAGAATT
1 TGTAAGTAGAATT
17501821 TGTAAGTAGAATT
1 TGTAAGTAGAATT
17501834 T
1 T
17501835 CCTGTTCTTG
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:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (13 bp):
TGTAAGTAGAATT
Found at i:17509830 original size:21 final size:21
Alignment explanation
Indices: 17509789--17509830 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17509779 CTTCCTCCAT
*
17509789 CTCCTCTTCATCAATTTCTTC
1 CTCCTCTTCATCAATTACTTC
17509810 CTCCTCTTCATC-ATATACTTC
1 CTCCTCTTCATCAAT-TACTTC
17509831 TTCTTCTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.17, C:0.38, G:0.00, T:0.45
Consensus pattern (21 bp):
CTCCTCTTCATCAATTACTTC
Found at i:17511354 original size:6 final size:6
Alignment explanation
Indices: 17511343--17511367 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17511333 GCTATAAATT
17511343 ATACAC ATACAC ATACAC ATACAC A
1 ATACAC ATACAC ATACAC ATACAC A
17511368 CGCACACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (6 bp):
ATACAC
Found at i:17513434 original size:3 final size:3
Alignment explanation
Indices: 17513426--17513459 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
17513416 TGCATTTTAG
17513426 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT A
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT A
17513460 AAGTTTCTCA
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:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
AGT
Found at i:17545156 original size:27 final size:26
Alignment explanation
Indices: 17545111--17545161 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
17545101 AAAATTAAAT
*
17545111 ATAAAATATTTTAGTAATATGAAAAAA
1 ATAAAATATTTTAGAAATAT-AAAAAA
17545138 ATAAAATCATTTTA-AAATATAAAA
1 ATAAAAT-ATTTTAGAAATATAAAA
17545162 GTAACTTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 4 0.18
27 12 0.55
28 6 0.27
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (26 bp):
ATAAAATATTTTAGAAATATAAAAAA
Found at i:17545561 original size:29 final size:27
Alignment explanation
Indices: 17545484--17545566 Score: 71
Period size: 28 Copynumber: 2.9 Consensus size: 27
17545474 ATATACCGAA
* *
17545484 AAAAAACTAAGAAAAAAAATT-AAATTT
1 AAAAAACT-ATAAAAATAATTAAAATTT
17545511 AAAAATACT-TAAATCAATAATTAAAATTT
1 AAAAA-ACTATAAA--AATAATTAAAATTT
17545540 AAAAAACTGATAAAAATGAATTGAAAA
1 AAAAAACT-ATAAAAAT-AATT-AAAA
17545567 AGAAAAACTA
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
26 3 0.07
27 5 0.11
28 15 0.33
29 15 0.33
30 8 0.17
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (27 bp):
AAAAAACTATAAAAATAATTAAAATTT
Found at i:17545696 original size:20 final size:20
Alignment explanation
Indices: 17545660--17545699 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
17545650 CTGGAATTTG
17545660 ATTAAAAATTAAGAAATAGA
1 ATTAAAAATTAAGAAATAGA
17545680 ATTAGAAAATTAA-AAATAGA
1 ATTA-AAAATTAAGAAATAGA
17545700 GAAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (20 bp):
ATTAAAAATTAAGAAATAGA
Found at i:17545709 original size:21 final size:21
Alignment explanation
Indices: 17545663--17545709 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
17545653 GAATTTGATT
**
17545663 AAAAATTAAGAAATAGAATTA
1 AAAAATTAAGAAATAGAAAAA
*
17545684 GAAAATTAA-AAATAGAGAAAA
1 AAAAATTAAGAAATAGA-AAAA
17545705 AAAAA
1 AAAAA
17545710 AGAAAAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (21 bp):
AAAAATTAAGAAATAGAAAAA
Found at i:17549345 original size:40 final size:39
Alignment explanation
Indices: 17549289--17549423 Score: 139
Period size: 40 Copynumber: 3.4 Consensus size: 39
17549279 ACCAGTTTGG
*
17549289 CACCCAGTGCCTCATCGGATAATTTGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGATAATCTGAAGT-ATAAATTGA
* * * * * *
17549329 TACCCAATGTCTCATCGGCTAAACTGAAG--TAAATTGG
1 CACCCAGTGCCTCATCGGATAATCTGAAGTATAAATTGA
* *
17549366 CACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGGA-TAATCTGAAGTA-TAAATTGA
*
17549407 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
17549424 ACTCGAAGTC
Statistics
Matches: 75, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
37 21 0.28
38 8 0.11
40 23 0.31
41 23 0.31
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAATCTGAAGTATAAATTGA
Found at i:17549411 original size:41 final size:40
Alignment explanation
Indices: 17549289--17549424 Score: 134
Period size: 41 Copynumber: 3.5 Consensus size: 40
17549279 ACCAGTTTGG
* * *
17549289 CACCCAGTGCCTCATCGGATAATTTGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAATAATCTGAAGTAGTAAATTGA
* * * ** * *
17549329 TACCCAATGTCTCATCGGCTAAACTG-A--AGTAAATTGG
1 CACCCAGTGCCTCATCGAATAATCTGAAGTAGTAAATTGA
*
17549366 CACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAA-TAATCTGAAGTAGTAAATTGA
*
17549407 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
17549425 CTCGAAGTCG
Statistics
Matches: 75, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
37 22 0.29
38 5 0.07
39 2 0.03
40 20 0.27
41 26 0.35
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATAATCTGAAGTAGTAAATTGA
Found at i:17549956 original size:18 final size:19
Alignment explanation
Indices: 17549930--17549965 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
17549920 TAAAATAAAT
*
17549930 TTAACTCCCT-AATTTCAC
1 TTAAATCCCTAAATTTCAC
17549948 TTAAATCCCTAAATTTCA
1 TTAAATCCCTAAATTTCA
17549966 AAATTTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAATCCCTAAATTTCAC
Found at i:17550263 original size:11 final size:10
Alignment explanation
Indices: 17550247--17550308 Score: 54
Period size: 11 Copynumber: 5.8 Consensus size: 10
17550237 GTCTTTCTCC
17550247 TTTTCTTTCCT
1 TTTTCTTT-CT
17550258 TTTTCTTTCT
1 TTTTCTTTCT
17550268 TTTTCCTTT-T
1 TTTT-CTTTCT
17550278 TGTTTCGTTTCT
1 T-TTTC-TTTCT
* *
17550290 ATCTTGTTTCT
1 -TTTTCTTTCT
17550301 TTTTCTTT
1 TTTTCTTT
17550309 TATTTAATCG
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
10 15 0.36
11 23 0.55
12 3 0.07
13 1 0.02
ACGTcount: A:0.02, C:0.19, G:0.05, T:0.74
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:17550344 original size:18 final size:17
Alignment explanation
Indices: 17550322--17550355 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
17550312 TTAATCGTTT
17550322 TATTATTAT-ATA-ATA
1 TATTATTATAATATATA
17550337 TATTATTATAATATATA
1 TATTATTATAATATATA
17550354 TA
1 TA
17550356 CTAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 3 0.18
17 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTATTATAATATATA
Found at i:17550348 original size:13 final size:13
Alignment explanation
Indices: 17550325--17550379 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
17550315 ATCGTTTTAT
17550325 TATTA-TATAATA
1 TATTATTATAATA
17550337 TATTATTATAATA
1 TATTATTATAATA
*
17550350 TATATACTA-AATA
1 TAT-TATTATAATA
17550363 TATTTTATTATAATA
1 TA--TTATTATAATA
17550378 TA
1 TA
17550380 CATTAAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
12 5 0.14
13 16 0.44
14 8 0.22
15 7 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
TATTATTATAATA
Found at i:17550386 original size:26 final size:27
Alignment explanation
Indices: 17550334--17550387 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
17550324 TTATTATATA
*
17550334 ATATATTATTATAATATATATACTAAAT
1 ATATATTATTATAATATACATA-TAAAT
*
17550362 ATATTTTATTATAATATACAT-TAAAT
1 ATATATTATTATAATATACATATAAAT
17550388 TTTACATAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.21
28 19 0.79
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATATTATTATAATATACATATAAAT
Found at i:17550599 original size:13 final size:13
Alignment explanation
Indices: 17550581--17550616 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
17550571 ACTAACTTCG
17550581 TAAATATTTATAA
1 TAAATATTTATAA
*
17550594 TAAATATTTATTA
1 TAAATATTTATAA
17550607 TAAATATTTA
1 TAAATATTTA
17550617 CGAGTCTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAAATATTTATAA
Found at i:17552068 original size:135 final size:135
Alignment explanation
Indices: 17551903--17552177 Score: 496
Period size: 135 Copynumber: 2.0 Consensus size: 135
17551893 CCCCGACTCA
* * *
17551903 GCAAAATTTGTGTAATTCTGTTTTGTTTTAAGTATGACATGTGTCTGGGTTGAGTCAATTTTTGA
1 GCAAAATTTGTGTAATTCTGTTTTGTTTTAAGTATAAAATGTGTCTGGGTTGAATCAATTTTTGA
*
17551968 CATAATATGTGACTTATGAACTTTTGGAGTTGGAATTGGTATTTTGAAAGTGACTATATGTTTGA
66 CATAATATGTGACTTATGAACTTTTGGAGTTGGAATTGGTATTTTGAAAGTGACTATATGTTTAA
17552033 ATTAT
131 ATTAT
*
17552038 GCAAAATTTGTGTAATTCTGTTTTGTTTTAAGTATAAAATGTGTCTGGGTTTAATCAATTTTTGA
1 GCAAAATTTGTGTAATTCTGTTTTGTTTTAAGTATAAAATGTGTCTGGGTTGAATCAATTTTTGA
17552103 CATAATATGTGACTTATGAACTTTTGGAGTTGGAATTGGTATTTTGAAAGTGACTATATGTTTAA
66 CATAATATGTGACTTATGAACTTTTGGAGTTGGAATTGGTATTTTGAAAGTGACTATATGTTTAA
*
17552168 ATTGT
131 ATTAT
17552173 GCAAA
1 GCAAA
17552178 CTAGGTTGTC
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
135 134 1.00
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.44
Consensus pattern (135 bp):
GCAAAATTTGTGTAATTCTGTTTTGTTTTAAGTATAAAATGTGTCTGGGTTGAATCAATTTTTGA
CATAATATGTGACTTATGAACTTTTGGAGTTGGAATTGGTATTTTGAAAGTGACTATATGTTTAA
ATTAT
Found at i:17555228 original size:25 final size:24
Alignment explanation
Indices: 17555199--17555245 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
17555189 TATAGCCCTG
17555199 ATAAGCTTCCTATTACATGGCTCAC
1 ATAAGCTTCCT-TTACATGGCTCAC
*
17555224 ATAAGCTTCCTTTATATGGCTC
1 ATAAGCTTCCTTTACATGGCTC
17555246 GAGAGAGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.36
Consensus pattern (24 bp):
ATAAGCTTCCTTTACATGGCTCAC
Found at i:17559807 original size:21 final size:20
Alignment explanation
Indices: 17559778--17559816 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
17559768 TTAGAAATGT
17559778 TTTCATTTT-GTCTTTTTTAA
1 TTTCATTTTAGT-TTTTTTAA
17559798 TTTCAATTTTAGTTTTTTT
1 TTTC-ATTTTAGTTTTTTT
17559817 CAACTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 11 0.65
22 2 0.12
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTCATTTTAGTTTTTTTAA
Found at i:17576084 original size:14 final size:15
Alignment explanation
Indices: 17576059--17576087 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17576049 ATGGTTACTC
17576059 TTTTTAATAATTTTA
1 TTTTTAATAATTTTA
17576074 TTTTTAA-AATTTTA
1 TTTTTAATAATTTTA
17576088 ACTTCATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTAATAATTTTA
Found at i:17577501 original size:85 final size:87
Alignment explanation
Indices: 17577295--17577509 Score: 208
Period size: 85 Copynumber: 2.5 Consensus size: 87
17577285 GCCTAAAGTG
* * * *
17577295 TAAAAAA-ACCCT-AAACTTTTTCAAAAAAAGTAATTAAGTCTTTGTTTTTTTTTTCACTTAATT
1 TAAAAAATACCCTCAAACTTTTTCAAAAAAAGCAATTAAG-C-CTGTTTTTTTTGTCACTCAATT
** *
17577358 AGATACTTAAGCTTTCAAAATGTA
64 AGATACTTAAAATTTCAAAATGCA
** ****
17577382 TAAAAAATGTCCTC-AACTTAAAAAAAGAAGAAGCAATTAAGCCT-TTTTTTTTGT-ACTCAATT
1 TAAAAAATACCCTCAAACTTTTTCAAA-AA-AAGCAATTAAGCCTGTTTTTTTTGTCACTCAATT
*
17577444 -GGTACTTAAAATTTCAAAATGCA
64 AGATACTTAAAATTTCAAAATGCA
*
17577467 TAAAAAAATACCCTCAAACTTTTTCAAAAAAAGCAAGTAAGCC
1 T-AAAAAATACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCC
17577510 ACTACTTTTT
Statistics
Matches: 101, Mismatches: 21, Indels: 14
0.74 0.15 0.10
Matches are distributed among these distances:
85 32 0.32
86 20 0.20
87 24 0.24
88 12 0.12
89 3 0.03
90 10 0.10
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (87 bp):
TAAAAAATACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCTGTTTTTTTTGTCACTCAATTAG
ATACTTAAAATTTCAAAATGCA
Found at i:17577704 original size:19 final size:20
Alignment explanation
Indices: 17577682--17577726 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
17577672 AAAATTATAA
17577682 AAAAAACAATAAATGTT-AT
1 AAAAAACAATAAATGTTAAT
** *
17577701 AAAAATTAATAAATTTTAAT
1 AAAAAACAATAAATGTTAAT
17577721 AAAAAA
1 AAAAAA
17577727 GTAAAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAAACAATAAATGTTAAT
Found at i:17577769 original size:20 final size:19
Alignment explanation
Indices: 17577719--17577810 Score: 73
Period size: 18 Copynumber: 4.7 Consensus size: 19
17577709 ATAAATTTTA
17577719 ATAAAAA-AGTAAAAAATAT
1 ATAAAAATA-TAAAAAATAT
*
17577738 TTAAAAAT-TAAAAAATAT
1 ATAAAAATATAAAAAATAT
*
17577756 ATAAAAATCATAAAATAT-T
1 ATAAAAAT-ATAAAAAATAT
* *
17577775 GTAAAAATTTATAAAAATCAT
1 ATAAAAATATA-AAAAAT-AT
*
17577796 AAAAAAATTATAAAA
1 ATAAAAA-TATAAAA
17577811 TGCATCAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
18 19 0.33
19 19 0.33
20 7 0.12
21 9 0.16
22 3 0.05
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (19 bp):
ATAAAAATATAAAAAATAT
Found at i:17577810 original size:10 final size:10
Alignment explanation
Indices: 17577719--17577810 Score: 54
Period size: 10 Copynumber: 9.6 Consensus size: 10
17577709 ATAAATTTTA
*
17577719 ATAAAAAAGT
1 ATAAAAAATT
17577729 A-AAAAATATT
1 ATAAAAA-ATT
17577739 -T-AAAAA-T
1 ATAAAAAATT
17577746 -TAAAAAA-T
1 ATAAAAAATT
*
17577754 ATATAAAAATC
1 ATA-AAAAATT
*
17577765 ATAAAATATT
1 ATAAAAAATT
* *
17577775 GTAAAAATTT
1 ATAAAAAATT
*
17577785 AT-AAAAATC
1 ATAAAAAATT
17577794 ATAAAAAAATT
1 AT-AAAAAATT
17577805 ATAAAA
1 ATAAAA
17577811 TGCATCAAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
7 2 0.03
8 7 0.11
9 18 0.29
10 25 0.40
11 11 0.17
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:17577810 original size:29 final size:28
Alignment explanation
Indices: 17577740--17577811 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
17577730 AAAAATATTT
*
17577740 AAAAATTAAAAAATATATAAAAATCATA
1 AAAAATTATAAAATATATAAAAATCATA
* * *
17577768 AAATATTGTAAAAATTTATAAAAATCATAA
1 AAAAATTAT-AAAATATATAAAAATCAT-A
17577798 AAAAATTATAAAAT
1 AAAAATTATAAAAT
17577812 GCATCAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 6 0.17
29 22 0.61
30 8 0.22
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (28 bp):
AAAAATTATAAAATATATAAAAATCATA
Found at i:17577821 original size:20 final size:20
Alignment explanation
Indices: 17577740--17577810 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
17577730 AAAAATATTT
*
17577740 AAAAATTA-AAAAAT-ATAT
1 AAAAATTATAAAAATCATAA
* **
17577758 AAAAATCATAAAATATTGT-A
1 AAAAATTATAAAA-ATCATAA
*
17577778 AAAATTTATAAAAATCATAA
1 AAAAATTATAAAAATCATAA
17577798 AAAAATTATAAAA
1 AAAAATTATAAAA
17577811 TGCATCAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
18 7 0.17
19 7 0.17
20 26 0.63
21 1 0.02
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (20 bp):
AAAAATTATAAAAATCATAA
Found at i:17581042 original size:49 final size:49
Alignment explanation
Indices: 17580910--17581044 Score: 216
Period size: 49 Copynumber: 2.8 Consensus size: 49
17580900 GATAATAACA
* * * * *
17580910 TGCCAAAGCCATGTCCCAAACATGGCCTTACATGAGATGTTTCCTGTAC
1 TGCCAATGCCATATCCCAGATATGGCCTTACATGGGATGTTTCCTGTAC
17580959 TGCCAATGCCATATCCCAGATATGGCCTTACATGGGATGTTTCCTGTAC
1 TGCCAATGCCATATCCCAGATATGGCCTTACATGGGATGTTTCCTGTAC
*
17581008 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGA
1 TGCCAATGCCATATCCCAGATATGGCCTTACATGGGA
17581045 GTTCTCATAT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 80 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (49 bp):
TGCCAATGCCATATCCCAGATATGGCCTTACATGGGATGTTTCCTGTAC
Found at i:17581148 original size:50 final size:53
Alignment explanation
Indices: 17581067--17581195 Score: 140
Period size: 50 Copynumber: 2.4 Consensus size: 53
17581057 GTGCCCATGC
* * *
17581067 CATGTCCCATACATGGTCTTACGGGGAACCTCTC-ATCTCAGTG-T-CAACGT
1 CATGTCCCAGACATGGTCTTACGGAGAACCTCTCAATCTCAATGATACAACGT
* * *
17581117 CATGTCCTAGACATGGTCTTACATGAG-ACCTCTCATAATCTCAATGATACCAATGT
1 CATGTCCCAGACATGGTCTTAC-GGAGAACCTCTC--AATCTCAATGATA-CAACGT
17581173 CATGTCCCAGACATGGTCTTACG
1 CATGTCCCAGACATGGTCTTACG
17581196 TGGGATCTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
50 27 0.42
51 2 0.03
53 8 0.12
54 1 0.02
56 26 0.41
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.29
Consensus pattern (53 bp):
CATGTCCCAGACATGGTCTTACGGAGAACCTCTCAATCTCAATGATACAACGT
Found at i:17583354 original size:23 final size:20
Alignment explanation
Indices: 17583320--17583373 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
17583310 TAGCAATTTT
*
17583320 TAAATATTTTTATCATTTTAA
1 TAAATATTTTTAT-AGTTTAA
17583341 TAAATATATATTTATAGTTTAA
1 TAAATAT-T-TTTATAGTTTAA
*
17583363 T-GATATTTTTA
1 TAAATATTTTTA
17583374 AAATTTCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 4 0.14
20 1 0.03
21 11 0.38
22 8 0.28
23 5 0.17
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TAAATATTTTTATAGTTTAA
Found at i:17596947 original size:51 final size:51
Alignment explanation
Indices: 17596903--17597002 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
17596893 AATTATTTAA
*
17596903 AAATAGGGATTTAAGAGAAATTTA-AGAGGAACTTGAGAGCAAATTGAGATT
1 AAATAGGAATTTAAGAGAAATTTAGA-AGGAACTTGAGAGCAAATTGAGATT
* * * *
17596954 AAATATGAATTTGAGAGAAATTTGGAAGGAATTTGAGAGCAAATTGAGA
1 AAATAGGAATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAGA
17597003 GGAAATTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.26, T:0.26
Consensus pattern (51 bp):
AAATAGGAATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAGATT
Found at i:17596975 original size:11 final size:11
Alignment explanation
Indices: 17596961--17597038 Score: 65
Period size: 11 Copynumber: 7.0 Consensus size: 11
17596951 ATTAAATATG
17596961 AATTTGAGAGA
1 AATTTGAGAGA
*
17596972 AATTTG-GAAGG
1 AATTTGAG-AGA
17596983 AATTTGAGAGCA
1 AATTTGAGAG-A
17596995 AA-TTGAGAGGA
1 AATTTGAGA-GA
*
17597006 AATTT-AAAGGA
1 AATTTGAGA-GA
17597017 AA-TTGAGAGGA
1 AATTTGAGA-GA
17597028 AATTTGAGAGA
1 AATTTGAGAGA
17597039 GGATTAGTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
10 3 0.05
11 41 0.73
12 12 0.21
ACGTcount: A:0.45, C:0.01, G:0.29, T:0.24
Consensus pattern (11 bp):
AATTTGAGAGA
Found at i:17597005 original size:22 final size:22
Alignment explanation
Indices: 17596961--17597038 Score: 90
Period size: 22 Copynumber: 3.5 Consensus size: 22
17596951 ATTAAATATG
17596961 AATTTGAGAGAAATTTG-GAAGG-
1 AATTTGAGAGAAA-TTGAG-AGGA
17596983 AATTTGAGAGCAAATTGAGAGGA
1 AATTTGAGAG-AAATTGAGAGGA
*
17597006 AATTT-AAAGGAAATTGAGAGGA
1 AATTTGAGA-GAAATTGAGAGGA
17597028 AATTTGAGAGA
1 AATTTGAGAGA
17597039 GGATTAGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
22 37 0.76
23 12 0.24
ACGTcount: A:0.45, C:0.01, G:0.29, T:0.24
Consensus pattern (22 bp):
AATTTGAGAGAAATTGAGAGGA
Found at i:17597016 original size:33 final size:35
Alignment explanation
Indices: 17596961--17597037 Score: 106
Period size: 33 Copynumber: 2.3 Consensus size: 35
17596951 ATTAAATATG
* *
17596961 AATTTGAGA-GAAATTTGGAAGGAATTTGAGAGCA
1 AATTTGAGAGGAAATTTGAAAGGAAATTGAGAGCA
*
17596995 AA-TTGAGAGGAAATTT-AAAGGAAATTGAGAGGA
1 AATTTGAGAGGAAATTTGAAAGGAAATTGAGAGCA
17597028 AATTTGAGAG
1 AATTTGAGAG
17597038 AGGATTAGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 22 0.58
34 16 0.42
ACGTcount: A:0.44, C:0.01, G:0.30, T:0.25
Consensus pattern (35 bp):
AATTTGAGAGGAAATTTGAAAGGAAATTGAGAGCA
Found at i:17602956 original size:22 final size:22
Alignment explanation
Indices: 17602931--17602986 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 22
17602921 AGTTTTCAAT
* *
17602931 ATTTATATATTTTGTCAATTTA
1 ATTTATATATTTTGTAAATTAA
*
17602953 ATTT-T-TATTTTTTAAATTAA
1 ATTTATATATTTTGTAAATTAA
17602973 ATTTAGTTATATTT
1 ATTTA--TATATTT
17602987 AAAAGTCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 16 0.59
21 1 0.04
22 4 0.15
23 1 0.04
24 5 0.19
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (22 bp):
ATTTATATATTTTGTAAATTAA
Found at i:17609669 original size:27 final size:27
Alignment explanation
Indices: 17609631--17609702 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
17609621 NNNNNNNNNN
* *
17609631 CAATATTCATACAAAATTATAATATTA
1 CAATATTCATACAAAATTACAAAATTA
17609658 CAATATTCATACAAAATTACAAAATTA
1 CAATATTCATACAAAATTACAAAATTA
*
17609685 CAATATTCATATAAAATT
1 CAATATTCATACAAAATT
17609703 GCAATATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (27 bp):
CAATATTCATACAAAATTACAAAATTA
Found at i:17609775 original size:22 final size:22
Alignment explanation
Indices: 17609750--17609836 Score: 129
Period size: 22 Copynumber: 3.7 Consensus size: 22
17609740 TCTATATTTA
17609750 GTATGAATATTGTAATTTTTTT
1 GTATGAATATTGTAATTTTTTT
17609772 GTATGAATATTGTAATTTTTTT
1 GTATGAATATTGTAATTTTTTT
17609794 GTATGAATATTGTAATATTATAATTTT
1 GTATGAATATTGT-A-ATT-T--TTTT
17609821 GTATGAATATTGTAAT
1 GTATGAATATTGTAAT
17609837 GTCGGTATAT
Statistics
Matches: 60, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
22 35 0.58
23 1 0.02
24 3 0.05
25 3 0.05
26 1 0.02
27 17 0.28
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (22 bp):
GTATGAATATTGTAATTTTTTT
Found at i:17609883 original size:47 final size:48
Alignment explanation
Indices: 17609755--17609883 Score: 165
Period size: 47 Copynumber: 2.7 Consensus size: 48
17609745 ATTTAGTATG
* **
17609755 AATATTGTAATTTTTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
1 AATATTGTAA-TTTTTTGTATGAATATTGTAA--TGTCGGTAT-AATATTGT
*
17609807 AATATTATAA--TTTTGTATGAATATTGTAATGTCGGTAT-ATATTGT
1 AATATTGTAATTTTTTGTATGAATATTGTAATGTCGGTATAATATTGT
17609852 AATATTGTAATTTTTTGTATGAATATTGTAAT
1 AATATTGTAATTTTTTGTATGAATATTGTAAT
17609884 TATTTTATAA
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
45 16 0.23
47 26 0.37
49 19 0.27
52 9 0.13
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (48 bp):
AATATTGTAATTTTTTGTATGAATATTGTAATGTCGGTATAATATTGT
Found at i:17609954 original size:19 final size:19
Alignment explanation
Indices: 17609932--17609969 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17609922 TATAAATTTA
*
17609932 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
17609951 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
17609970 AAATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAGTAACTTATTACTAAT
Found at i:17610221 original size:27 final size:27
Alignment explanation
Indices: 17610183--17610254 Score: 135
Period size: 27 Copynumber: 2.7 Consensus size: 27
17610173 CCGGCCCGGC
17610183 CCATTGGCGCCTCTCAGAATGGCACCA
1 CCATTGGCGCCTCTCAGAATGGCACCA
17610210 CCATTGGCGCCTCTCAGAATGGCACCA
1 CCATTGGCGCCTCTCAGAATGGCACCA
*
17610237 CCATTGGCGCCTCCCAGA
1 CCATTGGCGCCTCTCAGA
17610255 TAGGCGCCAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.21, C:0.39, G:0.22, T:0.18
Consensus pattern (27 bp):
CCATTGGCGCCTCTCAGAATGGCACCA
Found at i:17610331 original size:29 final size:29
Alignment explanation
Indices: 17610298--17610353 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
17610288 TACTAACCCG
*
17610298 AAAAAGTATAAAATTA-TATTTTATTCAA
1 AAAAAATATAAAATTATTATTTTATTCAA
* **
17610326 AAAAAATTTATTATTATTATTTTATTCA
1 AAAAAATATAAAATTATTATTTTATTCA
17610354 TTGGCGCCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (29 bp):
AAAAAATATAAAATTATTATTTTATTCAA
Found at i:17610462 original size:28 final size:29
Alignment explanation
Indices: 17610389--17610462 Score: 66
Period size: 28 Copynumber: 2.6 Consensus size: 29
17610379 TGAAAAAAGT
*
17610389 AACCTATTT-TGGTAAATATTTTTTCTGAC
1 AACCTATTTAT-GTAAAAATTTTTTCTGAC
* **
17610418 ACCCTATTTCA-GT-AAAATTTTTT-TTTC
1 AACCTATTT-ATGTAAAAATTTTTTCTGAC
17610445 AACCTATTTATGTAAAAA
1 AACCTATTTATGTAAAAA
17610463 ATCCAGAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
26 1 0.03
27 12 0.33
28 13 0.36
29 10 0.28
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.46
Consensus pattern (29 bp):
AACCTATTTATGTAAAAATTTTTTCTGAC
Found at i:17619534 original size:18 final size:17
Alignment explanation
Indices: 17619511--17619547 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
17619501 AATACCATTA
*
17619511 TATTAATATTAATTATTT
1 TATTAAAATTAATT-TTT
17619529 TATTAAAATTAATTTTT
1 TATTAAAATTAATTTTT
17619546 TA
1 TA
17619548 AATAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTAAAATTAATTTTT
Found at i:17619548 original size:14 final size:14
Alignment explanation
Indices: 17619521--17619560 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 14
17619511 TATTAATATT
17619521 AATT-ATTTTATTAA
1 AATTAATTTT-TTAA
17619535 AATTAATTTTTT-A
1 AATTAATTTTTTAA
17619548 AA-TAATTTTTTAA
1 AATTAATTTTTTAA
17619561 GTGAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 9 0.38
13 4 0.17
14 6 0.25
15 5 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AATTAATTTTTTAA
Found at i:17619953 original size:27 final size:28
Alignment explanation
Indices: 17619875--17619970 Score: 167
Period size: 28 Copynumber: 3.5 Consensus size: 28
17619865 AAAATAAAAT
*
17619875 TTTATCAAAATATTATAACTTTTTTTTA
1 TTTACCAAAATATTATAACTTTTTTTTA
17619903 TTTACCAAAATATTATAACTTTTTTTTA
1 TTTACCAAAATATTATAACTTTTTTTTA
*
17619931 TTTACTAAAATATTATAAC-TTTTTTTA
1 TTTACCAAAATATTATAACTTTTTTTTA
17619958 TTTACCAAAATAT
1 TTTACCAAAATAT
17619971 ACAAAAAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
27 20 0.31
28 45 0.69
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (28 bp):
TTTACCAAAATATTATAACTTTTTTTTA
Found at i:17625832 original size:44 final size:44
Alignment explanation
Indices: 17625769--17625855 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
17625759 TGAATGCATT
*
17625769 CATCTATGTTAATTACAATATAATCTGCAAATAAACAATCTATA
1 CATCTATATTAATTACAATATAATCTGCAAATAAACAATCTATA
17625813 CATCTATATTAATTACAATATAATCTGCAAATAAACAATCTAT
1 CATCTATATTAATTACAATATAATCTGCAAATAAACAATCTAT
17625856 CTTAATTAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.34
Consensus pattern (44 bp):
CATCTATATTAATTACAATATAATCTGCAAATAAACAATCTATA
Found at i:17632283 original size:19 final size:18
Alignment explanation
Indices: 17632246--17632284 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
17632236 AGTGAATATT
*
17632246 AAAATTAAATTAAACATA
1 AAAATTAAATCAAACATA
*
17632264 AAAATTAAACTCACACATA
1 AAAATTAAA-TCAAACATA
17632283 AA
1 AA
17632285 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.64, C:0.13, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAATTAAATCAAACATA
Found at i:17634500 original size:17 final size:17
Alignment explanation
Indices: 17634490--17634534 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
17634480 TTTGTTTTAA
17634490 TGTAATATTTGTATATT
1 TGTAATATTTGTATATT
17634507 TGTAATATTTGTATATT
1 TGTAATATTTGTATATT
17634524 TGTAAATATTT
1 TGT-AATATTT
17634535 ATGAATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 20 0.74
18 7 0.26
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (17 bp):
TGTAATATTTGTATATT
Found at i:17634502 original size:9 final size:9
Alignment explanation
Indices: 17634490--17634534 Score: 67
Period size: 8 Copynumber: 5.1 Consensus size: 9
17634480 TTTGTTTTAA
17634490 TGTAATATT
1 TGTAATATT
17634499 TGT-ATATT
1 TGTAATATT
17634507 TGTAATATT
1 TGTAATATT
17634516 TGT-ATATT
1 TGTAATATT
17634524 TGTAAATATT
1 TGT-AATATT
17634534 T
1 T
17634535 ATGAATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
8 16 0.48
9 11 0.33
10 6 0.18
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (9 bp):
TGTAATATT
Found at i:17638292 original size:2 final size:2
Alignment explanation
Indices: 17638285--17638312 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17638275 AGAATGCAGT
17638285 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
17638313 AAACAGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:17642946 original size:61 final size:60
Alignment explanation
Indices: 17642848--17642970 Score: 144
Period size: 61 Copynumber: 2.0 Consensus size: 60
17642838 GTCATTACAT
*
17642848 TGAATGCTTTAGCTGTTTTTAGTTTATGATTATGGAGTTGCATT-AAATTTTGAGCAAGGA
1 TGAATGCTTTAGCTGTTTTTAGTTTATGATTATGGAGTTGC-TTCAAATTTTGAACAAGGA
* ** *
17642908 TGAATGCTTTAG-TTTTTCTCTAGTTTATTTTTGA-GGAGTTGCTTCAAATTTTGAACGAGGA
1 TGAATGCTTTAGCTGTTT-T-TAGTTTATGATT-ATGGAGTTGCTTCAAATTTTGAACAAGGA
17642969 TG
1 TG
17642971 GACAAGGCTA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
59 4 0.07
60 15 0.28
61 34 0.63
62 1 0.02
ACGTcount: A:0.24, C:0.08, G:0.23, T:0.45
Consensus pattern (60 bp):
TGAATGCTTTAGCTGTTTTTAGTTTATGATTATGGAGTTGCTTCAAATTTTGAACAAGGA
Found at i:17643391 original size:17 final size:17
Alignment explanation
Indices: 17643369--17643402 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17643359 GAGGCTCATA
*
17643369 TCCGTCATTGCTCTGTT
1 TCCGTCATTGCTATGTT
*
17643386 TCCGTCCTTGCTATGTT
1 TCCGTCATTGCTATGTT
17643403 CCTCTAGCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.29, G:0.18, T:0.47
Consensus pattern (17 bp):
TCCGTCATTGCTATGTT
Found at i:17648165 original size:30 final size:30
Alignment explanation
Indices: 17648131--17648189 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
17648121 ATATATATAT
*
17648131 TAATT-TGGTACAATTATACACGTGAAACTC
1 TAATTGTGGTACAAATATACAC-TGAAACTC
* *
17648161 TAATTGTGGTTCAAATATATACTGAAACT
1 TAATTGTGGTACAAATATACACTGAAACT
17648190 TTAACTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (30 bp):
TAATTGTGGTACAAATATACACTGAAACTC
Found at i:17649472 original size:29 final size:30
Alignment explanation
Indices: 17649409--17649477 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
17649399 AAAACAATAC
* *
17649409 ATGAACTTTGATTTAATGTGCAATTATATAT
1 ATGAATTTTGATTTAATGT-CAATTATATAA
* *
17649440 ATGAATTTTGATTTTATGT-AATTTTATAA
1 ATGAATTTTGATTTAATGTCAATTATATAA
17649469 ATGAATTTT
1 ATGAATTTT
17649478 TTATTGATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 17 0.50
31 17 0.50
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.51
Consensus pattern (30 bp):
ATGAATTTTGATTTAATGTCAATTATATAA
Found at i:17649982 original size:25 final size:25
Alignment explanation
Indices: 17649954--17650006 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
17649944 TCTTTTCTTC
*
17649954 TTTTACAAAATTTAATCA-TTTTATT
1 TTTTACAAAAGTTAAT-ATTTTTATT
* *
17649979 TTTTCCATAAGTTAATATTTTTATT
1 TTTTACAAAAGTTAATATTTTTATT
17650004 TTT
1 TTT
17650007 GTGCAACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTACAAAAGTTAATATTTTTATT
Found at i:17650185 original size:21 final size:21
Alignment explanation
Indices: 17650159--17650202 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
17650149 TTCAGGATTT
*
17650159 GGGTTCGAGATTTAAGGTTTA
1 GGGTTCGAGATTCAAGGTTTA
17650180 GGGTTCGAGATTCAAGGTTTA
1 GGGTTCGAGATTCAAGGTTTA
17650201 GG
1 GG
17650203 TCTAGGGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.07, G:0.36, T:0.34
Consensus pattern (21 bp):
GGGTTCGAGATTCAAGGTTTA
Found at i:17651360 original size:16 final size:16
Alignment explanation
Indices: 17651336--17651366 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17651326 CCCGAAATAA
17651336 ACAGAGGCCCAAAATT
1 ACAGAGGCCCAAAATT
*
17651352 ACAGTGGCCCAAAAT
1 ACAGAGGCCCAAAAT
17651367 AGTTTCAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.26, G:0.19, T:0.13
Consensus pattern (16 bp):
ACAGAGGCCCAAAATT
Found at i:17675924 original size:6 final size:6
Alignment explanation
Indices: 17675913--17675941 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17675903 AGGAAGATAA
17675913 TGATGG TGATGG TGATGG TGATGG TGATG
1 TGATGG TGATGG TGATGG TGATGG TGATG
17675942 ATAAAGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.48, T:0.34
Consensus pattern (6 bp):
TGATGG
Found at i:17680766 original size:6 final size:6
Alignment explanation
Indices: 17680755--17680779 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17680745 TTAATATTGA
17680755 AATTTT AATTTT AATTTT AATTTT A
1 AATTTT AATTTT AATTTT AATTTT A
17680780 TAGAATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
AATTTT
Found at i:17688402 original size:17 final size:16
Alignment explanation
Indices: 17688377--17688413 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
17688367 ATTAATAAGT
*
17688377 TTATTATTATTTAATTA
1 TTATGATTATTT-ATTA
17688394 TTATGATTATTTATTA
1 TTATGATTATTTATTA
17688410 TTAT
1 TTAT
17688414 ATTTCTCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTATGATTATTTATTA
Found at i:17697164 original size:47 final size:47
Alignment explanation
Indices: 17697110--17697205 Score: 147
Period size: 47 Copynumber: 2.0 Consensus size: 47
17697100 AGCACAATAA
17697110 AAAATATCATAAAACTTATTATACGATGAAACTTGCAACAAAACAAG
1 AAAATATCATAAAACTTATTATACGATGAAACTTGCAACAAAACAAG
** * * *
17697157 AAAATATCATTGAATTTATTATATGATGAAACTTGTAACAAAACAAG
1 AAAATATCATAAAACTTATTATACGATGAAACTTGCAACAAAACAAG
17697204 AA
1 AA
17697206 GAACGAGTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.27
Consensus pattern (47 bp):
AAAATATCATAAAACTTATTATACGATGAAACTTGCAACAAAACAAG
Found at i:17698408 original size:7 final size:7
Alignment explanation
Indices: 17698396--17698435 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
17698386 AAAAATGTGC
17698396 AAAAAAT
1 AAAAAAT
17698403 AAAAAAT
1 AAAAAAT
17698410 AAAAAAT
1 AAAAAAT
17698417 AAAAAAT
1 AAAAAAT
17698424 AAAAAAT
1 AAAAAAT
17698431 AAAAA
1 AAAAA
17698436 GCAAGATAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:17702662 original size:2 final size:2
Alignment explanation
Indices: 17702655--17702683 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17702645 AGTTAAAGCA
17702655 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
17702684 ACACACACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:17718090 original size:16 final size:16
Alignment explanation
Indices: 17718069--17718099 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17718059 AAGGAACTGT
17718069 TTGTAACATCATTTGG
1 TTGTAACATCATTTGG
17718085 TTGTAACATCATTTG
1 TTGTAACATCATTTG
17718100 AGTAGAAAAA
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:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (16 bp):
TTGTAACATCATTTGG
Found at i:17720004 original size:30 final size:30
Alignment explanation
Indices: 17719959--17720022 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
17719949 TGATAGTTAC
* * *
17719959 ATAATAAATAAACTTACTTTTATTACTCAT
1 ATAACAAACAAACTTACTTTTATGACTCAT
*
17719989 ATAACAAACAAACTTACTTTTATGACTTAT
1 ATAACAAACAAACTTACTTTTATGACTCAT
17720019 ATAA
1 ATAA
17720023 AATAATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (30 bp):
ATAACAAACAAACTTACTTTTATGACTCAT
Found at i:17721081 original size:71 final size:70
Alignment explanation
Indices: 17720965--17721100 Score: 218
Period size: 71 Copynumber: 1.9 Consensus size: 70
17720955 CTTCCTCCAA
* *
17720965 CTTTTCGTCAAGCGAAGTGTTCGATAAAATGCTTCACTGATGAAAAAGTAAGGCCTTTCAAATTC
1 CTTTTCGTCAAGCGAAGTGTTCGATAAAATCCTTCACTGATGAAAAAG-AAAGCCTTTCAAATTC
17721030 TTTCAT
65 TTTCAT
* * *
17721036 CTTTTCGTCGAGCGAGGTGTTCGATAAAATCCTTCACTGTTGAAAAAGAAAGCCTTTCAAATTCT
1 CTTTTCGTCAAGCGAAGTGTTCGATAAAATCCTTCACTGATGAAAAAGAAAGCCTTTCAAATTCT
17721101 AACGTTTGTG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
70 16 0.27
71 44 0.73
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (70 bp):
CTTTTCGTCAAGCGAAGTGTTCGATAAAATCCTTCACTGATGAAAAAGAAAGCCTTTCAAATTCT
TTCAT
Found at i:17738144 original size:16 final size:16
Alignment explanation
Indices: 17738088--17738156 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
17738078 ATTTTTAAAT
*
17738088 TAAAA-ATATTTAAT-
1 TAAAATATAATTAATA
* *
17738102 TAAAATGTATTTAATA
1 TAAAATATAATTAATA
*
17738118 TTAAATATAATTACATA
1 TAAAATATAATTA-ATA
*
17738135 TAAAAT-TAATTGATTA
1 TAAAATATAATT-AATA
17738151 TAAAAT
1 TAAAAT
17738157 GATTTTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
14 5 0.11
15 8 0.18
16 23 0.51
17 9 0.20
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAAATATAATTAATA
Found at i:17738755 original size:17 final size:18
Alignment explanation
Indices: 17738735--17738775 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
17738725 ATCATTTAAA
17738735 AAAATT-ATT-TATTTTCT
1 AAAATTGATTCTATTTT-T
*
17738752 AAAATTGTTTCTATTTTT
1 AAAATTGATTCTATTTTT
17738770 AAAATT
1 AAAATT
17738776 CTTGCATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 9 0.43
19 6 0.29
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (18 bp):
AAAATTGATTCTATTTTT
Found at i:17739895 original size:58 final size:60
Alignment explanation
Indices: 17739755--17739900 Score: 174
Period size: 58 Copynumber: 2.5 Consensus size: 60
17739745 ATGTGCTACG
* * * *
17739755 TAACAATCGATTTAAACATATAAACAATTGATTCAAAAGAAGAAAAAGCAGTATTCTACTA
1 TAACAATTGATTTAAACATATAAACAATTGATTC-AAAGAACAAAAAGCAATATTCCACTA
* * *
17739816 TAAC-ATTCGATTTAAATATATAAACAATTTATTC-AA-AACAATAAGCAATATTCCA-TCA
1 TAACAATT-GATTTAAACATATAAACAATTGATTCAAAGAACAAAAAGCAATATTCCACT-A
17739874 TAACAATTGATTTAAACATATAAACAA
1 TAACAATTGATTTAAACATATAAACAA
17739901 CAAATTCGAA
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
57 1 0.01
58 38 0.51
59 5 0.07
60 2 0.03
61 28 0.38
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (60 bp):
TAACAATTGATTTAAACATATAAACAATTGATTCAAAGAACAAAAAGCAATATTCCACTA
Found at i:17741905 original size:14 final size:14
Alignment explanation
Indices: 17741886--17741918 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17741876 ATTGTTATAT
17741886 AAATTCATTT-AATA
1 AAATTC-TTTCAATA
17741900 AAATTCTTTCAATA
1 AAATTCTTTCAATA
17741914 AAATT
1 AAATT
17741919 AAATTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATTCTTTCAATA
Found at i:17745000 original size:69 final size:70
Alignment explanation
Indices: 17744915--17745051 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 70
17744905 TATCCGTATA
17744915 TAGTGGACTATCACAGTCACAGATACTGCCATGCCCCGTTAAAAATTTAAGAGTTGAGT-AGCTT
1 TAGTGGACTATCACAGTCACAGATACTGCCATGCCCCGTTAAAAATTTAAGAGTTGAGTAAGCTT
17744979 TTTTC
66 TTTTC
17744984 TAGTGGACTATCACAGTCACAGATACTGCCATGCCCCGTTAAAAATTTAAGAGTTGAGTAAGCTT
1 TAGTGGACTATCACAGTCACAGATACTGCCATGCCCCGTTAAAAATTTAAGAGTTGAGTAAGCTT
17745049 TTT
66 TTT
17745052 CAAATTAGAA
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
69 59 0.88
70 8 0.12
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (70 bp):
TAGTGGACTATCACAGTCACAGATACTGCCATGCCCCGTTAAAAATTTAAGAGTTGAGTAAGCTT
TTTTC
Found at i:17756423 original size:20 final size:17
Alignment explanation
Indices: 17756388--17756432 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 17
17756378 ATTTGTATGG
17756388 TTTTATGATTTTTAATAAT
1 TTTTAT-ATTTTTAAT-AT
17756407 TATTTATATTTTGTAATAT
1 T-TTTATATTTT-TAATAT
17756426 TTTTATA
1 TTTTATA
17756433 ATATTTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.25
19 9 0.38
20 9 0.38
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (17 bp):
TTTTATATTTTTAATAT
Done.