Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 59 of 310
Found at i:18599871 original size:82 final size:81
Alignment explanation
Indices: 18599758--18599913 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
18599748 AAATTGTACA
* *
18599758 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
18599822 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
18599839 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
18599904 TGCGAGTTGA
65 TGCGAATTGA
18599914 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:18610785 original size:39 final size:39
Alignment explanation
Indices: 18610621--18610803 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 39
18610611 TTGAATGCTG
* * * * * * *
18610621 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTATGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * * *
18610661 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTATG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* **
18610701 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTATGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
18610741 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
18610780 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTATGTCCCGAAGGCATT
18610804 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.31
40 74 0.61
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:18610823 original size:79 final size:80
Alignment explanation
Indices: 18610657--18610838 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
18610647 GCTAAGTGAA
* * * *
18610657 TATATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGG
1 TATATCCGGGTTAAG-TCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
** ** *
18610721 CATTCGTGCGAGTTGT
65 CATTCGAACGAGGAGC
* * * * *
18610737 TAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
*
18610801 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
*
18610816 TATATCC-GGTTAAATCCCGAAGG
1 TATATCCGGGTTAAGTCCCGAAGG
18610839 TACGTGATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 14 0.17
79 50 0.60
80 19 0.23
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:18615603 original size:34 final size:33
Alignment explanation
Indices: 18615565--18615642 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 33
18615555 CGAAGAGAAT
**
18615565 AAAATTTAAAA-AAAAGTTAAAAAATTGAGGATTG
1 AAAATTTAAAATAAAA-TT-AAAAATTGAAAATTG
* *
18615599 AAAATTCAAAATTAAAATTGAAAATTGAAAATTG
1 AAAATTTAAAA-TAAAATTAAAAATTGAAAATTG
18615633 AAAATTTAAA
1 AAAATTTAAA
18615643 TTTTAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
34 31 0.84
35 2 0.05
36 4 0.11
ACGTcount: A:0.60, C:0.01, G:0.10, T:0.28
Consensus pattern (33 bp):
AAAATTTAAAATAAAATTAAAAATTGAAAATTG
Found at i:18615609 original size:7 final size:7
Alignment explanation
Indices: 18615585--18615696 Score: 86
Period size: 7 Copynumber: 16.1 Consensus size: 7
18615575 AAAAAGTTAA
18615585 AAAATTG
1 AAAATTG
**
18615592 AGGATTG
1 AAAATTG
*
18615599 AAAATTC
1 AAAATTG
18615606 AAAATT-
1 AAAATTG
18615612 AAAATTG
1 AAAATTG
18615619 AAAATTG
1 AAAATTG
18615626 AAAATTG
1 AAAATTG
*
18615633 AAAATTT
1 AAAATTG
* *
18615640 AAATTTT
1 AAAATTG
*
18615647 AAATTTG
1 AAAATTG
*
18615654 AAGATTG
1 AAAATTG
18615661 AAAATCT-
1 AAAAT-TG
18615668 AAAATT-
1 AAAATTG
18615674 AGAAATTG
1 A-AAATTG
**
18615682 AGGATTG
1 AAAATTG
*
18615689 AAGATTG
1 AAAATTG
18615696 A
1 A
18615697 GGATTGAGAA
Statistics
Matches: 87, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
6 8 0.09
7 77 0.89
8 2 0.02
ACGTcount: A:0.51, C:0.02, G:0.15, T:0.32
Consensus pattern (7 bp):
AAAATTG
Found at i:18615687 original size:28 final size:27
Alignment explanation
Indices: 18615595--18615690 Score: 95
Period size: 28 Copynumber: 3.5 Consensus size: 27
18615585 AAAATTGAGG
* *
18615595 ATTGAAAATTCAAAATTAAAATT-GAAA
1 ATTGAAGATTGAAAATTAAAATTAG-AA
* * **
18615622 ATTGAAAATTGAAAATTTAAATTTTAA
1 ATTGAAGATTGAAAATTAAAATTAGAA
18615649 ATTTGAAGATTGAAAATCTAAAATTAGAA
1 A-TTGAAGATTGAAAAT-TAAAATTAGAA
*
18615678 ATTGAGGATTGAA
1 ATTGAAGATTGAA
18615691 GATTGAGGAT
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
27 24 0.41
28 25 0.43
29 9 0.16
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.33
Consensus pattern (27 bp):
ATTGAAGATTGAAAATTAAAATTAGAA
Found at i:18615713 original size:14 final size:13
Alignment explanation
Indices: 18615675--18615713 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
18615665 TCTAAAATTA
18615675 GAAATTGAGGATT
1 GAAATTGAGGATT
18615688 GAAGATTGAGGATT
1 GAA-ATTGAGGATT
*
18615702 GAGAATTTAGGA
1 GA-AATTGAGGA
18615714 AGGAAGAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 19 0.83
15 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.28
Consensus pattern (13 bp):
GAAATTGAGGATT
Found at i:18617563 original size:17 final size:17
Alignment explanation
Indices: 18617522--18617564 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
18617512 TTAAAGGTAT
*
18617522 ATATTTTTATTTTAAAA
1 ATATTTTTATTCTAAAA
*
18617539 ATACTTTTTCTTCTAAAA
1 ATA-TTTTTATTCTAAAA
*
18617557 TTATTTTT
1 ATATTTTT
18617565 TAGAAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATTTTTATTCTAAAA
Found at i:18620038 original size:43 final size:43
Alignment explanation
Indices: 18619990--18620090 Score: 141
Period size: 43 Copynumber: 2.3 Consensus size: 43
18619980 TTATTTGAAA
* * **
18619990 AAACGCTGCTAAAGGTC-GGAACCTTTAGCGGCGCTTTTCCCGT
1 AAACGCCGCTAAAGGTCAAG-ACCTTTAGCGGCGCTTTTCCCAC
*
18620033 AAACGCCGATAAAGGTCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCAAGACCTTTAGCGGCGCTTTTCCCAC
18620076 AAACGCCGCTAAAGG
1 AAACGCCGCTAAAGG
18620091 ACATAAAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
43 50 0.98
44 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:18620277 original size:16 final size:16
Alignment explanation
Indices: 18620252--18620282 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18620242 ACTACACCAG
*
18620252 AAATATAACAAAATAC
1 AAATAGAACAAAATAC
18620268 AAATAGAACAAAATA
1 AAATAGAACAAAATA
18620283 ATGATAGAAT
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:0.71, C:0.10, G:0.03, T:0.16
Consensus pattern (16 bp):
AAATAGAACAAAATAC
Found at i:18620773 original size:12 final size:12
Alignment explanation
Indices: 18620756--18620788 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
18620746 TTGAAGAACC
18620756 ATTAATCATGTT
1 ATTAATCATGTT
18620768 ATTAATCATGTT
1 ATTAATCATGTT
18620780 ATTAATCAT
1 ATTAATCAT
18620789 ATATGCAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (12 bp):
ATTAATCATGTT
Found at i:18620896 original size:13 final size:13
Alignment explanation
Indices: 18620878--18620923 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
18620868 TTATATGCCC
18620878 ATTTACATGCAGA
1 ATTTACATGCAGA
*
18620891 ATTT--A--CAGT
1 ATTTACATGCAGA
18620900 ATTTACATGCAGA
1 ATTTACATGCAGA
18620913 ATTTACATGCA
1 ATTTACATGCA
18620924 TCAACAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
9 7 0.26
11 2 0.07
13 18 0.67
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (13 bp):
ATTTACATGCAGA
Found at i:18620904 original size:22 final size:22
Alignment explanation
Indices: 18620878--18620919 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
18620868 TTATATGCCC
18620878 ATTTACATGCAGAATTTACAGT
1 ATTTACATGCAGAATTTACAGT
18620900 ATTTACATGCAGAATTTACA
1 ATTTACATGCAGAATTTACA
18620920 TGCATCAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (22 bp):
ATTTACATGCAGAATTTACAGT
Found at i:18625117 original size:15 final size:15
Alignment explanation
Indices: 18625074--18625120 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
18625064 AAGAATGATC
*
18625074 TAATTGGAATCGAAT
1 TAATTGGAATTGAAT
* *
18625089 TAAGTGTAGA-TGAAT
1 TAATTGGA-ATTGAAT
18625104 TAATTGGAATTGAAT
1 TAATTGGAATTGAAT
18625119 TA
1 TA
18625121 TTTTTAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.36
Consensus pattern (15 bp):
TAATTGGAATTGAAT
Found at i:18625484 original size:72 final size:70
Alignment explanation
Indices: 18625393--18625528 Score: 177
Period size: 72 Copynumber: 1.9 Consensus size: 70
18625383 CCTTAAACTC
* * *
18625393 TAACCCTAACCCCTAAACCCTAAATCATA-ATCCTTAAACTCATAATTCA-TCATAAACCTTCAA
1 TAACCCTAAACCCTAAACCCTAAACCATATAT-CTTAAAC-CATAATTAACTCATAAACCTT-AA
18625456 ACACTAGT
63 ACACTAGT
* *
18625464 TAACTCCTAAACCTTAAACCCTAAACCATATATCTTAAACCATAGTTAACTCATAAACCTTAAAC
1 TAAC-CCTAAACCCTAAACCCTAAACCATATATCTTAAACCATAATTAACTCATAAACCTTAAAC
18625529 CCTAAACCAT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
71 15 0.26
72 40 0.70
73 2 0.04
ACGTcount: A:0.42, C:0.29, G:0.01, T:0.27
Consensus pattern (70 bp):
TAACCCTAAACCCTAAACCCTAAACCATATATCTTAAACCATAATTAACTCATAAACCTTAAACA
CTAGT
Found at i:18625513 original size:46 final size:46
Alignment explanation
Indices: 18625460--18625553 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
18625450 CTTCAAACAC
*
18625460 TAGTTAACTCCTAAACCTTAAACCCTAAACCATATATCTTAAACCA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
18625506 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
18625552 TA
1 TA
18625554 AACCATAATG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.29
Consensus pattern (46 bp):
TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
Found at i:18625525 original size:25 final size:25
Alignment explanation
Indices: 18625417--18625529 Score: 94
Period size: 25 Copynumber: 4.6 Consensus size: 25
18625407 AAACCCTAAA
* * *
18625417 TCATAATCCTTAAACTCATAATTCA-
1 TCATAAACCTTAAAC-CATAGTTAAC
18625442 TCATAAACCTTCAAA-CACTAGTTAAC
1 TCATAAACCTT-AAACCA-TAGTTAAC
* *
18625468 TCCTAAACCTTAAACCCTA---AAC
1 TCATAAACCTTAAACCATAGTTAAC
* *
18625490 -CATATATCTTAAACCATAGTTAAC
1 TCATAAACCTTAAACCATAGTTAAC
18625514 TCATAAACCTTAAACC
1 TCATAAACCTTAAACC
18625530 CTAAACCATA
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
21 14 0.20
22 3 0.04
24 5 0.07
25 33 0.48
26 14 0.20
ACGTcount: A:0.42, C:0.27, G:0.02, T:0.29
Consensus pattern (25 bp):
TCATAAACCTTAAACCATAGTTAAC
Found at i:18625558 original size:7 final size:7
Alignment explanation
Indices: 18625471--18625561 Score: 56
Period size: 7 Copynumber: 12.4 Consensus size: 7
18625461 AGTTAACTCC
*
18625471 TAAACCT
1 TAAACCA
*
18625478 TAAACCC
1 TAAACCA
18625485 TAAACCA
1 TAAACCA
* * *
18625492 TATATCT
1 TAAACCA
18625499 TAAACCA
1 TAAACCA
18625506 TAGTTAACTCA
1 TA---AAC-CA
*
18625517 TAAACCT
1 TAAACCA
*
18625524 TAAACCC
1 TAAACCA
18625531 TAAACCA
1 TAAACCA
* * *
18625538 TATATCT
1 TAAACCA
18625545 TAAACCA
1 TAAACCA
18625552 TAAACCA
1 TAAACCA
18625559 TAA
1 TAA
18625562 TGATAATTAA
Statistics
Matches: 63, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
7 53 0.84
8 3 0.05
10 3 0.05
11 4 0.06
ACGTcount: A:0.46, C:0.26, G:0.01, T:0.26
Consensus pattern (7 bp):
TAAACCA
Found at i:18625782 original size:41 final size:41
Alignment explanation
Indices: 18625719--18625937 Score: 316
Period size: 41 Copynumber: 5.4 Consensus size: 41
18625709 GTTATATGAC
* *
18625719 TTTTAGCGGCGTTTTGTCAAAAGCGCCGCTAATGCTCCGGT
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGT
* * *
18625760 TTTTAGCAGCGTTTTGCTAAAAGCGCCGCTAATTCTCTGG-
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGT
* * *
18625800 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATTCTCTAGA
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGT
*
18625841 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGTT
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGT
*
18625882 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCT-AT
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGT
*
18625922 TTTTCGCGGCGCTTTT
1 TTTTAGCGGCG-TTTT
18625938 TACTAAAACG
Statistics
Matches: 162, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
40 48 0.30
41 114 0.70
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGT
Found at i:18625854 original size:81 final size:82
Alignment explanation
Indices: 18625719--18625968 Score: 335
Period size: 81 Copynumber: 3.1 Consensus size: 82
18625709 GTTATATGAC
* ** *
18625719 TTTTAGCGGCGTTTTGTCAAAAGCGCCGCTAATGCTCCGGTTTTTAGCAGCGTTTTGCTAAAAGC
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTAGTTTTTAGCGGCGTTTTGCTAAAAGC
*
18625784 GCCGCTAATTCTCTG-G
66 GCCGCTAATGCTCTGTG
* * *
18625800 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATTCTCTAGATTTTAGCGGCGTTTTGCCAAAAGC
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTAGTTTTTAGCGGCGTTTTGCTAAAAGC
*
18625865 GCCGCTAATGCTCTGTT
66 GCCGCTAATGCTCTGTG
* *
18625882 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTA-TTTTTCGCGGCGCTTTTTACTAAAA
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTAGTTTTTAGCGGCG--TTTTGCTAAAA
* * *
18625946 -CGCCGCTATTGCTATGAG
64 GCGCCGCTAATGCTCTGTG
18625964 TTTTA
1 TTTTA
18625969 CAATTTTTGC
Statistics
Matches: 148, Mismatches: 18, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
81 82 0.55
82 57 0.39
83 9 0.06
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.34
Consensus pattern (82 bp):
TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTAGTTTTTAGCGGCGTTTTGCTAAAAGC
GCCGCTAATGCTCTGTG
Found at i:18626249 original size:15 final size:15
Alignment explanation
Indices: 18626231--18626260 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18626221 TATCTGAACT
18626231 GATCATTTTCACTAA
1 GATCATTTTCACTAA
18626246 GATCATTTTCACTAA
1 GATCATTTTCACTAA
18626261 CTTCCTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
GATCATTTTCACTAA
Found at i:18631696 original size:43 final size:43
Alignment explanation
Indices: 18631642--18631789 Score: 129
Period size: 43 Copynumber: 3.4 Consensus size: 43
18631632 TATCCCAGAT
* *
18631642 ATGGTCTTTACATGTTATCATATATCGATGCCAACGT-CCTAGAC
1 ATGGTC-TTACATGTAATCATATAACGATGCCAACGTCCCT-GAC
* *** *
18631686 GTGGTCTTACACAAAATCATATAACGATGCCAATGTCCCTGAC
1 ATGGTCTTACATGTAATCATATAACGATGCCAACGTCCCTGAC
* * * * * * *
18631729 ATGTTCTTACATGTAAACACA-ATACAATGCCAATGGCCCAGAC
1 ATGGTCTTACATGTAATCATATA-ACGATGCCAACGTCCCTGAC
18631772 ATGGTCTTACATGTAATC
1 ATGGTCTTACATGTAATC
18631790 TCATCTTGAT
Statistics
Matches: 83, Mismatches: 19, Indels: 5
0.78 0.18 0.05
Matches are distributed among these distances:
42 1 0.01
43 74 0.89
44 8 0.10
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCATATAACGATGCCAACGTCCCTGAC
Found at i:18632086 original size:56 final size:56
Alignment explanation
Indices: 18632000--18632167 Score: 336
Period size: 56 Copynumber: 3.0 Consensus size: 56
18631990 TGACGTATCG
18632000 GATCAACTATTCGACAACTTTCGATTTCCCCCGATCCAAATATGATTTATTTCTTT
1 GATCAACTATTCGACAACTTTCGATTTCCCCCGATCCAAATATGATTTATTTCTTT
18632056 GATCAACTATTCGACAACTTTCGATTTCCCCCGATCCAAATATGATTTATTTCTTT
1 GATCAACTATTCGACAACTTTCGATTTCCCCCGATCCAAATATGATTTATTTCTTT
18632112 GATCAACTATTCGACAACTTTCGATTTCCCCCGATCCAAATATGATTTATTTCTTT
1 GATCAACTATTCGACAACTTTCGATTTCCCCCGATCCAAATATGATTTATTTCTTT
18632168 CTTGATCTAA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 112 1.00
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (56 bp):
GATCAACTATTCGACAACTTTCGATTTCCCCCGATCCAAATATGATTTATTTCTTT
Found at i:18633269 original size:62 final size:62
Alignment explanation
Indices: 18633172--18633479 Score: 616
Period size: 62 Copynumber: 5.0 Consensus size: 62
18633162 ATTGAAAAGG
18633172 TTAGCGTATTGTTCTTTCATAGCATCCTCGGGCTCCCACATAGCTTCTTCAATCCCGTATTA
1 TTAGCGTATTGTTCTTTCATAGCATCCTCGGGCTCCCACATAGCTTCTTCAATCCCGTATTA
18633234 TTAGCGTATTGTTCTTTCATAGCATCCTCGGGCTCCCACATAGCTTCTTCAATCCCGTATTA
1 TTAGCGTATTGTTCTTTCATAGCATCCTCGGGCTCCCACATAGCTTCTTCAATCCCGTATTA
18633296 TTAGCGTATTGTTCTTTCATAGCATCCTCGGGCTCCCACATAGCTTCTTCAATCCCGTATTA
1 TTAGCGTATTGTTCTTTCATAGCATCCTCGGGCTCCCACATAGCTTCTTCAATCCCGTATTA
18633358 TTAGCGTATTGTTCTTTCATAGCATCCTCGGGCTCCCACATAGCTTCTTCAATCCCGTATTA
1 TTAGCGTATTGTTCTTTCATAGCATCCTCGGGCTCCCACATAGCTTCTTCAATCCCGTATTA
18633420 TTAGCGTATTGTTCTTTCATAGCATCCTCGGGCTCCCACATAGCTTCTTCAATCCCGTAT
1 TTAGCGTATTGTTCTTTCATAGCATCCTCGGGCTCCCACATAGCTTCTTCAATCCCGTAT
18633480 CTATGCCAGA
Statistics
Matches: 246, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 246 1.00
ACGTcount: A:0.19, C:0.29, G:0.15, T:0.37
Consensus pattern (62 bp):
TTAGCGTATTGTTCTTTCATAGCATCCTCGGGCTCCCACATAGCTTCTTCAATCCCGTATTA
Found at i:18635504 original size:31 final size:31
Alignment explanation
Indices: 18635466--18635529 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
18635456 CCTTTTCATA
18635466 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
18635497 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
18635528 TT
1 TT
18635530 ACGGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:18636879 original size:27 final size:26
Alignment explanation
Indices: 18636801--18636930 Score: 91
Period size: 27 Copynumber: 4.7 Consensus size: 26
18636791 GTAAACCAAT
* * *
18636801 GGTATTTCTATAATTTTTAGAAAGTCAAG
1 GGTATTT-TGTAA-TTTTACAAA-TCAGG
* **
18636830 GGTATTTCTGTAACTTTGTAAATCAGG
1 GGTATTT-TGTAATTTTACAAATCAGG
*
18636857 GGTATTTTGGTAATTTTACAAAT-TGAG
1 GGTATTTT-GTAATTTTACAAATCAG-G
* *
18636884 GGTATTTCTGTAATTTTACAAACCAAG
1 GGTATTT-TGTAATTTTACAAATCAGG
*
18636911 GGTATTTTAGCAATTTTACA
1 GGTATTTT-GTAATTTTACA
18636931 GACTAGGGTA
Statistics
Matches: 83, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
26 3 0.04
27 61 0.73
28 7 0.08
29 12 0.14
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (26 bp):
GGTATTTTGTAATTTTACAAATCAGG
Found at i:18636951 original size:26 final size:26
Alignment explanation
Indices: 18636856--18636953 Score: 99
Period size: 27 Copynumber: 3.7 Consensus size: 26
18636846 TGTAAATCAG
* * *
18636856 GGGTATTTTGGTAATTTTACAAATTGA
1 GGGTATTCTAGTAATTTTACAAACT-A
*
18636883 GGGTATTTCT-GTAATTTTACAAACCAA
1 GGGTA-TTCTAGTAATTTTACAAA-CTA
* * *
18636910 GGGTATTTTAGCAATTTTACAGACTA
1 GGGTATTCTAGTAATTTTACAAACTA
18636936 GGGTATTCTAGTAATTTT
1 GGGTATTCTAGTAATTTT
18636954 GTAAATCGAG
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
26 21 0.36
27 35 0.59
28 3 0.05
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (26 bp):
GGGTATTCTAGTAATTTTACAAACTA
Found at i:18636966 original size:53 final size:53
Alignment explanation
Indices: 18636828--18636967 Score: 158
Period size: 54 Copynumber: 2.6 Consensus size: 53
18636818 TAGAAAGTCA
* * * *
18636828 AGGGTATTTCTGTAACTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTG
1 AGGGTATTTCTGTAATTTTGTAAATCA-GGGTATTTTAGCAATTTTACAAACTG
** * *
18636882 AGGGTATTTCTGTAATTTTACAAACCAAGGGTATTTTAGCAATTTTACAGACT-
1 AGGGTATTTCTGTAATTTTGTAAATC-AGGGTATTTTAGCAATTTTACAAACTG
18636935 AGGGTA-TTCTAGTAATTTTGTAAATCGAGGGTA
1 AGGGTATTTCT-GTAATTTTGTAAATC-AGGGTA
18636968 AAACAGTAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
52 4 0.06
53 24 0.33
54 43 0.60
55 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (53 bp):
AGGGTATTTCTGTAATTTTGTAAATCAGGGTATTTTAGCAATTTTACAAACTG
Found at i:18636975 original size:27 final size:27
Alignment explanation
Indices: 18636945--18637078 Score: 160
Period size: 27 Copynumber: 5.0 Consensus size: 27
18636935 AGGGTATTCT
*
18636945 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
18636972 AGTAATTCTGTAAATCAAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * * *
18636999 AGTAATTCTATATATCAAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
18637026 GGTACTTCTGTAAATCGATGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
18637053 GGTAATTCTGTAAGTCGAGGGTAAAA
1 AGTAATTCTGTAAATCGAGGGTAAAA
18637079 TGGGGGTAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 92 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.30
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:18637093 original size:65 final size:65
Alignment explanation
Indices: 18637017--18637140 Score: 167
Period size: 65 Copynumber: 1.9 Consensus size: 65
18637007 TATATATCAA
* * * * *
18637017 GGGTAAAATGGTACTTCTGTAAATCGATGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAATGG
1 GGGTAAAATGGTAATTATATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGG
* * * *
18637082 GGGTAAAATGGTAATTATATAAATTGGGGGTAAAATGGTAATTCTGTAAATCGGGGGTA
1 GGGTAAAATGGTAATTATATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTA
18637141 CTTTGGTAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
65 50 1.00
ACGTcount: A:0.35, C:0.06, G:0.30, T:0.29
Consensus pattern (65 bp):
GGGTAAAATGGTAATTATATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGG
Found at i:18637131 original size:27 final size:27
Alignment explanation
Indices: 18637073--18637140 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
18637063 TAAGTCGAGG
*
18637073 GTAAAATGGGGGTAAAATGGTAATTAT
1 GTAAATTGGGGGTAAAATGGTAATTAT
* *
18637100 ATAAATTGGGGGTAAAATGGTAATTCT
1 GTAAATTGGGGGTAAAATGGTAATTAT
*
18637127 GTAAATCGGGGGTA
1 GTAAATTGGGGGTA
18637141 CTTTGGTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.37, C:0.03, G:0.31, T:0.29
Consensus pattern (27 bp):
GTAAATTGGGGGTAAAATGGTAATTAT
Found at i:18637160 original size:92 final size:92
Alignment explanation
Indices: 18636990--18637167 Score: 203
Period size: 92 Copynumber: 1.9 Consensus size: 92
18636980 TGTAAATCAA
* * * *
18636990 GGGTAAAATAGTAATTCTATATATCAAGGGTAAAATGGTACTTCTGTAAATCGATGGTAAAACGG
1 GGGTAAAATAGTAATTATATAAATCAAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACGG
** *
18637055 TAATTCTGTAAGTCGAGGGTAAAATGG
66 TAATTCTACAAGTCGAAGGTAAAATGG
* *** * ****
18637082 GGGTAAAATGGTAATTATATAAATTGGGGGTAAAATGGTAATTCTGTAAATCGGGGGTACTTTGG
1 GGGTAAAATAGTAATTATATAAATCAAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACGG
*
18637147 TAATTTTACAAGTCGAAGGTA
66 TAATTCTACAAGTCGAAGGTA
18637168 CTTCAGTAAT
Statistics
Matches: 69, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
92 69 1.00
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.31
Consensus pattern (92 bp):
GGGTAAAATAGTAATTATATAAATCAAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACGG
TAATTCTACAAGTCGAAGGTAAAATGG
Found at i:18637167 original size:27 final size:27
Alignment explanation
Indices: 18637137--18637212 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
18637127 GTAAATCGGG
* *
18637137 GGTACTTTGGTAATTTTACAAGTCGAA
1 GGTACTTTAGTAATTTTACAAATCGAA
* *
18637164 GGTACTTCAGTAATTTTACAAATCGAG
1 GGTACTTTAGTAATTTTACAAATCGAA
*
18637191 GGTA-TTTCAGTATTTTTACAAA
1 GGTACTTT-AGTAATTTTACAAA
18637213 CTAAGCGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 2 0.05
27 40 0.95
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (27 bp):
GGTACTTTAGTAATTTTACAAATCGAA
Found at i:18637242 original size:28 final size:27
Alignment explanation
Indices: 18637146--18637244 Score: 85
Period size: 27 Copynumber: 3.6 Consensus size: 27
18637136 GGGTACTTTG
* * *
18637146 GTAATTTTACAAGTCGAAG-GTACTTCA
1 GTAATTTTACAA-ACTAAGCGTATTTCA
* *
18637173 GTAATTTTACAAA-TCGAGGGTATTTCA
1 GTAATTTTACAAACT-AAGCGTATTTCA
* *
18637200 GTATTTTTACAAACTAAGCGTATTTCG
1 GTAATTTTACAAACTAAGCGTATTTCA
*
18637227 GTAATTTTAGTAAACTAA
1 GTAATTTTA-CAAACTAA
18637245 AGTATTCTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
26 2 0.03
27 48 0.83
28 8 0.14
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (27 bp):
GTAATTTTACAAACTAAGCGTATTTCA
Found at i:18644498 original size:15 final size:16
Alignment explanation
Indices: 18644478--18644517 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
18644468 ATCTTAAGAA
18644478 AAAAATAAATA-AAAT
1 AAAAATAAATAGAAAT
*
18644493 AAAAATAAAAAGAAAT
1 AAAAATAAATAGAAAT
18644509 -AAAATAAAT
1 AAAAATAAAT
18644518 GGACTCAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAAATAAATAGAAAT
Found at i:18646181 original size:25 final size:24
Alignment explanation
Indices: 18646153--18646235 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 24
18646143 AATACTACTT
18646153 AATAAAAAATATAATGAATAATAA
1 AATAAAAAATATAATGAATAATAA
*
18646177 CAAT-AAAAATAATAATGAAGAATAA
1 -AATAAAAAAT-ATAATGAATAATAA
* *
18646202 TAATTAAAAATA-AATAAATAAATAA
1 -AATAAAAAATATAATGAAT-AATAA
18646227 ATATAAAAA
1 A-ATAAAAA
18646236 GGTAAAAAGG
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
24 12 0.24
25 31 0.63
26 6 0.12
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (24 bp):
AATAAAAAATATAATGAATAATAA
Found at i:18646203 original size:22 final size:23
Alignment explanation
Indices: 18646153--18646204 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
18646143 AATACTACTT
*
18646153 AATAA-AAAATATAATGAATAAT
1 AATAATAAAATATAATGAATAAG
*
18646175 AACAATAAAA-ATAAT-AATGAAG
1 AATAATAAAATATAATGAAT-AAG
18646197 AATAATAA
1 AATAATAA
18646205 TTAAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 3 0.12
22 18 0.72
23 4 0.16
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (23 bp):
AATAATAAAATATAATGAATAAG
Found at i:18646213 original size:13 final size:13
Alignment explanation
Indices: 18646152--18646214 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
18646142 TAATACTACT
*
18646152 TAATAAAAAAT-A
1 TAATGAAAAATAA
*
18646164 TAATGAATAATAA
1 TAATGAAAAATAA
*
18646177 CAAT-AAAAATAA
1 TAATGAAAAATAA
*
18646189 TAATGAAGAATAA
1 TAATGAAAAATAA
*
18646202 TAATTAAAAATAA
1 TAATGAAAAATAA
18646215 ATAAATAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
12 19 0.46
13 22 0.54
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (13 bp):
TAATGAAAAATAA
Found at i:18651888 original size:43 final size:43
Alignment explanation
Indices: 18651824--18651938 Score: 142
Period size: 43 Copynumber: 2.7 Consensus size: 43
18651814 AGCTCACACA
* * *** *
18651824 ATGCC-ATATCCCAGATATGGTCTTACATTTTATCATATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATGAAATCATATAACG
* *
18651866 ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCATATAACG
1 ATGCCAATGTCCCAGACATGGTCTTACATGAAATCATATAACG
*
18651909 ATGCCAATGTCCCAGACATGTTCTTACATG
1 ATGCCAATGTCCCAGACATGGTCTTACATG
18651939 TAAACACAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 5 0.08
43 56 0.92
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGAAATCATATAACG
Found at i:18651956 original size:43 final size:43
Alignment explanation
Indices: 18651821--18651967 Score: 120
Period size: 43 Copynumber: 3.4 Consensus size: 43
18651811 TAGAGCTCAC
* * **** *
18651821 ACAATGCC-ATATCCCAGATATGGTCTTACATTTTATCATATA
1 ACAATGCCAATGTCCCAGACATGGTCTTACACGAAATCAAATA
* * * *
18651863 TCGATGCCAATGTCCCAGACGTGGTCTTACACGAAATCATATA
1 ACAATGCCAATGTCCCAGACATGGTCTTACACGAAATCAAATA
* * *
18651906 ACGATGCCAATGTCCCAGACATGTTCTTACATGTAAA-CACAAT-
1 ACAATGCCAATGTCCCAGACATGGTCTTACACG-AAATCA-AATA
*
18651949 ACAATGCCAATGCCCCAGA
1 ACAATGCCAATGTCCCAGA
18651968 TGTAACACCC
Statistics
Matches: 86, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
42 6 0.07
43 75 0.87
44 5 0.06
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (43 bp):
ACAATGCCAATGTCCCAGACATGGTCTTACACGAAATCAAATA
Found at i:18653971 original size:50 final size:50
Alignment explanation
Indices: 18653917--18654242 Score: 323
Period size: 50 Copynumber: 6.5 Consensus size: 50
18653907 GGTACGCATG
*
18653917 GTAGCCTGCACTTAGTACTACATATGCGACCTATCAATCTGGTACACGTA
1 GTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTA
* *** * * * *
18653967 GTAGCCTGCACTTATTACTACACACATGACTTAACCATCTGATACACGTA
1 GTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTA
* * ** * * * *
18654017 GTAGCCTGCATTTAGTACTACACATGTGATCAAAGTTAA-CGGGTACGCATA
1 GTAGCCTGCACTTAGTACTACACATGCGA-CCTA-TCAATCTGGTACACGTA
18654068 GTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTA
1 GTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTA
* * * * ** * * * *
18654118 GTAGCATGCACTTAGTGCTACACACGTGATCAAAGTTAAT-GGGTACGCATA
1 GTAGCCTGCACTTAGTACTACACATGCGA-CCTA-TCAATCTGGTACACGTA
* * **
18654169 GTAGCTTGCACTTAGTACTACACATGCAACCTATCAATCTGGTACTTGTA
1 GTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTA
18654219 GTAGCCTGCACTTAGTACTACACA
1 GTAGCCTGCACTTAGTACTACACA
18654243 CGTGACTCAC
Statistics
Matches: 217, Mismatches: 53, Indels: 12
0.77 0.19 0.04
Matches are distributed among these distances:
49 7 0.03
50 134 0.62
51 71 0.33
52 5 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (50 bp):
GTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTA
Found at i:18654076 original size:51 final size:51
Alignment explanation
Indices: 18654015--18654194 Score: 220
Period size: 51 Copynumber: 3.5 Consensus size: 51
18654005 CTGATACACG
*
18654015 TAGTAGCCTGCATTTAGTACTACACATGTGATCAAAGTTAACGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGATCAAAGTTAACGGGTACGCA
* ** * * * *
18654066 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCTA-TCAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGATCAAAGTTAA-CGGGTACGCA
* * * *
18654116 TAGTAGCATGCACTTAGTGCTACACACGTGATCAAAGTTAATGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGATCAAAGTTAACGGGTACGCA
*
18654167 TAGTAGCTTGCACTTAGTACTACACATG
1 TAGTAGCCTGCACTTAGTACTACACATG
18654195 CAACCTATCA
Statistics
Matches: 104, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
49 3 0.03
50 36 0.35
51 62 0.60
52 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (51 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGATCAAAGTTAACGGGTACGCA
Found at i:18654091 original size:101 final size:101
Alignment explanation
Indices: 18653965--18654247 Score: 390
Period size: 101 Copynumber: 2.8 Consensus size: 101
18653955 CTGGTACACG
* * * * * *
18653965 TAGTAGCCTGCACTTATTACTACACACATGACTTAACCATCTGATACACGTAGTAGCCTGCATTT
1 TAGTAGCCTGCACTTAGTACTACACACATGACCTATCAATCTGGTACACGTAGTAGCCTGCACTT
*
18654030 AGTACTACACATGTGATCAAAGTTAACGGGTACGCA
66 AGTACTACACACGTGATCAAAGTTAACGGGTACGCA
*** *
18654066 TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGCATGCACTT
1 TAGTAGCCTGCACTTAGTACTACACACATGACCTATCAATCTGGTACACGTAGTAGCCTGCACTT
* *
18654131 AGTGCTACACACGTGATCAAAGTTAATGGGTACGCA
66 AGTACTACACACGTGATCAAAGTTAACGGGTACGCA
* **
18654167 TAGTAGCTTGCACTTAGTACT--ACACATGCAACCTATCAATCTGGTACTTGTAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACACATG--ACCTATCAATCTGGTACACGTAGTAGCCTGCAC
18654230 TTAGTACTACACACGTGA
64 TTAGTACTACACACGTGA
18654248 CTCACAACAG
Statistics
Matches: 159, Mismatches: 21, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
99 4 0.03
101 155 0.97
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (101 bp):
TAGTAGCCTGCACTTAGTACTACACACATGACCTATCAATCTGGTACACGTAGTAGCCTGCACTT
AGTACTACACACGTGATCAAAGTTAACGGGTACGCA
Found at i:18654213 original size:151 final size:152
Alignment explanation
Indices: 18653904--18654242 Score: 407
Period size: 151 Copynumber: 2.2 Consensus size: 152
18653894 ACCGAAGCTC
* *
18653904 TCTGGTACGCATGGTAGCCTGCACTTAGTACTACATATGCGACCTATCAATCTGGTACACGTAGT
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGT
* * * * * * *
18653969 AGCCTGCACTTATTACTACACACATGACTTAACCATCTGATACACGTAGTAGCCTGCATTTAGTA
66 AGCATGCACTTAGTACTACACACATGACTCAAACATATGATACACATAGTAGCCTGCACTTAGTA
* * *
18654034 CTACACATGTGATCAAAGTTAA
131 CTACACATGTCAACAAAGTCAA
*
18654056 -CGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGT
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGT
* * ** * * *
18654120 AGCATGCACTTAGTGCTACACACGTGA-TCAAAGTTAATGGGTACGCATAGTAGCTTGCACTTAG
66 AGCATGCACTTAGTACTACACACATGACTCAAACAT-AT-GATACACATAGTAGCCTGCACTTAG
**
18654184 TACTACACATG-CAACCTA-TCAA
129 TACTACACATGTCAACAAAGTCAA
***
18654206 TCTGGTACTTGTAGTAGCCTGCACTTAGTACTACACA
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACA
18654243 CGTGACTCAC
Statistics
Matches: 158, Mismatches: 26, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
150 7 0.04
151 120 0.76
152 31 0.20
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (152 bp):
TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGT
AGCATGCACTTAGTACTACACACATGACTCAAACATATGATACACATAGTAGCCTGCACTTAGTA
CTACACATGTCAACAAAGTCAA
Found at i:18657593 original size:69 final size:69
Alignment explanation
Indices: 18657510--18657643 Score: 223
Period size: 69 Copynumber: 1.9 Consensus size: 69
18657500 TAAAATAAAA
* *
18657510 TTTAAGAAACATCATTTAATCCAAACCAAACTATTTTAAAACTCTGAGATCACCGATTTGTCGAG
1 TTTAAGAAAAATCATTTAATCCAAACCAAACTATTTTAAAACTCTGAGATCACCGATTTGCCGAG
18657575 AAAT
66 AAAT
* * *
18657579 TTTAAGAAAAATCATTTAATCCAAACCAAGCTCTTTTAAAACTCTGAGATCACCGGTTTGCCGAG
1 TTTAAGAAAAATCATTTAATCCAAACCAAACTATTTTAAAACTCTGAGATCACCGATTTGCCGAG
18657644 TCCAACTTCT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (69 bp):
TTTAAGAAAAATCATTTAATCCAAACCAAACTATTTTAAAACTCTGAGATCACCGATTTGCCGAG
AAAT
Found at i:18661116 original size:24 final size:24
Alignment explanation
Indices: 18661096--18661155 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
18661086 CCTTTATCTG
*
18661096 CTCCTAAATCCTATGACTTATCAA
1 CTCCTAAATCCTATCACTTATCAA
*
18661120 CTCCTAAATCCTATCCCTTATCAA
1 CTCCTAAATCCTATCACTTATCAA
18661144 CTCCTAAATCCT
1 CTCCTAAATCCT
18661156 CTCCTGACAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.30, C:0.35, G:0.02, T:0.33
Consensus pattern (24 bp):
CTCCTAAATCCTATCACTTATCAA
Found at i:18661641 original size:178 final size:179
Alignment explanation
Indices: 18661342--18661699 Score: 673
Period size: 178 Copynumber: 2.0 Consensus size: 179
18661332 TTATTTTACA
18661342 CAATTAATACCTAAAAGCCCAATTAACCAGAACCCCTTTTTCTTATGGAATTAAAATTAATTAAA
1 CAATTAATACCTAAAAGCCCAATTAACCAGAACCCCTTTTTCTTATGGAATTAAAATTAATTAAA
*
18661407 ACTACCGGGTTTTACCTTAAGCTTGGGCCTTCTAGAGGCCCACTAACGTACTTAATCCTACGACA
66 ACTACCGGGTTTTACCTTAAGCTTGGGCCTTCTAGAGGCCCACCAACGTACTTAATCCTACGACA
* *
18661472 AACAAACAGGACACAGA-ATTTTTAAATTTTTCCAACATTTTTAAAATT
131 AACAAACAGGACACAGATAATTTTAAAATTTTCCAACATTTTTAAAATT
18661520 CAATTAATACCTAAAAGCCCAATTAACCAGAACCCCTTTTTCTTATGGAATTAAAATTAATTAAA
1 CAATTAATACCTAAAAGCCCAATTAACCAGAACCCCTTTTTCTTATGGAATTAAAATTAATTAAA
*
18661585 ACTACTGGGTTTTACCTTAAGCTTGGGCCTTCTAGAGGCCCACCAACGTACTTAATCCTACGACA
66 ACTACCGGGTTTTACCTTAAGCTTGGGCCTTCTAGAGGCCCACCAACGTACTTAATCCTACGACA
18661650 AACAAACAGGACACAGATAATTTTAAAATTTTCCAACATTTTTAAAATT
131 AACAAACAGGACACAGATAATTTTAAAATTTTCCAACATTTTTAAAATT
18661699 C
1 C
18661700 CCAAAAATTG
Statistics
Matches: 175, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
178 145 0.83
179 30 0.17
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (179 bp):
CAATTAATACCTAAAAGCCCAATTAACCAGAACCCCTTTTTCTTATGGAATTAAAATTAATTAAA
ACTACCGGGTTTTACCTTAAGCTTGGGCCTTCTAGAGGCCCACCAACGTACTTAATCCTACGACA
AACAAACAGGACACAGATAATTTTAAAATTTTCCAACATTTTTAAAATT
Found at i:18662936 original size:62 final size:62
Alignment explanation
Indices: 18662812--18662936 Score: 169
Period size: 62 Copynumber: 2.0 Consensus size: 62
18662802 GGCTCCAGGA
* * * ** * * *
18662812 GATAAAATTAGAAAACATGGGGCTGAAGAATTTAGGGCTACAGTGGATGACGATCTAGAGAG
1 GATAAAATCAAAAAACATGGGGCTGAAAAATTTAGGGCTACAGCAGATGACAATCCAAAGAG
*
18662874 GATAAAATCAAAAAACATGGGGCTGAAAAATTTAGGGCTACGGCAGATGACAATCCAAAGAG
1 GATAAAATCAAAAAACATGGGGCTGAAAAATTTAGGGCTACAGCAGATGACAATCCAAAGAG
18662936 G
1 G
18662937 GCTGAGTTCT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.42, C:0.12, G:0.28, T:0.18
Consensus pattern (62 bp):
GATAAAATCAAAAAACATGGGGCTGAAAAATTTAGGGCTACAGCAGATGACAATCCAAAGAG
Found at i:18665390 original size:16 final size:16
Alignment explanation
Indices: 18665369--18665411 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
18665359 ACAAAAGCCG
*
18665369 AAAAGCTGAAATGCCA
1 AAAAGCCGAAATGCCA
* *
18665385 AAAAGCCAAAATGTCA
1 AAAAGCCGAAATGCCA
18665401 AAAAGCCGAAA
1 AAAAGCCGAAA
18665412 GTTTGGCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.56, C:0.19, G:0.16, T:0.09
Consensus pattern (16 bp):
AAAAGCCGAAATGCCA
Found at i:18665664 original size:29 final size:28
Alignment explanation
Indices: 18665635--18665768 Score: 139
Period size: 28 Copynumber: 4.7 Consensus size: 28
18665625 ATAATGTGAT
*
18665635 TTGGGCCGGATGGGCCATATAAATGAGA
1 TTGGGCCTGATGGGCCATATAAATGAGA
* * * *
18665663 TTAGGCCTAATGGGCCATATGAATGTGAA
1 TTGGGCCTGATGGGCCATATAAATGAG-A
18665692 TTGGGCCTGATGGGCCATATGAACATGA-A
1 TTGGGCCTGATGGGCCATAT-AA-ATGAGA
* *
18665721 TTGGG-CTATATGGGCCATATAAGTGAGA
1 TTGGGCCT-GATGGGCCATATAAATGAGA
18665749 TTGGGCCT-AGTGGGCCATAT
1 TTGGGCCTGA-TGGGCCATAT
18665769 GCATGTATGT
Statistics
Matches: 88, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
27 4 0.05
28 42 0.48
29 38 0.43
30 1 0.01
31 3 0.03
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (28 bp):
TTGGGCCTGATGGGCCATATAAATGAGA
Found at i:18665752 original size:57 final size:58
Alignment explanation
Indices: 18665623--18665769 Score: 182
Period size: 57 Copynumber: 2.6 Consensus size: 58
18665613 GTGAGCATGA
* *
18665623 ATAT-AATGTGATTTGGGCCGGATGGGCCATAT-AAATGAGATTAGGCCTAATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCCATATGAAATGAGATTAGGCCTAATGGGCC
*
18665679 ATATGAATGTGAATTGGGCCTGATGGGCCATATGAACATGA-ATT-GGGCTATATGGGCC
1 ATATGAATGTGAATTGGGCCTGATGGGCCATATGAA-ATGAGATTAGGCCTA-ATGGGCC
18665737 ATAT-AA-GTGAGATTGGGCCT-AGTGGGCCATATG
1 ATATGAATGTGA-ATTGGGCCTGA-TGGGCCATATG
18665770 CATGTATGTT
Statistics
Matches: 82, Mismatches: 3, Indels: 11
0.85 0.03 0.11
Matches are distributed among these distances:
56 9 0.11
57 53 0.65
58 16 0.20
59 4 0.05
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.27
Consensus pattern (58 bp):
ATATGAATGTGAATTGGGCCTGATGGGCCATATGAAATGAGATTAGGCCTAATGGGCC
Found at i:18687591 original size:44 final size:44
Alignment explanation
Indices: 18687472--18687604 Score: 146
Period size: 44 Copynumber: 3.0 Consensus size: 44
18687462 TTAGGTGATA
*
18687472 TGTGTGCTAGTGTAAGACATGTCTGGGACAT-GCATCAGCCTAG
1 TGTGTGCTAGTGTAAGACCTGTCTGGGACATGGCATCAGCCTAG
* * *
18687515 AGATATACAAGCTAGTGTAA-ACCTGTCTGGGACATGGCATCAG-CTTG
1 TG-TGT----GCTAGTGTAAGACCTGTCTGGGACATGGCATCAGCCTAG
*
18687562 TTGTGTGCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCT
1 -TGTGTGCTAGTGTAAGACCTGTCTGGGACATGGCATCAGCCT
18687605 CGATATATGA
Statistics
Matches: 74, Mismatches: 7, Indels: 16
0.76 0.07 0.16
Matches are distributed among these distances:
43 11 0.15
44 24 0.32
45 2 0.03
47 19 0.26
48 18 0.24
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (44 bp):
TGTGTGCTAGTGTAAGACCTGTCTGGGACATGGCATCAGCCTAG
Found at i:18689186 original size:53 final size:54
Alignment explanation
Indices: 18689096--18689307 Score: 227
Period size: 53 Copynumber: 3.9 Consensus size: 54
18689086 TACGTGGTAT
* * * *
18689096 CCTTTTGAAACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCTTTG
1 CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCTTTG
* *
18689150 CCTTATG-AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGTCAT-TTT-
1 CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACAT-GGT-ATCTTTG
* * * * * *
18689203 CCTTATAGTAACTTATCAATGCAATGTCTTGACAT-GCCTTACATGGTATCCTTG
1 CCTTAT-GAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCTTTG
*
18689257 CCTTA-GAAACCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATC
1 CCTTATGAAA-CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATC
18689308 CTTAAACCCT
Statistics
Matches: 130, Mismatches: 19, Indels: 17
0.78 0.11 0.10
Matches are distributed among these distances:
52 5 0.04
53 49 0.38
54 39 0.30
55 37 0.28
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (54 bp):
CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCTTTG
Found at i:18689301 original size:109 final size:108
Alignment explanation
Indices: 18689104--18689303 Score: 296
Period size: 108 Copynumber: 1.8 Consensus size: 108
18689094 ATCCTTTTGA
* * * *
18689104 AACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCTTTGCCTTATGAACTCACCAATG
1 AACTTACCAATGCAATGTCTCGACATGGCCTTACATGGTATCCTTGCCTTATGAACTCACCAATG
18689169 CCATGCCTTGGCATGGTCTTACATGGGTCATTTTCCTTATAGT
66 CCATGCCTTGGCATGGTCTTACATGGGTCATTTTCCTTATAGT
* * *
18689212 AACTTATCAATGCAATGTCTTGACAT-GCCTTACATGGTATCCTTGCCTTA-GAAACCTTACCAA
1 AACTTACCAATGCAATGTCTCGACATGGCCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
18689275 TTGCCATGCCTTGGCATGGTCTTACATGG
64 -TGCCATGCCTTGGCATGGTCTTACATGG
18689304 TATCCTTAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
106 1 0.01
107 24 0.29
108 29 0.35
109 28 0.34
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (108 bp):
AACTTACCAATGCAATGTCTCGACATGGCCTTACATGGTATCCTTGCCTTATGAACTCACCAATG
CCATGCCTTGGCATGGTCTTACATGGGTCATTTTCCTTATAGT
Found at i:18689306 original size:55 final size:54
Alignment explanation
Indices: 18689073--18689310 Score: 219
Period size: 53 Copynumber: 4.5 Consensus size: 54
18689063 ATTTCCTTGA
* * *
18689073 CTTGTCATGGTCTTACGTGGTATCCTT---TT-GAAACTTACC-ATTGCCATGT
1 CTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAACTTACCAATTGCCATGC
* * *
18689122 CTCGACATGGTCTTACATGGTATCTTTGCCTTATG-AACTCACCAA-TGCCATGC
1 CTTGACATGGTCTTACATGGTATCCTTGCCTTA-GAAACTTACCAATTGCCATGC
* * * * * *
18689175 CTTGGCATGGTCTTACATGGGTCAT--TTTCCTTATAGTAACTTATCAA-TGCAATGT
1 CTTGACATGGTCTTACAT-GGT-ATCCTTGCC-T-TAGAAACTTACCAATTGCCATGC
*
18689230 CTTGACAT-GCCTTACATGGTATCCTTGCCTTAGAAACCTTACCAATTGCCATGC
1 CTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA-CTTACCAATTGCCATGC
*
18689284 CTTGGCATGGTCTTACATGGTATCCTT
1 CTTGACATGGTCTTACATGGTATCCTT
18689311 AAACCCTAAT
Statistics
Matches: 151, Mismatches: 22, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
49 23 0.15
52 9 0.06
53 45 0.30
54 32 0.21
55 42 0.28
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (54 bp):
CTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAACTTACCAATTGCCATGC
Found at i:18695049 original size:27 final size:25
Alignment explanation
Indices: 18694991--18695049 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
18694981 TAATCAATGA
*
18694991 GCACTAACGTGCTAATAATCAGAGG
1 GCACTAACGTGCTAAAAATCAGAGG
*
18695016 GTACTAACGTGCTAAAAATCAGAGAG
1 GCACTAACGTGCTAAAAATCAGAG-G
18695042 CGCACTAA
1 -GCACTAA
18695050 GGTTCCTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 22 0.76
26 1 0.03
27 6 0.21
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (25 bp):
GCACTAACGTGCTAAAAATCAGAGG
Found at i:18697391 original size:14 final size:15
Alignment explanation
Indices: 18697372--18697401 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18697362 CGGAAAGAAG
18697372 AAAT-AAAAATAAAA
1 AAATAAAAAATAAAA
18697386 AAATAAAAAATAAAA
1 AAATAAAAAATAAAA
18697401 A
1 A
18697402 CTACACTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
AAATAAAAAATAAAA
Found at i:18701887 original size:146 final size:146
Alignment explanation
Indices: 18701623--18701912 Score: 435
Period size: 146 Copynumber: 2.0 Consensus size: 146
18701613 CTTCTAGTGA
18701623 GATTACTGTACTAAGCCTATTGGGGCAGTCTGTTTGGGTTAGTAAACTCTATAGGAATGTCCTAT
1 GATTACTGTACTAAGCCTATTGGGGCAGTCTGTTTGGGTTAGTAAACTCTATAGGAATGTCCTAT
* *
18701688 TAGTGGTACAAAGGGTTGTCTTTCTGGAAAATCTGATAGAGCTTCCATTTGGGGAGTTCAATTTA
66 TAGTGGTACAAAGGGCTATCTTTCTGGAAAATCTGATAGAGCTTCCATTTGGGGAGTTCAATTTA
*
18701753 ATTTTGGGAATAGACT
131 ATTCTGGGAATAGACT
* * *
18701769 GATTATTGTACTAAGTCC-ATTGGGGCAGTTTGTTTGGGTTAGTAAACAT-TATAGGGATGT-CT
1 GATTACTGTACTAAG-CCTATTGGGGCAGTCTGTTTGGGTTAGTAAAC-TCTATAGGAATGTCCT
* * *
18701831 AGTTAGTGGTAC-AAGAGGCTATCTTTCTGGAAAATCTGATGGAGCTTCCGTTTGGGGAGTTCGA
64 A-TTAGTGGTACAAAG-GGCTATCTTTCTGGAAAATCTGATAGAGCTTCCATTTGGGGAGTTCAA
18701895 TTTAATTCTGGGAATAGA
127 TTTAATTCTGGGAATAGA
18701913 TTGGTTGGTT
Statistics
Matches: 131, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
145 6 0.05
146 122 0.93
147 3 0.02
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.36
Consensus pattern (146 bp):
GATTACTGTACTAAGCCTATTGGGGCAGTCTGTTTGGGTTAGTAAACTCTATAGGAATGTCCTAT
TAGTGGTACAAAGGGCTATCTTTCTGGAAAATCTGATAGAGCTTCCATTTGGGGAGTTCAATTTA
ATTCTGGGAATAGACT
Found at i:18708519 original size:12 final size:12
Alignment explanation
Indices: 18708504--18708572 Score: 77
Period size: 12 Copynumber: 5.6 Consensus size: 12
18708494 AGGAAAATAC
*
18708504 AAATAAACAGAA
1 AAATAAAAAGAA
18708516 AAATAAAAAGAA
1 AAATAAAAAGAA
*
18708528 AAATAAAAACTAA
1 AAATAAAAA-GAA
*
18708541 AAAGAAAAAAGAA
1 AAA-TAAAAAGAA
18708554 AAA-AGAAAAGAA
1 AAATA-AAAAGAA
18708566 AAATAAA
1 AAATAAA
18708573 TGGACTCAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
11 1 0.02
12 32 0.65
13 11 0.22
14 5 0.10
ACGTcount: A:0.81, C:0.03, G:0.09, T:0.07
Consensus pattern (12 bp):
AAATAAAAAGAA
Found at i:18708541 original size:19 final size:18
Alignment explanation
Indices: 18708514--18708572 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 18
18708504 AAATAAACAG
18708514 AAAAATAAAAAGAAAAAT
1 AAAAATAAAAAGAAAAAT
18708532 AAAAACTAAAAAGAAAAA-
1 AAAAA-TAAAAAGAAAAAT
*
18708550 AGAAAAAAGAAAAGAAAAAT
1 A-AAAATA-AAAAGAAAAAT
18708570 AAA
1 AAA
18708573 TGGACTCAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 7 0.19
19 28 0.78
20 1 0.03
ACGTcount: A:0.83, C:0.02, G:0.08, T:0.07
Consensus pattern (18 bp):
AAAAATAAAAAGAAAAAT
Found at i:18710169 original size:3 final size:3
Alignment explanation
Indices: 18710161--18710194 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
18710151 TAAATAAAGA
18710161 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
18710195 GAGTAAATAG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:18713258 original size:41 final size:41
Alignment explanation
Indices: 18713164--18713271 Score: 148
Period size: 41 Copynumber: 2.7 Consensus size: 41
18713154 GCTACTCGTT
* *
18713164 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTAGCA
* *
18713204 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTCACTTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAAC-TAGCA
*
18713245 CAAAAGCCTTCGGGACTTAGCCCGGAT
1 CAAATGCCTTCGGGACTTAGCCCGGAT
18713272 ATCATTCGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
40 29 0.48
41 31 0.52
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTAGCA
Found at i:18722920 original size:79 final size:81
Alignment explanation
Indices: 18722811--18722993 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 81
18722801 TACTCGTTCA
* *
18722811 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
18722874 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
18722891 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
18722954 TATAGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
18722970 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
18722994 CATCATTCGA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 3 0.03
79 60 0.66
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:18722993 original size:40 final size:40
Alignment explanation
Indices: 18722790--18722993 Score: 247
Period size: 40 Copynumber: 5.1 Consensus size: 40
18722780 CGGAATTTAA
** *
18722790 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
18722830 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
18722870 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
18722909 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
18722949 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
18722989 CCGGA
1 CCGGA
18722994 CATCATTCGA
Statistics
Matches: 142, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 95 0.67
41 12 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:18731653 original size:12 final size:13
Alignment explanation
Indices: 18731634--18731695 Score: 63
Period size: 13 Copynumber: 4.6 Consensus size: 13
18731624 TTTTTCTTGC
18731634 TAAGTTTTAAATT
1 TAAGTTTTAAATT
*
18731647 T-AGTTTTGAATT
1 TAAGTTTTAAATT
*
18731659 TAAGTTTTCTTTAATT
1 TAAG--TT-TTAAATT
*
18731675 TTAGTTTTAAATT
1 TAAGTTTTAAATT
18731688 TAAGTTTT
1 TAAGTTTT
18731696 TTAAAAATCC
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
12 11 0.28
13 16 0.40
14 2 0.05
15 2 0.05
16 9 0.22
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (13 bp):
TAAGTTTTAAATT
Found at i:18731672 original size:29 final size:29
Alignment explanation
Indices: 18731639--18731695 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
18731629 CTTGCTAAGT
*
18731639 TTTAAATTTAGTTTTGAATTTAAGTTTTC
1 TTTAAATTTAGTTTTAAATTTAAGTTTTC
*
18731668 TTTAATTTTAGTTTTAAATTTAAGTTTT
1 TTTAAATTTAGTTTTAAATTTAAGTTTT
18731696 TTAAAAATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.61
Consensus pattern (29 bp):
TTTAAATTTAGTTTTAAATTTAAGTTTTC
Found at i:18738473 original size:27 final size:25
Alignment explanation
Indices: 18738443--18738492 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
18738433 TTTAATGTAG
18738443 ATATTAATTAAATTTGGATTTCAAAGC
1 ATATTAA-TAAATTTGGA-TTCAAAGC
* *
18738470 ATATTTATGAATTTGGATTCAAA
1 ATATTAATAAATTTGGATTCAAA
18738493 ATTTGCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 9 0.43
27 6 0.29
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (25 bp):
ATATTAATAAATTTGGATTCAAAGC
Found at i:18743049 original size:28 final size:28
Alignment explanation
Indices: 18743001--18743077 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 28
18742991 GATAATTAAC
18743001 AGTGACTAAAATGTTACAACACATTAAT-ATA
1 AGTGACTAAAATG-T--AACA-ATTAATAATA
* *
18743032 AGTGACTAAAATGTAACATTTTATAATA
1 AGTGACTAAAATGTAACAATTAATAATA
18743060 AGTGACTAAAATGTAACA
1 AGTGACTAAAATGTAACA
18743078 TGAGAGAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 4 0.09
28 25 0.58
30 1 0.02
31 13 0.30
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (28 bp):
AGTGACTAAAATGTAACAATTAATAATA
Found at i:18743552 original size:43 final size:44
Alignment explanation
Indices: 18743468--18743566 Score: 112
Period size: 43 Copynumber: 2.2 Consensus size: 44
18743458 TATCACATTA
* **
18743468 AAAAATTTTAAAAAATTAATAATATTAATAATTAAACATAAATTT
1 AAAAA-TTTAAAAAATTAATAATATTAATAATTAAAAATAAAAAT
**
18743513 AAAAATTTAAAAAA-TAA-AATATTAAATTCTTAAAAATAAAAAT
1 AAAAATTTAAAAAATTAATAATATT-AATAATTAAAAATAAAAAT
*
18743556 AAAAAATTAAA
1 AAAAATTTAAA
18743567 TTTCGAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 6 0.13
43 27 0.57
44 9 0.19
45 5 0.11
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (44 bp):
AAAAATTTAAAAAATTAATAATATTAATAATTAAAAATAAAAAT
Found at i:18743561 original size:44 final size:44
Alignment explanation
Indices: 18743466--18743563 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 44
18743456 AATATCACAT
* *
18743466 TAAAAAATTTTAAAAAATTAATAATATTAATAATTAAACATAAAT
1 TAAAAAA-TTTAAAAAATTAATAATATTAATAATTAAAAATAAAA
* **
18743511 TTAAAAATTTAAAAAA-TAA-AATATTAAATTCTTAAAAATAAAAA
1 TAAAAAATTTAAAAAATTAATAATATT-AATAATTAAAAAT-AAAA
18743555 TAAAAAATT
1 TAAAAAATT
18743564 AAATTTCGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
42 6 0.13
43 13 0.29
44 20 0.44
45 6 0.13
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (44 bp):
TAAAAAATTTAAAAAATTAATAATATTAATAATTAAAAATAAAA
Found at i:18745153 original size:18 final size:18
Alignment explanation
Indices: 18745130--18745167 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
18745120 GTTTCTTTCC
18745130 TTATA-TTACATTTAAATT
1 TTATATTTA-ATTTAAATT
*
18745148 TTATATTTAATTTATATT
1 TTATATTTAATTTAAATT
18745166 TT
1 TT
18745168 TTAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATATTTAATTTAAATT
Found at i:18747033 original size:22 final size:21
Alignment explanation
Indices: 18746998--18747073 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
18746988 AAAAGGTATC
* *
18746998 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
18747019 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
18747042 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
18747061 TGC-AATCATATCT
1 TACAAATCATATCT
18747074 AAGATTGCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:18747070 original size:18 final size:19
Alignment explanation
Indices: 18747034--18747082 Score: 91
Period size: 18 Copynumber: 2.6 Consensus size: 19
18747024 AATCATATCT
18747034 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
18747053 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
18747071 TCTAAGATTGCA
1 TCTAAGATTGCA
18747083 CATTGAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 18 0.60
19 12 0.40
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:18749490 original size:3 final size:3
Alignment explanation
Indices: 18749482--18749537 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
18749472 GTACTCAGGC
18749482 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
18749530 GAT GAT GA
1 GAT GAT GA
18749538 AGTCTATAGG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:18754476 original size:21 final size:23
Alignment explanation
Indices: 18754442--18754502 Score: 81
Period size: 21 Copynumber: 2.7 Consensus size: 23
18754432 AACACTTCCC
* *
18754442 TAAAACCCTAAACCCTAAT-AAA
1 TAAAAACCTTAACCCTAATAAAA
*
18754464 -AAAAATCTTAACCCTAATAAAA
1 TAAAAACCTTAACCCTAATAAAA
18754486 TAAAAACCTTAACCCTA
1 TAAAAACCTTAACCCTA
18754503 GGAGAGATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 15 0.45
22 3 0.09
23 15 0.45
ACGTcount: A:0.54, C:0.25, G:0.00, T:0.21
Consensus pattern (23 bp):
TAAAAACCTTAACCCTAATAAAA
Found at i:18756421 original size:5 final size:5
Alignment explanation
Indices: 18756333--18756403 Score: 142
Period size: 5 Copynumber: 14.2 Consensus size: 5
18756323 ATTTAAAAAA
18756333 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
18756383 ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT A
18756404 ATTAAAGTAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 66 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:18756633 original size:13 final size:13
Alignment explanation
Indices: 18756617--18756658 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
18756607 GAAACAGGAG
18756617 AAAGAAAGAAGAA
1 AAAGAAAGAAGAA
*
18756630 AAAGATAGAAAGAA
1 AAAGAAAG-AAGAA
*
18756644 AAAGAAAGGAGAA
1 AAAGAAAGAAGAA
18756657 AA
1 AA
18756659 TTTAGGGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (13 bp):
AAAGAAAGAAGAA
Found at i:18756656 original size:17 final size:19
Alignment explanation
Indices: 18756607--18756657 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
18756597 ATTGGGGAAC
18756607 GAAACAGGAGAAAGAAAGAA
1 GAAA-AGGAGAAAGAAAGAA
*
18756627 GAAAAAGATAGAAAGAAA-AA
1 G-AAAAG-GAGAAAGAAAGAA
18756647 G-AAAGGAGAAA
1 GAAAAGGAGAAA
18756658 ATTTAGGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 5 0.19
18 4 0.15
20 6 0.22
21 12 0.44
ACGTcount: A:0.69, C:0.02, G:0.27, T:0.02
Consensus pattern (19 bp):
GAAAAGGAGAAAGAAAGAA
Found at i:18757623 original size:25 final size:25
Alignment explanation
Indices: 18757586--18757637 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
18757576 TGACCGATGA
18757586 GACACTGTATGTCAATTATTACTTC
1 GACACTGTATGTCAATTATTACTTC
*
18757611 GACACTGTGTGTCAATTATTACTTC
1 GACACTGTATGTCAATTATTACTTC
18757636 GA
1 GA
18757638 ATTATCCGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (25 bp):
GACACTGTATGTCAATTATTACTTC
Found at i:18757836 original size:21 final size:21
Alignment explanation
Indices: 18757810--18757860 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
18757800 AATAGAATGT
18757810 GAAATATGTTGACAATATATG
1 GAAATATGTTGACAATATATG
*
18757831 GAAATATGTTGATAATATATG
1 GAAATATGTTGACAATATATG
18757852 GAATATATG
1 GAA-ATATG
18757861 AATTATATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.35
Consensus pattern (21 bp):
GAAATATGTTGACAATATATG
Found at i:18760033 original size:2 final size:2
Alignment explanation
Indices: 18760028--18760175 Score: 296
Period size: 2 Copynumber: 74.0 Consensus size: 2
18760018 AATATATATA
18760028 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
18760070 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
18760112 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
18760154 TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG
18760176 NNNNNNNNNN
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 146 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:18765035 original size:13 final size:13
Alignment explanation
Indices: 18765019--18765060 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
18765009 GAAACAGGGG
18765019 AAAGAAAGAAGAA
1 AAAGAAAGAAGAA
*
18765032 AAAGATAGAAAGAA
1 AAAGAAAG-AAGAA
*
18765046 AAAGAAAGGAGAA
1 AAAGAAAGAAGAA
18765059 AA
1 AA
18765061 TTTAGGGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (13 bp):
AAAGAAAGAAGAA
Found at i:18792062 original size:21 final size:22
Alignment explanation
Indices: 18792037--18792082 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
18792027 TCCTTCAAGT
* *
18792037 TAACACTTTAAAAAATG-TTAA
1 TAACAATTTAAAAAAAGTTTAA
18792058 TAACAATTTAAAAAAAGTTTAA
1 TAACAATTTAAAAAAAGTTTAA
18792080 TAA
1 TAA
18792083 TAATAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (22 bp):
TAACAATTTAAAAAAAGTTTAA
Found at i:18796213 original size:26 final size:26
Alignment explanation
Indices: 18796175--18796308 Score: 207
Period size: 26 Copynumber: 5.2 Consensus size: 26
18796165 TGATACAAAT
*
18796175 TGATAATAGGTTAGGTAAATGTTCCT
1 TGATAATAGGTTAGGTAAATGTTCCA
*
18796201 TGATAATAAGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
18796227 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
18796253 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
18796279 TGATAAT-GGTTTAGGTAAATGTTCCA
1 TGATAATAGG-TTAGGTAAATGTTCCA
18796305 TGAT
1 TGAT
18796309 GGGAATTTCA
Statistics
Matches: 101, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
25 2 0.02
26 99 0.98
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:18797806 original size:26 final size:26
Alignment explanation
Indices: 18797743--18797818 Score: 98
Period size: 26 Copynumber: 2.8 Consensus size: 26
18797733 AAAAGTAGCT
* * *
18797743 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-GTGGA
*
18797771 AAATTACTGTTATACCCCTAGGTGTA
1 AAATTACTGTTATACCCCTAGGTGGA
18797797 AAATTACTGTTATACCCCTAGG
1 AAATTACTGTTATACCCCTAGG
18797819 GTTAATTTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 25 0.57
27 1 0.02
28 18 0.41
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGGTGGA
Found at i:18797962 original size:27 final size:27
Alignment explanation
Indices: 18797921--18798033 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 27
18797911 GAGGAAGCGT
*
18797921 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
18797948 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
18797975 TCTGGTGGCTCTGCCACGATTATCTGAA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
18798003 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
18798029 TCTGG
1 TCTGG
18798034 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
26 5 0.07
27 55 0.73
28 15 0.20
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:18798001 original size:54 final size:54
Alignment explanation
Indices: 18797919--18798033 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
18797909 TGGAGGAAGC
*
18797919 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGAATCTGGTGACTCTGCCACAT-TATCT
* * * *
18797973 GTTCTGGTGGCTCTGCCACGATTATCTGAATCTGGTGACTCTGTCACATTATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGAATCTGGTGACTCTGCCACATTATCT
18798027 GTTCTGG
1 GTTCTGG
18798034 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGAATCTGGTGACTCTGCCACATTATCT
Found at i:18802044 original size:26 final size:26
Alignment explanation
Indices: 18802006--18802089 Score: 116
Period size: 26 Copynumber: 3.2 Consensus size: 26
18801996 TGATACAAAT
**
18802006 TGATAATAGGTTAGGTAAATGTTCCT
1 TGATAATAGGTTAGGTAAATGTTCAA
*
18802032 TTATAATAGGTTAGGTAAATGTTCAA
1 TGATAATAGGTTAGGTAAATGTTCAA
*
18802058 TGATAATGGGTTAGGTAAATGTTTC-A
1 TGATAATAGGTTAGGTAAATG-TTCAA
18802084 TGATAA
1 TGATAA
18802090 GAATTTCATG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
26 49 0.94
27 3 0.06
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.38
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCAA
Found at i:18809529 original size:155 final size:154
Alignment explanation
Indices: 18809225--18809531 Score: 515
Period size: 155 Copynumber: 2.0 Consensus size: 154
18809215 GAAACCAATT
*
18809225 TAGAACCTAGAACAGTCGCTCACCCAACTCAGTCCAACATAAGGGAGTGCGACACTTACGACCAC
1 TAGAACCTAGAACAGTCGCTCACCCAACTCAGTCCAACATAAGGGAGTACGACACTTACGACCAC
18809290 ATAGTGCCTCGTAAGGTGCCATCTGGATGCTAGACTGGTAACTATTATTATAGGCAAACTCTGCT
66 ATAGTGCCTCGTAAGGTGCCATCTGGATGCTAGACTGGTAACTATTATTATAGGCAAACTCTGCT
* *
18809355 AACGGTAGATAATCCTCCTAACGG
131 AACAGCAGATAATCCTCCTAACGG
* ** * *
18809379 TAGAACCTGGAACACGTTTCTCGCCCAACTCAGTCCAACATAAGGGAGTACGACACTTATGACCA
1 TAGAACCTAGAACA-GTCGCTCACCCAACTCAGTCCAACATAAGGGAGTACGACACTTACGACCA
* *
18809444 TATAGTGCCTCGTAAGGTGCCATCTGGATGCTAGACTGGTAACTATTATTATAGGCAAATTCTGC
65 CATAGTGCCTCGTAAGGTGCCATCTGGATGCTAGACTGGTAACTATTATTATAGGCAAACTCTGC
18809509 TAACAGCAGATAATCCTCCTAAC
130 TAACAGCAGATAATCCTCCTAAC
18809532 TGCCTCAGAA
Statistics
Matches: 142, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
154 13 0.09
155 129 0.91
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (154 bp):
TAGAACCTAGAACAGTCGCTCACCCAACTCAGTCCAACATAAGGGAGTACGACACTTACGACCAC
ATAGTGCCTCGTAAGGTGCCATCTGGATGCTAGACTGGTAACTATTATTATAGGCAAACTCTGCT
AACAGCAGATAATCCTCCTAACGG
Found at i:18811366 original size:47 final size:47
Alignment explanation
Indices: 18811307--18811428 Score: 208
Period size: 47 Copynumber: 2.6 Consensus size: 47
18811297 CATTTGGCAC
*
18811307 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATTGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
18811354 TAAGACAAGGATACCTTGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* *
18811401 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
18811429 CCAAGGCATG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 70 1.00
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:18811536 original size:55 final size:54
Alignment explanation
Indices: 18811415--18811603 Score: 179
Period size: 55 Copynumber: 3.5 Consensus size: 54
18811405 ATAAGGATAT
* * * * *
18811415 CATGTAAGACCATGCCAAGGCATGGCATTGATAATTTCTATAAGGC-AAGG-CAAT
1 CATGTAAGACCATGCCAAGACATGGCATGGATGAGTTCTATAAGGCAAAGGTC--C
*
18811469 CATGTAAGACCATGGCAAGACATGGCATGGATGAGTTACTATAAGGCAAAGGTCC
1 CATGTAAGACCATGCCAAGACATGGCATGGATGAGTT-CTATAAGGCAAAGGTCC
* * * * * *
18811524 CATGTAAAACCATGCCAAGGCATGACATTGG-TGAGTTC-ATAAGGCAATGATAC
1 CATGTAAGACCATGCCAAGACATGGCA-TGGATGAGTTCTATAAGGCAAAGGTCC
** *
18811577 CACATAAGACCATGTCAAGACATGGCA
1 CATGTAAGACCATGCCAAGACATGGCA
18811604 ATGGTAAGTT
Statistics
Matches: 112, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
53 33 0.29
54 33 0.29
55 38 0.34
56 7 0.06
57 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (54 bp):
CATGTAAGACCATGCCAAGACATGGCATGGATGAGTTCTATAAGGCAAAGGTCC
Found at i:18811589 original size:53 final size:54
Alignment explanation
Indices: 18811410--18811614 Score: 191
Period size: 53 Copynumber: 3.8 Consensus size: 54
18811400 GTAAGATAAG
* * * * *
18811410 GATATCATGTAAGACCATGCCAAGGCATGGCATTGATAATTTCTATAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTATAAGGCAAA
* * *
18811464 GCA-ATCATGTAAGACCATGGCAAGACATGGCA-TGGATGAGTTACTATAAGGCAAA
1 G-ATACCATGTAAGACCATGCCAAGACATGGCATTGG-TAAGTT-CTATAAGGCAAA
* * * * * * *
18811519 GGTCCCATGTAAAACCATGCCAAGGCATGACATTGGTGAGTTC-ATAAGGCAAT
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTATAAGGCAAA
** * *
18811572 GATACCACATAAGACCATGTCAAGACATGGCAATGGTAAGTTC
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTC
18811615 AAAAAGGAAA
Statistics
Matches: 122, Mismatches: 24, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
53 44 0.36
54 33 0.27
55 42 0.34
56 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (54 bp):
GATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTATAAGGCAAA
Found at i:18816014 original size:27 final size:26
Alignment explanation
Indices: 18815958--18816108 Score: 115
Period size: 27 Copynumber: 5.6 Consensus size: 26
18815948 AAATTGTACA
* * *
18815958 GCACTAAGTGTGCG-ATTCTACTTTGTT
1 GCACTAAGTGTGCGAAAT-GACTATG-T
*
18815985 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGAAATGACTATG-T
* * *
18816012 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAAATGACTATG-T
*
18816039 GCACTAAGTGTGCGAGATGGACTATGT
1 GCACTAAGTGTGCGAAAT-GACTATGT
** * *
18816066 GGCACTAAGTGTGCGATTTGATTACGT
1 -GCACTAAGTGTGCGAAATGACTATGT
*
18816093 GGCACTAAATGTGCGA
1 -GCACTAAGTGTGCGA
18816109 GTTGATTATA
Statistics
Matches: 102, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
27 78 0.76
28 24 0.24
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (26 bp):
GCACTAAGTGTGCGAAATGACTATGT
Found at i:18816018 original size:54 final size:54
Alignment explanation
Indices: 18815958--18816083 Score: 148
Period size: 54 Copynumber: 2.3 Consensus size: 54
18815948 AAATTGTACA
* ** **
18815958 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAAT-GAATATGAT-
1 GCACTAAGTGTGCGATT-GACCATGCGGCACTAAGTGTGCGAAATGGAATATG-TG
* *
18816012 GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGATGGACTATGTG
1 GCACTAAGTGTGCG-ATTGACCATGCGGCACTAAGTGTGCGAAATGGAATATGTG
18816067 GCACTAAGTGTGCGATT
1 GCACTAAGTGTGCGATT
18816084 TGATTACGTG
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
54 39 0.63
55 23 0.37
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGATTGACCATGCGGCACTAAGTGTGCGAAATGGAATATGTG
Found at i:18816081 original size:55 final size:54
Alignment explanation
Indices: 18815985--18816134 Score: 160
Period size: 55 Copynumber: 2.8 Consensus size: 54
18815975 CTACTTTGTT
* *
18815985 GCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGATGAATATGATGCACTAAGTGTGCGAATTGACCACGCG
* * ** *
18816039 GCACTAAGTGTGCGAGATGGACTATG-TGGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAGAT-GAATATGAT-GCACTAAGTGTGCGAATTGACCACGCG
* * * *
18816094 GCACTAAATGTGCGAGTTGATTAT-ATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGATGAATATGAT-GCACTAAGTGTGCG
18816135 GGCTCAATAT
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
54 37 0.46
55 44 0.54
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGATGAATATGATGCACTAAGTGTGCGAATTGACCACGCG
Found at i:18816098 original size:82 final size:81
Alignment explanation
Indices: 18815958--18816113 Score: 188
Period size: 82 Copynumber: 1.9 Consensus size: 81
18815948 AAATTGTACA
* * * * * *
18815958 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGAATCGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
18816023 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
18816039 GCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAAT
1 GCACTAAGTGTGCGA-ATCGACTATGTGGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAAT
*
18816103 GTGCGAGTTGA
64 GTGCGAATTGA
18816114 TTATATAGCA
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
81 16 0.26
82 46 0.74
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGAATCGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:18816113 original size:27 final size:27
Alignment explanation
Indices: 18815985--18816134 Score: 113
Period size: 27 Copynumber: 5.5 Consensus size: 27
18815975 CTACTTTGTT
** * *
18815985 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAGTTGATTACG-TG
* ** * *
18816012 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGATTACGTG
* * *
18816039 GCACTAAGTGTGCGAGATGGACTATGTG
1 GCACTAAGTGTGCGAG-TTGATTACGTG
*
18816067 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAGTTGATTACGTG
* ** *
18816094 GCACTAAATGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGTTGATTACGTG
*
18816121 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
18816135 GGCTCAATAT
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
27 79 0.77
28 23 0.23
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGTTGATTACGTG
Found at i:18821128 original size:34 final size:34
Alignment explanation
Indices: 18821080--18821163 Score: 82
Period size: 34 Copynumber: 2.5 Consensus size: 34
18821070 ATCTCAGTAT
* * *
18821080 AGTATCAAATATGCAGT-AGTGTCTTAACCCATCAT
1 AGTATC-AGTATGCAGTAAG-GCCTTAACCCATCAC
* * *
18821115 GGTATCAGTATGCATTAAGGCCTTAGCCCATCAC
1 AGTATCAGTATGCAGTAAGGCCTTAACCCATCAC
18821149 AGTATCAGTA-GCAGT
1 AGTATCAGTATGCAGT
18821164 CATGCAGTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
33 4 0.10
34 29 0.73
35 7 0.17
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (34 bp):
AGTATCAGTATGCAGTAAGGCCTTAACCCATCAC
Found at i:18827280 original size:20 final size:20
Alignment explanation
Indices: 18827255--18827293 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
18827245 TACAAATTTG
*
18827255 CATATATAATACATAATATA
1 CATATATAATAAATAATATA
18827275 CATATATAATAAATAATAT
1 CATATATAATAAATAATAT
18827294 CGAATCCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (20 bp):
CATATATAATAAATAATATA
Found at i:18827758 original size:13 final size:14
Alignment explanation
Indices: 18827734--18827783 Score: 57
Period size: 13 Copynumber: 3.4 Consensus size: 14
18827724 TAATAACTGA
18827734 ATTTATTAATATTT
1 ATTTATTAATATTT
18827748 ATTTA-TAATATTT
1 ATTTATTAATATTT
18827761 ATAATTAATTAATATTT
1 AT--TT-ATTAATATTT
*
18827778 AATTAT
1 ATTTAT
18827784 ATTTAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
13 10 0.32
14 7 0.23
15 4 0.13
16 1 0.03
17 9 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTTATTAATATTT
Found at i:18835788 original size:40 final size:40
Alignment explanation
Indices: 18835733--18835914 Score: 314
Period size: 40 Copynumber: 4.6 Consensus size: 40
18835723 TATTCGAATG
18835733 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
18835773 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
18835813 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
18835853 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
18835893 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
18835915 TACTTGGGTT
Statistics
Matches: 137, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
39 14 0.10
40 121 0.88
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:18840589 original size:17 final size:17
Alignment explanation
Indices: 18840567--18840603 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
18840557 GTAAACTCAG
18840567 ACCTTTTGGTTGTTGAC
1 ACCTTTTGGTTGTTGAC
18840584 ACCTTTTGGTTGTTGAC
1 ACCTTTTGGTTGTTGAC
18840601 ACC
1 ACC
18840604 AGCAACAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.43
Consensus pattern (17 bp):
ACCTTTTGGTTGTTGAC
Found at i:18848958 original size:47 final size:46
Alignment explanation
Indices: 18848902--18849026 Score: 137
Period size: 47 Copynumber: 2.7 Consensus size: 46
18848892 CTGTCGAGGT
* * * *
18848902 CGATGCATGTCCCAGACATATCTTACTCTGGCACTCAT-CTCTGTGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCACTCATAATGTG-GC
* *
18848948 CGATGCCATGT-CCAAACATGGTCTTACACTGGCTCTCATAATGTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCACTCATAATGTGGC
* *
18848995 CGAAGCATGTCCCAGACATGTCTTACATTGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGC
18849027 GCACAACTCA
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
46 29 0.44
47 34 0.52
48 3 0.05
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCACTCATAATGTGGC
Found at i:18850655 original size:21 final size:21
Alignment explanation
Indices: 18850631--18850673 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
18850621 ATAGACCTAG
18850631 TGATCCTCCAAATATAGGAAC
1 TGATCCTCCAAATATAGGAAC
* * *
18850652 TGATCTTCTAGATATAGGAAC
1 TGATCCTCCAAATATAGGAAC
18850673 T
1 T
18850674 AAATGGGTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (21 bp):
TGATCCTCCAAATATAGGAAC
Found at i:18852805 original size:7 final size:7
Alignment explanation
Indices: 18852793--18852822 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
18852783 TAGACCCTAA
18852793 ATTTTTT
1 ATTTTTT
18852800 A-TTTTT
1 ATTTTTT
18852806 ATTTTTT
1 ATTTTTT
18852813 ATTTTTT
1 ATTTTTT
18852820 ATT
1 ATT
18852823 ATATATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (7 bp):
ATTTTTT
Found at i:18852811 original size:13 final size:13
Alignment explanation
Indices: 18852793--18852818 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18852783 TAGACCCTAA
18852793 ATTTTTTATTTTT
1 ATTTTTTATTTTT
18852806 ATTTTTTATTTTT
1 ATTTTTTATTTTT
18852819 TATTATATAT
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
ATTTTTTATTTTT
Found at i:18856099 original size:38 final size:39
Alignment explanation
Indices: 18856050--18856142 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 39
18856040 TATCTCCGTG
* * *
18856050 CAACCCAACACACCA-TGTGGGGATAAAATCAACCTACC
1 CAACCCTACACACCAGTATGAGGATAAAATCAACCTACC
* *
18856088 CAGCCCTACACACCAAGTATGAGGATAAAATCAACCTATC
1 CAACCCTACACACC-AGTATGAGGATAAAATCAACCTACC
18856128 CAACCCTACACACCA
1 CAACCCTACACACCA
18856143 AATGGTACCA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
38 12 0.26
39 2 0.04
40 33 0.70
ACGTcount: A:0.40, C:0.35, G:0.11, T:0.14
Consensus pattern (39 bp):
CAACCCTACACACCAGTATGAGGATAAAATCAACCTACC
Found at i:18860566 original size:36 final size:36
Alignment explanation
Indices: 18860526--18860597 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
18860516 TCCTTTCATC
18860526 ACCAGCTTCTCTGCCACTAACGCAGATATCACATTA
1 ACCAGCTTCTCTGCCACTAACGCAGATATCACATTA
18860562 ACCAGCTTCTCTGCCACTAACGCAGATATCACATTA
1 ACCAGCTTCTCTGCCACTAACGCAGATATCACATTA
18860598 GACAAATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.33, G:0.11, T:0.25
Consensus pattern (36 bp):
ACCAGCTTCTCTGCCACTAACGCAGATATCACATTA
Found at i:18863071 original size:79 final size:81
Alignment explanation
Indices: 18862962--18863144 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
18862952 TACTCGTTCA
* *
18862962 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
18863025 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
18863042 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
18863105 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
18863121 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
18863145 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:18863144 original size:40 final size:40
Alignment explanation
Indices: 18862941--18863144 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
18862931 CGGAATTTAA
** *
18862941 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
18862981 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
18863021 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
18863060 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
18863100 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
18863140 CCGGA
1 CCGGA
18863145 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:18865191 original size:47 final size:47
Alignment explanation
Indices: 18865117--18865206 Score: 162
Period size: 47 Copynumber: 1.9 Consensus size: 47
18865107 GCGAAGTCAC
* *
18865117 ATGAGAATGTATTTAAAACCGTGTTTACCCAAAAAAATTGTTATAGT
1 ATGAAAATGTATTTAAAACCGTGTTTACCCAAAAAAATCGTTATAGT
18865164 ATGAAAATGTATTTAAAACCGTGTTTACCCAAAAAAATCGTTA
1 ATGAAAATGTATTTAAAACCGTGTTTACCCAAAAAAATCGTTA
18865207 CAGTTACTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.32
Consensus pattern (47 bp):
ATGAAAATGTATTTAAAACCGTGTTTACCCAAAAAAATCGTTATAGT
Found at i:18867360 original size:11 final size:11
Alignment explanation
Indices: 18867344--18867376 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
18867334 AGAAATAAGT
18867344 TAAAAAAATAA
1 TAAAAAAATAA
18867355 TAAAAAAATAA
1 TAAAAAAATAA
18867366 -AAATAAAATAA
1 TAAA-AAAATAA
18867377 AGTCCAAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 3 0.14
11 18 0.86
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
TAAAAAAATAA
Found at i:18867524 original size:19 final size:19
Alignment explanation
Indices: 18867496--18867593 Score: 155
Period size: 19 Copynumber: 5.2 Consensus size: 19
18867486 AATCTTTAAG
*
18867496 GATATTCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
18867515 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
18867534 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
18867551 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
18867570 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
18867591 GAT
1 GAT
18867594 CTTGTAATCT
Statistics
Matches: 74, Mismatches: 1, Indels: 6
0.91 0.01 0.07
Matches are distributed among these distances:
17 17 0.23
19 48 0.65
21 9 0.12
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:18867526 original size:36 final size:36
Alignment explanation
Indices: 18867497--18867593 Score: 117
Period size: 36 Copynumber: 2.6 Consensus size: 36
18867487 ATCTTTAAGG
*
18867497 ATATTCAATCTTAGATATGATATGCAATC-TTAGAT
1 ATATACAATCTTAGATATGATATGCAATCTTTAGAT
18867532 ATGATACAATCTTAGATATGATATGCAATC-TTAGAT
1 AT-ATACAATCTTAGATATGATATGCAATCTTTAGAT
18867568 ATGATATGCAATCTTGAAGATATGAT
1 AT-ATA--CAATCTT--AGATATGAT
18867594 CTTGTAATCT
Statistics
Matches: 56, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
35 2 0.04
36 38 0.68
38 7 0.12
40 9 0.16
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.37
Consensus pattern (36 bp):
ATATACAATCTTAGATATGATATGCAATCTTTAGAT
Found at i:18867532 original size:14 final size:15
Alignment explanation
Indices: 18867515--18867571 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
18867505 TCTTAGATAT
18867515 GATATG-CAATCTTA
1 GATATGACAATCTTA
18867529 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
18867546 GATATGATATGCAATCTTA
1 GATATG--A--CAATCTTA
18867565 GATATGA
1 GATATGA
18867572 TATGCAATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.16
17 18 0.47
19 14 0.37
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:18870407 original size:21 final size:20
Alignment explanation
Indices: 18870379--18870419 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
18870369 AAAAGGTTAC
* *
18870379 AGAATTCTACTGGTAGAACT
1 AGAATTCTACTAGTACAACT
18870399 AGAAGTTCTACTAGTACAACT
1 AGAA-TTCTACTAGTACAACT
18870420 CTGGGTTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (20 bp):
AGAATTCTACTAGTACAACT
Found at i:18873280 original size:39 final size:40
Alignment explanation
Indices: 18873185--18873407 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
18873175 TTGAATGATG
*
18873185 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
18873223 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
18873264 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
18873303 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
18873342 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
18873381 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
18873408 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
39 93 0.57
40 59 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:18873371 original size:79 final size:81
Alignment explanation
Indices: 18873185--18873407 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
18873175 TTGAATGATG
* * *
18873185 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATATCCGGGCTAAGACCCGAAGGCAT
*
18873247 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAA
18873264 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATATCCGGGCTAAGACCCGAAGGCAT
*
18873325 TTGTGCGAGTTACTAAA
65 TTGTGCGAGATACTAAA
* * * * *
18873342 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
18873406 TG
66 TG
18873408 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
78 46 0.36
79 56 0.44
80 25 0.20
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:18873429 original size:79 final size:79
Alignment explanation
Indices: 18873185--18873440 Score: 217
Period size: 79 Copynumber: 3.3 Consensus size: 79
18873175 TTGAATGATG
* * * *
18873185 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
18873246 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
18873264 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
18873328 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
*
18873342 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
18873405 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
18873422 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
18873441 TACGTGATTT
Statistics
Matches: 153, Mismatches: 14, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
77 1 0.01
78 46 0.30
79 69 0.45
80 36 0.24
81 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:18875845 original size:44 final size:46
Alignment explanation
Indices: 18875780--18875868 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 46
18875770 CATTTTAACC
* *
18875780 TACTAAATAATTAACTAAATTATATAGTATTTATTATAAATTATTA
1 TACTAAATAATTAACTAAATTACATAGTACTTATTATAAATTATTA
* *
18875826 TACTAAAT-A-TAACTAAATTACATAGTACTTATTGTTAATTATT
1 TACTAAATAATTAACTAAATTACATAGTACTTATTATAAATTATT
18875869 TGTATTTGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 30 0.77
45 1 0.03
46 8 0.21
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (46 bp):
TACTAAATAATTAACTAAATTACATAGTACTTATTATAAATTATTA
Done.