Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold119
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: 3173904
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 20
Found at i:2162611 original size:19 final size:19
Alignment explanation
Indices: 2162587--2162652 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
2162577 AAAATTTCTT
2162587 CCCTTTAAACGATTATCTC
1 CCCTTTAAACGATTATCTC
** *
2162606 CCCTTTTATAAAAATTTTCTC
1 CCC-TTTA-AACGATTATCTC
*
2162627 CCCCTTAAACGATTATCTC
1 CCCTTTAAACGATTATCTC
2162646 CCCTTTA
1 CCCTTTA
2162653 TAAAAATTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 18 0.49
20 7 0.19
21 12 0.32
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.39
Consensus pattern (19 bp):
CCCTTTAAACGATTATCTC
Found at i:2162653 original size:39 final size:40
Alignment explanation
Indices: 2162574--2162661 Score: 142
Period size: 40 Copynumber: 2.2 Consensus size: 40
2162564 TCGTTTTTCT
* * *
2162574 TAAAAAATTTCTTCCCTTTAAACGATTATCTCCCCTTTTA
1 TAAAAATTTTCTCCCCCTTAAACGATTATCTCCCCTTTTA
2162614 TAAAAATTTTCTCCCCCTTAAACGATTATCTCCCC-TTTA
1 TAAAAATTTTCTCCCCCTTAAACGATTATCTCCCCTTTTA
2162653 TAAAAATTT
1 TAAAAATTT
2162662 ATTTTCACAT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 13 0.29
40 32 0.71
ACGTcount: A:0.32, C:0.25, G:0.02, T:0.41
Consensus pattern (40 bp):
TAAAAATTTTCTCCCCCTTAAACGATTATCTCCCCTTTTA
Found at i:2162663 original size:21 final size:21
Alignment explanation
Indices: 2162599--2162663 Score: 73
Period size: 19 Copynumber: 3.2 Consensus size: 21
2162589 CTTTAAACGA
2162599 TTATCTCCCCTTTTATAAAAAT
1 TTATCTCCCC-TTTATAAAAAT
* **
2162621 TT-TCTCCCCCTTA-AACGA-
1 TTATCTCCCCTTTATAAAAAT
2162639 TTATCTCCCCTTTATAAAAAT
1 TTATCTCCCCTTTATAAAAAT
2162660 TTAT
1 TTAT
2162664 TTTCACATAC
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 2 0.06
19 13 0.38
20 6 0.18
21 11 0.32
22 2 0.06
ACGTcount: A:0.29, C:0.26, G:0.02, T:0.43
Consensus pattern (21 bp):
TTATCTCCCCTTTATAAAAAT
Found at i:2164522 original size:13 final size:13
Alignment explanation
Indices: 2164504--2164545 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
2164494 AAATAGTACC
2164504 CAATGTATCGATA
1 CAATGTATCGATA
*
2164517 CAATGTATCAATA
1 CAATGTATCGATA
2164530 CAATGTATCGATA
1 CAATGTATCGATA
2164543 CAA
1 CAA
2164546 GGAATATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2170753 original size:19 final size:20
Alignment explanation
Indices: 2170709--2170764 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
2170699 CTGCCATTTT
* *
2170709 CATGTATCGATACAATTATC
1 CATGTATCGATACAATGATA
2170729 CATGTATCGATACAATGA-A
1 CATGTATCGATACAATGATA
*
2170748 CATGTATCGATGCAATG
1 CATGTATCGATACAATG
2170765 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATGATA
Found at i:2170771 original size:32 final size:33
Alignment explanation
Indices: 2170730--2170791 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
2170720 ACAATTATCC
*
2170730 ATGTATCGATACAATG-AACATGTATCGATGCA
1 ATGTATCGATACAAAGCAACATGTATCGATGCA
*
2170762 ATGTATCGATACAAAGCAGCATGTATCGAT
1 ATGTATCGATACAAAGCAACATGTATCGAT
2170792 ACATCTGGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.27
Consensus pattern (33 bp):
ATGTATCGATACAAAGCAACATGTATCGATGCA
Found at i:2171233 original size:31 final size:30
Alignment explanation
Indices: 2171177--2171234 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
2171167 TAAATATCCC
2171177 AAATAGATAAAATAATTAATAAAAAAATAT
1 AAATAGATAAAATAATTAATAAAAAAATAT
* * *
2171207 AAATAGCATGAAATTATTAATGAAAAAA
1 AAATAG-ATAAAATAATTAATAAAAAAA
2171235 GGTATTCGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.26
Consensus pattern (30 bp):
AAATAGATAAAATAATTAATAAAAAAATAT
Found at i:2175693 original size:13 final size:13
Alignment explanation
Indices: 2175675--2175700 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2175665 TACAAGCCAA
2175675 TGTATCGATACAT
1 TGTATCGATACAT
2175688 TGTATCGATACAT
1 TGTATCGATACAT
2175701 ACTTGGTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2178260 original size:13 final size:13
Alignment explanation
Indices: 2178242--2178266 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2178232 ATAATCCCCA
2178242 TGTATCGATACAT
1 TGTATCGATACAT
2178255 TGTATCGATACA
1 TGTATCGATACA
2178267 AAGAAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2183885 original size:13 final size:13
Alignment explanation
Indices: 2183867--2183892 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2183857 CAATTTTTTG
2183867 TGTATCGATACAT
1 TGTATCGATACAT
2183880 TGTATCGATACAT
1 TGTATCGATACAT
2183893 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2185622 original size:13 final size:13
Alignment explanation
Indices: 2185604--2185629 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2185594 CATTTTTTGG
2185604 TGTATCGATACAT
1 TGTATCGATACAT
2185617 TGTATCGATACAT
1 TGTATCGATACAT
2185630 ACTTGGTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2185641 original size:32 final size:33
Alignment explanation
Indices: 2185584--2185647 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2185574 TACAAGCCAA
**
2185584 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCGATACATTACTTGGTGTATCGATACAT
2185617 TGTATCGATACA-TACTTGGTGTATCGATACA
1 TGTATCGATACATTACTTGGTGTATCGATACA
2185648 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTACTTGGTGTATCGATACAT
Found at i:2187072 original size:16 final size:16
Alignment explanation
Indices: 2187047--2187136 Score: 83
Period size: 16 Copynumber: 5.5 Consensus size: 16
2187037 GGGTTAATTG
2187047 TTCGGGTCATTTCAGA
1 TTCGGGTCATTTCAGA
* *
2187063 TTCGGATCATTTCAGG
1 TTCGGGTCATTTCAGA
* *
2187079 TTCGGGTCATTTTTAAA
1 TTCGGGTCA-TTTCAGA
**
2187096 TTTAGGTCATTTC-GA
1 TTCGGGTCATTTCAGA
*
2187111 GTTCGGGTCATTTCGGA
1 -TTCGGGTCATTTCAGA
2187128 TTTCGGGTC
1 -TTCGGGTC
2187137 GGTCGGTTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
15 1 0.02
16 36 0.62
17 21 0.36
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.41
Consensus pattern (16 bp):
TTCGGGTCATTTCAGA
Found at i:2187308 original size:23 final size:23
Alignment explanation
Indices: 2187282--2187338 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
2187272 TATCATATTC
2187282 ATTTTTTATATTATGTTTTAATT
1 ATTTTTTATATTATGTTTTAATT
** * *
2187305 ATTTTTTACGTCATGTTTTTATT
1 ATTTTTTATATTATGTTTTAATT
*
2187328 -TTTTGTATATT
1 ATTTTTTATATT
2187339 CAAAGTAGTA
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.21, C:0.04, G:0.07, T:0.68
Consensus pattern (23 bp):
ATTTTTTATATTATGTTTTAATT
Found at i:2187361 original size:10 final size:10
Alignment explanation
Indices: 2187346--2187371 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2187336 ATTCAAAGTA
2187346 GTATAAATTT
1 GTATAAATTT
2187356 GTATAAATTT
1 GTATAAATTT
2187366 GTATAA
1 GTATAA
2187372 CTTTTTACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (10 bp):
GTATAAATTT
Found at i:2187842 original size:15 final size:16
Alignment explanation
Indices: 2187822--2187876 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 16
2187812 AGAAAGATGC
2187822 AAAGAAAA-AAAGAAA
1 AAAGAAAAGAAAGAAA
2187837 AAAGAAAAGAAAGAAA
1 AAAGAAAAGAAAGAAA
* *
2187853 AGGAGAGAGAGAAAGAAA
1 A-AAGA-AAAGAAAGAAA
2187871 TAAAGA
1 -AAAGA
2187877 GAAAATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 8 0.24
16 8 0.24
17 3 0.09
18 13 0.39
19 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (16 bp):
AAAGAAAAGAAAGAAA
Found at i:2188017 original size:21 final size:23
Alignment explanation
Indices: 2187991--2188032 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
2187981 CGTATCATAT
2187991 TTATTTTATAT-T-ATATTTTAA
1 TTATTTTATATGTCATATTTTAA
*
2188012 TTATTTTTTATGTCATATTTT
1 TTATTTTATATGTCATATTTT
2188033 TATTTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 1 0.06
23 7 0.39
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (23 bp):
TTATTTTATATGTCATATTTTAA
Found at i:2188020 original size:11 final size:12
Alignment explanation
Indices: 2187987--2188036 Score: 52
Period size: 11 Copynumber: 4.4 Consensus size: 12
2187977 TATTCGTATC
2187987 ATATT-TATTTT
1 ATATTATATTTT
2187998 ATATTATATTTT
1 ATATTATATTTT
*
2188010 A-ATTATTTTTT
1 ATATTATATTTT
* *
2188021 ATGTCATATTTT
1 ATATTATATTTT
2188033 -TATT
1 ATATT
2188037 TTTCATCTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 17 0.55
12 14 0.45
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:2188441 original size:18 final size:21
Alignment explanation
Indices: 2188400--2188442 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2188390 AATTTATTTT
*
2188400 ATAATTAAATTTTTATTAATA
1 ATAATTAAATATTTATTAATA
2188421 ATAATTAAA-ATTTA-TAA-A
1 ATAATTAAATATTTATTAATA
2188439 ATAA
1 ATAA
2188443 AAATAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 3 0.14
20 4 0.19
21 9 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATTAAATATTTATTAATA
Found at i:2188441 original size:21 final size:22
Alignment explanation
Indices: 2188400--2188451 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
2188390 AATTTATTTT
* *
2188400 ATAATT-AAATTTTTATTAATA
1 ATAATTAAAATTTATATAAATA
2188421 ATAATTAAAATTTATA-AAATA
1 ATAATTAAAATTTATATAAATA
* *
2188442 AAAATAAAAA
1 ATAATTAAAA
2188452 CTCCAACGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAATTAAAATTTATATAAATA
Found at i:2189045 original size:15 final size:15
Alignment explanation
Indices: 2188994--2189051 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
2188984 TTATGTTTGC
*
2188994 ATTTATAATTTTTTAT
1 ATTTAT-ATATTTTAT
* *
2189010 ATTTAAAATATTATAT
1 ATTT-ATATATTTTAT
*
2189026 TTTTATATATTTTAT
1 ATTTATATATTTTAT
2189041 ATTTATATATT
1 ATTTATATATT
2189052 AATAATTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
15 19 0.56
16 14 0.41
17 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTATATATTTTAT
Found at i:2189059 original size:15 final size:15
Alignment explanation
Indices: 2189007--2189101 Score: 65
Period size: 15 Copynumber: 6.3 Consensus size: 15
2188997 TATAATTTTT
*
2189007 TATATTTAAAATATTA
1 TATATTT-ATATATTA
* *
2189023 TATTTTTATATATTT
1 TATATTTATATATTA
2189038 TATATTTATATATTA
1 TATATTTATATATTA
*
2189053 -ATAATTTATTCTATTA
1 TAT-ATTTA-TATATTA
*
2189069 TATATATT-TTTATGTA
1 TATAT-TTATATAT-TA
2189085 TAT-TTTAT-T-TTA
1 TATATTTATATATTA
2189097 TATAT
1 TATAT
2189102 GGAAGAAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
12 5 0.08
13 2 0.03
14 5 0.08
15 30 0.46
16 19 0.29
17 4 0.06
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (15 bp):
TATATTTATATATTA
Found at i:2189086 original size:12 final size:12
Alignment explanation
Indices: 2189021--2189090 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 12
2189011 TTTAAAATAT
2189021 TATATTTTTATA
1 TATATTTTTATA
* *
2189033 TAT-TTTATATT
1 TATATTTTTATA
* *
2189044 TATATATTAATAA
1 TATATTTTTAT-A
*
2189057 TTTATTCTATTATA
1 TATATT-T-TTATA
*
2189071 TATATTTTTATG
1 TATATTTTTATA
2189083 TATATTTT
1 TATATTTT
2189091 ATTTTATATA
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
11 9 0.21
12 19 0.44
13 5 0.12
14 7 0.16
15 3 0.07
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (12 bp):
TATATTTTTATA
Found at i:2189447 original size:32 final size:32
Alignment explanation
Indices: 2189411--2189478 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 32
2189401 TTCGTGTCAT
*
2189411 TTTCAAGTTCGGGTCATTTCCG-GTTTAGGTTA
1 TTTCAAGTTCGGATCATTT-CGTGTTTAGGTTA
*
2189443 TTTCAGGTTCGGATCATTTCGTGTTTAGGTTA
1 TTTCAAGTTCGGATCATTTCGTGTTTAGGTTA
2189475 TTTC
1 TTTC
2189479 GGATACGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 2 0.06
32 31 0.94
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.47
Consensus pattern (32 bp):
TTTCAAGTTCGGATCATTTCGTGTTTAGGTTA
Found at i:2190013 original size:22 final size:22
Alignment explanation
Indices: 2189988--2190045 Score: 53
Period size: 24 Copynumber: 2.5 Consensus size: 22
2189978 TAATTAATTT
* *
2189988 TTTTTACAATAATAATTTAAAA
1 TTTTTACAATAAAAATTAAAAA
*
2190010 TTTTAAACTAATAAAAATTAAAAA
1 TTTT-TAC-AATAAAAATTAAAAA
* *
2190034 TTGTTATAATAA
1 TTTTTACAATAA
2190046 GCATGTATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
22 9 0.32
23 3 0.11
24 16 0.57
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (22 bp):
TTTTTACAATAAAAATTAAAAA
Found at i:2190757 original size:24 final size:24
Alignment explanation
Indices: 2190713--2190792 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
2190703 ATGTTCGTGT
* * *
2190713 TATTTTT-TATATTTAAAATATTA
1 TATTTTTATATTTTTTACATATTA
2190736 TATTTTTATATTTTTTACATATTA
1 TATTTTTATATTTTTTACATATTA
*
2190760 -ATAATTTAT-TTTATTT-CATA-TA
1 TAT-TTTTATATTT-TTTACATATTA
2190782 TATTTTTATAT
1 TATTTTTATAT
2190793 GTACGTGTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
22 7 0.15
23 19 0.40
24 21 0.45
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.64
Consensus pattern (24 bp):
TATTTTTATATTTTTTACATATTA
Found at i:2191439 original size:33 final size:33
Alignment explanation
Indices: 2191402--2191468 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2191392 TTCAACGATT
2191402 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
2191435 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
2191468 T
1 T
2191469 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:2191440 original size:13 final size:13
Alignment explanation
Indices: 2191422--2191446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2191412 CATAAAATGT
2191422 TGTATCGATACAA
1 TGTATCGATACAA
2191435 TGTATCGATACA
1 TGTATCGATACA
2191447 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2191527 original size:13 final size:13
Alignment explanation
Indices: 2191509--2191533 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2191499 ATTACTCAAA
2191509 TGTATCGATACAT
1 TGTATCGATACAT
2191522 TGTATCGATACA
1 TGTATCGATACA
2191534 CTGATCAAAT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2191531 original size:34 final size:34
Alignment explanation
Indices: 2191488--2191555 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
2191478 TGCCAAAAAA
*
2191488 TGTATCGATACA-TTACTCAAATGTATCGATACAT
1 TGTATCGATACACTGA-TCAAATGTATCGATACAT
2191522 TGTATCGATACACTGATCAAATGTATCGATACAT
1 TGTATCGATACACTGATCAAATGTATCGATACAT
2191556 GCAAGCAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 30 0.94
35 2 0.06
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (34 bp):
TGTATCGATACACTGATCAAATGTATCGATACAT
Found at i:2192295 original size:34 final size:34
Alignment explanation
Indices: 2192225--2192295 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
2192215 TATTTTTTTA
*
2192225 TAAATAAAATATTATAAATTATTTTAAAAATTAT
1 TAAATAAAATATTATAAATTATTTTAAAAATAAT
* *
2192259 TAAATAAAA-ATTTTACAATTATTATT-ATAATAAT
1 TAAATAAAATATTATA-AATTATT-TTAAAAATAAT
2192293 TAA
1 TAA
2192296 GTTTTACAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 5 0.16
34 25 0.78
35 2 0.06
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (34 bp):
TAAATAAAATATTATAAATTATTTTAAAAATAAT
Found at i:2192300 original size:28 final size:25
Alignment explanation
Indices: 2192254--2192305 Score: 68
Period size: 28 Copynumber: 2.0 Consensus size: 25
2192244 TATTTTAAAA
2192254 ATTATTAAATAAAAATTTTACAATT
1 ATTATTAAATAAAAATTTTACAATT
*
2192279 ATTATTATAATAATTAAGTTTTACAAT
1 ATTATTA-AATAA--AAATTTTACAAT
2192306 AAATTATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
26 5 0.22
28 11 0.48
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (25 bp):
ATTATTAAATAAAAATTTTACAATT
Found at i:2199587 original size:2 final size:2
Alignment explanation
Indices: 2199580--2199616 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2199570 GGGGGAAGGA
2199580 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2199617 AAGTTCTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2206765 original size:24 final size:23
Alignment explanation
Indices: 2206729--2206773 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2206719 ATCCATCACC
*
2206729 TATTAAATAATAAATATTTATCT
1 TATTAAATAATAAATAATTATCT
*
2206752 TATTACATCAATAAATAATTAT
1 TATTAAAT-AATAAATAATTAT
2206774 ACAGAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (23 bp):
TATTAAATAATAAATAATTATCT
Found at i:2206933 original size:3 final size:3
Alignment explanation
Indices: 2206925--2206962 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2206915 CTTAAGCTTC
2206925 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2206963 GCTTTTAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2207751 original size:2 final size:2
Alignment explanation
Indices: 2207700--2207732 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2207690 AATCTTTTTA
*
2207700 AT AT -T AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2207733 GTTTATCTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2208903 original size:16 final size:16
Alignment explanation
Indices: 2208884--2208923 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2208874 TATTTCTATA
2208884 TTAAATTTAAT-TGTAT
1 TTAAATTTAATAT-TAT
*
2208900 TTAAATTAAATATTAT
1 TTAAATTTAATATTAT
2208916 TTAAATTT
1 TTAAATTT
2208924 TTTGAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 20 0.95
17 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TTAAATTTAATATTAT
Found at i:2212313 original size:96 final size:97
Alignment explanation
Indices: 2212091--2212322 Score: 279
Period size: 96 Copynumber: 2.4 Consensus size: 97
2212081 ACATGGCTGG
* * *
2212091 AGTATCCCCTCGAAAGAATGGGGTTAGAGTGTCCTCGATGATAACAATTTAGGCAAAAATAAGAT
1 AGTATCCCCTCGAAAGAATGGGGTTAGAGTATCCTCGATGATAACAATTTAGGCAAAAATAAAAA
**
2212156 TTAAATCTTAACAAGTTTAAAAACAAGATTGG
66 TTAAATCTTAACAAGTTTAAAAACAAGATTAA
** * * *
2212188 AGTATCTTCTCGAAAGAGTAGGGTTAGAGTAT-CTCCGATGATGACAATTTAGGCAAAAA-AAAA
1 AGTATCCCCTCGAAAGAATGGGGTTAGAGTATCCT-CGATGATAACAATTTAGGCAAAAATAAAA
* *** *
2212251 ATTAAATCTTGACAAGTTTAAAAAGGGGGTTAA
65 ATTAAATCTTAACAAGTTTAAAAACAAGATTAA
* * *
2212284 AGTATCCCCTTGAAAGAATGGGGTGAGAGTATTCTCGAT
1 AGTATCCCCTCGAAAGAATGGGGTTAGAGTATCCTCGAT
2212323 AAATAAAATT
Statistics
Matches: 112, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
96 60 0.54
97 52 0.46
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.27
Consensus pattern (97 bp):
AGTATCCCCTCGAAAGAATGGGGTTAGAGTATCCTCGATGATAACAATTTAGGCAAAAATAAAAA
TTAAATCTTAACAAGTTTAAAAACAAGATTAA
Found at i:2214525 original size:52 final size:52
Alignment explanation
Indices: 2214468--2214607 Score: 167
Period size: 52 Copynumber: 2.7 Consensus size: 52
2214458 AATTGTTTGC
* *
2214468 ATGTATCGATACATTGAAGAATATATCGATACATTTAGGTTAAAAA-CTCAGA
1 ATGTATCGATACATTGAAAAATATATCGATACATTTAGGTCAAAAACCT-AGA
* * * * *
2214520 ATGTATCGATACAATGAATAATATATTGATAAATTTGGGTCAAAAACCTAGA
1 ATGTATCGATACATTGAAAAATATATCGATACATTTAGGTCAAAAACCTAGA
* *
2214572 ATGTATTGATAC-TATGAAAAATGTATCGATACATTT
1 ATGTATCGATACAT-TGAAAAATATATCGATACATTT
2214608 TCTTTCTAGA
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
52 72 0.97
53 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (52 bp):
ATGTATCGATACATTGAAAAATATATCGATACATTTAGGTCAAAAACCTAGA
Found at i:2215307 original size:38 final size:40
Alignment explanation
Indices: 2215260--2215334 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 40
2215250 TATTATTCAA
* *
2215260 TATTAT-AAAATATATTATTAGAA-ATTTTAAGATATATT
1 TATTATAAAAATATATTATTACAATATTTTAAAATATATT
2215298 TATTATAAAAATATATTATTACAATATTTTAAAATAT
1 TATTATAAAAATATATTATTACAATATTTTAAAATAT
2215335 TCTTAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 6 0.18
39 16 0.48
40 11 0.33
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (40 bp):
TATTATAAAAATATATTATTACAATATTTTAAAATATATT
Found at i:2215351 original size:9 final size:10
Alignment explanation
Indices: 2215170--2215907 Score: 141
Period size: 10 Copynumber: 73.7 Consensus size: 10
2215160 TTATTAAAAT
2215170 ATATTATTAA
1 ATATTATTAA
2215180 ATATT-TTAA
1 ATATTATTAA
2215189 TATATTA-TAA
1 -ATATTATTAA
2215199 ATTATT-TTAA
1 A-TATTATTAA
* *
2215209 TATATTTTTTA
1 -ATATTATTAA
2215220 ATA-TATTAA
1 ATATTATTAA
* *
2215229 A-A-TAATAG
1 ATATTATTAA
*
2215237 TTATTAATATAA
1 ATATT-AT-TAA
* *
2215249 TTATTATTCA
1 ATATTATTAA
*
2215259 ATATTATAAAA
1 ATATTAT-TAA
2215270 TATATTATTAGA
1 -ATATTATTA-A
2215282 A-ATT-TTAA
1 ATATTATTAA
*
2215290 GATA-TATTTA
1 -ATATTATTAA
* **
2215300 TTA-TAAAAA
1 ATATTATTAA
2215309 TATATTATTACA
1 -ATATTATTA-A
2215321 ATATT-TTAAA
1 ATATTATT-AA
*
2215331 ATATTCTTAA
1 ATATTATTAA
2215341 ATATT-TTAA
1 ATATTATTAA
*
2215350 ATATTATTAT
1 ATATTATTAA
*
2215360 AGATTATATAA
1 ATATTAT-TAA
2215371 ATATTA--AA
1 ATATTATTAA
* *
2215379 ATA-GATTGAG
1 ATATTATT-AA
* *
2215389 ATATTCTAAA
1 ATATTATTAA
2215399 ATATTA-T-A
1 ATATTATTAA
2215407 ATATT-TTAA
1 ATATTATTAA
2215416 A-ATTTATTAA
1 ATA-TTATTAA
*
2215426 ATA-CATTACA
1 ATATTATTA-A
**
2215436 ATATTACAAA
1 ATATTATTAA
*
2215446 ATATAATTAAA
1 ATATTATT-AA
2215457 ATATT-TTAATA
1 ATATTATT-A-A
*
2215468 ATTAATTATAAA
1 A-T-ATTATTAA
2215480 ATATTAATTAA
1 ATATT-ATTAA
* *
2215491 CTATCATTAA
1 ATATTATTAA
* * *
2215501 A-ATAAATAT
1 ATATTATTAA
*
2215510 CTATTATTAA
1 ATATTATTAA
2215520 ATATT-TT-A
1 ATATTATTAA
2215528 ATATATATT--
1 ATAT-TATTAA
*
2215537 -TATTATAAA
1 ATATTATTAA
*
2215546 ATATTA-TAT
1 ATATTATTAA
2215555 AT-TTATATAA
1 ATATTAT-TAA
2215565 ATATT-TTAA
1 ATATTATTAA
*
2215574 A-ATATATTGA
1 ATAT-TATTAA
*
2215584 ACATTA--AA
1 ATATTATTAA
*
2215592 ATATTATAAA
1 ATATTATTAA
2215602 ATATATATTAA
1 ATAT-TATTAA
*
2215613 A-ATT-TTTA
1 ATATTATTAA
2215621 ATAATTAATTATA
1 AT-ATT-ATTA-A
* *
2215634 AAATTAATAA
1 ATATTATTAA
*
2215644 TTAATTTCATTAAA
1 AT-A-TT-ATT-AA
*
2215658 ATACTATTAA
1 ATATTATTAA
2215668 A-A-TATTAA
1 ATATTATTAA
* * **
2215676 TTTTTATTTT
1 ATATTATTAA
* **
2215686 TTATT-TTTT
1 ATATTATTAA
2215695 A-ATTA-TAA
1 ATATTATTAA
*
2215703 A-A-TATAAA
1 ATATTATTAA
2215711 TATATTATTAA
1 -ATATTATTAA
2215722 ATTATT-TTAA
1 A-TATTATTAA
*
2215732 A-ATTTTATAA
1 ATATTAT-TAA
2215742 ATATTATTAA
1 ATATTATTAA
2215752 ATTATTATTAA
1 A-TATTATTAA
*
2215763 ATATTGTTAAA
1 ATATTATT-AA
*
2215774 ATATTGTTATAAA
1 ATA---TTATTAA
2215787 ATATT-TTAA
1 ATATTATTAA
2215796 TATAATTATTAA
1 -AT-ATTATTAA
*
2215808 ATCTTATGTAA
1 ATATTAT-TAA
*
2215819 TATATCATTAA
1 -ATATTATTAA
2215830 ATATT-TTAA
1 ATATTATTAA
* * *
2215839 AAATAATTAT
1 ATATTATTAA
* * **
2215849 TTCATAATTTT
1 AT-ATTATTAA
*
2215860 ATATTATGAA
1 ATATTATTAA
2215870 AT-TTATTAA
1 ATATTATTAA
*
2215879 GATATT-CTAA
1 -ATATTATTAA
2215889 TATATTATTAA
1 -ATATTATTAA
2215900 ATTATTAT
1 A-TATTAT
2215908 AATATGTTAT
Statistics
Matches: 532, Mismatches: 105, Indels: 181
0.65 0.13 0.22
Matches are distributed among these distances:
7 6 0.01
8 59 0.11
9 78 0.15
10 209 0.39
11 123 0.23
12 36 0.07
13 14 0.03
14 7 0.01
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (10 bp):
ATATTATTAA
Found at i:2215410 original size:18 final size:17
Alignment explanation
Indices: 2215389--2215422 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2215379 ATAGATTGAG
2215389 ATATTCTAAAATATTATA
1 ATATTCTAAAAT-TTATA
*
2215407 ATATTTTAAAATTTAT
1 ATATTCTAAAATTTAT
2215423 TAAATACATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTCTAAAATTTATA
Found at i:2215467 original size:29 final size:28
Alignment explanation
Indices: 2215395--2215467 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
2215385 TGAGATATTC
** *
2215395 TAAAATATTATAATATTTTAAAATTTAT
1 TAAAATATTATAATATTACAAAATTAAT
* *
2215423 TAAATACATTACAATATTACAAAATATAAT
1 TAAA-ATATTATAATATTACAAAAT-TAAT
*
2215453 TAAAATATTTTAATA
1 TAAAATATTATAATA
2215468 ATTAATTATA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
28 4 0.11
29 24 0.69
30 7 0.20
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAAATATTATAATATTACAAAATTAAT
Found at i:2215530 original size:26 final size:26
Alignment explanation
Indices: 2215501--2215550 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2215491 CTATCATTAA
*
2215501 AATAAATATCTATTATTAAATATTTT
1 AATAAATATCTATTATAAAATATTTT
* *
2215527 AATATATATTTATTATAAAATATT
1 AATAAATATCTATTATAAAATATT
2215551 ATATATTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
AATAAATATCTATTATAAAATATTTT
Found at i:2215568 original size:45 final size:45
Alignment explanation
Indices: 2215513--2215637 Score: 125
Period size: 45 Copynumber: 2.8 Consensus size: 45
2215503 TAAATATCTA
* *
2215513 TTAT-TAAATATTTTAATATATATTTATTATAAAATATTAT-ATAT
1 TTATATAAATATTTTAA-ATATATTAATTATAAAATATTATAAAAT
*
2215557 TTATATAAATATTTTAAAATATATTGAA-CATTAAAATATTATAAAAT
1 TTATATAAATATTTT-AAATATATT-AATTA-TAAAATATTATAAAAT
* *
2215604 ATATATTAAA-ATTTTTAATA-ATTAATTATAAAAT
1 TTATA-TAAATATTTTAAATATATTAATTATAAAAT
2215638 TAATAATTAA
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
44 12 0.18
45 22 0.32
46 18 0.26
47 12 0.18
48 4 0.06
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (45 bp):
TTATATAAATATTTTAAATATATTAATTATAAAATATTATAAAAT
Found at i:2215613 original size:12 final size:11
Alignment explanation
Indices: 2215586--2215674 Score: 55
Period size: 11 Copynumber: 8.1 Consensus size: 11
2215576 TATATTGAAC
2215586 ATTAAAATATT
1 ATTAAAATATT
2215597 A-TAAAATATAT
1 ATTAAAATAT-T
2215608 ATTAAAAT-TT
1 ATTAAAATATT
*
2215618 -TTAATAAT-TA
1 ATTAA-AATATT
2215628 ATTATAAA-ATT
1 ATTA-AAATATT
*
2215639 AATAATTAAT-TT
1 ATTAA--AATATT
*
2215651 CATTAAAATACT
1 -ATTAAAATATT
2215663 ATTAAAATATT
1 ATTAAAATATT
2215674 A
1 A
2215675 ATTTTTATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 22
0.69 0.07 0.25
Matches are distributed among these distances:
9 4 0.07
10 14 0.23
11 27 0.44
12 12 0.20
13 4 0.07
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTAAAATATT
Found at i:2215674 original size:156 final size:158
Alignment explanation
Indices: 2215400--2215778 Score: 393
Period size: 156 Copynumber: 2.4 Consensus size: 158
2215390 TATTCTAAAA
* *
2215400 TATTATAATATTTTAAAATTTATTAAATACATTACAATATTACAAAATATAATTAAAATATTTTA
1 TATTA-AATATTTTAAAATATATTAAATACATTAAAATATTACAAAATATAATTAAAATATTTTA
* *
2215465 ATAATTAATTATAAAATATTAATTAACTATCATTAAAATAAATATCTATTATTAAATATTTTA-A
65 ATAATTAATTATAAAATAATAATTAACTATCATTAAAATAAATATCTAATATT-AAT-TTTTATA
*
2215529 TATA-TATTT-ATTATAAAATAT-TATATATT
128 TATATTATTTAATTATAAAATATAAATATA-T
* *
2215558 TATATAAATATTTTAAAATATATT-GA-ACATTAAAATATTATAAAATATATATTAAAAT-TTTT
1 TAT-TAAATATTTTAAAATATATTAAATACATTAAAATATTACAAAATATA-ATTAAAATATTTT
* *
2215620 AATAATTAATTATAAAATTAATAATTAA-TTTCATTAAAAT-ACTAT-TAAAATATTAATTTTTA
64 AATAATTAATTATAAAA-TAATAATTAACTATCATTAAAATAAATATCT--AATATTAATTTTTA
* * *
2215682 TTTTTTATTTTTTAATTATAAAATATAAATATAT
126 -TATATATTATTTAATTATAAAATATAAATATAT
* * * ** **
2215716 TATTAAATTATTTTAAAAT-TTTATAAATATTATTAAATTATTATTAAATATTGTTAAAATATT
1 TATTAAA-TATTTTAAAATATAT-TAAATA-CATTAAAATATTACAAAATATAATTAAAATATT
2215779 GTTATAAAAT
Statistics
Matches: 186, Mismatches: 19, Indels: 29
0.79 0.08 0.12
Matches are distributed among these distances:
154 6 0.03
155 7 0.04
156 61 0.33
157 28 0.15
158 48 0.26
159 8 0.04
160 8 0.04
161 20 0.11
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (158 bp):
TATTAAATATTTTAAAATATATTAAATACATTAAAATATTACAAAATATAATTAAAATATTTTAA
TAATTAATTATAAAATAATAATTAACTATCATTAAAATAAATATCTAATATTAATTTTTATATAT
ATTATTTAATTATAAAATATAAATATAT
Found at i:2215778 original size:21 final size:20
Alignment explanation
Indices: 2215170--2215840 Score: 148
Period size: 21 Copynumber: 33.0 Consensus size: 20
2215160 TTATTAAAAT
*
2215170 ATATTATTAAATATTTTAAT
1 ATATTATTAAATATTTTAAA
*
2215190 ATATTA-TAAATTATTTTAAT
1 ATATTATTAAA-TATTTTAAA
* * *
2215210 ATATTTTTTAATATATTAAA
1 ATATTATTAAATATTTTAAA
* * * *
2215230 ATAATAGTT-ATTAATAT-AA
1 ATATTA-TTAAATATTTTAAA
* * *
2215249 TTATTATTCAATATTATAAAA
1 ATATTATTAAATATT-TTAAA
*
2215270 TATATTATTAGAA-ATTTTAAG
1 -ATATTATTA-AATATTTTAAA
* * **
2215291 ATA-TATTTATTA-TAAAAA
1 ATATTATTAAATATTTTAAA
2215309 TATATTATTACAATATTTTAAA
1 -ATATTATTA-AATATTTTAAA
*
2215331 ATATTCTTAAATATTTT-AA
1 ATATTATTAAATATTTTAAA
* * *
2215350 ATATTATTATAGATTATATAA
1 ATATTATTAAATATTTTA-AA
** * *
2215371 ATATTA--AAATAGATTGAG
1 ATATTATTAAATATTTTAAA
* * *
2215389 ATATT-CTAAA-ATATTATA
1 ATATTATTAAATATTTTAAA
*
2215407 ATATT-TTAAA-ATTTATTAA
1 ATATTATTAAATATTT-TAAA
* **
2215426 ATA-CATTACAATATTACAAA
1 ATATTATTA-AATATTTTAAA
*
2215446 ATATAATTAAAATATTTTAATA
1 ATATTATT-AAATATTTTAA-A
*
2215468 ATTAATTATAAAATATTAATT-AA
1 A-T-ATTATTAAATATT--TTAAA
* *
2215491 CTATCATTAAA-A---TAAA
1 ATATTATTAAATATTTTAAA
2215507 TATCTATTATTAAATATTTTAATA
1 -A--TATTATTAAATATTTTAA-A
* * *
2215531 TATATTTATTATAAAATATT-AT
1 -ATA-TTATTA-AATATTTTAAA
2215553 ATATTTATATAAATATTTTAAA
1 ATA-TTAT-TAAATATTTTAAA
* *
2215575 ATA-TATTGAACA--TTAAA
1 ATATTATTAAATATTTTAAA
*
2215592 ATATTATAAAATATATATTAAA
1 ATATTATTAAATAT-T-TTAAA
* * * *
2215614 ATTTTTAATAATTAATTATAAA
1 A-TATTATTAAAT-ATTTTAAA
*
2215636 ATTAATAATT-AAT-TTCATTAAA
1 A-T-ATTATTAAATATT--TTAAA
* *
2215658 ATACTATTAAA-ATATT-AA
1 ATATTATTAAATATTTTAAA
* * *** **
2215676 TTTTTATTTTTTATTTT-TT
1 ATATTATTAAATATTTTAAA
*
2215695 A-ATTA-TAAA-A-TATAAA
1 ATATTATTAAATATTTTAAA
2215711 TATATTATTAAATTATTTTAAA
1 -ATATTATTAAA-TATTTTAAA
*
2215733 ATTTTA-TAAATATTATTAAA
1 ATATTATTAAATATT-TTAAA
*
2215753 TTATTATTAAATATTGTTAAA
1 ATATTATTAAATATT-TTAAA
* *
2215774 ATATTGTTATAAAATATTTTAAT
1 ATA---TTATTAAATATTTTAAA
* *
2215797 ATAATTATTAAATCTTATGTAAT
1 AT-ATTATTAAATATT-T-TAAA
*
2215820 ATATCATTAAATATTTTAAA
1 ATATTATTAAATATTTTAAA
2215840 A
1 A
2215841 ATAATTATTT
Statistics
Matches: 465, Mismatches: 117, Indels: 138
0.65 0.16 0.19
Matches are distributed among these distances:
15 3 0.01
16 3 0.01
17 10 0.02
18 48 0.10
19 79 0.17
20 85 0.18
21 100 0.22
22 63 0.14
23 44 0.09
24 28 0.06
25 2 0.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
ATATTATTAAATATTTTAAA
Found at i:2215897 original size:21 final size:21
Alignment explanation
Indices: 2215872--2215918 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2215862 ATTATGAAAT
*
2215872 TTATTAAGA-TATTCTAATATA
1 TTATTAA-ATTATTATAATATA
*
2215893 TTATTAAATTATTATAATATG
1 TTATTAAATTATTATAATATA
2215914 TTATT
1 TTATT
2215919 TTATATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (21 bp):
TTATTAAATTATTATAATATA
Found at i:2215938 original size:18 final size:19
Alignment explanation
Indices: 2215902--2215951 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
2215892 ATTATTAAAT
*
2215902 TATTATAATATGTTATTTTA
1 TATTTTAATAT-TTATTTTA
2215922 TATTTTAATATTT-TTTTA
1 TATTTTAATATTTATTTTA
2215940 T-TTTTATATATT
1 TATTTTA-ATATT
2215952 ATTAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 5 0.18
18 11 0.39
19 2 0.07
20 10 0.36
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TATTTTAATATTTATTTTA
Found at i:2215947 original size:24 final size:25
Alignment explanation
Indices: 2215917--2215976 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
2215907 TAATATGTTA
* *
2215917 TTTTATATTTTAAT-ATTTTTTTAT
1 TTTTATATATTAATAAATTTTTTAT
*
2215941 TTTTATATATTATTAAATTTTTTAT
1 TTTTATATATTAATAAATTTTTTAT
*
2215966 TTGTAATATAT
1 TT-TTATATAT
2215977 AACTAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 12 0.40
25 11 0.37
26 7 0.23
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (25 bp):
TTTTATATATTAATAAATTTTTTAT
Found at i:2215960 original size:18 final size:18
Alignment explanation
Indices: 2215888--2215962 Score: 53
Period size: 18 Copynumber: 4.0 Consensus size: 18
2215878 AGATATTCTA
2215888 ATATATTATTAAATTATTAT
1 ATATATTATTAAATT-TT-T
* **
2215908 AATATGTTATTTTATATTTT
1 -ATATATTATTAAAT-TTTT
* **
2215928 A-ATATTTTTTTATTTTT
1 ATATATTATTAAATTTTT
2215945 ATATATTATTAAATTTTT
1 ATATATTATTAAATTTTT
2215963 TATTTGTAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
17 5 0.11
18 23 0.52
19 1 0.02
20 1 0.02
21 13 0.30
22 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (18 bp):
ATATATTATTAAATTTTT
Found at i:2216069 original size:12 final size:12
Alignment explanation
Indices: 2216025--2216091 Score: 64
Period size: 12 Copynumber: 5.2 Consensus size: 12
2216015 ATTAGATTTA
2216025 TATATTAATTAAT
1 TATATT-ATTAAT
2216038 TATATGAATATTTAAT
1 TATAT---TA-TTAAT
*
2216054 TATATTATTAAG
1 TATATTATTAAT
2216066 TATATTATTAAT
1 TATATTATTAAT
*
2216078 TATTTTATT-AT
1 TATATTATTAAT
2216089 TAT
1 TAT
2216092 TTTCTTTATA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
11 5 0.11
12 23 0.49
13 7 0.15
15 1 0.02
16 11 0.23
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (12 bp):
TATATTATTAAT
Found at i:2216177 original size:15 final size:16
Alignment explanation
Indices: 2216157--2216189 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2216147 TTTAGATAGA
2216157 TTTAAAAAA-ATTATT
1 TTTAAAAAATATTATT
2216172 TTTAAAAAATATTATT
1 TTTAAAAAATATTATT
2216188 TT
1 TT
2216190 GATGTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAAAAAATATTATT
Found at i:2217747 original size:18 final size:19
Alignment explanation
Indices: 2217717--2217754 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2217707 CATCATATAA
2217717 TATTTATTATA-TTATTTT
1 TATTTATTATATTTATTTT
2217735 TATTT-TTACTATTTATTTT
1 TATTTATTA-TATTTATTTT
2217754 T
1 T
2217755 TTATATCGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.17
18 7 0.39
19 8 0.44
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTATTATATTTATTTT
Found at i:2218161 original size:19 final size:20
Alignment explanation
Indices: 2218139--2218176 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2218129 TAAAAATTAT
*
2218139 TATA-TATTTATAAAATTTG
1 TATAGTATTAATAAAATTTG
*
2218158 TATAGTATTAATTAAATTT
1 TATAGTATTAATAAAATTT
2218177 TAAATATGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
TATAGTATTAATAAAATTTG
Found at i:2218864 original size:14 final size:15
Alignment explanation
Indices: 2218845--2218876 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2218835 TTTTTTTATA
2218845 TTTTTTTC-TTTTTC
1 TTTTTTTCATTTTTC
2218859 TTTTTTTCATTTTTC
1 TTTTTTTCATTTTTC
2218874 TTT
1 TTT
2218877 AATCAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTTCATTTTTC
Found at i:2219880 original size:15 final size:15
Alignment explanation
Indices: 2219860--2219933 Score: 80
Period size: 15 Copynumber: 5.1 Consensus size: 15
2219850 TATTTAACAC
2219860 AAATATTTTTGATAT
1 AAATATTTTTGATAT
2219875 AAATATTTTTGATAT
1 AAATATTTTTGATAT
* * *
2219890 AGATA-TTTTAACAT
1 AAATATTTTTGATAT
*
2219904 AGATA-TTTTGATAT
1 AAATATTTTTGATAT
* *
2219918 AAATATCTTCGATAT
1 AAATATTTTTGATAT
2219933 A
1 A
2219934 TGTACTTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
14 23 0.46
15 27 0.54
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (15 bp):
AAATATTTTTGATAT
Found at i:2219914 original size:43 final size:44
Alignment explanation
Indices: 2219852--2219963 Score: 131
Period size: 43 Copynumber: 2.6 Consensus size: 44
2219842 ATAAATTTTA
* * * *
2219852 TTTAACACAAATATTTTTGATATAAATATTTTTGATATA-GATAT
1 TTTAACATAAATATTTTTGATATAAATATCTTCGATATATG-TAC
*
2219896 TTTAACATAGATA-TTTTGATATAAATATCTTCGATATATGTAC
1 TTTAACATAAATATTTTTGATATAAATATCTTCGATATATGTAC
*
2219939 TTTAACATAAGTATCTTTT-ATATAA
1 TTTAACATAAATAT-TTTTGATATAA
2219964 TTATATTAGT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
43 36 0.62
44 18 0.31
45 4 0.07
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (44 bp):
TTTAACATAAATATTTTTGATATAAATATCTTCGATATATGTAC
Found at i:2221436 original size:2 final size:2
Alignment explanation
Indices: 2221429--2221460 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2221419 TGTGCTTTAT
2221429 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2221461 GATCTTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2221859 original size:2 final size:2
Alignment explanation
Indices: 2221852--2221884 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2221842 TAATTGAAGG
2221852 AT AT 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 AT AT A
2221885 GATTACAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2222383 original size:63 final size:62
Alignment explanation
Indices: 2222307--2222439 Score: 198
Period size: 63 Copynumber: 2.1 Consensus size: 62
2222297 TTTCAATTTT
* * *
2222307 TCATGAAATTAATTAAGT-TTATGATAG-TAGTAAATTAAAACTATATTTGGGTTATAAGCAAA
1 TCATTAAATTAATTAAGTCGT-TGATAGAT-GTAAATTAAAACTATATTTGAGTTATAAGCAAA
2222369 TCATTAAATTTAATTAAGTCGTTGATAGATGTAAATTAAAACTATATTTGAGTTATAAGCAAA
1 TCATTAAA-TTAATTAAGTCGTTGATAGATGTAAATTAAAACTATATTTGAGTTATAAGCAAA
2222432 TCATTAAA
1 TCATTAAA
2222440 GATATATAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
62 7 0.11
63 56 0.86
64 2 0.03
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.38
Consensus pattern (62 bp):
TCATTAAATTAATTAAGTCGTTGATAGATGTAAATTAAAACTATATTTGAGTTATAAGCAAA
Found at i:2223296 original size:18 final size:18
Alignment explanation
Indices: 2223273--2223308 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2223263 AATGTAAAAT
* *
2223273 TTAATAATTTTTTATTTA
1 TTAATAAATATTTATTTA
2223291 TTAATAAATATTTATTTA
1 TTAATAAATATTTATTTA
2223309 ATAAAATTAA
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTAATAAATATTTATTTA
Found at i:2223304 original size:14 final size:15
Alignment explanation
Indices: 2223285--2223313 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2223275 AATAATTTTT
2223285 TATTTA-TTAATAAA
1 TATTTATTTAATAAA
2223299 TATTTATTTAATAAA
1 TATTTATTTAATAAA
2223314 ATTAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTATTTAATAAA
Found at i:2223434 original size:6 final size:6
Alignment explanation
Indices: 2223423--2223457 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
2223413 TTTAAAAAAT
*
2223423 TATTTA TATTTA TACTTA TATTTA TATTTA TATTT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTT
2223458 GTGTATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (6 bp):
TATTTA
Found at i:2223818 original size:26 final size:26
Alignment explanation
Indices: 2223760--2223818 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 26
2223750 TTAAATAAAA
*
2223760 ATATTTTATTATATAAATAATAATTT
1 ATATTTAATTATATAAATAATAATTT
*
2223786 A-AATTAATT-TATATAATAA-AATATT
1 ATATTTAATTATATA-AATAATAAT-TT
2223811 ATATTTAA
1 ATATTTAA
2223819 ACTCAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
24 7 0.26
25 14 0.52
26 6 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATATTTAATTATATAAATAATAATTT
Found at i:2223884 original size:26 final size:26
Alignment explanation
Indices: 2223831--2223902 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
2223821 TCAATTTAAA
*
2223831 TTAATTTATAAATTAAA--TAAATAAC
1 TTAATTTTTAAA-TAAATTTAAATAAC
2223856 TTAATTTTTAAATAAATTTAAATAAC
1 TTAATTTTTAAATAAATTTAAATAAC
**
2223882 TTAACCTTTAAATAAATTTAA
1 TTAATTTTTAAATAAATTTAA
2223903 TATGAGTGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
24 4 0.10
25 11 0.26
26 27 0.64
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (26 bp):
TTAATTTTTAAATAAATTTAAATAAC
Found at i:2224340 original size:2 final size:2
Alignment explanation
Indices: 2224333--2224362 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2224323 CTCGTGCGTA
*
2224333 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2224363 GAAAATGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2226204 original size:2 final size:2
Alignment explanation
Indices: 2226197--2226234 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2226187 AACCATCAAA
2226197 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2226235 TACTTGAGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2227554 original size:23 final size:23
Alignment explanation
Indices: 2227528--2227584 Score: 55
Period size: 23 Copynumber: 2.4 Consensus size: 23
2227518 AATCATAAAA
2227528 AAATATAAATTATTAAATAT-ATT
1 AAATATAAATTA-TAAATATAATT
*
2227551 AAATTTTAAA-TATAAATATAATT
1 AAA-TATAAATTATAAATATAATT
*
2227574 ACATAATAAAT
1 AAAT-ATAAAT
2227585 GTAGCATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
22 8 0.30
23 14 0.52
24 5 0.19
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATATAAATTATAAATATAATT
Found at i:2227559 original size:16 final size:17
Alignment explanation
Indices: 2227533--2227564 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2227523 TAAAAAAATA
2227533 TAAATTATTAAATATAT
1 TAAATTATTAAATATAT
2227550 TAAATT-TTAAATATA
1 TAAATTATTAAATATA
2227565 AATATAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATTATTAAATATAT
Found at i:2229434 original size:31 final size:31
Alignment explanation
Indices: 2229376--2229434 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
2229366 ATATAAATTT
* * *
2229376 TTTTAATATATTAATAATGTATGAATATAAA
1 TTTTAACATAATAATAATATATGAATATAAA
* *
2229407 TTTTAACATAATATTAATATATTAATAT
1 TTTTAACATAATAATAATATATGAATAT
2229435 TATATTTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (31 bp):
TTTTAACATAATAATAATATATGAATATAAA
Found at i:2229439 original size:19 final size:18
Alignment explanation
Indices: 2229406--2229481 Score: 66
Period size: 19 Copynumber: 4.2 Consensus size: 18
2229396 ATGAATATAA
* *
2229406 ATTTTAACATAATATTAAT
1 ATTTTAATATTATATT-AT
* *
2229425 ATATTAATATTATATTTTT
1 ATTTTAATATTATA-TTAT
*
2229444 ATTTTTATATTATATTAT
1 ATTTTAATATTATATTAT
2229462 ATTTTAATTATT-T-TTAT
1 ATTTTAA-TATTATATTAT
2229479 ATT
1 ATT
2229482 ATATTTAAAC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
17 7 0.15
18 10 0.21
19 28 0.60
20 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTAATATTATATTAT
Found at i:2229471 original size:16 final size:16
Alignment explanation
Indices: 2229424--2229472 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 16
2229414 ATAATATTAA
* *
2229424 TATATTAATATTATAT
1 TATATTATTTTTATAT
2229440 T-T-TTATTTTTATAT
1 TATATTATTTTTATAT
2229454 TATATTATATTTTA-AT
1 TATATTAT-TTTTATAT
2229470 TAT
1 TAT
2229473 TTTTATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 11 0.39
15 2 0.07
16 10 0.36
17 5 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATATTATTTTTATAT
Found at i:2229472 original size:27 final size:24
Alignment explanation
Indices: 2229424--2229486 Score: 90
Period size: 27 Copynumber: 2.5 Consensus size: 24
2229414 ATAATATTAA
2229424 TATATTAATATTATATTTTTATTTT
1 TATATT-ATATTATATTTTTATTTT
2229449 TATATTATATTATATTTTAATTATTTT
1 TATATTATATTATA-TTT--TTATTTT
2229476 TATATTATATT
1 TATATTATATT
2229487 TAAACTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
24 8 0.23
25 9 0.26
27 18 0.51
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TATATTATATTATATTTTTATTTT
Found at i:2229481 original size:22 final size:24
Alignment explanation
Indices: 2229419--2229497 Score: 90
Period size: 24 Copynumber: 3.3 Consensus size: 24
2229409 TTAACATAAT
* *
2229419 ATTAATATATTAATATTATATTTTT
1 ATTATTATATT-ATATTATATTTTA
*
2229444 ATTTTTATATTATATTATATTTTA
1 ATTATTATATTATATTATATTTTA
*
2229468 ATTATT-T-TTATATTATATTTAA
1 ATTATTATATTATATTATATTTTA
2229490 ACTTATTA
1 A-TTATTA
2229498 AATGTACAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.32
23 6 0.13
24 17 0.36
25 9 0.19
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTATTATATTATATTATATTTTA
Found at i:2229488 original size:11 final size:11
Alignment explanation
Indices: 2229424--2229488 Score: 60
Period size: 11 Copynumber: 5.7 Consensus size: 11
2229414 ATAATATTAA
*
2229424 TATATTAATAT
1 TATATTTATAT
*
2229435 TATATTTTTATT
1 TATATTTATA-T
*
2229447 TTTATATTATAT
1 TATAT-TTATAT
2229459 TATATTT-TAAT
1 TATATTTAT-AT
*
2229470 TATTTTTATAT
1 TATATTTATAT
2229481 TATATTTA
1 TATATTTA
2229489 AACTTATTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
10 1 0.02
11 27 0.63
12 11 0.26
13 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATATTTATAT
Found at i:2232656 original size:14 final size:14
Alignment explanation
Indices: 2232637--2232665 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2232627 TGAAAAAAGG
2232637 TAAGTGGACAAAAC
1 TAAGTGGACAAAAC
2232651 TAAGTGGACAAAAC
1 TAAGTGGACAAAAC
2232665 T
1 T
2232666 CATCCCGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.14, G:0.21, T:0.17
Consensus pattern (14 bp):
TAAGTGGACAAAAC
Found at i:2233500 original size:10 final size:10
Alignment explanation
Indices: 2233482--2233518 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
2233472 CTTTTCTTAC
*
2233482 CTCTCTATCT
1 CTCTATATCT
2233492 CTCTATATCT
1 CTCTATATCT
2233502 CTCTAT-TC-
1 CTCTATATCT
2233510 CTCTATATC
1 CTCTATATC
2233519 CTTTCTTACC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
8 6 0.24
9 4 0.16
10 15 0.60
ACGTcount: A:0.16, C:0.35, G:0.00, T:0.49
Consensus pattern (10 bp):
CTCTATATCT
Found at i:2233505 original size:18 final size:18
Alignment explanation
Indices: 2233482--2233518 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2233472 CTTTTCTTAC
2233482 CTCTCTA-TCTCTCTATAT
1 CTCTCTATTC-CTCTATAT
2233500 CTCTCTATTCCTCTATAT
1 CTCTCTATTCCTCTATAT
2233518 C
1 C
2233519 CTTTCTTACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.16, C:0.35, G:0.00, T:0.49
Consensus pattern (18 bp):
CTCTCTATTCCTCTATAT
Found at i:2233804 original size:10 final size:10
Alignment explanation
Indices: 2233791--2233882 Score: 53
Period size: 10 Copynumber: 9.2 Consensus size: 10
2233781 TCTAGAACAC
2233791 TCTAGAATCT
1 TCTAGAATCT
**
2233801 TCTAGAGCCT
1 TCTAGAATCT
* * *
2233811 TCCATAATAT
1 TCTAGAATCT
2233821 TCTAGAA-CAT
1 TCTAGAATC-T
2233831 TCTAGAATCT
1 TCTAGAATCT
* **
2233841 TCCAGAGCCT
1 TCTAGAATCT
* * *
2233851 TCCACAATAT
1 TCTAGAATCT
2233861 TCTAGAA-CAT
1 TCTAGAATC-T
2233871 TCTAGAATCT
1 TCTAGAATCT
2233881 TC
1 TC
2233883 CAAAGCCTTT
Statistics
Matches: 58, Mismatches: 20, Indels: 8
0.67 0.23 0.09
Matches are distributed among these distances:
10 56 0.97
11 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.34
Consensus pattern (10 bp):
TCTAGAATCT
Found at i:2233804 original size:40 final size:40
Alignment explanation
Indices: 2233764--2233992 Score: 329
Period size: 40 Copynumber: 5.7 Consensus size: 40
2233754 ATAAAGTTCT
* *
2233764 AGAACCTTCCAC-ATTATTCTAGAACACTCTAGAATCTTCT
1 AGAACCTTCCACGA-TATTCTAGAACATTCTAGAATCTTCC
* **
2233804 AGAGCCTTCCATAATATTCTAGAACATTCTAGAATCTTCC
1 AGAACCTTCCACGATATTCTAGAACATTCTAGAATCTTCC
* *
2233844 AGAGCCTTCCACAATATTCTAGAACATTCTAGAATCTTCC
1 AGAACCTTCCACGATATTCTAGAACATTCTAGAATCTTCC
*
2233884 A-AAGCCTTTCACGATATTCTAGAACATTCTAGAATCTTCC
1 AGAA-CCTTCCACGATATTCTAGAACATTCTAGAATCTTCC
*
2233924 AGAGCCTTCCACGATATTCTAGAACATTCTAGAATCTTCC
1 AGAACCTTCCACGATATTCTAGAACATTCTAGAATCTTCC
2233964 A-AAGCCTTCCACGATATTCTAGAACATTC
1 AGAA-CCTTCCACGATATTCTAGAACATTC
2233993 CAAAGTGTTC
Statistics
Matches: 174, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
39 2 0.01
40 170 0.98
41 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.31
Consensus pattern (40 bp):
AGAACCTTCCACGATATTCTAGAACATTCTAGAATCTTCC
Found at i:2233843 original size:30 final size:29
Alignment explanation
Indices: 2233714--2233844 Score: 75
Period size: 30 Copynumber: 4.4 Consensus size: 29
2233704 CTAGTCTTGG
* *
2233714 AGAATTTTCCATAAGCTTCTAGAACATTCC
1 AGAATCTTCCATAA-ATTCTAGAACATTCC
* * *
2233744 ATAATCCTCCATAAAGTTCTAGAACCTTCC
1 AGAATCTTCCATAAA-TTCTAGAACATTCC
* * * * * * *
2233774 ACATTATTCTAGAACACTCTAGAATC-TTCT
1 AGAATCTTCCATAA-ATTCTAGAA-CATTCC
** *
2233804 AGAGCCTTCCATAATATTCTAGAACATTCT
1 AGAATCTTCCATAA-ATTCTAGAACATTCC
2233834 AGAATCTTCCA
1 AGAATCTTCCA
2233845 GAGCCTTCCA
Statistics
Matches: 74, Mismatches: 23, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
29 1 0.01
30 71 0.96
31 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.33
Consensus pattern (29 bp):
AGAATCTTCCATAAATTCTAGAACATTCC
Found at i:2233875 original size:80 final size:80
Alignment explanation
Indices: 2233768--2233992 Score: 378
Period size: 80 Copynumber: 2.8 Consensus size: 80
2233758 AGTTCTAGAA
* * * * **
2233768 CCTTCCACATTATTCTAGAACACTCTAGAATCTTCTAGAGCCTTCCATAATATTCTAGAACATTC
1 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTTCCACGATATTCTAGAACATTC
2233833 TAGAATCTTCCAGAG
66 TAGAATCTTCCAGAG
*
2233848 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTTTCACGATATTCTAGAACATTC
1 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTTCCACGATATTCTAGAACATTC
2233913 TAGAATCTTCCAGAG
66 TAGAATCTTCCAGAG
*
2233928 CCTTCCACGATATTCTAGAACATTCTAGAATCTTCCAAAGCCTTCCACGATATTCTAGAACATTC
1 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTTCCACGATATTCTAGAACATTC
2233993 CAAAGTGTTC
Statistics
Matches: 136, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 136 1.00
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.32
Consensus pattern (80 bp):
CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTTCCACGATATTCTAGAACATTC
TAGAATCTTCCAGAG
Found at i:2237575 original size:10 final size:10
Alignment explanation
Indices: 2237557--2237593 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
2237547 CTTTTCTTAC
*
2237557 CTCTCTATCT
1 CTCTATATCT
2237567 CTCTATATCT
1 CTCTATATCT
2237577 CTCTAT-TC-
1 CTCTATATCT
2237585 CTCTATATC
1 CTCTATATC
2237594 CTTTCTTACC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
8 6 0.24
9 4 0.16
10 15 0.60
ACGTcount: A:0.16, C:0.35, G:0.00, T:0.49
Consensus pattern (10 bp):
CTCTATATCT
Found at i:2237580 original size:18 final size:18
Alignment explanation
Indices: 2237557--2237593 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2237547 CTTTTCTTAC
2237557 CTCTCTA-TCTCTCTATAT
1 CTCTCTATTC-CTCTATAT
2237575 CTCTCTATTCCTCTATAT
1 CTCTCTATTCCTCTATAT
2237593 C
1 C
2237594 CTTTCTTACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.16, C:0.35, G:0.00, T:0.49
Consensus pattern (18 bp):
CTCTCTATTCCTCTATAT
Found at i:2237869 original size:10 final size:10
Alignment explanation
Indices: 2237854--2237952 Score: 67
Period size: 10 Copynumber: 9.9 Consensus size: 10
2237844 CTTCCACATT
2237854 ATTCTAGAAC
1 ATTCTAGAAC
2237864 ATTCTAGAATC
1 ATTCTAGAA-C
*
2237875 -TTCTAGAGC
1 ATTCTAGAAC
* * * *
2237884 CTTCCATAAT
1 ATTCTAGAAC
2237894 ATTCTAGAAC
1 ATTCTAGAAC
2237904 ATTCTAGAATC
1 ATTCTAGAA-C
* *
2237915 -TTCCAGAGC
1 ATTCTAGAAC
* * * *
2237924 CTTCCACAAT
1 ATTCTAGAAC
2237934 ATTCTAGAAC
1 ATTCTAGAAC
2237944 ATTCTAGAA
1 ATTCTAGAA
2237953 TCTTCCAAAG
Statistics
Matches: 67, Mismatches: 18, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
9 2 0.03
10 63 0.94
11 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.32
Consensus pattern (10 bp):
ATTCTAGAAC
Found at i:2237879 original size:40 final size:40
Alignment explanation
Indices: 2237839--2238067 Score: 338
Period size: 40 Copynumber: 5.7 Consensus size: 40
2237829 ATAAAGTTCT
*
2237839 AGAACCTTCCAC-ATTATTCTAGAACATTCTAGAATCTTCT
1 AGAACCTTCCACGA-TATTCTAGAACATTCTAGAATCTTCC
* **
2237879 AGAGCCTTCCATAATATTCTAGAACATTCTAGAATCTTCC
1 AGAACCTTCCACGATATTCTAGAACATTCTAGAATCTTCC
* *
2237919 AGAGCCTTCCACAATATTCTAGAACATTCTAGAATCTTCC
1 AGAACCTTCCACGATATTCTAGAACATTCTAGAATCTTCC
*
2237959 A-AAGCCTTTCACGATATTCTAGAACATTCTAGAATCTTCC
1 AGAA-CCTTCCACGATATTCTAGAACATTCTAGAATCTTCC
*
2237999 AGAGCCTTCCACGATATTCTAGAACATTCTAGAATCTTCC
1 AGAACCTTCCACGATATTCTAGAACATTCTAGAATCTTCC
2238039 A-AAGCCTTCCACGATATTCTAGAACATTC
1 AGAA-CCTTCCACGATATTCTAGAACATTC
2238068 CAAAGTGTTC
Statistics
Matches: 175, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
39 2 0.01
40 171 0.98
41 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.31
Consensus pattern (40 bp):
AGAACCTTCCACGATATTCTAGAACATTCTAGAATCTTCC
Found at i:2237918 original size:30 final size:29
Alignment explanation
Indices: 2237789--2237919 Score: 84
Period size: 30 Copynumber: 4.4 Consensus size: 29
2237779 CTAGTCTTGG
* *
2237789 AGAATTTTCCATAAGCTTCTAGAACATTCC
1 AGAATCTTCCATAA-ATTCTAGAACATTCC
* * *
2237819 ATAATCCTCCATAAAGTTCTAGAACCTTCC
1 AGAATCTTCCATAAA-TTCTAGAACATTCC
* * * * * *
2237849 ACATTATTCTAGAACATTCTAGAATC-TTCT
1 AGAATCTTCCATAA-ATTCTAGAA-CATTCC
** *
2237879 AGAGCCTTCCATAATATTCTAGAACATTCT
1 AGAATCTTCCATAA-ATTCTAGAACATTCC
2237909 AGAATCTTCCA
1 AGAATCTTCCA
2237920 GAGCCTTCCA
Statistics
Matches: 76, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
29 1 0.01
30 73 0.96
31 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (29 bp):
AGAATCTTCCATAAATTCTAGAACATTCC
Found at i:2237947 original size:80 final size:80
Alignment explanation
Indices: 2237843--2238067 Score: 387
Period size: 80 Copynumber: 2.8 Consensus size: 80
2237833 AGTTCTAGAA
* * * **
2237843 CCTTCCACATTATTCTAGAACATTCTAGAATCTTCTAGAGCCTTCCATAATATTCTAGAACATTC
1 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTTCCACGATATTCTAGAACATTC
2237908 TAGAATCTTCCAGAG
66 TAGAATCTTCCAGAG
*
2237923 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTTTCACGATATTCTAGAACATTC
1 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTTCCACGATATTCTAGAACATTC
2237988 TAGAATCTTCCAGAG
66 TAGAATCTTCCAGAG
*
2238003 CCTTCCACGATATTCTAGAACATTCTAGAATCTTCCAAAGCCTTCCACGATATTCTAGAACATTC
1 CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTTCCACGATATTCTAGAACATTC
2238068 CAAAGTGTTC
Statistics
Matches: 137, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 137 1.00
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.32
Consensus pattern (80 bp):
CCTTCCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTTCCACGATATTCTAGAACATTC
TAGAATCTTCCAGAG
Found at i:2238484 original size:25 final size:25
Alignment explanation
Indices: 2238456--2238504 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2238446 CTGTGACATG
* *
2238456 TAAA-AAATAATTATATTAGAAAACC
1 TAAATAAATAAATATA-GAGAAAACC
2238481 TAAATAAATAAATATAGAGAAAAC
1 TAAATAAATAAATATAGAGAAAAC
2238505 ATATACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.24
Consensus pattern (25 bp):
TAAATAAATAAATATAGAGAAAACC
Found at i:2239444 original size:17 final size:16
Alignment explanation
Indices: 2239408--2239448 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2239398 ATCCGAACAT
*
2239408 AAAATAACCAAAACCC
1 AAAATGACCAAAACCC
*
2239424 AAAATGACCCAAACCC
1 AAAATGACCAAAACCC
2239440 GAAAATGAC
1 -AAAATGAC
2239449 TCGAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.56, C:0.29, G:0.07, T:0.07
Consensus pattern (16 bp):
AAAATGACCAAAACCC
Found at i:2239920 original size:27 final size:24
Alignment explanation
Indices: 2239886--2239954 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 24
2239876 TTTTACTTTA
2239886 ATAATATAAAAAATAATATAAACAC
1 ATAATATAAAAAATAATATAAA-AC
* *
2239911 GATATTTATAAAAAAT-ATTTAAAAC
1 -ATA-ATATAAAAAATAATATAAAAC
2239936 ATAATAT-AAAAATAATATA
1 ATAATATAAAAAATAATATA
2239955 CAAATGACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
22 6 0.16
23 7 0.19
24 3 0.08
25 2 0.05
26 9 0.24
27 10 0.27
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.30
Consensus pattern (24 bp):
ATAATATAAAAAATAATATAAAAC
Found at i:2239950 original size:11 final size:11
Alignment explanation
Indices: 2239885--2239959 Score: 53
Period size: 11 Copynumber: 6.3 Consensus size: 11
2239875 TTTTTACTTT
2239885 AATAATATAAAA
1 AATAATAT-AAA
2239897 AATAATATAAA
1 AATAATATAAA
*
2239908 CACGATATTTATAAA
1 -A--ATA-ATATAAA
*
2239923 AA-ATATTTAAA
1 AATA-ATATAAA
2239934 ACATAATATAAA
1 A-ATAATATAAA
*
2239946 AATAATATACA
1 AATAATATAAA
2239957 AAT
1 AAT
2239960 GACATGAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
11 23 0.44
12 18 0.35
13 1 0.02
14 4 0.08
15 6 0.12
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.29
Consensus pattern (11 bp):
AATAATATAAA
Found at i:2240097 original size:18 final size:18
Alignment explanation
Indices: 2240057--2240096 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2240047 AAATACAAAC
*
2240057 TTTTTCTTTATTTCTTTA
1 TTTTTCTTTATTTATTTA
*
2240075 TTTTTCTTTTTTTATTT-
1 TTTTTCTTTATTTATTTA
2240092 TTTTT
1 TTTTT
2240097 TTCACTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTCTTTATTTATTTA
Found at i:2240619 original size:27 final size:28
Alignment explanation
Indices: 2240576--2240689 Score: 71
Period size: 27 Copynumber: 4.1 Consensus size: 28
2240566 TAAAAAAAAA
*
2240576 ATTAAATTTGATA-ATTTACATATTTAT
1 ATTAAATTTAATATATTTACATATTTAT
* *
2240603 ATTATATTT-ATATATTTTATCATA-TCAT
1 ATTAAATTTAATATA-TTTA-CATATTTAT
* * *
2240631 AATTATATTTAAAATATTT-TATATTTAT
1 -ATTAAATTTAATATATTTACATATTTAT
*
2240659 A-TAAATTTTAT-TATGTTA-ATAATTTAT
1 ATTAAATTTAATATAT-TTACAT-ATTTAT
2240686 ATTA
1 ATTA
2240690 CATAAATTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
25 3 0.04
26 14 0.20
27 20 0.29
28 12 0.17
29 16 0.23
30 4 0.06
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (28 bp):
ATTAAATTTAATATATTTACATATTTAT
Found at i:2242373 original size:24 final size:24
Alignment explanation
Indices: 2242340--2242394 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
2242330 GAAAGAATCT
* *
2242340 CTAATAAAAAT-TCTTAATATTATG
1 CTAATTAAAATCTC-TAATATAATG
2242364 CTAATTAAAATCTCTAATATAATG
1 CTAATTAAAATCTCTAATATAATG
*
2242388 TTAATTA
1 CTAATTA
2242395 CAAAATTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (24 bp):
CTAATTAAAATCTCTAATATAATG
Found at i:2244376 original size:50 final size:51
Alignment explanation
Indices: 2244297--2244407 Score: 179
Period size: 50 Copynumber: 2.2 Consensus size: 51
2244287 TAAAAGTCGT
* * *
2244297 GGTTGGAGTATCCCTGAGATGAAACATTTAATATTTTGAAAATAAAAATGG
1 GGTTGGAGTATCCCTGAGATGAAAAATTTAATATTTTGAAAATAAAAACGA
*
2244348 GGTTGGAGTATCTC-GAGATGAAAAATTTAATATTTTGAAAATAAAAACGA
1 GGTTGGAGTATCCCTGAGATGAAAAATTTAATATTTTGAAAATAAAAACGA
2244398 GGTTGGAGTA
1 GGTTGGAGTA
2244408 CCCCCCTTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
50 43 0.77
51 13 0.23
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCTGAGATGAAAAATTTAATATTTTGAAAATAAAAACGA
Found at i:2249020 original size:80 final size:80
Alignment explanation
Indices: 2248873--2249056 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
2248863 TTCATTGATG
* * ** *
2248873 TTTTTATTTCTAAAACACTAATTTTTTATAATCGGAGATACTCTAACCTCGTTATTTTTGAGGAG
1 TTTTTATTTCTAAAACACTAATTTTTCATAATCGGAGATACTCCAACCTCGTTATTTTCAAAGAG
2248938 ATACTCCAACCTAGA
66 ATACTCCAACCTAGA
* * * * *
2248953 TTTTTATTTTTAAAACA-TCGATTTTTCATAATCGGGGATGCTCCAACCTCGTTATTTTCAAATA
1 TTTTTATTTCTAAAACACT-AATTTTTCATAATCGGAGATACTCCAACCTCGTTATTTTCAAAGA
* *
2249017 GATACTCCAATCTCG-
65 GATACTCCAACCTAGA
* *
2249032 GTTTTACTTCTAAAACACTAATTTT
1 TTTTTATTTCTAAAACACTAATTTT
2249057 CCACCATCGG
Statistics
Matches: 86, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
79 20 0.23
80 66 0.77
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.41
Consensus pattern (80 bp):
TTTTTATTTCTAAAACACTAATTTTTCATAATCGGAGATACTCCAACCTCGTTATTTTCAAAGAG
ATACTCCAACCTAGA
Found at i:2249231 original size:186 final size:186
Alignment explanation
Indices: 2248954--2249292 Score: 414
Period size: 186 Copynumber: 1.8 Consensus size: 186
2248944 CAACCTAGAT
* * * * * * *
2248954 TTTTATTTTTAAAACATCGATTTTTCATAATCGGGGATGCTCCAACCTCGTTATTTTCAAATAGA
1 TTTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTCGTTATTTTCAAAGAGA
* * * *
2249019 TACTCCAATCTCGGTTTTACTTCTAAAACACTAATTTTCCACCA-TCGGGGGTGCTCCAAC-CAT
66 TACTCCAACCTCGGTTTTACTTCTAAAACACTAATTTTCCA-CATTCGAGGATACTCCAACTC-T
2249082 GTTATTTTCGAGGGGATACTCTAACGCCGTTACTTTTAAAGGGATACTCTAACCCCGG
129 GTTATTTTCGAGGGGATACTCTAACGCCGTTACTTTTAAAGGGATACTCTAACCCCGG
* * * * *
2249140 TTTTATTTCTAAAACACCAATTTTCCACCATTGGGGATACTCCAACC-CTGTTATTTTCGAGGGG
1 TTTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTC-GTTATTTTCAAAGAG
* * * * * *
2249204 ATACTCTAACCTCGGTTTTATTTCTAAAACATTGATTTTTCACATTCGAGGATACTTCAACTCTG
65 ATACTCCAACCTCGGTTTTACTTCTAAAACACTAATTTTCCACATTCGAGGATACTCCAACTCTG
**
2249269 TTATTTTTTAGGGGATACTCTAAC
130 TTATTTTCGAGGGGATACTCTAAC
2249293 TCCGGTTTAT
Statistics
Matches: 126, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
185 3 0.02
186 122 0.97
187 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (186 bp):
TTTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTCGTTATTTTCAAAGAGA
TACTCCAACCTCGGTTTTACTTCTAAAACACTAATTTTCCACATTCGAGGATACTCCAACTCTGT
TATTTTCGAGGGGATACTCTAACGCCGTTACTTTTAAAGGGATACTCTAACCCCGG
Found at i:2249322 original size:158 final size:157
Alignment explanation
Indices: 2249122--2249604 Score: 516
Period size: 158 Copynumber: 3.1 Consensus size: 157
2249112 TACTTTTAAA
*
2249122 GGGATACTCTAACCCCGGTTTTATTTCTAAAACACCAATTTTCCACCATTGGGGATACTCCAACC
1 GGGATACTCTAACCCCGGTTTTATTTCTAAAACACTAATTTT-CACCATTGGGGATACTCCAACC
**
2249187 CTGTTATTTTCGAGGGGATACTCTAACCTCGGTTTTATTTCTAAAACATTGATTTTTCACATTCG
65 CTGTTATTTTCGAGGGGATACTCTAACCTCGGTTTTATTTCTAAAACATCAATTTTTCACATTCG
* **
2249252 AGGATACTTCAACTCTGTTATTTTTTAG
130 GGGATACTTCAACTCTGTTATTTTCGAG
* * * *
2249280 GGGATACTCTAACTCCGG-TTTATTT-TCAAAACACTAATTTTTCAGCATCGGGGATACTTCAAC
1 GGGATACTCTAACCCCGGTTTTATTTCT-AAAACACTAA-TTTTCACCATTGGGGATACTCCAAC
* * * *
2249343 CCTATTATTTTCGAGGGAATACTCCAATCC-CAGTTTTATTT-TCAAAACATCAATTTTTC-CAT
64 CCTGTTATTTTCGAGGGGATACTCTAA-CCTCGGTTTTATTTCT-AAAACATCAATTTTTCACAT
* * *
2249405 AATTGGGGATAC-TCTAACCCCGTTATTTTCGAG
127 --TCGGGGATACTTC-AACTCTGTTATTTTCGAG
*** * * * * **
2249438 AAAATACTCCAACCCCGATTTTATTTCTAAAATACTGATTTTGCATAATTGGGGATACTCCAACG
1 GGGATACTCTAACCCCGGTTTTATTTCTAAAACACTAATTTT-CACCATTGGGGATACTCCAAC-
* * * *
2249503 CC-GTTATTTTTGAGGGGATATTTTAACCTCGGTTTTATTTCCAAAACATCAATTTTTCACCA-T
64 CCTGTTATTTTCGAGGGGATACTCTAACCTCGGTTTTATTTCTAAAACATCAATTTTTCA-CATT
*
2249566 CGGGGATACTTTAA-TCTTGTTATTTTCGAG
128 CGGGGATACTTCAACTC-TGTTATTTTCGAG
2249596 GGGATACTC
1 GGGATACTC
2249605 CGATCCCATT
Statistics
Matches: 264, Mismatches: 44, Indels: 34
0.77 0.13 0.10
Matches are distributed among these distances:
156 5 0.02
157 85 0.32
158 92 0.35
159 77 0.29
160 3 0.01
161 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (157 bp):
GGGATACTCTAACCCCGGTTTTATTTCTAAAACACTAATTTTCACCATTGGGGATACTCCAACCC
TGTTATTTTCGAGGGGATACTCTAACCTCGGTTTTATTTCTAAAACATCAATTTTTCACATTCGG
GGATACTTCAACTCTGTTATTTTCGAG
Found at i:2249618 original size:79 final size:79
Alignment explanation
Indices: 2249122--2249641 Score: 396
Period size: 79 Copynumber: 6.6 Consensus size: 79
2249112 TACTTTTAAA
* * * * *
2249122 GGGATACT-CTAACCCCGGTTTTATTTCTAAAACACCAATTTTCCACCATTGGGGATACTCCAAC
1 GGGATACTCCTAA-CCCAGTTTTATTTCCAAAACATCAATTTTTCACCATCGGGGATACTCCAAC
2249186 CCTGTTATTTTCGAG
65 CCTGTTATTTTCGAG
* * ** * *
2249201 GGGATACT-CTAACCTCGGTTTTATTTCTAAAACATTGATTTTTCA-CATTCGAGGATACTTCAA
1 GGGATACTCCTAACC-CAGTTTTATTTCCAAAACATCAATTTTTCACCA-TCGGGGATACTCCAA
* **
2249264 CTCTGTTATTTTTTAG
64 CCCTGTTATTTTCGAG
* * * *
2249280 GGGATACT-CTAACTCC-GGTTTATTTTCAAAACA-CTAATTTTTCAGCATCGGGGATACTTCAA
1 GGGATACTCCTAAC-CCAGTTTTATTTCCAAAACATC-AATTTTTCACCATCGGGGATACTCCAA
*
2249342 CCCTATTATTTTCGAG
64 CCCTGTTATTTTCGAG
* * ** * *
2249358 GGAATACTCC-AATCCCAGTTTTATTTTCAAAACATCAATTTTTCCATAATTGGGGATACTCTAA
1 GGGATACTCCTAA-CCCAGTTTTATTTCCAAAACATCAATTTTT-CACCATCGGGGATACTCCAA
*
2249422 CCCCGTTATTTTCGAG
64 CCCTGTTATTTTCGAG
*** * * * * * ** *
2249438 AAAATACTCC-AACCCCGATTTTATTTCTAAAATA-CTGATTTTGCATAATTGGGGATACTCCAA
1 GGGATACTCCTAACCCAG-TTTTATTTCCAAAACATC-AATTTTTCACCATCGGGGATACTCCAA
*
2249501 CGCC-GTTATTTTTGAG
64 C-CCTGTTATTTTCGAG
** * ** *
2249517 GGGATA-TTTTAACCTCGGTTTTATTTCCAAAACATCAATTTTTCACCATCGGGGATACTTTAAT
1 GGGATACTCCTAACC-CAGTTTTATTTCCAAAACATCAATTTTTCACCATCGGGGATACTCCAAC
*
2249581 CTTGTTATTTTCGAG
65 CCTGTTATTTTCGAG
* * * * * *
2249596 GGGATACTCCGATCCCATTTTTATCTCCAAAATATTAAATTTTTCA
1 GGGATACTCCTAACCCAGTTTTATTTCCAAAACA-TCAATTTTTCA
2249642 TCGAAGGATG
Statistics
Matches: 356, Mismatches: 66, Indels: 37
0.78 0.14 0.08
Matches are distributed among these distances:
78 65 0.18
79 213 0.60
80 78 0.22
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (79 bp):
GGGATACTCCTAACCCAGTTTTATTTCCAAAACATCAATTTTTCACCATCGGGGATACTCCAACC
CTGTTATTTTCGAG
Found at i:2251568 original size:52 final size:50
Alignment explanation
Indices: 2251495--2251613 Score: 157
Period size: 52 Copynumber: 2.3 Consensus size: 50
2251485 GTCAAAATAG
* * * *
2251495 CCTGCATGTATTGATACAATGAAGAATGTATCGATACATTTAGGTAAAAAA
1 CCTGAATGTATAGATACAATGAAAAATGTATCGATACATTTAAGT-AAAAA
*
2251546 TCCTGAATGTATAGATACAATGAAAAATGTATCGATACATTTAAGTTAAAA
1 -CCTGAATGTATAGATACAATGAAAAATGTATCGATACATTTAAGTAAAAA
*
2251597 CCTAGAATGTATCGATA
1 CCT-GAATGTATAGATA
2251614 AATTTTCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
50 3 0.05
51 16 0.27
52 41 0.68
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (50 bp):
CCTGAATGTATAGATACAATGAAAAATGTATCGATACATTTAAGTAAAAA
Found at i:2251726 original size:21 final size:20
Alignment explanation
Indices: 2251674--2251728 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
2251664 ATATTTCAGA
*
2251674 TATGTTTCGATACATTCACT
1 TATGTATCGATACATTCACT
2251694 TATGTATCGATACATTCACT
1 TATGTATCGATACATTCACT
* *
2251714 ATTTGTATTGATACA
1 -TATGTATCGATACA
2251729 AATTGTAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (20 bp):
TATGTATCGATACATTCACT
Found at i:2252420 original size:30 final size:29
Alignment explanation
Indices: 2252369--2252425 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
2252359 TTTGAGGAAA
*
2252369 AAAAGAATAAAATAACGAAAATAGATAAAG
1 AAAAGAAAAAAATAACGAAAATA-ATAAAG
**
2252399 AAAAGAAAAAAATAATTAAAATAATAA
1 AAAAGAAAAAAATAACGAAAATAATAA
2252426 TAATAATAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.16
Consensus pattern (29 bp):
AAAAGAAAAAAATAACGAAAATAATAAAG
Found at i:2252988 original size:17 final size:18
Alignment explanation
Indices: 2252948--2252990 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
2252938 TCATAAACAT
* *
2252948 GATAAAAAGTGGAAAAAA
1 GATAAAAAATAGAAAAAA
2252966 GA-AAAAAATAGAAAAAA
1 GATAAAAAATAGAAAAAA
2252983 -ATAAAAAA
1 GATAAAAAA
2252991 AAATTATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 1 0.05
17 19 0.86
18 2 0.09
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (18 bp):
GATAAAAAATAGAAAAAA
Found at i:2255866 original size:21 final size:20
Alignment explanation
Indices: 2255826--2255883 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
2255816 AATAATCTTC
2255826 TTGAAAAG-AAATCAAATGAG
1 TTGAAAAGAAAAT-AAATGAG
*
2255846 TTAGAAAAGAAAATAAGTGAG
1 TT-GAAAAGAAAATAAATGAG
2255867 TTGCAAAATGAAAATAA
1 TTG-AAAA-GAAAATAA
2255884 TGAATTGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.09
21 18 0.55
22 12 0.36
ACGTcount: A:0.57, C:0.03, G:0.19, T:0.21
Consensus pattern (20 bp):
TTGAAAAGAAAATAAATGAG
Found at i:2257381 original size:13 final size:13
Alignment explanation
Indices: 2257363--2257388 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2257353 CAAATAGTGG
2257363 ATGTATCGATACA
1 ATGTATCGATACA
2257376 ATGTATCGATACA
1 ATGTATCGATACA
2257389 TGCCTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2257459 original size:20 final size:20
Alignment explanation
Indices: 2257434--2257489 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
2257424 ACTGCTAAGG
2257434 AAATGTATCGATACATTAGT
1 AAATGTATCGATACATTAGT
2257454 AAATGTATCGATACATTAGT
1 AAATGTATCGATACATTAGT
2257474 AAATGTATCGATACAT
1 AAATGTATCGATACAT
2257490 GTTTACAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (20 bp):
AAATGTATCGATACATTAGT
Found at i:2263399 original size:20 final size:20
Alignment explanation
Indices: 2263374--2263425 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2263364 AACCCTGATT
*
2263374 TGTATCGATATAC-ATGCAGA
1 TGTATCGATACACGATGCA-A
*
2263394 TGTATCGATACACGTTGCAA
1 TGTATCGATACACGATGCAA
2263414 TGTATCGATACA
1 TGTATCGATACA
2263426 TTGTATTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (20 bp):
TGTATCGATACACGATGCAA
Found at i:2263437 original size:33 final size:33
Alignment explanation
Indices: 2263394--2263456 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
2263384 TACATGCAGA
*
2263394 TGTATCGATACACGTTGCAATGTATCGATACAT
1 TGTATCGATACACATTGCAATGTATCGATACAT
* *
2263427 TGTATTGATACATATTGCAATGTATCGATA
1 TGTATCGATACACATTGCAATGTATCGATA
2263457 TACGATGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (33 bp):
TGTATCGATACACATTGCAATGTATCGATACAT
Found at i:2263552 original size:21 final size:20
Alignment explanation
Indices: 2263504--2263581 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
2263494 GCTACCCTTC
* *
2263504 GATTGTATCAATACAAACGTGT
1 GATTGTATCGATAC-AA-GTCT
2263526 GATTGTATCGATACAAGTCT
1 GATTGTATCGATACAAGTCT
2263546 AGATTGTATCGATAC-A-TCT
1 -GATTGTATCGATACAAGTCT
2263565 GGAATTGTATCGATACA
1 -G-ATTGTATCGATACA
2263582 CTTGGTCCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
19 4 0.08
20 17 0.34
21 16 0.32
22 13 0.26
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
GATTGTATCGATACAAGTCT
Found at i:2264245 original size:41 final size:41
Alignment explanation
Indices: 2264183--2264261 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
2264173 TAGGTACCAA
2264183 GTTTAATCTCTTTCTCATTTGCATTATTTTATTTATCCGGT
1 GTTTAATCTCTTTCTCATTTGCATTATTTTATTTATCCGGT
*
2264224 GTTTGATCTCTTTCTCATTTGCATTATTTTATTTATCC
1 GTTTAATCTCTTTCTCATTTGCATTATTTTATTTATCC
2264262 ATTATTCCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.16, C:0.18, G:0.09, T:0.57
Consensus pattern (41 bp):
GTTTAATCTCTTTCTCATTTGCATTATTTTATTTATCCGGT
Found at i:2268434 original size:13 final size:13
Alignment explanation
Indices: 2268418--2268447 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2268408 ATACATTGTT
2268418 CATTGTATCGATA
1 CATTGTATCGATA
2268431 CATTGTATCGATA
1 CATTGTATCGATA
2268444 CATT
1 CATT
2268448 TTGGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:2268488 original size:20 final size:19
Alignment explanation
Indices: 2268463--2268569 Score: 91
Period size: 20 Copynumber: 5.7 Consensus size: 19
2268453 TTTACCCAGA
2268463 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
* *
2268483 TGTATCGATAGATTGCTCAT
1 TGTATCGATACATT-TTCAT
2268503 TGTATCGATACA--TT-A-
1 TGTATCGATACATTTTCAT
**
2268518 --TATCGATACATTGCCCAT
1 TGTATCGATACATT-TTCAT
*
2268536 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
2268556 TGTATCGATACATT
1 TGTATCGATACATT
2268570 CAGGCATTTT
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
13 10 0.14
16 1 0.01
17 2 0.03
20 55 0.80
21 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:2268516 original size:13 final size:13
Alignment explanation
Indices: 2268500--2268530 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2268490 ATAGATTGCT
2268500 CATTGTATCGATA
1 CATTGTATCGATA
*
2268513 CATTATATCGATA
1 CATTGTATCGATA
2268526 CATTG
1 CATTG
2268531 CCCATTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:2268531 original size:33 final size:33
Alignment explanation
Indices: 2268480--2268549 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
2268470 ATACATTTTG
* * *
2268480 CATTGTATCGATAGATTGCTCATTGTATCGATA
1 CATTATATCGATACATTGCCCATTGTATCGATA
2268513 CATTATATCGATACATTGCCCATTGTATCGATA
1 CATTATATCGATACATTGCCCATTGTATCGATA
2268546 CATT
1 CATT
2268550 TTACAATGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.39
Consensus pattern (33 bp):
CATTATATCGATACATTGCCCATTGTATCGATA
Found at i:2268537 original size:53 final size:53
Alignment explanation
Indices: 2268465--2268569 Score: 140
Period size: 53 Copynumber: 2.0 Consensus size: 53
2268455 TACCCAGATG
*** * *
2268465 TATCGATACATTTTGCATTGTATCGATAGATTGCT-CATTGTATCGATACATTA
1 TATCGATACATTGCCCATTGTATCGATACATT-CTACAATGTATCGATACATTA
*
2268518 TATCGATACATTGCCCATTGTATCGATACATTTTACAATGTATCGATACATT
1 TATCGATACATTGCCCATTGTATCGATACATTCTACAATGTATCGATACATT
2268570 CAGGCATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
52 1 0.02
53 44 0.98
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (53 bp):
TATCGATACATTGCCCATTGTATCGATACATTCTACAATGTATCGATACATTA
Found at i:2270945 original size:51 final size:51
Alignment explanation
Indices: 2270890--2271034 Score: 150
Period size: 51 Copynumber: 2.8 Consensus size: 51
2270880 ATCCCGGTTC
** *
2270890 TATTTCCAAAACATCAATTTTTCTTAATCG-GAGATACTCCAACTATGATTT
1 TATTTCCAAAACATCAATTTTTCGCAATCGAG-GATACTCCAACTACGATTT
* * * ** *
2270941 TATTTCTAAAGCATCGATTTACCGCAATCGAGGATACTCCAACTCCGATTT
1 TATTTCCAAAACATCAATTTTTCGCAATCGAGGATACTCCAACTACGATTT
* * *
2270992 TATTTCCAAAACACCAATTTTTCACAA-CTGGGGATACTCCAAC
1 TATTTCCAAAACATCAATTTTTCGCAATC-GAGGATACTCCAAC
2271035 CCCATTATTT
Statistics
Matches: 75, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
50 1 0.01
51 73 0.97
52 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.33
Consensus pattern (51 bp):
TATTTCCAAAACATCAATTTTTCGCAATCGAGGATACTCCAACTACGATTT
Found at i:2271053 original size:28 final size:28
Alignment explanation
Indices: 2271021--2271093 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
2271011 TTTCACAACT
**
2271021 GGGGATACTCCAACCCCATTATTTAATC
1 GGGGATACTCCAACCCCATTATTTAAGA
**
2271049 GGGGATACTCCAACCCCATTATTTCCGA
1 GGGGATACTCCAACCCCATTATTTAAGA
2271077 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
2271094 GGCTTTATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (28 bp):
GGGGATACTCCAACCCCATTATTTAAGA
Done.