Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, whole genome shotgun sequence
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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 21 of 32
Found at i:10998657 original size:31 final size:31
Alignment explanation
Indices: 10998576--10998762 Score: 126
Period size: 31 Copynumber: 6.0 Consensus size: 31
10998566 GTCTAATTAA
* * *
10998576 ACTAGCATCCAAAATATTTAAGCCTAGTTAT
1 ACTAGCATCCAAGATGTTTAAGCCCAGTTAT
*** ** * * *
10998607 AAGGGCATAAAAAAAGTTTAAGCCCATTTAT
1 ACTAGCATCCAAGATGTTTAAGCCCAGTTAT
10998638 ACTAGCATCCAAGATGTTTAAGCCCAGTTAT
1 ACTAGCATCCAAGATGTTTAAGCCCAGTTAT
* * * * * **
10998669 ATTGGCA-CAAAGAGATGTATAAACTGAGTTAT
1 ACTAGCATC-CA-AGATGTTTAAGCCCAGTTAT
* * *
10998701 ACTAGCATTCACGATGTTTAAGCCCAATT-T
1 ACTAGCATCCAAGATGTTTAAGCCCAGTTAT
* *
10998731 AGCTGGCATCCAAGATGTTTAAGCCTAGTTAT
1 A-CTAGCATCCAAGATGTTTAAGCCCAGTTAT
10998763 CTTAGTATAA
Statistics
Matches: 112, Mismatches: 39, Indels: 9
0.70 0.24 0.06
Matches are distributed among these distances:
30 3 0.03
31 86 0.77
32 23 0.21
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (31 bp):
ACTAGCATCCAAGATGTTTAAGCCCAGTTAT
Found at i:10999539 original size:21 final size:20
Alignment explanation
Indices: 10999514--10999576 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 20
10999504 GCGGCACGGG
10999514 GAGAAGAAAAAGGAAGAGAAA
1 GAGAAGAAAAAGGAA-AGAAA
*
10999535 GAGAAGGAAAAGGAAAG-AA
1 GAGAAGAAAAAGGAAAGAAA
*
10999554 -AGAA-AAAAAGAAAAGAAA
1 GAGAAGAAAAAGGAAAGAAA
*
10999572 AAGAA
1 GAGAA
10999577 AGAAGAAGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 9 0.24
18 6 0.16
19 6 0.16
20 2 0.05
21 14 0.38
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (20 bp):
GAGAAGAAAAAGGAAAGAAA
Found at i:10999570 original size:13 final size:12
Alignment explanation
Indices: 10999515--10999580 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
10999505 CGGCACGGGG
*
10999515 AGAAGAAAAAGGA
1 AGAA-AAAAAGAA
* *
10999528 AGAGAAAGAGAA
1 AGAAAAAAAGAA
*
10999540 GGAAAAGGAAAGAA
1 AGAAAA--AAAGAA
10999554 AGAAAAAAAGAA
1 AGAAAAAAAGAA
*
10999566 A-AGAAAAAGAA
1 AGAAAAAAAGAA
10999577 AGAA
1 AGAA
10999581 GAAGACAGAG
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
11 10 0.24
12 18 0.44
13 3 0.07
14 10 0.24
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAGAA
Found at i:10999649 original size:17 final size:17
Alignment explanation
Indices: 10999629--10999678 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
10999619 GAATAAATGG
10999629 AAGGAAAGAAAGAGAAA
1 AAGGAAAGAAAGAGAAA
10999646 AAGGAAAG-AAGA-AAA
1 AAGGAAAGAAAGAGAAA
10999661 AAGAGAGAA-AAAGAGAAA
1 AAG-GA-AAGAAAGAGAAA
10999679 TAACACATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.21
16 6 0.21
17 14 0.48
18 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
AAGGAAAGAAAGAGAAA
Found at i:10999651 original size:21 final size:22
Alignment explanation
Indices: 10999613--10999661 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
10999603 GCAAAGGGAG
*
10999613 GAAAAAGAATAAATGGAAGGAAA
1 GAAAAAGAATAAATGGAAAG-AA
*
10999636 GAAAGAGAA-AAA-GGAAAGAA
1 GAAAAAGAATAAATGGAAAGAA
10999656 GAAAAA
1 GAAAAA
10999662 AGAGAGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 7 0.30
21 5 0.22
22 3 0.13
23 8 0.35
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (22 bp):
GAAAAAGAATAAATGGAAAGAA
Found at i:10999662 original size:16 final size:17
Alignment explanation
Indices: 10999629--10999662 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
10999619 GAATAAATGG
*
10999629 AAGGAAAGAAAGAGAAA
1 AAGGAAAGAAAGAAAAA
10999646 AAGGAAAG-AAGAAAAA
1 AAGGAAAGAAAGAAAAA
10999662 A
1 A
10999663 GAGAGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAGGAAAGAAAGAAAAA
Found at i:10999677 original size:8 final size:8
Alignment explanation
Indices: 10999637--10999678 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
10999627 GGAAGGAAAG
10999637 AAAGAGAA
1 AAAGAGAA
10999645 AAAG-GAA
1 AAAGAGAA
*
10999652 AGAAGAAAA
1 A-AAGAGAA
10999661 AAGAGAGAA
1 AA-AGAGAA
10999670 AAAGAGAA
1 AAAGAGAA
10999678 A
1 A
10999679 TAACACATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
7 4 0.14
8 15 0.52
9 10 0.34
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (8 bp):
AAAGAGAA
Found at i:10999754 original size:15 final size:15
Alignment explanation
Indices: 10999701--10999847 Score: 65
Period size: 14 Copynumber: 9.5 Consensus size: 15
10999691 AGCAAAGAAT
*
10999701 AAGAGAAGAAGAAGA
1 AAGAGAAGAAAAAGA
*
10999716 AA-AGGAAG-GAAAGA
1 AAGA-GAAGAAAAAGA
*
10999730 AGGAGAA-AAAAA-A
1 AAGAGAAGAAAAAGA
*
10999743 GAGAGAAGAAAAAGA
1 AAGAGAAGAAAAAGA
*
10999758 AAGAGAAGAAACCAATAA
1 AAGAGAAGAAA--AA-GA
*
10999776 AAGGAGAGAGGAAGAAGA
1 AA-GAGA-A-GAAAAAGA
10999794 AAGAGAAGGAAGGAAAGA
1 AAGAGAA-GAA--AAAGA
*
10999812 AAAAG-AGAAAGAGAGA
1 AAGAGAAGAAA-A-AGA
*
10999828 AAGA-AAG-GAAAGA
1 AAGAGAAGAAAAAGA
10999841 AAGAGAA
1 AAGAGAA
10999848 AAGAAGGCAG
Statistics
Matches: 101, Mismatches: 14, Indels: 35
0.67 0.09 0.23
Matches are distributed among these distances:
13 13 0.13
14 21 0.21
15 20 0.20
16 16 0.16
17 7 0.07
18 14 0.14
19 6 0.06
20 1 0.01
21 3 0.03
ACGTcount: A:0.66, C:0.01, G:0.32, T:0.01
Consensus pattern (15 bp):
AAGAGAAGAAAAAGA
Found at i:10999816 original size:20 final size:20
Alignment explanation
Indices: 10999780--10999852 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
10999770 CAATAAAAGG
*
10999780 AGAGAGGAAGAAGAAAGAGAA
1 AGAGAGAAAGAA-AAAGAGAA
*
10999801 GGA-AGGAAAGAAAAAGAGAA
1 AGAGA-GAAAGAAAAAGAGAA
10999821 AGAGAGAAAGAAAGGAA-AGAA
1 AGAGAGAAAGAAA--AAGAGAA
10999842 AGAGA-AAAGAA
1 AGAGAGAAAGAA
10999853 GGCAGGAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
20 25 0.56
21 18 0.40
22 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (20 bp):
AGAGAGAAAGAAAAAGAGAA
Found at i:10999843 original size:33 final size:34
Alignment explanation
Indices: 10999782--10999851 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
10999772 ATAAAAGGAG
* *
10999782 AGAGGAAGAAGAAAGAGAAGGAAGGAAAGA-AAA
1 AGAGAAAGAAGAAAGAGAAGGAAAGAAAGAGAAA
10999815 AGAGAAAGAGAGAAAGA-AAGGAAAGAAAGAGAAA
1 AGAGAAAGA-AGAAAGAGAAGGAAAGAAAGAGAAA
10999849 AGA
1 AGA
10999852 AGGCAGGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 20 0.61
34 13 0.39
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (34 bp):
AGAGAAAGAAGAAAGAGAAGGAAAGAAAGAGAAA
Found at i:10999859 original size:23 final size:21
Alignment explanation
Indices: 10999817--10999878 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 21
10999807 AAAGAAAAAG
10999817 AGAAAGAGAGAAAGAA-AGGAA
1 AGAAAGAGA-AAAGAAGAGGAA
10999838 AGAAAGAGAAAAGAAGGCAGGAA
1 AGAAAGAGAAAAGAA-G-AGGAA
* *
10999861 AAAAAAAGAAAAAGAAGA
1 AGAAAGAG-AAAAGAAGA
10999879 ACAACCAGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
20 6 0.17
21 9 0.26
22 1 0.03
23 12 0.34
24 7 0.20
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (21 bp):
AGAAAGAGAAAAGAAGAGGAA
Found at i:10999861 original size:19 final size:19
Alignment explanation
Indices: 10999713--10999854 Score: 61
Period size: 19 Copynumber: 7.6 Consensus size: 19
10999703 GAGAAGAAGA
*
10999713 AGAAAAGGAAGGAAAGAAGG
1 AGAAAA-GAAGGAAAGAAAG
* * *
10999733 AGAAAAAAAAGAGAG-AAG
1 AGAAAAGAAGGAAAGAAAG
* *
10999751 A-AAAAGAAAGAGAAGAAACC
1 AGAAAAGAAGGA-AAGAAA-G
* *
10999771 A-ATAA-AAGGAGAGAGGAAG
1 AGAAAAGAAGGA-A-AGAAAG
*
10999790 AAGAAAGAGAAGGAAGGAAAG
1 -AGAAA-AGAAGGAAAGAAAG
10999811 A-AAAAG-A-GAAAG--AG
1 AGAAAAGAAGGAAAGAAAG
10999825 AG-AAAGAAAGGAAAGAAAG
1 AGAAAAG-AAGGAAAGAAAG
10999844 AGAAAAGAAGG
1 AGAAAAGAAGG
10999855 CAGGAAAAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 31
0.67 0.11 0.22
Matches are distributed among these distances:
14 7 0.08
16 5 0.05
17 15 0.16
18 7 0.08
19 25 0.27
20 20 0.22
21 6 0.07
22 2 0.02
23 5 0.05
ACGTcount: A:0.65, C:0.01, G:0.32, T:0.01
Consensus pattern (19 bp):
AGAAAAGAAGGAAAGAAAG
Found at i:11000401 original size:28 final size:27
Alignment explanation
Indices: 11000366--11000419 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
11000356 TTAGATACTC
11000366 GTAAATATAATTAATAAAAATACATGAT
1 GTAAATATAATTAATAAAAA-ACATGAT
* *
11000394 GTAAATATAATTATTATAAAACATGA
1 GTAAATATAATTAATAAAAAACATGA
11000420 AATGATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (27 bp):
GTAAATATAATTAATAAAAAACATGAT
Found at i:11012342 original size:29 final size:29
Alignment explanation
Indices: 11012290--11012384 Score: 86
Period size: 32 Copynumber: 3.2 Consensus size: 29
11012280 TATTAAAGTA
* *
11012290 TAACAA-AATA-TTTTTGAATATGGCGTG
1 TAACAACAATATTTTTTCAACATGGCGTG
11012317 TAACAACAATATTTTTTCAACATGGCGTG
1 TAACAACAATATTTTTTCAACATGGCGTG
* * * * *
11012346 AAATAATAGTATTTTTTTTTCAACATAGCGTG
1 TAACAACA--A-TATTTTTTCAACATGGCGTG
11012378 TAACAAC
1 TAACAAC
11012385 CTTTTTTAAC
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
27 6 0.11
28 4 0.08
29 20 0.38
31 1 0.02
32 22 0.42
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (29 bp):
TAACAACAATATTTTTTCAACATGGCGTG
Found at i:11012583 original size:45 final size:44
Alignment explanation
Indices: 11012453--11012586 Score: 142
Period size: 45 Copynumber: 3.0 Consensus size: 44
11012443 TTTAACATAG
* * *
11012453 CATGTAATAACCTAATCATGGTGTGTAACATGTTTTTATACATGA
1 CATGTAATAACCTAACCAT-GCGTGTAACATGTTTTTGTACATGA
* * * *
11012498 CGTGTAATAACCTAACCATGACGTTTTACACGTTTTTGTACATGA
1 CATGTAATAACCTAACCATG-CGTGTAACATGTTTTTGTACATGA
* * * *
11012543 CATGTAACAACCTAACCATAGCATGTAATATGTTTCTGTACATG
1 CATGTAATAACCTAACCAT-GCGTGTAACATGTTTTTGTACATG
11012587 GTGTGTAACA
Statistics
Matches: 72, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
44 1 0.01
45 70 0.97
46 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (44 bp):
CATGTAATAACCTAACCATGCGTGTAACATGTTTTTGTACATGA
Found at i:11015741 original size:15 final size:15
Alignment explanation
Indices: 11015699--11015735 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
11015689 TCTAATTAAA
*
11015699 TTATATTATAAT-AT
1 TTATTTTATAATAAT
11015713 TTATTTTATAATAAT
1 TTATTTTATAATAAT
11015728 TTATTTTA
1 TTATTTTA
11015736 ATATAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTTTATAATAAT
Found at i:11015897 original size:5 final size:5
Alignment explanation
Indices: 11015887--11015965 Score: 54
Period size: 5 Copynumber: 15.2 Consensus size: 5
11015877 CTATTATAAT
* * * *
11015887 TAAAA TAAAA TATAT TAAAA TAAAA T-ATA TAATA TAAGAA TCAAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA-AA T--AAAA
*
11015934 TTAAAA TAAAA TAAAA TATAAA -AAAT TAAAA T
1 -TAAAA TAAAA TAAAA TA-AAA TAAAA TAAAA T
11015966 TTATATAATA
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
4 5 0.08
5 40 0.68
6 9 0.15
7 2 0.03
8 3 0.05
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (5 bp):
TAAAA
Found at i:11015905 original size:15 final size:15
Alignment explanation
Indices: 11015885--11015916 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
11015875 TACTATTATA
11015885 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
11015900 ATTAAAATAAAATAT
1 ATTAAAATAAAATAT
11015915 AT
1 AT
11015917 AATATAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATTAAAATAAAATAT
Found at i:11015918 original size:33 final size:33
Alignment explanation
Indices: 11015881--11015954 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
11015871 GAAATACTAT
11015881 TATAAT-TAA-AATAAAATATATTAAAATAAAATA
1 TATAATATAAGAATAAAA-A-ATTAAAATAAAATA
*
11015914 TATAATATAAGAATCAAAAATTAAAATAAAATA
1 TATAATATAAGAATAAAAAATTAAAATAAAATA
11015947 -A-AATATAA
1 TATAATATAA
11015955 AAAATTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
31 7 0.18
32 1 0.03
33 20 0.53
34 4 0.11
35 6 0.16
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (33 bp):
TATAATATAAGAATAAAAAATTAAAATAAAATA
Found at i:11016035 original size:50 final size:50
Alignment explanation
Indices: 11015884--11016038 Score: 147
Period size: 50 Copynumber: 3.0 Consensus size: 50
11015874 ATACTATTAT
11015884 AATTAAAATAAAATATATTAAAATAAAATATATAATATAAG-AATCAAAAATTA
1 AATTAAAATAAAATATA-TAAAATAAAAT-TAT-ATATAAGAAATCAAAAA-TA
* * * ** **
11015937 AAATAAAATAAAATATAAAAAATTAAAATT-TATATAATATCTGTAAAATA
1 AATTAAAATAAAATATATAAAA-TAAAATTATATATAAGAAATCAAAAATA
*
11015987 AATTAAAATAAAATATATAATATAAAAATTATAT-TAAAGAAAT-AAAAATA
1 AATTAAAATAAAATATATAAAAT-AAAATTATATAT-AAGAAATCAAAAATA
11016037 AA
1 AA
11016039 ATACATAAGA
Statistics
Matches: 83, Mismatches: 14, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
49 1 0.01
50 42 0.51
51 13 0.16
52 5 0.06
53 22 0.27
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.30
Consensus pattern (50 bp):
AATTAAAATAAAATATATAAAATAAAATTATATATAAGAAATCAAAAATA
Found at i:11016072 original size:88 final size:91
Alignment explanation
Indices: 11015888--11016074 Score: 196
Period size: 88 Copynumber: 2.1 Consensus size: 91
11015878 TATTATAATT
* *
11015888 AAAATAAAATATATTAAAATAAAATATATAATATAAGAATCAAAAATTAAAATAAAATAAAATAT
1 AAAATAAAATAAATTAAAATAAAATATATAATATAAAAAT-AAAAATTAAAATAAAATAAAATAT
**
11015953 AAAAAATTAAAATTTATATAATATCTG
65 AAAAAATTAAAATTTATATAATAAATG
* * *
11015980 ----TAAAATAAATTAAAATAAAATATATAATATAAAAAT-TATATT-AAA-GAAATAAAA-ATA
1 AAAATAAAATAAATTAAAATAAAATATATAATATAAAAATAAAAATTAAAATAAAATAAAATATA
*
11016037 AAATACA-TAAGA-TTATAATAATAAATG
66 AAA-A-ATTAAAATTTAT-ATAATAAATG
11016064 AAAATAAAATA
1 AAAATAAAATA
11016075 TATGACATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
83 10 0.12
84 21 0.26
85 4 0.05
86 4 0.05
88 41 0.51
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (91 bp):
AAAATAAAATAAATTAAAATAAAATATATAATATAAAAATAAAAATTAAAATAAAATAAAATATA
AAAAATTAAAATTTATATAATAAATG
Found at i:11016328 original size:15 final size:15
Alignment explanation
Indices: 11016300--11016351 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
11016290 CCCTACAATC
*
11016300 ACATTGCTTATAATT
1 ACATTACTTATAATT
*
11016315 ACATTACTTGTAATT
1 ACATTACTTATAATT
*
11016330 ACATTACTTATAATC
1 ACATTACTTATAATT
11016345 ACATTAC
1 ACATTAC
11016352 ATTGTAAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.42
Consensus pattern (15 bp):
ACATTACTTATAATT
Found at i:11016340 original size:30 final size:31
Alignment explanation
Indices: 11016300--11016358 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
11016290 CCCTACAATC
* *
11016300 ACATTGCTTATAATTACATTAC-TTGTAATT
1 ACATTACTTATAATCACATTACATTGTAATT
11016330 ACATTACTTATAATCACATTACATTGTAA
1 ACATTACTTATAATCACATTACATTGTAA
11016359 AGTATCGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.42
Consensus pattern (31 bp):
ACATTACTTATAATCACATTACATTGTAATT
Found at i:11027281 original size:21 final size:21
Alignment explanation
Indices: 11027228--11027286 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
11027218 GTATGGAGTG
* *
11027228 AGGTGAACGTTACACAAAATA
1 AGGTGAACGTTGCACCAAATA
11027249 AGGTGAACGTTGCACCAAATA
1 AGGTGAACGTTGCACCAAATA
* *
11027270 AGGTGCACGTTGAACCA
1 AGGTGAACGTTGCACCA
11027287 GATTAGGGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.19
Consensus pattern (21 bp):
AGGTGAACGTTGCACCAAATA
Found at i:11027451 original size:101 final size:101
Alignment explanation
Indices: 11027271--11027466 Score: 311
Period size: 101 Copynumber: 1.9 Consensus size: 101
11027261 CACCAAATAA
* * *
11027271 GGTGCACGTTGAACCAGATTAGGGAGTTGAGAAAAACACTTAGGAGTTAAAGAAAAACTTGGTCA
1 GGTGCACGTTAAACCAGATTAGGGAGTTGAGAAAAACACTCAAGAGTTAAAGAAAAACTTGGTCA
* *
11027336 ACTATTTACTGAGTCAGATAAACGTTGGAGCATTTT
66 ACTATTCACCGAGTCAGATAAACGTTGGAGCATTTT
* *
11027372 GGTGCATGTTAAACCAGATTAGGGAGTTGAGAAAAACACTCAAGAGTTAGAGAAAAACTTGGTCA
1 GGTGCACGTTAAACCAGATTAGGGAGTTGAGAAAAACACTCAAGAGTTAAAGAAAAACTTGGTCA
* *
11027437 GCTATTCACCGAGTCAGATAAATGTTGGAG
66 ACTATTCACCGAGTCAGATAAACGTTGGAG
11027467 ACTCAGTAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 86 1.00
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (101 bp):
GGTGCACGTTAAACCAGATTAGGGAGTTGAGAAAAACACTCAAGAGTTAAAGAAAAACTTGGTCA
ACTATTCACCGAGTCAGATAAACGTTGGAGCATTTT
Found at i:11027572 original size:70 final size:70
Alignment explanation
Indices: 11027459--11027591 Score: 266
Period size: 70 Copynumber: 1.9 Consensus size: 70
11027449 GTCAGATAAA
11027459 TGTTGGAGACTCAGTAAACGTTGGAGCATATCCAGGTAAGGTAGGTAGAAAAATTAATGCCAAAA
1 TGTTGGAGACTCAGTAAACGTTGGAGCATATCCAGGTAAGGTAGGTAGAAAAATTAATGCCAAAA
11027524 GGTAC
66 GGTAC
11027529 TGTTGGAGACTCAGTAAACGTTGGAGCATATCCAGGTAAGGTAGGTAGAAAAATTAATGCCAA
1 TGTTGGAGACTCAGTAAACGTTGGAGCATATCCAGGTAAGGTAGGTAGAAAAATTAATGCCAA
11027592 GGTACAAAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.23
Consensus pattern (70 bp):
TGTTGGAGACTCAGTAAACGTTGGAGCATATCCAGGTAAGGTAGGTAGAAAAATTAATGCCAAAA
GGTAC
Found at i:11030018 original size:21 final size:21
Alignment explanation
Indices: 11029992--11030035 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
11029982 GAGTCAGATA
*
11029992 AACATTGGAGCATTTCCAGGT
1 AACATTGGAGCATATCCAGGT
*
11030013 AACATTGGAGCATATCTAGGT
1 AACATTGGAGCATATCCAGGT
11030034 AA
1 AA
11030036 GGTAGGTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (21 bp):
AACATTGGAGCATATCCAGGT
Found at i:11030060 original size:25 final size:25
Alignment explanation
Indices: 11030031--11030106 Score: 143
Period size: 25 Copynumber: 3.0 Consensus size: 25
11030021 AGCATATCTA
11030031 GGTAAGGTAGGTAGAGTTTTAGAAT
1 GGTAAGGTAGGTAGAGTTTTAGAAT
*
11030056 GGTAAGGTCGGTAGAGTTTTAGAAT
1 GGTAAGGTAGGTAGAGTTTTAGAAT
11030081 GGTAAGGTAGGTAGAGTTTTAGAAT
1 GGTAAGGTAGGTAGAGTTTTAGAAT
11030106 G
1 G
11030107 ATTCAATCAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.30, C:0.01, G:0.37, T:0.32
Consensus pattern (25 bp):
GGTAAGGTAGGTAGAGTTTTAGAAT
Found at i:11031629 original size:12 final size:12
Alignment explanation
Indices: 11031612--11031636 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11031602 AATGAGATTC
11031612 TTAAATTGGATA
1 TTAAATTGGATA
11031624 TTAAATTGGATA
1 TTAAATTGGATA
11031636 T
1 T
11031637 GATGAAAGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (12 bp):
TTAAATTGGATA
Found at i:11034195 original size:29 final size:29
Alignment explanation
Indices: 11034162--11034221 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
11034152 AATATTTTTT
*
11034162 ATTTTTTTGCTACTTTAAATTAAATATTA
1 ATTTTTTTACTACTTTAAATTAAATATTA
* *
11034191 ATTTTTTTATTATTTTAAATTAAATATTA
1 ATTTTTTTACTACTTTAAATTAAATATTA
11034220 AT
1 AT
11034222 ACTCATCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (29 bp):
ATTTTTTTACTACTTTAAATTAAATATTA
Found at i:11034792 original size:19 final size:19
Alignment explanation
Indices: 11034770--11034807 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
11034760 AATAATTTTT
*
11034770 AAAAATAATTAATATAATTA
1 AAAAATAA-TAAAATAATTA
11034790 AAAAATAATAAAATAATT
1 AAAAATAATAAAATAATT
11034808 TTATAAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATAATAAAATAATTA
Found at i:11034815 original size:20 final size:21
Alignment explanation
Indices: 11034760--11034815 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
11034750 TATATTTTTT
11034760 AATAATTTTTAAAAATAATTAA
1 AATAA-TTTTAAAAATAATTAA
* *
11034782 TATAA-TTAAAAAATAA-TAA
1 AATAATTTTAAAAATAATTAA
*
11034801 AATAATTTTATAAAT
1 AATAATTTTAAAAAT
11034816 CTCATTCAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 7 0.25
20 17 0.61
22 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AATAATTTTAAAAATAATTAA
Found at i:11035655 original size:15 final size:15
Alignment explanation
Indices: 11035635--11035673 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
11035625 GTTTAATATA
11035635 TTAATTTTAAAATTT
1 TTAATTTTAAAATTT
* *
11035650 TTAATTTTTATATTTT
1 TTAA-TTTTAAAATTT
11035666 TTAATTTT
1 TTAATTTT
11035674 TTGACTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTAATTTTAAAATTT
Found at i:11036741 original size:16 final size:18
Alignment explanation
Indices: 11036722--11036758 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
11036712 TAATTTTTTT
11036722 AAAAAAT-AAAATTTA-A
1 AAAAAATAAAAATTTATA
11036738 AAAAAATAAAAATTTATA
1 AAAAAATAAAAATTTATA
11036756 AAA
1 AAA
11036759 TTGTAAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 4 0.21
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAAATAAAAATTTATA
Found at i:11036981 original size:30 final size:30
Alignment explanation
Indices: 11036947--11037005 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
11036937 CTATCAAAAA
* *
11036947 TTTTAATTATAATAATTAATAATTAAATAT
1 TTTTAATTATAATAATTAAAAATAAAATAT
* * *
11036977 TTTTATTTTTTATAATTAAAAATAAAATA
1 TTTTAATTATAATAATTAAAAATAAAATA
11037006 AGAGATATCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TTTTAATTATAATAATTAAAAATAAAATAT
Found at i:11037212 original size:27 final size:27
Alignment explanation
Indices: 11037156--11037261 Score: 124
Period size: 28 Copynumber: 3.9 Consensus size: 27
11037146 TTTATTATTG
* *
11037156 ATATGTAATAATTATTATTTTTAATATA
1 ATATGTAATAATTA-AATTTTTAATTTA
*
11037184 ATATGTAATAATTAAAATTTTAATTTA
1 ATATGTAATAATTAAATTTTTAATTTA
* *
11037211 ATATATAATAATTATATTTTTAAATATT-
1 ATATGTAATAATTAAATTTTT-AAT-TTA
*
11037239 ACATGTAATAATTAAATTTTTAA
1 ATATGTAATAATTAAATTTTTAA
11037262 GATGATGTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
27 30 0.45
28 35 0.52
29 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (27 bp):
ATATGTAATAATTAAATTTTTAATTTA
Found at i:11037225 original size:55 final size:56
Alignment explanation
Indices: 11037156--11037285 Score: 165
Period size: 55 Copynumber: 2.4 Consensus size: 56
11037146 TTTATTATTG
* * **
11037156 ATATGTAATAATTATTATTTTT-AATATAATATGTAATAATTAAAATTTTAATTTA
1 ATATATAATAATTATTATTTTTAAATATAACATGTAATAATTAAAATTTTAAGATA
* * *
11037211 ATATATAATAATTA-TATTTTTAAATATTACATGTAATAATTAAATTTTTAAGATG
1 ATATATAATAATTATTATTTTTAAATATAACATGTAATAATTAAAATTTTAAGATA
* *
11037266 ATGTATAATAATTATAATTT
1 ATATATAATAATTATTATTT
11037286 CAATGTAATT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
54 7 0.11
55 53 0.83
56 4 0.06
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (56 bp):
ATATATAATAATTATTATTTTTAAATATAACATGTAATAATTAAAATTTTAAGATA
Found at i:11037259 original size:28 final size:27
Alignment explanation
Indices: 11037144--11037285 Score: 133
Period size: 27 Copynumber: 5.1 Consensus size: 27
11037134 TATAATAATG
* *
11037144 TTTTTATTATTGATATGTAATAATTATTA
1 TTTTTAATATT-ATATGTAATAATTA-AA
*
11037173 TTTTTAATATAATATGTAATAATTAAA
1 TTTTTAATATTATATGTAATAATTAAA
* * *
11037200 ATTTTAAT-TTAATATATAATAATTATA
1 TTTTTAATATT-ATATGTAATAATTAAA
*
11037227 TTTTTAAATATTACATGTAATAATTAAA
1 TTTTT-AATATTATATGTAATAATTAAA
* * * *
11037255 TTTTTAAGATGATGTATAATAATTATAA
1 TTTTTAATATTATATGTAATAATTA-AA
11037283 TTT
1 TTT
11037286 CAATGTAATT
Statistics
Matches: 93, Mismatches: 16, Indels: 9
0.79 0.14 0.08
Matches are distributed among these distances:
26 1 0.01
27 41 0.44
28 40 0.43
29 11 0.12
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (27 bp):
TTTTTAATATTATATGTAATAATTAAA
Found at i:11039170 original size:15 final size:15
Alignment explanation
Indices: 11039150--11039188 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
11039140 GTTTAATATA
11039150 TTAATTTTAAAATTT
1 TTAATTTTAAAATTT
* *
11039165 TTAATTTTTATATTTT
1 TTAA-TTTTAAAATTT
11039181 TTAATTTT
1 TTAATTTT
11039189 GATTTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTAATTTTAAAATTT
Found at i:11039196 original size:16 final size:16
Alignment explanation
Indices: 11039162--11039196 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
11039152 AATTTTAAAA
*
11039162 TTTTTAATTTTTATAT
1 TTTTTAATTTTGATAT
11039178 TTTTTAATTTTGAT-T
1 TTTTTAATTTTGATAT
11039193 TTTT
1 TTTT
11039197 CAATAAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTTAATTTTGATAT
Found at i:11040255 original size:18 final size:19
Alignment explanation
Indices: 11040234--11040271 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
11040224 TAATTTTTTT
11040234 AAAAAAT-AAAA-TTTAAA
1 AAAAAATAAAAATTTTAAA
11040251 AAAAAATAAAAATTTATAAA
1 AAAAAATAAAAATTT-TAAA
11040271 A
1 A
11040272 TTGTAAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 4 0.22
19 2 0.11
20 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAAATAAAAATTTTAAA
Found at i:11040256 original size:17 final size:19
Alignment explanation
Indices: 11040234--11040271 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
11040224 TAATTTTTTT
11040234 AAAAAAT-AAAATTTA-AA
1 AAAAAATAAAAATTTATAA
11040251 AAAAAATAAAAATTTATAA
1 AAAAAATAAAAATTTATAA
11040270 AA
1 AA
11040272 TTGTAAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 8 0.42
19 4 0.21
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAAATAAAAATTTATAA
Found at i:11040493 original size:30 final size:30
Alignment explanation
Indices: 11040459--11040517 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
11040449 CTATCAAAAA
*
11040459 TTTTAATTATAATAATTAAATATTAAATAT
1 TTTTAATTATAATAATTAAAAATTAAATAT
* * *
11040489 TTTTATTTTTTATAATTAAAAATTAAATA
1 TTTTAATTATAATAATTAAAAATTAAATA
11040518 AGAGATATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TTTTAATTATAATAATTAAAAATTAAATAT
Found at i:11040685 original size:27 final size:27
Alignment explanation
Indices: 11040655--11040793 Score: 143
Period size: 27 Copynumber: 5.1 Consensus size: 27
11040645 TATAATAATG
* * * *
11040655 TTTTTATTATGATATGTAATAATTTAT
1 TTTTTAATATAATATGTAATAATTAAA
11040682 TTTTTAATATAATATGTAATAATTAAA
1 TTTTTAATATAATATGTAATAATTAAA
* * * *
11040709 ATTTTAATTTAATATATAATAATTATA
1 TTTTTAATATAATATGTAATAATTAAA
* *
11040736 TTTTTAATATTACATGTAATAATTAAA
1 TTTTTAATATAATATGTAATAATTAAA
* * * *
11040763 TTTTTAAGATGATGTATAATAATTATAA
1 TTTTTAATATAATATGTAATAATTA-AA
11040791 TTT
1 TTT
11040794 CAATGTAATT
Statistics
Matches: 92, Mismatches: 19, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
27 87 0.95
28 5 0.05
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (27 bp):
TTTTTAATATAATATGTAATAATTAAA
Found at i:11040730 original size:54 final size:54
Alignment explanation
Indices: 11040666--11040789 Score: 160
Period size: 54 Copynumber: 2.3 Consensus size: 54
11040656 TTTTATTATG
* *
11040666 ATATGTAATAATT-TATTTTTTAATATAATATGTAATAATTAAAATTTTAATTTA
1 ATATATAATAATTATA-TTTTTAATATAACATGTAATAATTAAAATTTTAATTTA
* * ** *
11040720 ATATATAATAATTATATTTTTAATATTACATGTAATAATTAAATTTTTAAGATG
1 ATATATAATAATTATATTTTTAATATAACATGTAATAATTAAAATTTTAATTTA
*
11040774 ATGTATAATAATTATA
1 ATATATAATAATTATA
11040790 ATTTCAATGT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 59 0.97
55 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (54 bp):
ATATATAATAATTATATTTTTAATATAACATGTAATAATTAAAATTTTAATTTA
Found at i:11040754 original size:81 final size:80
Alignment explanation
Indices: 11040642--11040802 Score: 187
Period size: 81 Copynumber: 2.0 Consensus size: 80
11040632 TTATGATGTG
* * * * * * *
11040642 ATATATAATAATGTTTTTATTATGATATGTAATAATTTATTTTTTAATATAATATGTAATAATTA
1 ATATATAATAATATTTTTAATATGACATGTAATAATTAAATTTTTAAGATAATATATAATAATTA
* *
11040707 AAATTTTAATTTAAT
66 AAATTTCAATGTAAT
* * * *
11040722 ATATAATAATTATATTTTTAATATTACATGTAATAATTAAATTTTTAAGATGATGTATAATAATT
1 ATAT-ATAATAATATTTTTAATATGACATGTAATAATTAAATTTTTAAGATAATATATAATAATT
*
11040787 ATAATTTCAATGTAAT
65 AAAATTTCAATGTAAT
11040803 TTTTTTTTGT
Statistics
Matches: 66, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
80 4 0.06
81 62 0.94
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (80 bp):
ATATATAATAATATTTTTAATATGACATGTAATAATTAAATTTTTAAGATAATATATAATAATTA
AAATTTCAATGTAAT
Found at i:11041788 original size:13 final size:14
Alignment explanation
Indices: 11041770--11041803 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
11041760 TATATTTTTT
11041770 AATAATTTTTA-AA
1 AATAATTTTTATAA
*
11041783 AATAATTTTTATTA
1 AATAATTTTTATAA
11041797 AATAATT
1 AATAATT
11041804 AATATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATAATTTTTATAA
Found at i:11041839 original size:20 final size:21
Alignment explanation
Indices: 11041781--11041839 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
11041771 ATAATTTTTA
11041781 AAAATAATTTTTATTAAATAATT
1 AAAATAA-TTTTA-TAAATAATT
* * *
11041804 AATATAA-TTAAAAAATAA-T
1 AAAATAATTTTATAAATAATT
11041823 AAAATAATTTTATAAAT
1 AAAATAATTTTATAAAT
11041840 TTCATTTAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
19 7 0.24
20 13 0.45
21 3 0.10
23 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAATAATTTTATAAATAATT
Found at i:11041869 original size:19 final size:20
Alignment explanation
Indices: 11041847--11041885 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
11041837 AATTTCATTT
11041847 AATTTTACTTAATTT-TTTA
1 AATTTTACTTAATTTGTTTA
**
11041866 AATTTTTTTTAATTTGTTTA
1 AATTTTACTTAATTTGTTTA
11041886 TTCATATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
AATTTTACTTAATTTGTTTA
Found at i:11044383 original size:17 final size:16
Alignment explanation
Indices: 11044361--11044429 Score: 66
Period size: 17 Copynumber: 4.0 Consensus size: 16
11044351 ATCATTATCC
11044361 TTTTTTCAAATTTTTCT
1 TTTTTTCAAATTTTT-T
*
11044378 TTTTTTTAAATAATTTTT
1 TTTTTTCAAAT--TTTTT
*
11044396 TTGTTTTCAATTTTTTT
1 TT-TTTTCAAATTTTTT
*
11044413 TCTTTTTCTAATTTTTT
1 T-TTTTTCAAATTTTTT
11044430 CTGAATTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
17 28 0.65
18 4 0.09
19 11 0.26
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.74
Consensus pattern (16 bp):
TTTTTTCAAATTTTTT
Found at i:11044384 original size:18 final size:17
Alignment explanation
Indices: 11044361--11044429 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 17
11044351 ATCATTATCC
11044361 TTTTTTCAAATTTTTCTT
1 TTTTTTCAAATTTTT-TT
11044379 TTTTTT-AAATAATTTTTT
1 TTTTTTCAAAT--TTTTTT
*
11044397 TGTTTTC-AATTTTTTT
1 TTTTTTCAAATTTTTTT
*
11044413 TCTTTTTCTAATTTTTT
1 T-TTTTTCAAATTTTTT
11044430 CTGAATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
16 7 0.16
17 9 0.20
18 24 0.55
19 4 0.09
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.74
Consensus pattern (17 bp):
TTTTTTCAAATTTTTTT
Found at i:11044686 original size:44 final size:43
Alignment explanation
Indices: 11044555--11044676 Score: 149
Period size: 43 Copynumber: 2.8 Consensus size: 43
11044545 ATACTTTTTT
* *
11044555 AAATG-AAAAGCTCATCATCTGGAATGAAGCTATGTCACTTTAA
1 AAATGAAAAAACTCCTCATCTGGAATGAAGCTATGTCACTTT-A
* * * *
11044598 AAATGAAAAAACTCCTCATCTAGAATGAGGTTACGTCACTTTA
1 AAATGAAAAAACTCCTCATCTGGAATGAAGCTATGTCACTTTA
*
11044641 AAAT-AAATAAACTCCTCATTTGGAATGAAGCTATGT
1 AAATGAAA-AAACTCCTCATCTGGAATGAAGCTATGT
11044677 GAAATTTAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 3 0.05
43 33 0.50
44 30 0.45
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (43 bp):
AAATGAAAAAACTCCTCATCTGGAATGAAGCTATGTCACTTTA
Found at i:11044852 original size:93 final size:93
Alignment explanation
Indices: 11044752--11045038 Score: 259
Period size: 92 Copynumber: 3.1 Consensus size: 93
11044742 TGGCATCCAT
* *
11044752 AGGATTTGAAAATGATTACTCAAAGGTTTTAAAAATGGTTACTTCG-AGGTTTTGAAAAATAGTA
1 AGGATTTGAAAATGATTACTCAGAGGTTTTAAAAATGGTTACTCCGAAGGTTTTGAAAAATAGTA
* * * *
11044816 ACCTAGAAGATGTTGAAATATTTACTTAA
66 ACCTAGAAGAT-TTAAAAGATGTACTCAA
* * * * * *
11044845 AGGATTTGAAAATGGTTAC-CTGGAGGTTTTGAAAATGGTT-GTCCGAAGGTTTTGAAATATGGT
1 AGGATTTGAAAATGATTACTC-AGAGGTTTTAAAAATGGTTACTCCGAAGGTTTTGAAAAATAGT
* * *
11044908 TACCTTGAGGATTTAAAAGATGTACTCAA
65 AACCTAGAAGATTTAAAAGATGTACTCAA
* * * * *
11044937 AGGATTTGAAATTGATTACTTAGAGGTTTTAAAAATAGTTACAT--GAAGGATTTGAAAGAT-GT
1 AGGATTTGAAAATGATTACTCAGAGGTTTTAAAAATGGTTAC-TCCGAAGGTTTTGAAAAATAGT
*
11044999 -ACCT-GAAAGATATAAAA-ATGATTACTCAA
65 AACCTAG-AAGATTTAAAAGATG--TACTCAA
*
11045028 AGCATTTGAAA
1 AGGATTTGAAA
11045039 TGGATTTTGA
Statistics
Matches: 159, Mismatches: 27, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
89 4 0.03
90 13 0.08
91 19 0.12
92 64 0.40
93 58 0.36
94 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (93 bp):
AGGATTTGAAAATGATTACTCAGAGGTTTTAAAAATGGTTACTCCGAAGGTTTTGAAAAATAGTA
ACCTAGAAGATTTAAAAGATGTACTCAA
Found at i:11044857 original size:23 final size:23
Alignment explanation
Indices: 11044752--11044993 Score: 77
Period size: 23 Copynumber: 10.5 Consensus size: 23
11044742 TGGCATCCAT
*
11044752 AGGATTTGAAAAT-GATTACTCAA
1 AGGATTTGAAAATAG-TTACTTAA
* * * **
11044775 AGGTTTTAAAAATGGTTACTTCG
1 AGGATTTGAAAATAGTTACTTAA
* * *
11044798 AGGTTTTGAAAAATAGTAACCTAGA
1 AGGATTTG-AAAATAGTTACTTA-A
*
11044823 A-GATGTTG-AAATATTTACTTAA
1 AGGAT-TTGAAAATAGTTACTTAA
* * **
11044845 AGGATTTGAAAATGGTTACCTGG
1 AGGATTTGAAAATAGTTACTTAA
* * * **
11044868 AGGTTTTGAAAATGGTT-GTCCGA
1 AGGATTTGAAAATAGTTACT-TAA
* * *
11044891 AGGTTTTGAAATATGGTTACCTT-G
1 AGGATTTGAAA-ATAGTTA-CTTAA
* *
11044915 AGGATTT-AAAAGA-TGTACTCAA
1 AGGATTTGAAAATAGT-TACTTAA
* *
11044937 AGGATTTG-AAATTGATTACTTAG
1 AGGATTTGAAAATAG-TTACTTAA
* * * *
11044960 AGGTTTTAAAAATAGTTACATGA
1 AGGATTTGAAAATAGTTACTTAA
11044983 AGGATTTGAAA
1 AGGATTTGAAA
11044994 GATGTACCTG
Statistics
Matches: 158, Mismatches: 45, Indels: 32
0.67 0.19 0.14
Matches are distributed among these distances:
21 3 0.02
22 18 0.11
23 101 0.64
24 31 0.20
25 4 0.03
26 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (23 bp):
AGGATTTGAAAATAGTTACTTAA
Found at i:11044945 original size:46 final size:47
Alignment explanation
Indices: 11044838--11044970 Score: 134
Period size: 46 Copynumber: 2.9 Consensus size: 47
11044828 TTGAAATATT
* * *
11044838 TACTTAAAGGATTTGAAA-ATGGTTACCTGGAGGTTTTGAAAATGGTTG
1 TACTCAAAGGATTTGAAATATGGTTACCTTGAGGTTTT-AAAA-GGATG
* * *
11044886 T-C-CGAAGGTTTTGAAATATGGTTACCTTGAGGATTTAAAA-GATG
1 TACTCAAAGGATTTGAAATATGGTTACCTTGAGGTTTTAAAAGGATG
*
11044930 TACTCAAAGGATTTGAAAT-TGATTA-CTTAGAGGTTTTAAAA
1 TACTCAAAGGATTTGAAATATGGTTACCTT-GAGGTTTTAAAA
11044971 ATAGTTACAT
Statistics
Matches: 71, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
44 7 0.10
45 17 0.24
46 28 0.39
47 18 0.25
48 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (47 bp):
TACTCAAAGGATTTGAAATATGGTTACCTTGAGGTTTTAAAAGGATG
Found at i:11054861 original size:8 final size:8
Alignment explanation
Indices: 11054827--11054870 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
11054817 CTATCATTTT
11054827 ATTTATTA
1 ATTTATTA
* *
11054835 AATTACTA
1 ATTTATTA
11054843 ATTTAATTA
1 ATTT-ATTA
11054852 ATTTATTA
1 ATTTATTA
*
11054860 ATTGATTA
1 ATTTATTA
11054868 ATT
1 ATT
11054871 ACTAATGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
8 23 0.77
9 7 0.23
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (8 bp):
ATTTATTA
Found at i:11054861 original size:17 final size:16
Alignment explanation
Indices: 11054827--11054876 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
11054817 CTATCATTTT
11054827 ATTTATTAAATTACTA
1 ATTTATTAAATTACTA
* *
11054843 ATTTAATTAATTTATTA
1 ATTT-ATTAAATTACTA
*
11054860 ATTGATT-AATTACTA
1 ATTTATTAAATTACTA
11054875 AT
1 AT
11054877 GCATTAGTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 13 0.46
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (16 bp):
ATTTATTAAATTACTA
Found at i:11055420 original size:17 final size:17
Alignment explanation
Indices: 11055377--11055429 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 17
11055367 TAATTTATTG
*
11055377 CTTAATTACTTATAATATA
1 CTTAATTACTTA-ATTA-A
11055396 -TTACATTACTTAATTAA
1 CTTA-ATTACTTAATTAA
11055413 CTTAATTACTTAATTAA
1 CTTAATTACTTAATTAA
11055430 GTCATGAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 14 0.45
18 9 0.29
19 8 0.26
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (17 bp):
CTTAATTACTTAATTAA
Found at i:11055423 original size:8 final size:8
Alignment explanation
Indices: 11055377--11055428 Score: 52
Period size: 8 Copynumber: 6.0 Consensus size: 8
11055367 TAATTTATTG
11055377 CTTAATTA
1 CTTAATTA
11055385 CTTATAATATA
1 C-T-TAAT-TA
11055396 -TTACATTA
1 CTTA-ATTA
11055404 CTTAATTAA
1 CTTAATT-A
11055413 CTTAATTA
1 CTTAATTA
11055421 CTTAATTA
1 CTTAATTA
11055429 AGTCATGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
8 17 0.45
9 15 0.39
10 4 0.11
11 2 0.05
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (8 bp):
CTTAATTA
Found at i:11072477 original size:23 final size:23
Alignment explanation
Indices: 11072442--11072485 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
11072432 AAAATAAAAA
* * *
11072442 TTTTTCTTTTTTCTTTTTTTTTC
1 TTTTTCATCTTTCTATTTTTTTC
11072465 TTTTTCATCTTTCTATTTTTT
1 TTTTTCATCTTTCTATTTTTT
11072486 ACACTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTTCATCTTTCTATTTTTTTC
Found at i:11072528 original size:12 final size:11
Alignment explanation
Indices: 11072508--11072571 Score: 57
Period size: 11 Copynumber: 6.1 Consensus size: 11
11072498 CATTCTATTC
11072508 TCTT-TTTTTT
1 TCTTCTTTTTT
11072518 T-TTACTTTTTT
1 TCTT-CTTTTTT
11072529 TCTTC-TTTTT
1 TCTTCTTTTTT
11072539 TC--CTTTTTT
1 TCTTCTTTTTT
* *
11072548 ACCTTCTATTTT
1 -TCTTCTTTTTT
11072560 TCTTCTTTTTT
1 TCTTCTTTTTT
11072571 T
1 T
11072572 TCCTCTCATA
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
8 1 0.02
9 7 0.16
10 9 0.21
11 18 0.42
12 8 0.19
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (11 bp):
TCTTCTTTTTT
Found at i:11072546 original size:31 final size:31
Alignment explanation
Indices: 11072442--11072570 Score: 84
Period size: 31 Copynumber: 3.9 Consensus size: 31
11072432 AAAATAAAAA
*
11072442 TTTTTCTTTTTTCTTTTTTT-TTC-TTTTTCATC
1 TTTTT-TTTTTACTTTTTTTCTTCTTTTTTC--C
* * *
11072474 TTTCTATTTTTTACACTTTTTTGTCATTCTATTCTCT
1 TTT-T-TTTTTT--ACTTTTTT-TC-TTCTTTTTTCC
11072511 TTTTTTTTTTACTTTTTTTCTTCTTTTTTCC
1 TTTTTTTTTTACTTTTTTTCTTCTTTTTTCC
** *
11072542 TTTTTTACCTT-CTATTTTTCTTCTTTTTT
1 TTTTTT-TTTTACTTTTTTTCTTCTTTTTT
11072571 TTCCTCTCAT
Statistics
Matches: 78, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
31 31 0.40
32 7 0.09
33 14 0.18
34 1 0.01
35 13 0.17
36 2 0.03
37 3 0.04
38 3 0.04
39 4 0.05
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.75
Consensus pattern (31 bp):
TTTTTTTTTTACTTTTTTTCTTCTTTTTTCC
Found at i:11073096 original size:25 final size:27
Alignment explanation
Indices: 11073041--11073107 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 27
11073031 GCTTGACTCC
* *
11073041 TTCAATTTATTCTATTTTCTTTTTTTTCT
1 TTCAATTT-TTTTA-TTTCTTTTCTTTCT
11073070 TTC-ATTTTTTTATTTC-TTTCTTTCT
1 TTCAATTTTTTTATTTCTTTTCTTTCT
11073095 TTCAATTTTTTTA
1 TTCAATTTTTTTA
11073108 ATCTTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 11 0.31
26 13 0.37
27 4 0.11
28 4 0.11
29 3 0.09
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (27 bp):
TTCAATTTTTTTATTTCTTTTCTTTCT
Found at i:11073112 original size:25 final size:25
Alignment explanation
Indices: 11073065--11073113 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
11073055 TTTTCTTTTT
*
11073065 TTTCTTTCATTTTTTTATTTCTTTC
1 TTTCTTTCATTTTTTTATATCTTTC
11073090 TTTCTTTCAATTTTTTTA-ATCTTT
1 TTTCTTTC-ATTTTTTTATATCTTT
11073114 TAAACTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTCTTTCATTTTTTTATATCTTTC
Found at i:11074936 original size:81 final size:81
Alignment explanation
Indices: 11074797--11075056 Score: 332
Period size: 81 Copynumber: 3.2 Consensus size: 81
11074787 AATTTGATTT
* * * *
11074797 TTATCTCTAAATTAATATAA-TTA-TTAGAGATAAATTGGATGACCAATAATTAAATTTTGATT-
1 TTATCTCTAAATTATTTTAATTTATTTAGAGATAAATTGGATGACCAATAACTAATTTTTGATTA
11074859 GATCAAAAATATAAATA
66 G-TCAAAAATATAAATA
* * *
11074876 TTATCTCTAAATTATTTTAATTTATTTATAGATAAACTGGGTGACCAATAACTAATTTTTGATTA
1 TTATCTCTAAATTATTTTAATTTATTTAGAGATAAATTGGATGACCAATAACTAATTTTTGATTA
*
11074941 GTTAAAAATATAAATA
66 GTCAAAAATATAAATA
* * * *
11074957 TTATTTTTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAACTAAATTTTTTATT
1 TTATCTCTAAATTATTTTAATTTATTTAGAGATAAATTGGATGACCAATAACT-AATTTTTGATT
* *
11075022 AGTC--CAATTTAAATA
65 AGTCAAAAATATAAATA
*
11075037 TTATCTCTAAATTATCTTAA
1 TTATCTCTAAATTATTTTAA
11075057 GAGATGAATA
Statistics
Matches: 155, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
79 18 0.12
80 28 0.18
81 95 0.61
82 14 0.09
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.43
Consensus pattern (81 bp):
TTATCTCTAAATTATTTTAATTTATTTAGAGATAAATTGGATGACCAATAACTAATTTTTGATTA
GTCAAAAATATAAATA
Found at i:11079168 original size:35 final size:35
Alignment explanation
Indices: 11079121--11079283 Score: 148
Period size: 35 Copynumber: 4.6 Consensus size: 35
11079111 ATTAAGTTAT
11079121 ACTTAATTAATTAAATTGTTTAATTAAATCATTAG
1 ACTTAATTAATTAAATTGTTTAATTAAATCATTAG
* * ** *
11079156 TCTTAATTAATTAAATTATTTAATTAAGCCATTGG
1 ACTTAATTAATTAAATTGTTTAATTAAATCATTAG
* * *
11079191 ACCTAATTGATTAAAATTGTTTAATTAAGTCATTA-
1 ACTTAATTAATT-AAATTGTTTAATTAAATCATTAG
* * * * ** *
11079226 CCCTAATTGATTAAAATTATTTAATTAAATTGTTGG
1 ACTTAATTAATT-AAATTGTTTAATTAAATCATTAG
* *
11079262 GCTTAATGAATTAAATTGTTTA
1 ACTTAATTAATTAAATTGTTTA
11079284 GTCAAGTTAT
Statistics
Matches: 104, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
35 77 0.74
36 27 0.26
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (35 bp):
ACTTAATTAATTAAATTGTTTAATTAAATCATTAG
Found at i:11079275 original size:71 final size:69
Alignment explanation
Indices: 11079094--11079283 Score: 201
Period size: 71 Copynumber: 2.7 Consensus size: 69
11079084 TCTCAAGCAC
** * *
11079094 TTGATTAAAATTATTTAATT-AAGTTATACTTAATTAATTAAATTGTTTAATTAAATCATTAGTC
1 TTGATTAAAATTATTTAATTAAAGTTGGACTTAATGAATTAAATTGTTTAATTAAATCATTAGCC
*
11079158 TTAA
66 CTAA
* * *
11079162 TTAATT-AAATTATTTAATT-AAGCCATTGGACCTAATTG-ATTAAAATTGTTTAATTAAGTCAT
1 TTGATTAAAATTATTTAATTAAAG---TTGGACTTAA-TGAATT-AAATTGTTTAATTAAATCAT
11079224 TA-CCCTAA
61 TAGCCCTAA
*
11079232 TTGATTAAAATTATTTAATTAAATTGTTGGGCTTAATGAATTAAATTGTTTA
1 TTGATTAAAATTATTTAATTAAA--GTTGGACTTAATGAATTAAATTGTTTA
11079284 GTCAAGTTAT
Statistics
Matches: 101, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
67 16 0.16
68 5 0.05
70 31 0.31
71 46 0.46
72 2 0.02
74 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (69 bp):
TTGATTAAAATTATTTAATTAAAGTTGGACTTAATGAATTAAATTGTTTAATTAAATCATTAGCC
CTAA
Found at i:11079276 original size:106 final size:103
Alignment explanation
Indices: 11079094--11079311 Score: 256
Period size: 106 Copynumber: 2.1 Consensus size: 103
11079084 TCTCAAGCAC
* * * *
11079094 TTGATTAAAATTATTTAATTAAGTTATACTTAATTAATTAAATTGTTTAATTAAATCATTAGTCT
1 TTGATTAAAATTATTTAATTAAGTCATACCTAATTAATTAAATTATTTAATTAAATCATTAGGCT
* *
11079159 TAATTAATTAAATTATTTAATTAAGCCATTGGACCTAA
66 TAATGAATTAAATTATTTAATCAAGCCATTGGACCTAA
* * ** *
11079197 TTGATTAAAATTGTTTAATTAAGTCATTACCCTAATTGATTAAAATTATTTAATTAAATTGTTGG
1 TTGATTAAAATTATTTAATTAAGTCA-TA-CCTAATTAATT-AAATTATTTAATTAAATCATTAG
* * ** *
11079262 GCTTAATGAATTAAATTGTTTAGTCAAGTTATTGGGCCTAA
63 GCTTAATGAATTAAATTATTTAATCAAGCCATTGGACCTAA
*
11079303 TTAATTAAA
1 TTGATTAAA
11079312 TTAAGCAATT
Statistics
Matches: 95, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
103 24 0.25
104 2 0.02
105 9 0.09
106 60 0.63
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (103 bp):
TTGATTAAAATTATTTAATTAAGTCATACCTAATTAATTAAATTATTTAATTAAATCATTAGGCT
TAATGAATTAAATTATTTAATCAAGCCATTGGACCTAA
Found at i:11092473 original size:14 final size:15
Alignment explanation
Indices: 11092454--11092483 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
11092444 AGAAAGAAGG
11092454 GAAGAAAAA-AAAAA
1 GAAGAAAAAGAAAAA
11092468 GAAGAAAAAGAAAAA
1 GAAGAAAAAGAAAAA
11092483 G
1 G
11092484 GAAAGGGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
GAAGAAAAAGAAAAA
Found at i:11097541 original size:20 final size:20
Alignment explanation
Indices: 11097504--11097542 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11097494 AAAAAAAAGA
*
11097504 TATATAGTAAATAGTTCTTG
1 TATATAGTAAATAATTCTTG
* *
11097524 TATATATTAATTAATTCTT
1 TATATAGTAAATAATTCTT
11097543 CCTTAATAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (20 bp):
TATATAGTAAATAATTCTTG
Found at i:11107805 original size:13 final size:14
Alignment explanation
Indices: 11107771--11107806 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
11107761 CAAAATTTTT
11107771 AAAATTTTTTTAAC
1 AAAATTTTTTTAAC
11107785 AAATATTTTTTTAA-
1 AAA-ATTTTTTTAAC
11107799 AAAATTTT
1 AAAATTTT
11107807 AAAATTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.24
14 6 0.29
15 10 0.48
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
AAAATTTTTTTAAC
Found at i:11107832 original size:37 final size:36
Alignment explanation
Indices: 11107762--11107834 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
11107752 TGGGTTCTAC
* *
11107762 AAAATTTTTAAAATTTTTTTAACAAATATTTTTTTA
1 AAAAATTTTAAAATTTTTTTAACAAATAATTTTTTA
*
11107798 AAAAATTTTAAAATTTTACTTTTAC-AATAATTTTTTA
1 AAAAATTTTAAAATTTT--TTTAACAAATAATTTTTTA
11107835 TTTGATGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 16 0.50
37 11 0.34
38 5 0.16
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (36 bp):
AAAAATTTTAAAATTTTTTTAACAAATAATTTTTTA
Found at i:11111141 original size:17 final size:18
Alignment explanation
Indices: 11111120--11111166 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
11111110 TATTTGTATA
11111120 AATATTATATATATACAT
1 AATATTATATATATACAT
*
11111138 -ATATT-TAATTTATACAT
1 AATATTAT-ATATATACAT
11111155 AATATTACTATA
1 AATATTA-TATA
11111167 AACTTATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
16 1 0.04
17 14 0.61
18 5 0.22
19 2 0.09
20 1 0.04
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (18 bp):
AATATTATATATATACAT
Found at i:11111512 original size:17 final size:18
Alignment explanation
Indices: 11111506--11111539 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11111496 AATTTTATTA
11111506 TTATTAACAATTATTTAT
1 TTATTAACAATTATTTAT
*
11111524 TTATTAATAA-TATTTA
1 TTATTAACAATTATTTA
11111540 AAATATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATTAACAATTATTTAT
Found at i:11114127 original size:33 final size:34
Alignment explanation
Indices: 11114059--11114128 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
11114049 ATAAATAAAG
*
11114059 TTATCCCATAGTGGGCTTTATTCATATGGTATTC
1 TTATCCCACAGTGGGCTTTATTCATATGGTATTC
11114093 TTATCCCACAGTGGGCTTTA-TCA-AGTGGTATTC
1 TTATCCCACAGTGGGCTTTATTCATA-TGGTATTC
11114126 TTA
1 TTA
11114129 CCTCCACAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 1 0.03
33 14 0.41
34 19 0.56
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (34 bp):
TTATCCCACAGTGGGCTTTATTCATATGGTATTC
Found at i:11114136 original size:34 final size:34
Alignment explanation
Indices: 11114063--11114136 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
11114053 ATAAAGTTAT
* *
11114063 CCCATAGTGGGCTTTATTCATATGGTATTCTTAT
1 CCCACAGTGGGCTTTATTCATATGGTATTCTTAC
11114097 CCCACAGTGGGCTTTA-TCA-AGTGGTATTCTTAC
1 CCCACAGTGGGCTTTATTCATA-TGGTATTCTTAC
11114130 CTCCACA
1 C-CCACA
11114137 ATGAGTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
32 1 0.03
33 15 0.42
34 20 0.56
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (34 bp):
CCCACAGTGGGCTTTATTCATATGGTATTCTTAC
Found at i:11118080 original size:11 final size:11
Alignment explanation
Indices: 11118064--11118089 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11118054 TAAACTTATT
11118064 TAAAAATTAAC
1 TAAAAATTAAC
11118075 TAAAAATTAAC
1 TAAAAATTAAC
11118086 TAAA
1 TAAA
11118090 TCCTAACCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAAATTAAC
Found at i:11124792 original size:18 final size:18
Alignment explanation
Indices: 11124771--11124812 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
11124761 ATTTAATTAT
11124771 TAATAATTAAAAAATTTA
1 TAATAATTAAAAAATTTA
* * *
11124789 TAATAAATAATAATTTTA
1 TAATAATTAAAAAATTTA
11124807 T-ATAAT
1 TAATAAT
11124813 ATATAAATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAATTAAAAAATTTA
Found at i:11125095 original size:14 final size:14
Alignment explanation
Indices: 11125041--11125096 Score: 62
Period size: 14 Copynumber: 4.0 Consensus size: 14
11125031 TACTTTTATT
11125041 TAAAT-ATAAAATA
1 TAAATAATAAAATA
11125054 TTAAAT-ATAAAATTA
1 -TAAATAATAAAA-TA
*
11125069 TAATTAATAAAATA
1 TAAATAATAAAATA
*
11125083 TAAATAATTAAATA
1 TAAATAATAAAATA
11125097 GTAGATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 29 0.78
15 8 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAATAATAAAATA
Found at i:11125284 original size:11 final size:10
Alignment explanation
Indices: 11125268--11125334 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 10
11125258 TTATATGATT
11125268 AAAATTAATAA
1 AAAATT-ATAA
11125279 AAAATT-TAA
1 AAAATTATAA
*
11125288 AAAATTATCA
1 AAAATTATAA
**
11125298 AAAA-TATGT
1 AAAATTATAA
*
11125307 AATA-TATATA
1 AAAATTATA-A
*
11125317 AAAATTTTAA
1 AAAATTATAA
11125327 AAAATTAT
1 AAAATTAT
11125335 GGGAGCCAAG
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
9 18 0.41
10 17 0.39
11 9 0.20
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (10 bp):
AAAATTATAA
Found at i:11132201 original size:21 final size:21
Alignment explanation
Indices: 11132175--11132220 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
11132165 CATAGGCAGA
*
11132175 AAATGA-AGTGAACATTGCACC
1 AAATGAGA-TGAACATTGCAAC
*
11132196 AAATGAGATGAACGTTGCAAC
1 AAATGAGATGAACATTGCAAC
11132217 AAAT
1 AAAT
11132221 CAGGGAGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (21 bp):
AAATGAGATGAACATTGCAAC
Found at i:11156922 original size:10 final size:10
Alignment explanation
Indices: 11156892--11156932 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
11156882 TACATAATAC
11156892 TTAAA-AAAT
1 TTAAATAAAT
*
11156901 CTTAAAT-TAT
1 -TTAAATAAAT
11156911 TTAAATAAAT
1 TTAAATAAAT
11156921 TTAAATAAAT
1 TTAAATAAAT
11156931 TT
1 TT
11156933 TATTTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 6 0.22
10 21 0.78
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (10 bp):
TTAAATAAAT
Found at i:11156996 original size:18 final size:18
Alignment explanation
Indices: 11156969--11157004 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11156959 TAAATAAATT
11156969 TTAATAATTAATAATTAA
1 TTAATAATTAATAATTAA
* *
11156987 TTAATTATTATTAATTAA
1 TTAATAATTAATAATTAA
11157005 AATTTATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATAATTAATAATTAA
Found at i:11159726 original size:49 final size:49
Alignment explanation
Indices: 11159657--11159757 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
11159647 CAGAGAAAGT
* *
11159657 TTATCTATAACAATAGTACAATAATACTTTTATTCATATTCGTTTTATG
1 TTATCTATAACAATAATACAATAATACTTTTATTCATATTCATTTTATG
11159706 TTATCTATAACAATAATACAATAATACTTTTATTCATATTCATTTTATG
1 TTATCTATAACAATAATACAATAATACTTTTATTCATATTCATTTTATG
11159755 TTA
1 TTA
11159758 CTTAAACTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.48
Consensus pattern (49 bp):
TTATCTATAACAATAATACAATAATACTTTTATTCATATTCATTTTATG
Found at i:11164499 original size:21 final size:21
Alignment explanation
Indices: 11164470--11164509 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11164460 GAATGGAAAC
*
11164470 AATTTTTAATATTATATAAAT
1 AATTATTAATATTATATAAAT
11164491 AATTATTAATATTATATAA
1 AATTATTAATATTATATAA
11164510 TACGTGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTATTAATATTATATAAAT
Found at i:11173354 original size:2 final size:2
Alignment explanation
Indices: 11173347--11173376 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11173337 AGTTGTATAA
11173347 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
11173377 AAGTATAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:11174255 original size:18 final size:18
Alignment explanation
Indices: 11174224--11174260 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11174214 ATGACGTGGC
* *
11174224 ATTAATATGTTAGATTAT
1 ATTAACATGATAGATTAT
11174242 ATTAACATGATAGATTAT
1 ATTAACATGATAGATTAT
11174260 A
1 A
11174261 CTAATATGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (18 bp):
ATTAACATGATAGATTAT
Found at i:11176089 original size:30 final size:30
Alignment explanation
Indices: 11176049--11176106 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
11176039 TATATTAATC
11176049 AAGTTATTATATTTTTATTCTGAGTCAAGT
1 AAGTTATTATATTTTTATTCTGAGTCAAGT
* *
11176079 AAGTTTTTATATTTTTATTTTGAGTCAA
1 AAGTTATTATATTTTTATTCTGAGTCAA
11176107 ATTATTACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.53
Consensus pattern (30 bp):
AAGTTATTATATTTTTATTCTGAGTCAAGT
Found at i:11179665 original size:16 final size:17
Alignment explanation
Indices: 11179637--11179680 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
11179627 TGATATTTCT
11179637 AAAA-TAAATAAATTAA
1 AAAATTAAATAAATTAA
11179653 AAAATTAAA-AAATTAA
1 AAAATTAAATAAATTAA
11179669 AAATATTAAATA
1 AAA-ATTAAATA
11179681 TTTATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 14 0.56
17 10 0.40
18 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATTAAATAAATTAA
Found at i:11179670 original size:7 final size:8
Alignment explanation
Indices: 11179637--11179678 Score: 59
Period size: 8 Copynumber: 5.1 Consensus size: 8
11179627 TGATATTTCT
11179637 AAAA-TAA
1 AAAATTAA
11179644 ATAAATTAA
1 A-AAATTAA
11179653 AAAATTAA
1 AAAATTAA
11179661 AAAATTAA
1 AAAATTAA
11179669 AAATATTAA
1 AAA-ATTAA
11179678 A
1 A
11179679 TATTTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 1 0.03
8 21 0.66
9 10 0.31
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAATTAA
Found at i:11179726 original size:12 final size:12
Alignment explanation
Indices: 11179711--11179743 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
11179701 TTTAAAAATA
11179711 ATATATAATAAT
1 ATATATAATAAT
*
11179723 ATATATATTAAT
1 ATATATAATAAT
11179735 ATATATAAT
1 ATATATAAT
11179744 TAATTTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATATAATAAT
Found at i:11183355 original size:2 final size:2
Alignment explanation
Indices: 11183350--11183375 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11183340 GTGTGTGCAA
11183350 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
11183376 GTATTTCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11190840 original size:218 final size:219
Alignment explanation
Indices: 11190448--11190890 Score: 667
Period size: 218 Copynumber: 2.0 Consensus size: 219
11190438 AAAAGAACAC
* * **
11190448 TTGCCTGTTTGGTATTTCACCAGGAAGTTCCATGAAACGCACAGCACGATCTAAGTAGCTGGCAA
1 TTGCATGTTTGGTATTTCACCAGGAAGTTCCATGAAACGCACAGCACGATCGAAGTAGCCAGCAA
*
11190513 AAACAGTCTAGCATGCAAAAAACTTTAAATTAGAAAAAAAAAAAGGTACCTTTCCACAATGTAAT
66 AAACAGTCTAGCATGCAAAAAACTTTAAATT---AAAAAAAAAAGGTACCTTTCCACAATATAAT
* * *
11190578 GCACCAATCTAGACAGATGGCTATGCAAATCATGAGAAGAGAACTTCAGAGTGAGAA-AAAATCA
128 GCACCAAGCTAGACAGAAGGCTATGCAAATCATGAGAAGAGAACTTCAAAGTGAGAACAAAATCA
*
11190642 GGAAAATAATAAAATTTATGCACACAG
193 GGAAAACAATAAAATTTATGCACACAG
* * *
11190669 TTGCATGTTTGGTATTTCACCAGGAAAGTTCCATGAAATGCACAGCATGATCGAAGTAGCCAGTA
1 TTGCATGTTTGGTATTTCACCAGG-AAGTTCCATGAAACGCACAGCACGATCGAAGTAGCCAGCA
*
11190734 AAAACAGTCTAGCATGCAAAAAA-TATTAAATT-AAAAAAAAAGGTACGTTTCCACAATATAATG
65 AAAACAGTCTAGCATGCAAAAAACT-TTAAATTAAAAAAAAAAGGTACCTTTCCACAATATAATG
* * * *
11190797 CACCAAGCTAGACAGAAGGCTATGCAAATCGTGGGAAGAGAACTTCAAAGTGAGAACAAATTTAG
129 CACCAAGCTAGACAGAAGGCTATGCAAATCATGAGAAGAGAACTTCAAAGTGAGAACAAAATCAG
11190862 GAAAACAATAAAATTTATGCACACAG
194 GAAAACAATAAAATTTATGCACACAG
11190888 TTG
1 TTG
11190891 GCACTTAGAT
Statistics
Matches: 202, Mismatches: 17, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
218 80 0.40
219 34 0.17
221 24 0.12
222 64 0.32
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.23
Consensus pattern (219 bp):
TTGCATGTTTGGTATTTCACCAGGAAGTTCCATGAAACGCACAGCACGATCGAAGTAGCCAGCAA
AAACAGTCTAGCATGCAAAAAACTTTAAATTAAAAAAAAAAGGTACCTTTCCACAATATAATGCA
CCAAGCTAGACAGAAGGCTATGCAAATCATGAGAAGAGAACTTCAAAGTGAGAACAAAATCAGGA
AAACAATAAAATTTATGCACACAG
Found at i:11191646 original size:60 final size:60
Alignment explanation
Indices: 11191553--11191672 Score: 179
Period size: 60 Copynumber: 2.0 Consensus size: 60
11191543 TAGTTCCATT
* * *
11191553 GCTTAAGATAGCTGTTTCCATCTGTACAAAGCCACAATGCCAATT-ATTACGAAGAAAGAA
1 GCTTAAGATAGCTATTCCCATCTGTACAAAGCCACAATGCC-ATTAATTAAGAAGAAAGAA
* *
11191613 GCTTAAGATAGCTATTCCCATCTGTACAAAGCCACACTGTCATTAATTAAGAAGAAAGAA
1 GCTTAAGATAGCTATTCCCATCTGTACAAAGCCACAATGCCATTAATTAAGAAGAAAGAA
11191673 CAGGTTAATG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 3 0.06
60 51 0.94
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (60 bp):
GCTTAAGATAGCTATTCCCATCTGTACAAAGCCACAATGCCATTAATTAAGAAGAAAGAA
Found at i:11198391 original size:13 final size:14
Alignment explanation
Indices: 11198373--11198411 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
11198363 TTATATTAAA
11198373 ATTAATATAATAT-
1 ATTAATATAATATG
*
11198386 ATTAATTTAATATG
1 ATTAATATAATATG
11198400 A-TAATATAATAT
1 ATTAATATAATAT
11198412 TTTTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 22 0.96
14 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (14 bp):
ATTAATATAATATG
Found at i:11198511 original size:25 final size:25
Alignment explanation
Indices: 11198465--11198513 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
11198455 AAGTGATATT
*
11198465 TTAATTAATAATAATTAATTAATTA
1 TTAATTAATAAAAATTAATTAATTA
*
11198490 TTAATTAA-AAAAAGTTATTTAATT
1 TTAATTAATAAAAA-TTAATTAATT
11198514 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TTAATTAATAAAAATTAATTAATTA
Found at i:11198535 original size:20 final size:19
Alignment explanation
Indices: 11198510--11198550 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
11198500 AAAGTTATTT
*
11198510 AATTTAAAATAAAATATAAA
1 AATTT-AAATAAAAAATAAA
*
11198530 AATTTAATTAAAAAATAAA
1 AATTTAAATAAAAAATAAA
11198549 AA
1 AA
11198551 AATTATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AATTTAAATAAAAAATAAA
Found at i:11201845 original size:29 final size:30
Alignment explanation
Indices: 11201803--11201864 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
11201793 CTCCTTAACG
11201803 GTGCTCCCCTAACC-TGAGAGCACCGTCAA
1 GTGCTCCCCTAACCATGAGAGCACCGTCAA
* **
11201832 GTGCT-CCCTAAACCATGGGAGCATTGTCAA
1 GTGCTCCCCT-AACCATGAGAGCACCGTCAA
11201862 GTG
1 GTG
11201865 TTCCTCAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 4 0.14
29 9 0.32
30 15 0.54
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (30 bp):
GTGCTCCCCTAACCATGAGAGCACCGTCAA
Found at i:11202453 original size:2 final size:2
Alignment explanation
Indices: 11202446--11202474 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11202436 TTGATACCCA
11202446 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11202475 AAGAACAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11204204 original size:22 final size:22
Alignment explanation
Indices: 11204176--11204221 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
11204166 TTGTCATACC
11204176 TGCGAATTGAAATGAGAGGAGA
1 TGCGAATTGAAATGAGAGGAGA
11204198 TGCGAATTGAAATGAGAGGAGA
1 TGCGAATTGAAATGAGAGGAGA
11204220 TG
1 TG
11204222 TTCTGACTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.37, T:0.20
Consensus pattern (22 bp):
TGCGAATTGAAATGAGAGGAGA
Found at i:11217771 original size:45 final size:46
Alignment explanation
Indices: 11217694--11217819 Score: 112
Period size: 45 Copynumber: 2.8 Consensus size: 46
11217684 TGTTATATGC
* * * * * * **
11217694 CATGATTAAGTTGTTACACATTAT-ATATAAAAATATGTGACATTT
1 CATGGTTAAGTTGTTACACGTCATGTTAAAAAAATATATGACACAT
* * * * * *
11217739 TATGGTTAGGTTGTTACATGTCATG-TACAAAAACATATTACACAT
1 CATGGTTAAGTTGTTACACGTCATGTTAAAAAAATATATGACACAT
11217784 CATGGTTAAGTTGTTACACGTCATGTTAAAAAAATA
1 CATGGTTAAGTTGTTACACGTCATGTTAAAAAAATA
11217820 CTGTTATTAC
Statistics
Matches: 62, Mismatches: 17, Indels: 3
0.76 0.21 0.04
Matches are distributed among these distances:
45 54 0.87
46 8 0.13
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (46 bp):
CATGGTTAAGTTGTTACACGTCATGTTAAAAAAATATATGACACAT
Found at i:11217838 original size:29 final size:27
Alignment explanation
Indices: 11217797--11217852 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
11217787 GGTTAAGTTG
11217797 TTACACGTCATGTTAAAAAAATACTGTTA
1 TTACACGTCATG-TAAAAAAATA-TGTTA
*
11217826 TTACACG-CTATGTACAAAAATATGTTA
1 TTACACGTC-ATGTAAAAAAATATGTTA
11217853 CACGCCATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 5 0.20
28 10 0.40
29 10 0.40
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (27 bp):
TTACACGTCATGTAAAAAAATATGTTA
Found at i:11217877 original size:26 final size:25
Alignment explanation
Indices: 11217793--11217881 Score: 74
Period size: 29 Copynumber: 3.4 Consensus size: 25
11217783 TCATGGTTAA
*
11217793 GTTGTTACACGTCATGTTAAAAAAATACT
1 GTTGTTACACGCCATGTT--AAAAA-A-T
* *
11217822 GTTATTACACGCTATG-TACAAAAAT
1 GTTGTTACACGCCATGTTA-AAAAAT
*
11217847 -ATGTTACACGCCATGATTAAAAAAT
1 GTTGTTACACGCCATG-TTAAAAAAT
11217872 GTTGTTACAC
1 GTTGTTACAC
11217882 TGTTAAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
24 12 0.24
25 7 0.14
26 12 0.24
27 4 0.08
28 1 0.02
29 13 0.27
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (25 bp):
GTTGTTACACGCCATGTTAAAAAAT
Found at i:11217932 original size:29 final size:29
Alignment explanation
Indices: 11217889--11217951 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
11217879 CACTGTTAAA
* * * *
11217889 AAAAAATATTGTTATTACATGTTATATTG
1 AAAAAATAATATTATTACATGTCATATTC
11217918 AAAAAATAATATTATTACATGTCATATTC
1 AAAAAATAATATTATTACATGTCATATTC
11217947 AAAAA
1 AAAAA
11217952 CATTTTGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (29 bp):
AAAAAATAATATTATTACATGTCATATTC
Found at i:11218553 original size:10 final size:10
Alignment explanation
Indices: 11218538--11218567 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
11218528 TTATTAAGTC
11218538 ATAATTAAAT
1 ATAATTAAAT
*
11218548 ATAATTAAAA
1 ATAATTAAAT
11218558 ATAATTAAAT
1 ATAATTAAAT
11218568 TTATTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATAATTAAAT
Found at i:11219005 original size:2 final size:2
Alignment explanation
Indices: 11219000--11219024 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11218990 TGGTCATGAT
11219000 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 T
11219025 TAATGATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11225110 original size:16 final size:16
Alignment explanation
Indices: 11225085--11225142 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
11225075 TGTAAAAATT
11225085 TATTAATTAATTTAAA
1 TATTAATTAATTTAAA
*
11225101 TATTATTTAA-TTAATA
1 TATTAATTAATTTAA-A
* *
11225117 AATT-ATTAATTTATA
1 TATTAATTAATTTAAA
11225132 TATTAATTAAT
1 TATTAATTAAT
11225143 AAAAAATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 12 0.35
16 22 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTAATTAATTTAAA
Found at i:11225125 original size:15 final size:15
Alignment explanation
Indices: 11225102--11225160 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
11225092 TAATTTAAAT
11225102 ATTATTTAATTAATAA
1 ATTA-TTAATTAATAA
*
11225118 ATTATTAATT--TAT
1 ATTATTAATTAATAA
11225131 A-TATTAATTAATAA
1 ATTATTAATTAATAA
** *
11225145 AAAATTAATTTATAA
1 ATTATTAATTAATAA
11225160 A
1 A
11225161 GATATTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
12 8 0.22
13 3 0.08
14 3 0.08
15 18 0.50
16 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATTAATTAATAA
Found at i:11225128 original size:31 final size:30
Alignment explanation
Indices: 11225090--11225151 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
11225080 AAATTTATTA
* *
11225090 ATTAATTTAAATATTATTTAATTAATAAATT
1 ATTAATTTAAATATTAATTAA-TAAAAAATT
*
11225121 ATTAATTTATATATTAATTAATAAAAAATT
1 ATTAATTTAAATATTAATTAATAAAAAATT
11225151 A
1 A
11225152 ATTTATAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 9 0.32
31 19 0.68
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
ATTAATTTAAATATTAATTAATAAAAAATT
Found at i:11225142 original size:27 final size:27
Alignment explanation
Indices: 11225089--11225158 Score: 86
Period size: 27 Copynumber: 2.4 Consensus size: 27
11225079 AAAATTTATT
*
11225089 AATTAATTTAAATATTATTTAATTAATAAAT
1 AATTAATTT--ATA-TA-TTAATTAATAAAA
*
11225120 TATTAATTTATATATTAATTAATAAAA
1 AATTAATTTATATATTAATTAATAAAA
11225147 AATTAATTTATA
1 AATTAATTTATA
11225159 AAGATATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 23 0.64
28 2 0.06
29 3 0.08
31 8 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
AATTAATTTATATATTAATTAATAAAA
Found at i:11256881 original size:8 final size:8
Alignment explanation
Indices: 11256870--11256896 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
11256860 TATTATTTAA
11256870 TTAATAAT
1 TTAATAAT
11256878 TTAATAAT
1 TTAATAAT
11256886 TTAATAAT
1 TTAATAAT
11256894 TTA
1 TTA
11256897 TATATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTAATAAT
Found at i:11256909 original size:16 final size:15
Alignment explanation
Indices: 11256867--11256905 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
11256857 AAATATTATT
11256867 TAATTAATAATTTAA
1 TAATTAATAATTTAA
11256882 TAATTTAATAATTT-A
1 TAA-TTAATAATTTAA
11256897 TATATTAAT
1 TA-ATTAAT
11256906 TAATAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TAATTAATAATTTAA
Found at i:11257449 original size:17 final size:18
Alignment explanation
Indices: 11257427--11257462 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
11257417 AGTCAAAATC
11257427 AATCAAAACTATT-ATTT
1 AATCAAAACTATTAATTT
*
11257444 AATCAAAATTATTAATTT
1 AATCAAAACTATTAATTT
11257462 A
1 A
11257463 TTGAGTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (18 bp):
AATCAAAACTATTAATTT
Found at i:11270914 original size:2 final size:2
Alignment explanation
Indices: 11270907--11270931 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11270897 AGAATTTATC
11270907 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11270932 CCTACTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11272784 original size:18 final size:19
Alignment explanation
Indices: 11272757--11272793 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
11272747 TTTTTTAAAA
11272757 AAAAAAAAGTTA-TTTTTT
1 AAAAAAAAGTTACTTTTTT
*
11272775 AAAAATAAGTTACTTTTTT
1 AAAAAAAAGTTACTTTTTT
11272794 TTTTTTGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (19 bp):
AAAAAAAAGTTACTTTTTT
Found at i:11280644 original size:151 final size:151
Alignment explanation
Indices: 11280370--11280680 Score: 532
Period size: 151 Copynumber: 2.1 Consensus size: 151
11280360 ATCAAAATTA
* * *
11280370 GTTTTGGTTAGCAAAAGAGGTGTTACACCTTAAATACCTTAGAATAACCAGCCGAGAGTTATGGT
1 GTTTTGGTTAGCAAAAGAGGTGCTACACCTTAAATACCTTAGAATAACCAACCGAGAGTCATGGT
* **
11280435 TCATTTTGTTAAGCTAATAGTGTGGTTTTAATTCTAAGTATTTTGAATTAATAGGCTTTAAGATG
66 TCATTTTGTTAAGCTAATAGTGTGGTTTTAATTCCAAGTATTTTGAATTAATAGGCTTTAAGACA
11280500 ATTTCGATTCTTAATCCTTTG
131 ATTTCGATTCTTAATCCTTTG
* *
11280521 GTTTTGGTTAGCGAAAGAGGTGCTACACCTTAAATGCCTTAGAATAACCAACCGAGAGTCATGGT
1 GTTTTGGTTAGCAAAAGAGGTGCTACACCTTAAATACCTTAGAATAACCAACCGAGAGTCATGGT
* *
11280586 TCATTTTGTTAAGCTAGTAGTGTGGTTTTAATTCCAAGTATTTTGAATTAATAGGCTTTAGGACA
66 TCATTTTGTTAAGCTAATAGTGTGGTTTTAATTCCAAGTATTTTGAATTAATAGGCTTTAAGACA
11280651 ATTTCGATTCTTAATCCTTTG
131 ATTTCGATTCTTAATCCTTTG
11280672 GTTTTGGTT
1 GTTTTGGTT
11280681 TGGCAAATCA
Statistics
Matches: 150, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
151 150 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (151 bp):
GTTTTGGTTAGCAAAAGAGGTGCTACACCTTAAATACCTTAGAATAACCAACCGAGAGTCATGGT
TCATTTTGTTAAGCTAATAGTGTGGTTTTAATTCCAAGTATTTTGAATTAATAGGCTTTAAGACA
ATTTCGATTCTTAATCCTTTG
Found at i:11288971 original size:15 final size:16
Alignment explanation
Indices: 11288940--11288973 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11288930 ATAATTTTTT
*
11288940 AATTTTTAAAAATTAA
1 AATTATTAAAAATTAA
11288956 AATTATTAAAAA-TAA
1 AATTATTAAAAATTAA
11288971 AAT
1 AAT
11288974 CTACATAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTATTAAAAATTAA
Found at i:11289132 original size:14 final size:14
Alignment explanation
Indices: 11289115--11289169 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
11289105 ATAGAATTGA
11289115 AAAAATAAATAAAT
1 AAAAATAAATAAAT
11289129 AAAAAT-AATAATAT
1 AAAAATAAATAA-AT
* *
11289143 TAATATAAATAGAA-
1 AAAAATAAATA-AAT
*
11289157 AAAATTAAATAAA
1 AAAAATAAATAAA
11289170 AACTGTACGG
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
13 7 0.21
14 20 0.61
15 5 0.15
16 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (14 bp):
AAAAATAAATAAAT
Found at i:11289347 original size:13 final size:13
Alignment explanation
Indices: 11289329--11289353 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11289319 TATTATTCAA
11289329 TGAAAAATTATTT
1 TGAAAAATTATTT
11289342 TGAAAAATTATT
1 TGAAAAATTATT
11289354 AAAAAAATAT
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
TGAAAAATTATTT
Found at i:11291509 original size:13 final size:13
Alignment explanation
Indices: 11291491--11291516 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11291481 TTCTTTAGCA
11291491 ACTCATCAGCAGG
1 ACTCATCAGCAGG
11291504 ACTCATCAGCAGG
1 ACTCATCAGCAGG
11291517 TTGGCATCAT
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:0.31, C:0.31, G:0.23, T:0.15
Consensus pattern (13 bp):
ACTCATCAGCAGG
Done.