Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 7 of 173
Found at i:1843632 original size:23 final size:23
Alignment explanation
Indices: 1843606--1843664 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
1843596 GCTTGGAGGC
1843606 CTGCTGGCCTGCTAGGGGCTGGG
1 CTGCTGGCCTGCTAGGGGCTGGG
*
1843629 CTGCTGGCCTGTTAGGGGCTGGG
1 CTGCTGGCCTGCTAGGGGCTGGG
*
1843652 CTGCTGGCTTGCT
1 CTGCTGGCCTGCT
1843665 GGGCTGCCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.03, C:0.25, G:0.44, T:0.27
Consensus pattern (23 bp):
CTGCTGGCCTGCTAGGGGCTGGG
Found at i:1843801 original size:21 final size:21
Alignment explanation
Indices: 1843777--1843848 Score: 117
Period size: 21 Copynumber: 3.3 Consensus size: 21
1843767 GGGTTGCTGT
1843777 TCGGGTCGGATCGTCGGTGGG
1 TCGGGTCGGATCGTCGGTGGG
1843798 TCGGGTCGGATCGTCGGTGGG
1 TCGGGTCGGATCGTCGGTGGG
1843819 TCGGGTCGGATCGATTCGGTCGGG
1 TCGGGTCGGATCG--TCGGT-GGG
1843843 TCGGGT
1 TCGGGT
1843849 TGACCCGACT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
21 34 0.71
23 5 0.10
24 9 0.19
ACGTcount: A:0.06, C:0.19, G:0.50, T:0.25
Consensus pattern (21 bp):
TCGGGTCGGATCGTCGGTGGG
Found at i:1843879 original size:8 final size:8
Alignment explanation
Indices: 1843866--1843916 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
1843856 ACTGTTATAA
1843866 TATTTTTT
1 TATTTTTT
1843874 TATTTTTT
1 TATTTTTT
1843882 TATTATTTT
1 TATT-TTTT
1843891 T-TTTCTTT
1 TATTT-TTT
*
1843899 TTTCTTTTT
1 TAT-TTTTT
*
1843908 TCTTTTTT
1 TATTTTTT
1843916 T
1 T
1843917 CTTTCTGCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
7 1 0.03
8 24 0.63
9 11 0.29
10 2 0.05
ACGTcount: A:0.08, C:0.06, G:0.00, T:0.86
Consensus pattern (8 bp):
TATTTTTT
Found at i:1843899 original size:6 final size:7
Alignment explanation
Indices: 1843889--1843920 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1843879 TTTTATTATT
1843889 TTTTTTC
1 TTTTTTC
1843896 TTTTTTC
1 TTTTTTC
1843903 TTTTTTC
1 TTTTTTC
1843910 TTTTTTTC
1 -TTTTTTC
1843918 TTT
1 TTT
1843921 CTGCTTCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:1843906 original size:14 final size:15
Alignment explanation
Indices: 1843889--1843920 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1843879 TTTTATTATT
1843889 TTTTTTC-TTTTTTC
1 TTTTTTCTTTTTTTC
1843903 TTTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
1843918 TTT
1 TTT
1843921 CTGCTTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTTCTTTTTTTC
Found at i:1844370 original size:30 final size:30
Alignment explanation
Indices: 1844284--1844371 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 30
1844274 GGCCAAAACA
* *
1844284 TAATTTTGAGG-AAGTTTATGGGTCAAAATG
1 TAATTTT-AGGAAAATTTATGGGTTAAAATG
**
1844314 TAATTTTA--AAAAGTTTATATGTTAAAATG
1 TAATTTTAGGAAAA-TTTATGGGTTAAAATG
*
1844343 TAATTTTAGGAAAATTTAGGGGTTAAAAT
1 TAATTTTAGGAAAATTTATGGGTTAAAAT
1844372 ACAATTTCAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
28 2 0.04
29 22 0.47
30 19 0.40
31 4 0.09
ACGTcount: A:0.40, C:0.01, G:0.19, T:0.40
Consensus pattern (30 bp):
TAATTTTAGGAAAATTTATGGGTTAAAATG
Found at i:1844378 original size:30 final size:30
Alignment explanation
Indices: 1844295--1844409 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 30
1844285 AATTTTGAGG
* * *
1844295 AAGTTTA-TGGGTCAAAATGTAATTTTAAA
1 AAGTTTAGGGGGTTAAAATATAATTTTAAA
*** *
1844324 AAGTTTA-TATGTTAAAATGTAATTTTAGGAA
1 AAGTTTAGGGGGTTAAAATATAATTTTA--AA
* *
1844355 AA-TTTA-GGGGTTAAAATACAATTTCAAA
1 AAGTTTAGGGGGTTAAAATATAATTTTAAA
*
1844383 AAGTTTAGGGGGTCAAAATATAATTTT
1 AAGTTTAGGGGGTTAAAATATAATTTT
1844410 TTTTATTTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
28 4 0.06
29 28 0.40
30 34 0.49
31 4 0.06
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.37
Consensus pattern (30 bp):
AAGTTTAGGGGGTTAAAATATAATTTTAAA
Found at i:1844420 original size:8 final size:8
Alignment explanation
Indices: 1844407--1844436 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
1844397 AAAATATAAT
1844407 TTTTTTTA
1 TTTTTTTA
1844415 TTTTTTGTA
1 TTTTTT-TA
1844424 TTTTTTTA
1 TTTTTTTA
1844432 TTTTT
1 TTTTT
1844437 ATATATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1844428 original size:18 final size:19
Alignment explanation
Indices: 1844400--1844451 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 19
1844390 GGGGGTCAAA
1844400 ATATAATTTTTTTTATTTTT
1 ATAT-ATTTTTTTTATTTTT
*
1844420 -TGTA-TTTTTTTATTTTT
1 ATATATTTTTTTTATTTTT
1844437 ATATATATTTTTTTA
1 ATATAT-TTTTTTTA
1844452 AAAAAGCACG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 13 0.48
18 4 0.15
19 2 0.07
20 8 0.30
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (19 bp):
ATATATTTTTTTTATTTTT
Found at i:1844755 original size:75 final size:75
Alignment explanation
Indices: 1844629--1844783 Score: 256
Period size: 75 Copynumber: 2.1 Consensus size: 75
1844619 TGATTCCCCC
* * * * * *
1844629 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCCTTGGTGGTTGTTAAGTGCTGATTCCACTGTAAC
1 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTGATCCCACCGTAAC
1844694 TTGAATGTGA
66 TTGAATGTGA
1844704 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTGATCCCACCGTAAC
1 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTGATCCCACCGTAAC
1844769 TTGAATGTGA
66 TTGAATGTGA
1844779 AAGGG
1 AAGGG
1844784 ATCCCACCGT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTGATCCCACCGTAAC
TTGAATGTGA
Found at i:1844795 original size:28 final size:28
Alignment explanation
Indices: 1844755--1844811 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1844745 GCTAACTGCT
1844755 GATCCCACCGTAACTTGAATGTGAAAGG
1 GATCCCACCGTAACTTGAATGTGAAAGG
1844783 GATCCCACCGTAACTTGAATGTGAAAGG
1 GATCCCACCGTAACTTGAATGTGAAAGG
1844811 G
1 G
1844812 GTTGCTAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (28 bp):
GATCCCACCGTAACTTGAATGTGAAAGG
Found at i:1844808 original size:103 final size:103
Alignment explanation
Indices: 1844684--1844886 Score: 379
Period size: 103 Copynumber: 2.0 Consensus size: 103
1844674 AGTGCTGATT
*
1844684 CCACTGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTA
1 CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTA
1844749 ACTGCTGATCCCACCGTAACTTGAATGTGAAAGGGATC
66 ACTGCTGATCCCACCGTAACTTGAATGTGAAAGGGATC
1844787 CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTA
1 CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTA
* *
1844852 AGTGCTGATCCTACCGTAACTTGAATGTGAAAGGG
66 ACTGCTGATCCCACCGTAACTTGAATGTGAAAGGG
1844887 GTTGCTAAGT
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (103 bp):
CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTA
ACTGCTGATCCCACCGTAACTTGAATGTGAAAGGGATC
Found at i:1844943 original size:178 final size:179
Alignment explanation
Indices: 1844629--1844962 Score: 546
Period size: 178 Copynumber: 1.9 Consensus size: 179
1844619 TGATTCCCCC
* * * *
1844629 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCCTTGGTGGTTGTTAAGTGCTGATTCCACTGTAAC
1 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCGTAAC
1844694 TTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTGATC
66 TTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTGATC
1844759 CCACCGTAACTT-GAATGTGAAAGGGATCCCACCGTAACTTGAATGTGA
131 CCACCGTAACTTCGAATGTGAAAGGGATCCCACCGTAACTTGAATGTGA
1844807 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGA-TCCTACCGTAA
1 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCC-ACCGTAA
* * * * *
1844871 CTTGAATGTGAAAGGGGTTGCTAAGTGCTTATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGAT
65 CTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTGAT
* *
1844936 TCCACCGTATCTTCGAATGTGAAAGGG
130 CCCACCGTAACTTCGAATGTGAAAGGG
1844963 GTTGCTAAGT
Statistics
Matches: 143, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
177 3 0.02
178 127 0.89
179 13 0.09
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (179 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCGTAAC
TTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTGATC
CCACCGTAACTTCGAATGTGAAAGGGATCCCACCGTAACTTGAATGTGA
Found at i:1844982 original size:76 final size:74
Alignment explanation
Indices: 1844787--1845017 Score: 354
Period size: 75 Copynumber: 3.1 Consensus size: 74
1844777 GAAAGGGATC
* *
1844787 CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTA
1 CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTA
1844852 AGTGCTGAT
66 AGTGCTGAT
*
1844861 CCTACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTTATTCCCCGAATCATTGGTGGTTGCT
1 CC-ACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCT
*
1844926 AAGTGTTGATT
65 AAGTGCTGA-T
* * * *
1844937 CCACCGTATCTTCGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTAGTGGTTGCG
1 CCACCGTAACTT-GAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCT
1845002 AAGTGCTGAAT
65 AAGTGCTG-AT
1845013 CCACC
1 CCACC
1845018 AAATAACGGT
Statistics
Matches: 143, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
74 2 0.01
75 76 0.53
76 64 0.45
77 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.29
Consensus pattern (74 bp):
CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTA
AGTGCTGAT
Found at i:1847266 original size:19 final size:18
Alignment explanation
Indices: 1847238--1847274 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1847228 TTCATTTATT
*
1847238 TTTATTTTATTTGTTTAA
1 TTTATTTTATTTCTTTAA
1847256 TTTATTATTATTTCTTTAA
1 TTTATT-TTATTTCTTTAA
1847275 ATTTTTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTATTTTATTTCTTTAA
Found at i:1849386 original size:29 final size:29
Alignment explanation
Indices: 1849326--1849409 Score: 77
Period size: 31 Copynumber: 2.9 Consensus size: 29
1849316 AAATTAAAAC
* *
1849326 AAAA-ATTAAAAAAATATTT--TAAAATT
1 AAAATATTAAAAAAGTATTTAAAAAAATT
*
1849352 AAAAAAATT-AAAAAGTATTTTTAAAAAAATT
1 -AAAATATTAAAAAAGTA--TTTAAAAAAATT
*
1849383 AAAATTTTAAAAAAGTATTTAAAAAAA
1 AAAATATTAAAAAAGTATTTAAAAAAA
1849410 GTATTTTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
27 11 0.23
28 3 0.06
29 13 0.28
30 6 0.13
31 14 0.30
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAATATTAAAAAAGTATTTAAAAAAATT
Found at i:1849408 original size:14 final size:14
Alignment explanation
Indices: 1849361--1849420 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 14
1849351 TAAAAAAATT
1849361 AAAAAGTATTTTTAA
1 AAAAAGTA-TTTTAA
*
1849376 AAAAATTAAAATTTT-A
1 AAAAAGT---ATTTTAA
1849392 AAAAAGTA-TTTAA
1 AAAAAGTATTTTAA
1849405 AAAAAGTATTTTAA
1 AAAAAGTATTTTAA
1849419 AA
1 AA
1849421 GTATTTCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
12 3 0.08
13 10 0.26
14 7 0.18
15 6 0.16
16 7 0.18
17 4 0.11
18 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (14 bp):
AAAAAGTATTTTAA
Found at i:1849420 original size:11 final size:11
Alignment explanation
Indices: 1849406--1849442 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1849396 AGTATTTAAA
1849406 AAAAGTATTTT
1 AAAAGTATTTT
*
1849417 AAAAGTATTTC
1 AAAAGTATTTT
*
1849428 AAAAGCATTTT
1 AAAAGTATTTT
1849439 AAAA
1 AAAA
1849443 TTAAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.35
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:1849459 original size:17 final size:17
Alignment explanation
Indices: 1849434--1849471 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1849424 TTTCAAAAGC
* *
1849434 ATTTTAAAATTAAAAA-
1 ATTTAAAAAATAAAAAT
1849450 ATTTAAAAAATAAAAAT
1 ATTTAAAAAATAAAAAT
1849467 ATTTA
1 ATTTA
1849472 TTATATTCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTTAAAAAATAAAAAT
Found at i:1852515 original size:20 final size:21
Alignment explanation
Indices: 1852485--1852525 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1852475 TTTATTAATT
1852485 TAATATTTATAAAAAATTAAA
1 TAATATTTATAAAAAATTAAA
*
1852506 TAAT-TTTATAAATAATTAAA
1 TAATATTTATAAAAAATTAAA
1852526 ATTTTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATATTTATAAAAAATTAAA
Found at i:1854053 original size:39 final size:39
Alignment explanation
Indices: 1854010--1854086 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
1854000 AGCAGAAGTT
1854010 ACAAGGCTCCA-CAGAAGCCAAACAAGCTGGGTGAATGTG
1 ACAAGGCT-CAGCAGAAGCCAAACAAGCTGGGTGAATGTG
* * * * *
1854049 ACAAGGGTTAGCAGAAGCTAAACCAGTTGGGTGAATGT
1 ACAAGGCTCAGCAGAAGCCAAACAAGCTGGGTGAATGT
1854087 TAGTGATTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.03
39 31 0.97
ACGTcount: A:0.35, C:0.18, G:0.30, T:0.17
Consensus pattern (39 bp):
ACAAGGCTCAGCAGAAGCCAAACAAGCTGGGTGAATGTG
Found at i:1857663 original size:18 final size:17
Alignment explanation
Indices: 1857621--1857657 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
1857611 TGGTTTTTAA
1857621 TTATTTTTAAATATATT
1 TTATTTTTAAATATATT
1857638 TTATTTTT-AATATATT
1 TTATTTTTAAATATATT
1857654 TTAT
1 TTAT
1857658 AATTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTTTTAAATATATT
Found at i:1865001 original size:59 final size:60
Alignment explanation
Indices: 1864923--1865046 Score: 164
Period size: 59 Copynumber: 2.1 Consensus size: 60
1864913 CAAGTCAGTT
* * * *
1864923 AACTATTTCCCATTTTCTTTTTTGGTCACTCAATTAT-AATTTTTTTAATTTGA-TCACCC
1 AACTATTTCCCACTTTCTTTTTTGGTCACCCAACTATCAATTTTTCTAATTT-ACTCACCC
*
1864982 AACTATTGTCCC-CTTTCTTTTTTGGTCACCCAACTATCAATTTTTCTAATTTACTCATCC
1 AACTATT-TCCCACTTTCTTTTTTGGTCACCCAACTATCAATTTTTCTAATTTACTCACCC
1865042 AACTA
1 AACTA
1865047 ATCAAGATTG
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
59 30 0.53
60 27 0.47
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.47
Consensus pattern (60 bp):
AACTATTTCCCACTTTCTTTTTTGGTCACCCAACTATCAATTTTTCTAATTTACTCACCC
Found at i:1865450 original size:4 final size:4
Alignment explanation
Indices: 1865441--1865465 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1865431 GCTACTGCTA
1865441 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
1865466 GACCGCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1865630 original size:29 final size:31
Alignment explanation
Indices: 1865560--1865647 Score: 83
Period size: 29 Copynumber: 2.9 Consensus size: 31
1865550 AAAAAATGAT
1865560 ATTGATTAGTTGAGTGACGAAAAAAAAAAAAG
1 ATTGA-TAGTTGAGTGACGAAAAAAAAAAAAG
* * **
1865592 AGTTAATAGTTGAGTGA-GCAAATTAAAAAA-
1 A-TTGATAGTTGAGTGACGAAAAAAAAAAAAG
* *
1865622 ATTGATAGTTGAATGA-TAAAAAAAAA
1 ATTGATAGTTGAGTGACGAAAAAAAAA
1865648 TAATAATTGG
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
29 19 0.42
30 1 0.02
31 10 0.22
32 12 0.27
33 3 0.07
ACGTcount: A:0.53, C:0.02, G:0.19, T:0.25
Consensus pattern (31 bp):
ATTGATAGTTGAGTGACGAAAAAAAAAAAAG
Found at i:1865730 original size:19 final size:21
Alignment explanation
Indices: 1865708--1865748 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
1865698 AGTAGTAGAA
1865708 AGAGAAATGGA-AGTG-GTGG
1 AGAGAAATGGAGAGTGAGTGG
*
1865727 AGAGAAGTGGAGAGTGAGTGG
1 AGAGAAATGGAGAGTGAGTGG
1865748 A
1 A
1865749 CTGATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 4 0.21
21 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.49, T:0.15
Consensus pattern (21 bp):
AGAGAAATGGAGAGTGAGTGG
Found at i:1869260 original size:61 final size:60
Alignment explanation
Indices: 1869185--1869305 Score: 233
Period size: 61 Copynumber: 2.0 Consensus size: 60
1869175 AAGTATCCCC
1869185 CTGAAGATGAGATCTAAAGAAAAGTTGGATTCAAAGAAGGTAGCATCCATTGAAACAATCA
1 CTGAAGATGAGATCTAAAGAAAAGTTGGATTCAAAGAA-GTAGCATCCATTGAAACAATCA
1869246 CTGAAGATGAGATCTAAAGAAAAGTTGGATTCAAAGAAGTAGCATCCATTGAAACAATCA
1 CTGAAGATGAGATCTAAAGAAAAGTTGGATTCAAAGAAGTAGCATCCATTGAAACAATCA
1869306 TTCTTTTTGT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 22 0.37
61 38 0.63
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (60 bp):
CTGAAGATGAGATCTAAAGAAAAGTTGGATTCAAAGAAGTAGCATCCATTGAAACAATCA
Found at i:1884783 original size:26 final size:26
Alignment explanation
Indices: 1884754--1884805 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1884744 TAATAAATTT
1884754 GAATTTTCTATTAATATA-CTGAAAAG
1 GAATTTTCTATTAATATATC-GAAAAG
*
1884780 GAATTTTCTGTTAATATATCGAAAAG
1 GAATTTTCTATTAATATATCGAAAAG
1884806 AAAAGAGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (26 bp):
GAATTTTCTATTAATATATCGAAAAG
Found at i:1895074 original size:45 final size:45
Alignment explanation
Indices: 1895023--1895130 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
1895013 GATGTGGAAA
** *
1895023 AACCACTAATCGGTGCAGATAAAAGCTGTTAATACGAAGTGGATT
1 AACCACTAATCGGTGCAGATAAAAGCTACTAATACGAAGTAGATT
* * * * *
1895068 GACCACTAAAT-GATACATATAAAAGCTACTAATACGATGTAGATT
1 AACCACT-AATCGGTGCAGATAAAAGCTACTAATACGAAGTAGATT
*
1895113 AACCACTAAACGGTGCAG
1 AACCACTAATCGGTGCAG
1895131 GCAAGCTGCT
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
44 2 0.04
45 43 0.90
46 3 0.06
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.23
Consensus pattern (45 bp):
AACCACTAATCGGTGCAGATAAAAGCTACTAATACGAAGTAGATT
Found at i:1897227 original size:15 final size:16
Alignment explanation
Indices: 1897207--1897237 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1897197 ACGTGTCTTT
1897207 TTTTTAATATT-TACA
1 TTTTTAATATTATACA
1897222 TTTTTAATATTATACA
1 TTTTTAATATTATACA
1897238 CCCCTATAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTTAATATTATACA
Found at i:1897998 original size:20 final size:20
Alignment explanation
Indices: 1897975--1898012 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1897965 TTTGTAAAAA
*
1897975 TAAAAAAATTATAAAATTAT
1 TAAAAAAATTAAAAAATTAT
*
1897995 TAAAAAATTTAAAAAATT
1 TAAAAAAATTAAAAAATT
1898013 TAAAAGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAAAATTAAAAAATTAT
Found at i:1898010 original size:9 final size:9
Alignment explanation
Indices: 1897975--1898017 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
1897965 TTTGTAAAAA
*
1897975 TAAAAAAAT
1 TAAAAAATT
*
1897984 TATAAAATTAT
1 TA-AAAAAT-T
1897995 TAAAAAATT
1 TAAAAAATT
1898004 TAAAAAATT
1 TAAAAAATT
1898013 TAAAA
1 TAAAA
1898018 GTAATTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 17 0.59
10 9 0.31
11 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TAAAAAATT
Found at i:1904631 original size:44 final size:44
Alignment explanation
Indices: 1904529--1904632 Score: 136
Period size: 44 Copynumber: 2.4 Consensus size: 44
1904519 ATATGTTTCG
* * * *
1904529 ATATGAAATCTGATATGCTATCATATGTTGTAAGTTATGCTCCA
1 ATATGAAATCTGATATGCTATAATATGTTGTAAGATAAGCACCA
* *
1904573 TTACGAAATCTGATATGCTATAATATGTTGTAAGATAAGCACCA
1 ATATGAAATCTGATATGCTATAATATGTTGTAAGATAAGCACCA
* *
1904617 ATATGTAATATGATAT
1 ATATGAAATCTGATAT
1904633 ATTTTGACCT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (44 bp):
ATATGAAATCTGATATGCTATAATATGTTGTAAGATAAGCACCA
Found at i:1923918 original size:131 final size:129
Alignment explanation
Indices: 1923739--1924053 Score: 453
Period size: 125 Copynumber: 2.5 Consensus size: 129
1923729 AAAATCGAAG
* * * * * *
1923739 CCCAGTAAGTTAGGGCACGATTTCTCGAATCTTCTA-AATACGGAATATTGCCTTCATTTTTTTT
1 CCCAGTAAGTTAGGGTACAATTTCTCGAA-ATTCCAGAACACGAAATATTGCCTT-A-TTTTTTT
*
1923803 TTAAATTT-TATATGTTTGGAAATTTAAAAGGATATTTTGCTATTTAGGTTTAACGAGCAAATTG
63 TGAAATTTGT-TATGTTTGGAAATTTAAAAGGATATTTTGCTATTTAGGTTTAACGAGCAAATTG
1923867 AGA
127 AGA
1923870 CCCAGTAAGTTAGGGTACAATTTCTCGAAATTCCAGAACACGAAATATTGCCTTA----TTTTGA
1 CCCAGTAAGTTAGGGTACAATTTCTCGAAATTCCAGAACACGAAATATTGCCTTATTTTTTTTGA
*
1923931 AATTTGTTATGTTTGGAAATTTAAAAGGATATTTTGCTATTTAGGTTTAACGAGTAAATTGAGA
66 AATTTGTTATGTTTGGAAATTTAAAAGGATATTTTGCTATTTAGGTTTAACGAGCAAATTGAGA
* * *
1923995 CCCAGTAAGTTAGGGTACAATTTCTCGAAGTTCCAGAACGCGAAACATTGCCTTATTTT
1 CCCAGTAAGTTAGGGTACAATTTCTCGAAATTCCAGAACACGAAATATTGCCTTATTTT
1924054 GAAATTTGTT
Statistics
Matches: 167, Mismatches: 11, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
125 118 0.71
126 1 0.01
130 5 0.03
131 43 0.26
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (129 bp):
CCCAGTAAGTTAGGGTACAATTTCTCGAAATTCCAGAACACGAAATATTGCCTTATTTTTTTTGA
AATTTGTTATGTTTGGAAATTTAAAAGGATATTTTGCTATTTAGGTTTAACGAGCAAATTGAGA
Found at i:1923967 original size:125 final size:125
Alignment explanation
Indices: 1923800--1924064 Score: 469
Period size: 125 Copynumber: 2.1 Consensus size: 125
1923790 CTTCATTTTT
*
1923800 TTTTTAAATTT-TATATGTTTGGAAATTTAAAAGGATATTTTGCTATTTAGGTTTAACGAGCAAA
1 TTTTGAAATTTGT-TATGTTTGGAAATTTAAAAGGATATTTTGCTATTTAGGTTTAACGAGCAAA
*
1923864 TTGAGACCCAGTAAGTTAGGGTACAATTTCTCGAAATTCCAGAACACGAAATATTGCCTTA
65 TTGAGACCCAGTAAGTTAGGGTACAATTTCTCGAAATTCCAGAACACGAAACATTGCCTTA
*
1923925 TTTTGAAATTTGTTATGTTTGGAAATTTAAAAGGATATTTTGCTATTTAGGTTTAACGAGTAAAT
1 TTTTGAAATTTGTTATGTTTGGAAATTTAAAAGGATATTTTGCTATTTAGGTTTAACGAGCAAAT
* *
1923990 TGAGACCCAGTAAGTTAGGGTACAATTTCTCGAAGTTCCAGAACGCGAAACATTGCCTTA
66 TGAGACCCAGTAAGTTAGGGTACAATTTCTCGAAATTCCAGAACACGAAACATTGCCTTA
1924050 TTTTGAAATTTGTTA
1 TTTTGAAATTTGTTA
1924065 CGAATTTAGG
Statistics
Matches: 134, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
125 133 0.99
126 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (125 bp):
TTTTGAAATTTGTTATGTTTGGAAATTTAAAAGGATATTTTGCTATTTAGGTTTAACGAGCAAAT
TGAGACCCAGTAAGTTAGGGTACAATTTCTCGAAATTCCAGAACACGAAACATTGCCTTA
Found at i:1934923 original size:20 final size:21
Alignment explanation
Indices: 1934888--1934926 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1934878 ACTTTACCAC
*
1934888 TTATTTAGATATTTTTTATAT
1 TTATTTAGACATTTTTTATAT
1934909 TTATTTA-ACATTTTTTAT
1 TTATTTAGACATTTTTTAT
1934927 TTAATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (21 bp):
TTATTTAGACATTTTTTATAT
Found at i:1938884 original size:16 final size:16
Alignment explanation
Indices: 1938865--1938898 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1938855 TAGTTGATTA
1938865 GACAATATTTTGACAT
1 GACAATATTTTGACAT
* *
1938881 GACATTATTTTGATAT
1 GACAATATTTTGACAT
1938897 GA
1 GA
1938899 GCATTTCACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (16 bp):
GACAATATTTTGACAT
Found at i:1948855 original size:31 final size:31
Alignment explanation
Indices: 1948819--1948888 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
1948809 GTTACAAAAT
* **
1948819 AATCACTGAATTATTTGAAAGTTTTCATTTA
1 AATCACTGAACTATTCAAAAGTTTTCATTTA
* *
1948850 AATCACTAAACTATTCAAAAGTTTTTATTTA
1 AATCACTGAACTATTCAAAAGTTTTCATTTA
*
1948881 AGTCACTG
1 AATCACTG
1948889 GGATGTTAAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (31 bp):
AATCACTGAACTATTCAAAAGTTTTCATTTA
Found at i:1962419 original size:30 final size:30
Alignment explanation
Indices: 1962385--1962448 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
1962375 TCTTTACAAC
1962385 TTGTTGGATAGCTTGAGATGAACCAAAAAT
1 TTGTTGGATAGCTTGAGATGAACCAAAAAT
*
1962415 TTGTTGGATAGCTTGAGATGACCCAAAAAT
1 TTGTTGGATAGCTTGAGATGAACCAAAAAT
1962445 TTGT
1 TTGT
1962449 GTCACCATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (30 bp):
TTGTTGGATAGCTTGAGATGAACCAAAAAT
Found at i:1964156 original size:17 final size:17
Alignment explanation
Indices: 1964128--1964165 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
1964118 AATAAAAAGA
*
1964128 AAAAGAAAGAAATAATTG
1 AAAAGAAAGAAA-AAATG
1964146 AAAAG-AAGAAAAAATG
1 AAAAGAAAGAAAAAATG
1964162 AAAA
1 AAAA
1964166 CCTAAACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.11
Consensus pattern (17 bp):
AAAAGAAAGAAAAAATG
Found at i:1968658 original size:19 final size:20
Alignment explanation
Indices: 1968599--1968658 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 20
1968589 CTAATTTTTT
*
1968599 AAAATTTAAAAAT--TTTAA
1 AAAATATAAAAATGATTTAA
* * * *
1968617 AAATTATAAAGATTATTTTA
1 AAAATATAAAAATGATTTAA
1968637 AAAATA-AAAAATGATTTAA
1 AAAATATAAAAATGATTTAA
1968656 AAA
1 AAA
1968659 TAATTTAATC
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
18 10 0.31
19 13 0.41
20 9 0.28
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
AAAATATAAAAATGATTTAA
Found at i:1970643 original size:34 final size:35
Alignment explanation
Indices: 1970600--1970667 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 35
1970590 TAAGCATGAC
* * *
1970600 TTTTGCTACTGAGTTGATCTATTATAAGCATATTA
1 TTTTGCTACTAAATTGAACTATTATAAGCATATTA
* *
1970635 TTTT-CTACTAAATTGAACTGTTATAATCATATT
1 TTTTGCTACTAAATTGAACTATTATAAGCATATT
1970668 GAATGCTACT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 24 0.86
35 4 0.14
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (35 bp):
TTTTGCTACTAAATTGAACTATTATAAGCATATTA
Found at i:1971078 original size:86 final size:85
Alignment explanation
Indices: 1970786--1971098 Score: 394
Period size: 86 Copynumber: 3.6 Consensus size: 85
1970776 ACAAGTGGCA
* * * *
1970786 GTTTAATCTGCAAACAGTGTGGTTCAATCACGAACCAAGTGGCAGTAACTGCAAATATGTGGTTC
1 GTTTAATCTGCAAATA-TGTTGTGCACTCAC-AA-CAAGTGGCAGTAACTGCAAATATGTGGTTC
* * *
1970851 AATCACGAACCGAGTGGTAGTTT
63 AATCATGAACCAAGTGGCAGTTT
* * * *
1970874 GTTTAATCTGCAAATATGCTGCGCACTCACAAAAAAATGGCAGTAACTGCAAATATGTGGTTCAA
1 GTTTAATCTGCAAATATGTTGTGCACTCAC-AACAAGTGGCAGTAACTGCAAATATGTGGTTCAA
** *
1970939 TCATGAACCAAGTCACAATTT
65 TCATGAACCAAGTGGCAGTTT
*
1970960 GTTTAATCTGCAAATATGTTGTGCACTCACAACAAGTGGCAGTAACTGCAAGCA-ATATGGTTCA
1 GTTTAATCTGCAAATATGTTGTGCACTCACAACAAGTGGCAGTAACTGCAA--ATATGTGGTTCA
1971024 ATCATGAACCAAGTGGCAGTTT
64 ATCATGAACCAAGTGGCAGTTT
* * * *
1971046 GTTTAATCTGAAAATATGTTGTGCACCCACAACAAGTGGCTGTAACTACAAAT
1 GTTTAATCTGCAAATATGTTGTGCACTCACAACAAGTGGCAGTAACTGCAAAT
1971099 CAGCTGTGGT
Statistics
Matches: 195, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
84 1 0.01
85 19 0.10
86 148 0.76
87 12 0.06
88 15 0.08
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (85 bp):
GTTTAATCTGCAAATATGTTGTGCACTCACAACAAGTGGCAGTAACTGCAAATATGTGGTTCAAT
CATGAACCAAGTGGCAGTTT
Found at i:1971715 original size:57 final size:57
Alignment explanation
Indices: 1971627--1971737 Score: 204
Period size: 57 Copynumber: 1.9 Consensus size: 57
1971617 TGAAATATGG
*
1971627 TTTTTAATTATTTATACATATACTCAGATTAAATCTAAATTGAATATCACTTTTCTA
1 TTTTTAATTATTTATACATATAATCAGATTAAATCTAAATTGAATATCACTTTTCTA
*
1971684 TTTTTAATTATTTATACATATAATCAGATTAAATCTAAATTGAATATCATTTTT
1 TTTTTAATTATTTATACATATAATCAGATTAAATCTAAATTGAATATCACTTTT
1971738 TCGCTGCTAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.49
Consensus pattern (57 bp):
TTTTTAATTATTTATACATATAATCAGATTAAATCTAAATTGAATATCACTTTTCTA
Found at i:1972176 original size:32 final size:31
Alignment explanation
Indices: 1972119--1972179 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
1972109 GGCACGTGTC
*
1972119 ATAAAAAATAATATTTTTTAGAAAATAAAAAA
1 ATAAAAAAT-ATATTTTTTACAAAATAAAAAA
1972151 ATAAAAAAT-TATTTTTCATACAAAATAAA
1 ATAAAAAATATATTTTT--TACAAAATAAA
1972180 CTTAGACAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 7 0.27
32 19 0.73
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (31 bp):
ATAAAAAATATATTTTTTACAAAATAAAAAA
Found at i:1972358 original size:19 final size:18
Alignment explanation
Indices: 1972319--1972363 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1972309 AACTCTTGAA
*
1972319 TTTTATAAAAATTTTATT
1 TTTTATAAAAATTTTAGT
*
1972337 TTTTTTAAAAATTTTAAGT
1 TTTTATAAAAATTTT-AGT
*
1972356 TTTCATAA
1 TTTTATAA
1972364 TTTTTATTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTTATAAAAATTTTAGT
Found at i:1972569 original size:18 final size:18
Alignment explanation
Indices: 1972527--1972569 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1972517 AATATGAAAT
*
1972527 ATTTTTAAAATAAATTTC
1 ATTTTTAAAATAAATTTA
*
1972545 ATATTTAAAATAAATTTA
1 ATTTTTAAAATAAATTTA
1972563 ATTTTTA
1 ATTTTTA
1972570 TTATTTAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTTAAAATAAATTTA
Found at i:1973613 original size:2 final size:2
Alignment explanation
Indices: 1973606--1973636 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1973596 TCTTCAAGAT
1973606 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1973637 TGCCTATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1973883 original size:47 final size:47
Alignment explanation
Indices: 1973814--1973908 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
1973804 GTCAACAAAA
*
1973814 TATGTTAATAATAGAAACTGTGCTTTATTAATTCTTTTTTTTCTCTC
1 TATGTTAATAATAGAAACTGTGCTTTATTAATTCTTTTTTCTCTCTC
1973861 TATGTTAATAATAGAAACTGTGCTTTATTAATTCTTTTTTCTCTCTC
1 TATGTTAATAATAGAAACTGTGCTTTATTAATTCTTTTTTCTCTCTC
1973908 T
1 T
1973909 CTTTATATTG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.25, C:0.14, G:0.08, T:0.53
Consensus pattern (47 bp):
TATGTTAATAATAGAAACTGTGCTTTATTAATTCTTTTTTCTCTCTC
Found at i:1976002 original size:19 final size:20
Alignment explanation
Indices: 1975980--1976031 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
1975970 ATTTTATTTT
*
1975980 AAAACACGAGAA-TTTTTGA
1 AAAACACGAAAATTTTTTGA
1975999 AAAACACGAAAATTTTTTG-
1 AAAACACGAAAATTTTTTGA
1976018 -AAACAC-AAAATTTT
1 AAAACACGAAAATTTT
1976032 GATAAATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 8 0.26
18 6 0.19
19 11 0.35
20 6 0.19
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.29
Consensus pattern (20 bp):
AAAACACGAAAATTTTTTGA
Found at i:1976014 original size:18 final size:18
Alignment explanation
Indices: 1975980--1976033 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
1975970 ATTTTATTTT
*
1975980 AAAACACGAGAATTTTTGA
1 AAAACACGA-AAATTTTGA
**
1975999 AAAACACGAAAATTTTTT
1 AAAACACGAAAATTTTGA
*
1976017 GAAACAC-AAAATTTTGA
1 AAAACACGAAAATTTTGA
1976034 TAAATTATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
17 8 0.28
18 12 0.41
19 9 0.31
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (18 bp):
AAAACACGAAAATTTTGA
Found at i:1976048 original size:124 final size:123
Alignment explanation
Indices: 1975894--1976511 Score: 733
Period size: 124 Copynumber: 4.8 Consensus size: 123
1975884 ATCCGATTGT
* *
1975894 AACACGAAAATTTTGATAAACTACATATTATTATATATCCATTTAAATATAATTTGATAATTTAC
1 AACACGAAAATTTTGATAAATTATATATTATTATATATCCATTTAAATATAATTTGATAATTTAC
1975959 AAAAAATAAACATTTTATTTTAAAACACGAGAATTTTTGAAAAACACGAAAATTTTTTG-A
66 AAAAAATAAACATTTTATTTTAAAACACGAGAATTTTTG--AAACACGAAAA-TTTTTGAA
*
1976019 AACAC-AAAATTTTGATAAATTATATATTATTATATATCCATTTAAATATAATTTGATAAGTTAC
1 AACACGAAAATTTTGATAAATTATATATTATTATATATCCATTTAAATATAATTTGATAATTTAC
* *
1976083 AAAAAATAAACATTTTATTTTAAAACACGAGAATTTTTAAAAAACAC-AAATTTTTTG-A
66 AAAAAATAAACATTTTATTTTAAAACACGAGAATTTTT--GAAACACGAAAATTTTTGAA
1976141 AACAC-AAAATTTTGATAAATTATATATTATTATATATCCATTTAAATATAATTTGATAATTTAC
1 AACACGAAAATTTTGATAAATTATATATTATTATATATCCATTTAAATATAATTTGATAATTTAC
* * *
1976205 AAAAAATAAACATTTTATTTTAAAACACAAGAATTTTTGAAACACTAGAATTTTTGAA
66 AAAAAATAAACATTTTATTTTAAAACACGAGAATTTTTGAAACACGAAAATTTTTGAA
** * *
1976263 AACACGAATTTTTTTTGAAACACGAAAATTTTGATAAATTACATATTATTATATATCCATTTAAA
1 AACACGAA--AATTTTG----A--TAAA--TT-AT--A-TA-TTATTA-TATA--TCCATTTAAA
* * *
1976328 TATAATTTGATAAATTAGAAAAAAAAATTAAACATTTTATTTTAAAACATGAGAATTTTTGAAAC
48 TATAATTTGAT-AATT--TACAAAAAA-TAAACATTTTATTTTAAAACACGAGAATTTTTGAAAC
*
1976393 ACGAGAATTTTTGAA
109 ACGAAAATTTTTGAA
* * * **
1976408 AACACGAAAACTTTGATAAATTACATATTATTATATCTCTTTTTAAATATAATTTGATAATTTTA
1 AACACGAAAATTTTGATAAATTATATATTATTATATATCCATTTAAATATAATTTGATAA-TTTA
* * *
1976473 AAAAAAATAAACATTTTATTTTAAAACACTAAAATTTTT
65 CAAAAAATAAACATTTTATTTTAAAACACGAGAATTTTT
1976512 TAATTTTTTA
Statistics
Matches: 433, Mismatches: 32, Indels: 57
0.83 0.06 0.11
Matches are distributed among these distances:
120 6 0.01
121 8 0.02
122 113 0.26
123 5 0.01
124 129 0.30
125 18 0.04
126 2 0.00
127 21 0.05
129 4 0.01
130 5 0.01
131 5 0.01
132 1 0.00
133 2 0.00
134 3 0.01
135 2 0.00
136 1 0.00
137 5 0.01
138 5 0.01
139 5 0.01
141 21 0.05
142 4 0.01
143 4 0.01
144 7 0.02
145 57 0.13
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (123 bp):
AACACGAAAATTTTGATAAATTATATATTATTATATATCCATTTAAATATAATTTGATAATTTAC
AAAAAATAAACATTTTATTTTAAAACACGAGAATTTTTGAAACACGAAAATTTTTGAA
Found at i:1976112 original size:105 final size:113
Alignment explanation
Indices: 1975924--1976258 Score: 370
Period size: 122 Copynumber: 2.8 Consensus size: 113
1975914 CTACATATTA
*
1975924 TTATATATCCATTTAAATATAATTTGATAATTTACAAAAAATAAACATTTTATTTTAAAACACGA
1 TTATATATCCATTTAAATATAATTTGATAAGTTACAAAAAATAAACATTTTATTTTAAAACACGA
*
1975989 GAA-TTTTTGAAAAACACGAAAATTTTTTGAAACACAAAATTTTGATAAATTATATATT
66 AAATTTTTTG--AAACAC-AAAA--TTTTG--A-ACAAAA-TTTGAT-AATTATATA-T
1976047 ATTATATATCCATTTAAATATAATTTGATAAGTTACAAAAAATAAACATTTTATTTTAAAACACG
1 -TTATATATCCATTTAAATATAATTTGATAAGTTACAAAAAATAAACATTTTATTTTAAAACACG
* ** *
1976112 AGAATTTTTAAAAAACACAAATTTTTTGAAACACAAAATTTTGATAAATTATATATT
65 AAAATTTTT-TGAAACACAAA-ATTTTG--A-ACAAAA-TTTGAT-AATTATATA-T
*
1976169 ATTATATATCCATTTAAATATAATTTGATAATTTACAAAAAATAAACATTTTATTTTAAAACAC-
1 -TTATATATCCATTTAAATATAATTTGATAAGTTACAAAAAATAAACATTTTATTTTAAAACACG
*
1976233 AAGAA-TTTTTGAAACACTAGAATTTT
65 AA-AATTTTTTGAAACAC-AAAATTTT
1976259 TGAAAACACG
Statistics
Matches: 196, Mismatches: 10, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
120 10 0.05
121 7 0.04
122 99 0.51
123 3 0.02
124 73 0.37
125 4 0.02
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (113 bp):
TTATATATCCATTTAAATATAATTTGATAAGTTACAAAAAATAAACATTTTATTTTAAAACACGA
AAATTTTTTGAAACACAAAATTTTGAACAAAATTTGATAATTATATAT
Found at i:1976258 original size:16 final size:17
Alignment explanation
Indices: 1976222--1976275 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
1976212 AAACATTTTA
*
1976222 TTTTAAAACACAAGAAT
1 TTTTGAAACACAAGAAT
*
1976239 TTTTGAAACACTAGAAT
1 TTTTGAAACACAAGAAT
*
1976256 TTTTGAAA-ACACGAAT
1 TTTTGAAACACAAGAAT
1976272 TTTT
1 TTTT
1976276 TTTGAAACAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
16 10 0.30
17 23 0.70
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (17 bp):
TTTTGAAACACAAGAAT
Found at i:1976294 original size:17 final size:18
Alignment explanation
Indices: 1976222--1976294 Score: 71
Period size: 17 Copynumber: 4.2 Consensus size: 18
1976212 AAACATTTTA
*
1976222 TTTTAAAACAC-AAGAAT
1 TTTTGAAACACGAAGAAT
*
1976239 TTTTGAAACAC-TAGAAT
1 TTTTGAAACACGAAGAAT
***
1976256 TTTTGAAAACACGAATTTT
1 TTTTG-AAACACGAAGAAT
1976275 TTTTGAAACACGAA-AAT
1 TTTTGAAACACGAAGAAT
1976292 TTT
1 TTT
1976295 GATAAATTAC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
17 24 0.52
18 15 0.33
19 7 0.15
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (18 bp):
TTTTGAAACACGAAGAAT
Found at i:1976294 original size:18 final size:18
Alignment explanation
Indices: 1976238--1976294 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
1976228 AACACAAGAA
* *
1976238 TTTTTGAAACACTAGAA-
1 TTTTTGAAACACGAAAAT
**
1976255 TTTTTGAAAACACGAATTT
1 TTTTTG-AAACACGAAAAT
1976274 TTTTTGAAACACGAAAAT
1 TTTTTGAAACACGAAAAT
1976292 TTT
1 TTT
1976295 GATAAATTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 6 0.19
18 20 0.62
19 6 0.19
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.40
Consensus pattern (18 bp):
TTTTTGAAACACGAAAAT
Found at i:1976299 original size:141 final size:142
Alignment explanation
Indices: 1976100--1976511 Score: 492
Period size: 145 Copynumber: 3.0 Consensus size: 142
1976090 AAACATTTTA
* * *
1976100 TTTTAAAACACGAGAATTTTTAAAAAACAC-AAATTTTTTGAAACACAAAATTTTGATAAATTAT
1 TTTTGAAACACGAGAATTTTT-GAAAACACGAAATTTTTTGAAACACAAAATTTTGATAAATTAC
* *
1976164 ATATTATTATATATCCATTTAAATATAATTTGAT-AATT-TACAAAAAA-TAAACATTTTATTTT
65 ATATTATTATATATCCATTTAAATATAATTTGATAAATTAAAAAAAAAATTAAACATTTTATTTT
1976226 AAAACACAAGAAT
130 AAAACACAAGAAT
* *
1976239 TTTTGAAACACTAGAATTTTTGAAAACACGAATTTTTTTTGAAACACGAAAATTTTGATAAATTA
1 TTTTGAAACACGAGAATTTTTGAAAACACGAA-ATTTTTTGAAACAC-AAAATTTTGATAAATTA
1976304 CATATTATTATATATCCATTTAAATATAATTTGATAAATTAGAAAAAAAAATTAAACATTTTATT
64 CATATTATTATATATCCATTTAAATATAATTTGATAAATTA-AAAAAAAAATTAAACATTTTATT
**
1976369 TTAAAACATGAGAAT
128 TTAAAACACAAGAAT
1976384 TTTTGAAACACGAGAATTTTTGAAAACAC----------GAAA-AC-----TTTGATAAATTACA
1 TTTTGAAACACGAGAATTTTTGAAAACACGAAATTTTTTGAAACACAAAATTTTGATAAATTACA
* ** **
1976433 TATTATTATATCTCTTTTTAAATATAATTTGAT-AATTTTAAAAAAAA-TAAACATTTTATTTTA
66 TATTATTATATATCCATTTAAATATAATTTGATAAATTAAAAAAAAAATTAAACATTTTATTTTA
1976496 AAACACTAA-AAT
131 AAACAC-AAGAAT
1976508 TTTT
1 TTTT
1976512 TAATTTTTTA
Statistics
Matches: 248, Mismatches: 17, Indels: 31
0.84 0.06 0.10
Matches are distributed among these distances:
124 28 0.11
125 9 0.04
126 4 0.02
127 44 0.18
133 2 0.01
134 4 0.02
138 7 0.03
139 21 0.08
140 13 0.05
141 51 0.21
142 4 0.02
144 7 0.03
145 54 0.22
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (142 bp):
TTTTGAAACACGAGAATTTTTGAAAACACGAAATTTTTTGAAACACAAAATTTTGATAAATTACA
TATTATTATATATCCATTTAAATATAATTTGATAAATTAAAAAAAAAATTAAACATTTTATTTTA
AAACACAAGAAT
Found at i:1976410 original size:18 final size:18
Alignment explanation
Indices: 1976367--1976414 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 18
1976357 AAACATTTTA
*
1976367 TTTT-AAAACATGAGAAT
1 TTTTGAAAACACGAGAAT
1976384 TTTTG-AAACACGAGAAT
1 TTTTGAAAACACGAGAAT
1976401 TTTTGAAAACACGA
1 TTTTGAAAACACGA
1976415 AAACTTTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 20 0.71
18 8 0.29
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (18 bp):
TTTTGAAAACACGAGAAT
Found at i:1976853 original size:16 final size:17
Alignment explanation
Indices: 1976832--1976873 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
1976822 GGAATTTTTA
1976832 TTTTTTTTCTTTCTT-C
1 TTTTTTTTCTTTCTTCC
1976848 TTTTTTTTCTTTCTTCCC
1 TTTTTTTTCTTTCTT-CC
1976866 TTTTTTTT
1 TTTTTTTT
1976874 TCTGGCCTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 15 0.62
18 9 0.38
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTTTCTTTCTTCC
Found at i:1980796 original size:27 final size:27
Alignment explanation
Indices: 1980756--1980830 Score: 123
Period size: 27 Copynumber: 2.8 Consensus size: 27
1980746 CCACCGAGAC
* * *
1980756 ACTAAATACAGGGTAGTCTATCGGGAT
1 ACTAAACACGGGGTAGTCCATCGGGAT
1980783 ACTAAACACGGGGTAGTCCATCGGGAT
1 ACTAAACACGGGGTAGTCCATCGGGAT
1980810 ACTAAACACGGGGTAGTCCAT
1 ACTAAACACGGGGTAGTCCAT
1980831 TTGGACATCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (27 bp):
ACTAAACACGGGGTAGTCCATCGGGAT
Found at i:1983140 original size:21 final size:20
Alignment explanation
Indices: 1983116--1983177 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
1983106 CTTTCCGTTT
1983116 AACTCTCACGAGTTTCTGTTC
1 AACTCT-ACGAGTTTCTGTTC
*
1983137 AACTCTTATGAGTCTT-TGTTC
1 AACTC-TACGAGT-TTCTGTTC
*
1983158 AACTCTACTGAGCTTCTGTT
1 AACTCTAC-GAGTTTCTGTT
1983178 TAACCCTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
20 4 0.12
21 27 0.79
22 3 0.09
ACGTcount: A:0.19, C:0.24, G:0.15, T:0.42
Consensus pattern (20 bp):
AACTCTACGAGTTTCTGTTC
Found at i:1983255 original size:42 final size:42
Alignment explanation
Indices: 1983166--1983257 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
1983156 TCAACTCTAC
** * *
1983166 TGAGCTTCTGTTTAACCCTTATGGGTTTTCGCTCAGCTTTTA
1 TGAGCTTCCATTTAACCCTTATGGGTTTTCGCTCAGCTCTCA
* * *
1983208 CGAGCTTCCATTTAACCCTTATGGG-TTTCTGTTTAGCTCTCA
1 TGAGCTTCCATTTAACCCTTATGGGTTTTC-GCTCAGCTCTCA
1983250 TGAGCTTC
1 TGAGCTTC
1983258 TGTTCAGCCT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 4 0.10
42 37 0.90
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.42
Consensus pattern (42 bp):
TGAGCTTCCATTTAACCCTTATGGGTTTTCGCTCAGCTCTCA
Found at i:1990560 original size:30 final size:30
Alignment explanation
Indices: 1990524--1990585 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1990514 TTTGTTGTAA
1990524 GAATGATTATAAAGAAACTCTATTAAGTTT
1 GAATGATTATAAAGAAACTCTATTAAGTTT
1990554 GAATGATTATAAAGAAACTCTATTAAGTTT
1 GAATGATTATAAAGAAACTCTATTAAGTTT
1990584 GA
1 GA
1990586 TGTTTCTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (30 bp):
GAATGATTATAAAGAAACTCTATTAAGTTT
Found at i:1994566 original size:13 final size:13
Alignment explanation
Indices: 1994550--1994602 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
1994540 TTAGTATTGT
1994550 AGTGTTTTTAAAA
1 AGTGTTTTTAAAA
*** **
1994563 AGTGACGTGGAAA
1 AGTGTTTTTAAAA
1994576 AGTGTTTTTAAAA
1 AGTGTTTTTAAAA
*
1994589 AGTATTTTTAAAA
1 AGTGTTTTTAAAA
1994602 A
1 A
1994603 TTTTGATTTA
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.38
Consensus pattern (13 bp):
AGTGTTTTTAAAA
Found at i:1996014 original size:32 final size:32
Alignment explanation
Indices: 1995962--1996027 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
1995952 TAAAATCATT
*
1995962 AAAAATGTTAAAAAACTTATAAA-ATTATAAA
1 AAAAATGTTAAAAAAATTATAAATATTATAAA
*
1995993 AAAAATTTGTAAAAAAATTATAAATATTATAAA
1 AAAAATGT-TAAAAAAATTATAAATATTATAAA
1996026 AA
1 AA
1996028 CTTATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 7 0.23
32 14 0.45
33 10 0.32
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (32 bp):
AAAAATGTTAAAAAAATTATAAATATTATAAA
Found at i:1998987 original size:21 final size:21
Alignment explanation
Indices: 1998962--1999012 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1998952 TAAAAACAAG
*
1998962 AAAATATTAAAGTACACTGAA
1 AAAATATTAAAGTACACTAAA
1998983 AAAATATTAAAGTACACTAAA
1 AAAATATTAAAGTACACTAAA
1999004 AAAATATTA
1 AAAATATTA
1999013 TAAGATTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.25
Consensus pattern (21 bp):
AAAATATTAAAGTACACTAAA
Found at i:2003476 original size:18 final size:18
Alignment explanation
Indices: 2003439--2003476 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2003429 CTCGATCTTG
*
2003439 ATTTTTGTATTTTCTATC
1 ATTTTTGTATTCTCTATC
*
2003457 ATTTTTGTATTCTCTGTC
1 ATTTTTGTATTCTCTATC
2003475 AT
1 AT
2003477 AATTTCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.13, G:0.08, T:0.63
Consensus pattern (18 bp):
ATTTTTGTATTCTCTATC
Found at i:2003583 original size:21 final size:21
Alignment explanation
Indices: 2003559--2003601 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2003549 GGTATAAACC
2003559 TTCTTTTATATCTTTTATATT
1 TTCTTTTATATCTTTTATATT
* *
2003580 TTCTTTTATATTTTTTGTATT
1 TTCTTTTATATCTTTTATATT
2003601 T
1 T
2003602 CTTCTGAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.74
Consensus pattern (21 bp):
TTCTTTTATATCTTTTATATT
Found at i:2003586 original size:12 final size:12
Alignment explanation
Indices: 2003569--2003593 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2003559 TTCTTTTATA
2003569 TCTTTTATATTT
1 TCTTTTATATTT
2003581 TCTTTTATATTT
1 TCTTTTATATTT
2003593 T
1 T
2003594 TTGTATTTCT
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TCTTTTATATTT
Found at i:2003746 original size:12 final size:12
Alignment explanation
Indices: 2003731--2003757 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2003721 CTTTACATTT
2003731 TTCTTCCATTAA
1 TTCTTCCATTAA
2003743 TTCTTCCATTAA
1 TTCTTCCATTAA
2003755 TTC
1 TTC
2003758 ATTAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.26, G:0.00, T:0.52
Consensus pattern (12 bp):
TTCTTCCATTAA
Found at i:2008660 original size:25 final size:26
Alignment explanation
Indices: 2008610--2008663 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
2008600 TTCAAAAAAA
* *
2008610 AAAACAAGAAAATATTAAACCTTTAT
1 AAAACAAAAAAATATTAAACCATTAT
2008636 AAAACAAAAAAAT-TTATAA-CATTAT
1 AAAACAAAAAAATATTA-AACCATTAT
2008661 AAA
1 AAA
2008664 GAATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (26 bp):
AAAACAAAAAAATATTAAACCATTAT
Found at i:2008699 original size:39 final size:39
Alignment explanation
Indices: 2008641--2008715 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
2008631 TTTATAAAAC
*
2008641 AAAAAAATTTATAACATTATAAAGAATT-TTAAAAAATTT
1 AAAAAAATTTATAACATTATAAA-AATTAGTAAAAAATTT
*
2008680 AAAAAAATTTATGGA-ATTATAAAAATTAGTAAAAAA
1 AAAAAAATTTAT-AACATTATAAAAATTAGTAAAAAA
2008716 AAATGTGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 4 0.12
39 27 0.84
40 1 0.03
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.32
Consensus pattern (39 bp):
AAAAAAATTTATAACATTATAAAAATTAGTAAAAAATTT
Found at i:2010527 original size:140 final size:141
Alignment explanation
Indices: 2010363--2010621 Score: 457
Period size: 140 Copynumber: 1.8 Consensus size: 141
2010353 TAGTTCTTAA
*
2010363 GAATAAGAAAAAAAATGAACCTAGAAATGTTCTTAAATTTCTTTTCAAAGCAATTCAGAAATGTT
1 GAATAAGAAAAAAAATGAACCTAGAAATGTTCTTAAATTTCTTTTCAAAGCAATCCAGAAATGTT
* * *
2010428 GAAAAAATCCAAAAAAGAAAAAGGCAAAGTGACGAGAGGAAGAAGGAAGAAGAATTGAATTATCG
66 GAAAAAATCCAAAAAAGAAAAAGGCAAAGTGACAAGAAGAAAAAGGAAGAAGAATTGAATTATCG
2010493 AAAAAAAGAAG
131 AAAAAAAGAAG
2010504 GAATAAG-AAAAAAATGAACCTAGAAATGTTCTTAAATTTCTTTTCAAAGCAATCCAGAAATGTT
1 GAATAAGAAAAAAAATGAACCTAGAAATGTTCTTAAATTTCTTTTCAAAGCAATCCAGAAATGTT
* *
2010568 GAAAGAATCCATAAAAGAAAAAGGCAAAGTGACAAGAAGAAAAAGGAAGAAGAA
66 GAAAAAATCCAAAAAAGAAAAAGGCAAAGTGACAAGAAGAAAAAGGAAGAAGAA
2010622 GAATAAAGGA
Statistics
Matches: 112, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
140 105 0.94
141 7 0.06
ACGTcount: A:0.53, C:0.09, G:0.19, T:0.19
Consensus pattern (141 bp):
GAATAAGAAAAAAAATGAACCTAGAAATGTTCTTAAATTTCTTTTCAAAGCAATCCAGAAATGTT
GAAAAAATCCAAAAAAGAAAAAGGCAAAGTGACAAGAAGAAAAAGGAAGAAGAATTGAATTATCG
AAAAAAAGAAG
Found at i:2010620 original size:16 final size:17
Alignment explanation
Indices: 2010601--2010632 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2010591 GCAAAGTGAC
2010601 AAGAAGAA-AAAGGAAG
1 AAGAAGAATAAAGGAAG
2010617 AAGAAGAATAAAGGAA
1 AAGAAGAATAAAGGAA
2010633 TAGGGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (17 bp):
AAGAAGAATAAAGGAAG
Found at i:2010679 original size:140 final size:137
Alignment explanation
Indices: 2010363--2010661 Score: 402
Period size: 140 Copynumber: 2.1 Consensus size: 137
2010353 TAGTTCTTAA
*
2010363 GAATAAGAAAAAAAATGAACCTAGAAATGTTCTTAAATTTCTTTTCAAAGCAATTCAGAAATGTT
1 GAATAAG-AAAAAAATGAA-C-AGAAATGTTCTTAAATTTCTTTTCAAAGCAATCCAGAAATGTT
* * * * *
2010428 GAAAAAATCCAAAAAAGAAAAAGGCAAAGTGACGAGAGGAAGAAGGAAGAAGAATTGAATTATCG
63 GAAAAAATCCAAAAAAGAAAAAGGCAAAGTGACAAGAAGAAAAAGGAAGAAGAA-TGAATAAACG
2010493 AAAAAAAGAAG
127 AAAAAAAGAAG
2010504 GAATAAGAAAAAAATGAACCTAGAAATGTTCTTAAATTTCTTTTCAAAGCAATCCAGAAATGTTG
1 GAATAAGAAAAAAATGAA-C-AGAAATGTTCTTAAATTTCTTTTCAAAGCAATCCAGAAATGTTG
* * *
2010569 AAAGAATCCATAAAAGAAAAAGGCAAAGTGACAAGAAGAAAAAGGAAGAAGAA-GAATAAAGGAA
64 AAAAAATCCAAAAAAGAAAAAGGCAAAGTGACAAGAAGAAAAAGGAAGAAGAATGAATAAACG-A
2010633 TAGGGAAAAAGAAG
128 -A---AAAAAGAAG
2010647 GAAATAAGAAAAAAA
1 G-AATAAGAAAAAAA
2010662 ATTAAAATAA
Statistics
Matches: 143, Mismatches: 9, Indels: 9
0.89 0.06 0.06
Matches are distributed among these distances:
138 6 0.04
139 1 0.01
140 106 0.74
141 7 0.05
143 10 0.07
144 13 0.09
ACGTcount: A:0.55, C:0.08, G:0.19, T:0.17
Consensus pattern (137 bp):
GAATAAGAAAAAAATGAACAGAAATGTTCTTAAATTTCTTTTCAAAGCAATCCAGAAATGTTGAA
AAAATCCAAAAAAGAAAAAGGCAAAGTGACAAGAAGAAAAAGGAAGAAGAATGAATAAACGAAAA
AAAGAAG
Found at i:2014409 original size:24 final size:25
Alignment explanation
Indices: 2014355--2014409 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
2014345 AATTGGTTAT
* *
2014355 AATTTTATAAATCATTAAATTTTTT
1 AATTTTATAAATCATTAAATATTTA
* **
2014380 ATTTTTAT-AATTTTTAAATATTTA
1 AATTTTATAAATCATTAAATATTTA
2014404 AATTTT
1 AATTTT
2014410 TTTAAAAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
AATTTTATAAATCATTAAATATTTA
Found at i:2014969 original size:3 final size:3
Alignment explanation
Indices: 2014961--2014987 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2014951 CGTTATATCC
2014961 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
2014988 TAATGAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:2018161 original size:17 final size:17
Alignment explanation
Indices: 2018128--2018160 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2018118 TTTATTATTT
2018128 TATTTATATAAATAAAA
1 TATTTATATAAATAAAA
*
2018145 TATTTAT-TAATTAAAA
1 TATTTATATAAATAAAA
2018161 AGATGAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATTTATATAAATAAAA
Found at i:2018496 original size:14 final size:15
Alignment explanation
Indices: 2018473--2018505 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2018463 GTTTCAAAAG
*
2018473 AAAATGTGTTTTGTA
1 AAAATGTGTTTTGCA
2018488 AAAAT-TGTTTTGCA
1 AAAATGTGTTTTGCA
2018502 AAAA
1 AAAA
2018506 GCGTTTTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.39
Consensus pattern (15 bp):
AAAATGTGTTTTGCA
Found at i:2018667 original size:10 final size:11
Alignment explanation
Indices: 2018647--2018688 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 11
2018637 TCTTCTTAAA
2018647 AATTAATATTT
1 AATTAATATTT
2018658 AATT-ATATTT
1 AATTAATATTT
*
2018668 AAATAATA-TT
1 AATTAATATTT
2018678 -ATTAATATTT
1 AATTAATATTT
2018688 A
1 A
2018689 TTTATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 6 0.23
10 13 0.50
11 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTAATATTT
Found at i:2021064 original size:18 final size:18
Alignment explanation
Indices: 2021041--2021078 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2021031 TGCCAGGTGC
* *
2021041 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
2021059 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
2021077 GT
1 GT
2021079 TTTCTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:2021714 original size:116 final size:117
Alignment explanation
Indices: 2021511--2021720 Score: 268
Period size: 116 Copynumber: 1.8 Consensus size: 117
2021501 CTAAAATAGA
* * *
2021511 AATTTACTTATACATTTTTAATATAATAGAAATTCTTTTAAATAAGGCAATATGTTGAATATTTC
1 AATTTACTTATACATTTTTAATAAAATAGAAATTATTTTAAATAAGGCAATATGTTAAATATTTC
*
2021576 TATATTATTTCATTTAATAAAATA-AAATGTTATTTTGAATAAAGTAATTGT
66 TATAATATTTCATTTAATAAAATATAAATGTTATTTTGAATAAAGTAATTGT
* ** *
2021627 AATTTACTT-TAATATTTTTAATAAAATAGATTTTATTTTAAATAAGTCAATAT-TCTAAATATT
1 AATTTACTTAT-ACATTTTTAATAAAATAGAAATTATTTTAAATAAGGCAATATGT-TAAATATT
*
2021690 TGTATCAAT-TTTCGATTTAA-AAAATATAAAT
64 TCTAT-AATATTTC-ATTTAATAAAATATAAAT
2021721 AATAAATTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
115 2 0.03
116 66 0.82
117 12 0.15
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (117 bp):
AATTTACTTATACATTTTTAATAAAATAGAAATTATTTTAAATAAGGCAATATGTTAAATATTTC
TATAATATTTCATTTAATAAAATATAAATGTTATTTTGAATAAAGTAATTGT
Found at i:2025317 original size:12 final size:11
Alignment explanation
Indices: 2025296--2025329 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
2025286 GTTAGTTAGG
2025296 TTTTTTTTATT
1 TTTTTTTTATT
2025307 TTTTATTTTATT
1 TTTT-TTTTATT
2025319 TATTTTTTTAT
1 T-TTTTTTTAT
2025330 GCCGATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 14 0.67
13 3 0.14
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:2025320 original size:16 final size:16
Alignment explanation
Indices: 2025296--2025326 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2025286 GTTAGTTAGG
*
2025296 TTTTTTTTATTTTTTA
1 TTTTATTTATTTTTTA
2025312 TTTTATTTATTTTTT
1 TTTTATTTATTTTTT
2025327 TATGCCGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTATTTATTTTTTA
Found at i:2027617 original size:126 final size:126
Alignment explanation
Indices: 2027391--2027932 Score: 861
Period size: 126 Copynumber: 4.3 Consensus size: 126
2027381 CCAAACATGC
* * * * * *
2027391 GCTACTGCAGCAAAAGCACGTTCTCGTGGGAGCTTCTATCAGTACTTGTGCTGACAATGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCCT
* * *
2027456 GCTTAAAGCGTTTTTAACACTATTTGCTCACAAACGTCTACTCGAAATTATTTTTTTAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
*
2027517 GCTACTGCT-GCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTAACAATGCATCC
1 GCTACTG-TAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCC
* *
2027581 TGCTTAAAGTGTTTTTGACATTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
65 TGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
* * *
2027643 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTCCAGTACTTTTCCTGACAATGCATCTT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCCT
2027708 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
* * *
2027769 GCTACTATAGCAAAAGTGCGTCCACGTGGGAGCTTCTTTCGGTACTTTTGCTGACAATGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCCT
* *
2027834 GCTTAAAGCGTTTTTGACACTATTTGCTCAAAAACGTCTACTCGAAATTATTTTTTTAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
* * *
2027895 GCTACTGTAGCAAAAGCACGTCAACATGGGAGCTTCTT
1 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTT
2027933 CCCTTAAAAT
Statistics
Matches: 383, Mismatches: 31, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
125 1 0.00
126 382 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (126 bp):
GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCCT
GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAGGA
Found at i:2028161 original size:14 final size:14
Alignment explanation
Indices: 2028101--2028174 Score: 51
Period size: 14 Copynumber: 4.8 Consensus size: 14
2028091 ATTTTTTCTT
2028101 TAAAACCCTAAACC
1 TAAAACCCTAAACC
*
2028115 TAAAAACACCAAAACTC
1 T-AAAAC-CCTAAAC-C
*
2028132 TAACCCTAATCCTAAACC
1 TAA----AACCCTAAACC
2028150 -ATAAACCCTAAACC
1 TA-AAACCCTAAACC
2028164 TAAAACCCTAA
1 TAAAACCCTAA
2028175 TTGCAGGAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 18
0.68 0.06 0.26
Matches are distributed among these distances:
14 20 0.43
15 6 0.13
16 8 0.17
17 3 0.06
18 2 0.04
19 6 0.13
20 2 0.04
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (14 bp):
TAAAACCCTAAACC
Found at i:2029596 original size:18 final size:17
Alignment explanation
Indices: 2029563--2029601 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2029553 TTGTATAAAT
2029563 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
2029581 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
2029598 TGTG
1 TGTG
2029602 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:2029854 original size:23 final size:23
Alignment explanation
Indices: 2029827--2029924 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
2029817 AGTGTTATTG
2029827 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
2029850 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2029873 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2029895 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2029918 ATCAGTG
1 ATCAGTG
2029925 TGGCACTTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 20 0.29
23 48 0.71
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2029893 original size:45 final size:45
Alignment explanation
Indices: 2029829--2029917 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
2029819 TGTTATTGAT
* **
2029829 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCAGCTACATC
2029874 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCAGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCAGCTACAT
2029918 ATCAGTGTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCAGCTACATC
Found at i:2033473 original size:23 final size:23
Alignment explanation
Indices: 2033424--2033474 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
2033414 ACAAATGTCC
***
2033424 GTAACCCCTAAATTCATTATCTT
1 GTAACCCCTAAATTCATTATAAA
2033447 GTAACCCCTAAATT-ATTTATAAA
1 GTAACCCCTAAATTCA-TTATAAA
2033470 GTAAC
1 GTAAC
2033475 TTAATGCTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (23 bp):
GTAACCCCTAAATTCATTATAAA
Found at i:2040928 original size:11 final size:11
Alignment explanation
Indices: 2040914--2040939 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2040904 TTATTTTTAT
2040914 TTTTAAAATAC
1 TTTTAAAATAC
2040925 TTTTAAAATAC
1 TTTTAAAATAC
2040936 TTTT
1 TTTT
2040940 TTTAATTTTT
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:2044507 original size:14 final size:14
Alignment explanation
Indices: 2044490--2044522 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2044480 TGTAATATGA
2044490 AAGTTTGACCATTT
1 AAGTTTGACCATTT
*
2044504 AAGTTTGACCGTTT
1 AAGTTTGACCATTT
2044518 AAGTT
1 AAGTT
2044523 CAGTCTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (14 bp):
AAGTTTGACCATTT
Found at i:2051475 original size:14 final size:13
Alignment explanation
Indices: 2051441--2051482 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
2051431 ACTATCAAGC
2051441 TTAAATTA-TAAA
1 TTAAATTATTAAA
*
2051453 TTTAATTATTAAA
1 TTAAATTATTAAA
2051466 TCTAAATTATTAAA
1 T-TAAATTATTAAA
2051480 TTA
1 TTA
2051483 TAAATTTAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 7 0.27
13 7 0.27
14 12 0.46
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAATTATTAAA
Found at i:2054137 original size:17 final size:17
Alignment explanation
Indices: 2054111--2054152 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
2054101 ATACTACAAA
*
2054111 AATTATTTCGATTAATT
1 AATTAATTCGATTAATT
2054128 AATTAATTCGATTAATT
1 AATTAATTCGATTAATT
*
2054145 ACTTAATT
1 AATTAATT
2054153 TCGAACCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (17 bp):
AATTAATTCGATTAATT
Found at i:2055751 original size:18 final size:18
Alignment explanation
Indices: 2055728--2055781 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
2055718 AAATCGTGTC
2055728 ATTCATTTTCAAAACATT
1 ATTCATTTTCAAAACATT
* * *
2055746 ATTCATTTACAAACCTTT
1 ATTCATTTTCAAAACATT
*
2055764 ATTCAATTTCAAAACATT
1 ATTCATTTTCAAAACATT
2055782 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTCATTTTCAAAACATT
Found at i:2067457 original size:26 final size:26
Alignment explanation
Indices: 2067427--2067477 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
2067417 ACCAATGAAC
*
2067427 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
2067453 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
2067478 CTTTTCACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:2067484 original size:104 final size:104
Alignment explanation
Indices: 2067290--2067556 Score: 439
Period size: 104 Copynumber: 2.6 Consensus size: 104
2067280 TAACCGTTAT
* **
2067290 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
2067355 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
*
2067394 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTC-GGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
2067458 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
* **
2067498 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
2067557 TTATATACAA
Statistics
Matches: 153, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
103 25 0.16
104 127 0.83
105 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.19
Consensus pattern (104 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:2074480 original size:104 final size:105
Alignment explanation
Indices: 2074300--2074567 Score: 450
Period size: 104 Copynumber: 2.6 Consensus size: 105
2074290 TAACCGTTAT
* **
2074300 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
2074365 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
*
2074404 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
2074469 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* **
2074509 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
2074568 TTATATACAA
Statistics
Matches: 154, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
104 82 0.53
105 71 0.46
106 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.19
Consensus pattern (105 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:2076700 original size:44 final size:44
Alignment explanation
Indices: 2076563--2076874 Score: 189
Period size: 44 Copynumber: 7.2 Consensus size: 44
2076553 ACTTGATGCG
* * *
2076563 ATCTGCTCTACTGCAACTTCAGAGATATAAGATCTATTACTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTCA
* * * * *
2076607 ATCCGCTCCACTACAACTTCAGGGAGATAGGAT-TATCGAATTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTAT-TACTTCA
* * *
2076651 ATCTGCTCCACTGCAACCTCAGGGAGATAAGAT-TTTCTTCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTAT-TACTTCA
* * *** * *
2076695 GTCTGCCCCACTATGACTTCAGGGGGATAAGACTCGT-TTTC-TCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TC-TATTACTTCA
* * * * *
2076739 GTCTGCTCTACTGTAACTTCAGGGAGATAAGACCTGATGTGA--TCC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-AT-T-ACTTCA
* * *
2076784 A-CT-CT--ACTGCAAGTTCAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTCA
* * * *
2076824 ATCCGCTCCACTACAACTTCA-GGAGGATAGGAT-TATCAACTTCA
1 ATCTGCTCCACTGCAACTTCAGGGA-GATAAGATCTAT-TACTTCA
2076868 ATCTGCT
1 ATCTGCT
2076875 TCCTTACACT
Statistics
Matches: 206, Mismatches: 46, Indels: 32
0.73 0.16 0.11
Matches are distributed among these distances:
38 1 0.00
39 1 0.00
40 4 0.02
41 23 0.11
42 3 0.01
43 11 0.05
44 154 0.75
45 7 0.03
46 1 0.00
47 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTCA
Found at i:2077350 original size:87 final size:87
Alignment explanation
Indices: 2077128--2077550 Score: 580
Period size: 87 Copynumber: 4.9 Consensus size: 87
2077118 TGCAATCTTT
* * * * *
2077128 GATCTGCTTCACTGTCAGTGCAGGAAGGCAAGATCTGCTATCTTTAATCTGCTCCACTGCAACTG
1 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
* *
2077193 AGGGAGGCAAGGC-TAGTATCTTT
66 AGGGAGGCAAGGCTTTGT-T-TTC
* ** * * * * *
2077216 GATTTGCTTCGCTGTCAGCGCAAGAAGGCAATATCTGCTATCTTTAACCTGTTCCACCGCAACTC
1 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAAC-C
2077281 -AGGGAGGCAAGGCTTTGTTTTC
65 GAGGGAGGCAAGGCTTTGTTTTC
* *
2077303 GATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCG
1 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
* * *
2077368 ATGGAGGCAAGACTTTGTTTGC
66 AGGGAGGCAAGGCTTTGTTTTC
*
2077390 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCCATCTTTAACCAGCTCCACTGCAACCG
1 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
**
2077455 ATAGAGGCAAGGCTTTGTTTTC
66 AGGGAGGCAAGGCTTTGTTTTC
*
2077477 GATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
1 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
*
2077542 ATGGAGGCA
66 AGGGAGGCA
2077551 GGATGGCATG
Statistics
Matches: 299, Mismatches: 33, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
86 1 0.00
87 226 0.76
88 69 0.23
89 3 0.01
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.27
Consensus pattern (87 bp):
GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCG
AGGGAGGCAAGGCTTTGTTTTC
Found at i:2079622 original size:29 final size:26
Alignment explanation
Indices: 2079575--2079648 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 26
2079565 TTTTTTCTCT
* *
2079575 TTTTTCATATTTTTATTTTAACTTCGA
1 TTTTTC-TTTTTTTCTTTTAACTTCGA
* *
2079602 TTGATTTCTTTTTTTGCTTTTGACTTTGA
1 TT--TTTCTTTTTTT-CTTTTAACTTCGA
2079631 TTTTTCTTTTTTTCTTTT
1 TTTTTCTTTTTTTCTTTT
2079649 TTATTTTTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 5 0.12
27 13 0.32
28 6 0.15
29 16 0.40
ACGTcount: A:0.12, C:0.11, G:0.07, T:0.70
Consensus pattern (26 bp):
TTTTTCTTTTTTTCTTTTAACTTCGA
Found at i:2079657 original size:34 final size:34
Alignment explanation
Indices: 2079606--2079677 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
2079596 CTTCGATTGA
**
2079606 TTTCTTTTTTTGCTTTTGACTTTGATTTTTCTTTT
1 TTTCTTTTTTT-CTTTTGACTTTGATTTTGATTTT
*
2079641 TTTCTTTTTTAT-TTTTGATTTTGATTTTGATTTT
1 TTTCTTTTTT-TCTTTTGACTTTGATTTTGATTTT
2079675 TTT
1 TTT
2079678 TATTGAATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 22 0.67
35 10 0.30
36 1 0.03
ACGTcount: A:0.08, C:0.07, G:0.08, T:0.76
Consensus pattern (34 bp):
TTTCTTTTTTTCTTTTGACTTTGATTTTGATTTT
Found at i:2088541 original size:22 final size:22
Alignment explanation
Indices: 2088509--2088564 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
2088499 GTGACGATTC
* *
2088509 TCAGTGACACAACATCCACTAG
1 TCAGTGTCACAAAATCCACTAG
2088531 TCAGTGTCACAAAATCCACTAG
1 TCAGTGTCACAAAATCCACTAG
**
2088553 TTGGTGTCACAA
1 TCAGTGTCACAA
2088565 TTTCTTCACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (22 bp):
TCAGTGTCACAAAATCCACTAG
Found at i:2092154 original size:30 final size:31
Alignment explanation
Indices: 2092120--2092187 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
2092110 TTACCCAAGA
** * **
2092120 GTAAATACTCAAAATTTGAGGGATTAA-AGT
1 GTAAATACAAAAAATTTGAAGGACCAATAGT
2092150 GTAAATACAAAAAATTTGAAGGACCAATAGT
1 GTAAATACAAAAAATTTGAAGGACCAATAGT
2092181 GTAAATA
1 GTAAATA
2092188 TTTTTAAGGG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (31 bp):
GTAAATACAAAAAATTTGAAGGACCAATAGT
Found at i:2095347 original size:3 final size:3
Alignment explanation
Indices: 2095339--2095374 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2095329 ATTTTAGAGC
2095339 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2095375 GAACCCACCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2098376 original size:26 final size:27
Alignment explanation
Indices: 2098341--2098407 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 27
2098331 TTTGGAATAA
2098341 ATTTTAATTAT-ATT-TTTATAATGTGG
1 ATTTTAATTATAATTATTTA-AATGTGG
*
2098367 ATTTTGATTATAATTATTTAAATGT--
1 ATTTTAATTATAATTATTTAAATGTGG
*
2098392 ATATTAATTAT-ATTAT
1 ATTTTAATTATAATTAT
2098408 AATTGTGCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
24 5 0.14
25 9 0.25
26 10 0.28
27 8 0.22
28 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (27 bp):
ATTTTAATTATAATTATTTAAATGTGG
Found at i:2104886 original size:67 final size:68
Alignment explanation
Indices: 2104764--2104894 Score: 165
Period size: 67 Copynumber: 1.9 Consensus size: 68
2104754 TATTTAATTA
* * * * * *
2104764 AAAGATGTATTTAATTAATATTTTTATATATGAAATATTTACATATATTATAATTT-AGTGCATA
1 AAAGATGTAATTAATTAACATTTTTATATATAAAATATTTACACATACTACAATTTAAGTGCATA
2104828 TAT
66 TAT
* * * *
2104831 AAAGATTTAATTAATTCACATTTTTATATATAAAATATTTACGCATGCTACAATTTAAGTGCAT
1 AAAGATGTAATTAATTAACATTTTTATATATAAAATATTTACACATACTACAATTTAAGTGCAT
2104895 TTACTAATAT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
67 46 0.87
68 7 0.13
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (68 bp):
AAAGATGTAATTAATTAACATTTTTATATATAAAATATTTACACATACTACAATTTAAGTGCATA
TAT
Found at i:2105157 original size:44 final size:44
Alignment explanation
Indices: 2105093--2105177 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
2105083 CTAGTCAATA
* * *
2105093 TGGGATTGAAATTAACTTTTTTTAATAAAAATAGTGAAGAATTG
1 TGGGATTAAAATTAAATTTTTTTAATAAAAATAGTAAAGAATTG
2105137 TGGGATTAAAATTAAATTTTTTTAATAAAAATAGTAAAGAA
1 TGGGATTAAAATTAAATTTTTTTAATAAAAATAGTAAAGAA
2105178 GTGAGCTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.46, C:0.01, G:0.15, T:0.38
Consensus pattern (44 bp):
TGGGATTAAAATTAAATTTTTTTAATAAAAATAGTAAAGAATTG
Found at i:2105242 original size:115 final size:111
Alignment explanation
Indices: 2105026--2105245 Score: 273
Period size: 115 Copynumber: 1.9 Consensus size: 111
2105016 AACACATCAA
** * * *
2105026 GGGATTAAAATTAATTTTTAATGGAAATAATGAAGAAGTGAGCTATGGAAGTCTTCTCTAGTCAA
1 GGGATTAAAATTAATTTTTAATAAAAATAATAAAGAAGTGAGCTATAGAAGTATTCTCTAGTCAA
*
2105091 TATGGGATTGAAATTAACTTTTTTTAATAAAAATAGTGAAGAATTGT
66 TATGGGATTAAAATTAAC-TTTTTTAATAAAAATAGTGAAGAATTGT
*
2105138 GGGATTAAAATTAAATTTTTTTAATAAAAATAGTAAAGAAGTGAGCTATA-AGAGTATTCTCTAG
1 GGGATTAAAATT-AA--TTTTTAATAAAAATAATAAAGAAGTGAGCTATAGA-AGTATTCTCTAG
* **
2105202 TCAATGTGGGATTAAAAATTTAAC-TTTTTAATGGAAATAGTGAA
62 TCAATATGGGATT-AAAA-TTAACTTTTTTAATAAAAATAGTGAA
2105246 TAAATTGTCA
Statistics
Matches: 92, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
112 12 0.13
113 2 0.02
114 1 0.01
115 69 0.75
116 3 0.03
117 5 0.05
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (111 bp):
GGGATTAAAATTAATTTTTAATAAAAATAATAAAGAAGTGAGCTATAGAAGTATTCTCTAGTCAA
TATGGGATTAAAATTAACTTTTTTAATAAAAATAGTGAAGAATTGT
Found at i:2105327 original size:93 final size:93
Alignment explanation
Indices: 2105194--2105422 Score: 250
Period size: 93 Copynumber: 2.5 Consensus size: 93
2105184 TATAAGAGTA
* * * *
2105194 TTCTCTAGTCAATGTGGGATTAAAAATTTAACTTTTTAATGGAAATAGTGAATAAATTG-TCACT
1 TTCTATAGTAAATGTGGGATT-AAAA-TTAACTTTTTAATGGAAATAGTGAAGAAA-TGAACACT
* * *
2105258 TGTTTATAAGGAAAATGTGAA-ATATAGGAGTG
63 TATTTATAAGGAAAATGTGAACAT-GA-GAGCG
* * *
2105290 TT-TATAGTTAATGTGAGATTAAAATTAACTTTTTAATGAAAATAGTGAAGAAATGAACACTTAT
1 TTCTATAGTAAATGTGGGATTAAAATTAACTTTTTAATGGAAATAGTGAAGAAATGAACACTTAT
* * *
2105354 TTATAGGGTAAGTGTGAACATGAGAGCG
66 TTATAAGGAAAATGTGAACATGAGAGCG
* *
2105382 TTCTCTAGCAAATGTGGGATTAAAATTAACTTTTTAA-GGAA
1 TTCTATAGTAAATGTGGGATTAAAATTAACTTTTTAATGGAA
2105423 TCAAAATTTA
Statistics
Matches: 113, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
92 11 0.10
93 79 0.70
94 6 0.05
95 15 0.13
96 2 0.02
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (93 bp):
TTCTATAGTAAATGTGGGATTAAAATTAACTTTTTAATGGAAATAGTGAAGAAATGAACACTTAT
TTATAAGGAAAATGTGAACATGAGAGCG
Found at i:2105965 original size:40 final size:40
Alignment explanation
Indices: 2105921--2106013 Score: 150
Period size: 40 Copynumber: 2.3 Consensus size: 40
2105911 TTGAGGGAAT
2105921 CATATTTTGTAAAGATTACATTAGATTAGATTTGATATGA
1 CATATTTTGTAAAGATTACATTAGATTAGATTTGATATGA
* * *
2105961 CATATTTTGTAAAGATTAGATTAGATTATATTTGATATGG
1 CATATTTTGTAAAGATTACATTAGATTAGATTTGATATGA
*
2106001 CATATCTTGTAAA
1 CATATTTTGTAAA
2106014 TCCTTAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (40 bp):
CATATTTTGTAAAGATTACATTAGATTAGATTTGATATGA
Found at i:2109104 original size:21 final size:22
Alignment explanation
Indices: 2109065--2109105 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2109055 GTCAATGTAG
2109065 GATTAAAATTAACTTTTTAAGA
1 GATTAAAATTAACTTTTTAAGA
*
2109087 GATTAGAATTAA-TTTTTAA
1 GATTAAAATTAACTTTTTAA
2109106 TGAAAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (22 bp):
GATTAAAATTAACTTTTTAAGA
Found at i:2109408 original size:22 final size:23
Alignment explanation
Indices: 2109364--2109411 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
2109354 TTAGCCAATG
*
2109364 AGGGATTAAAATTTACTTTTTTA
1 AGGGATTAAAATTTAATTTTTTA
*
2109387 AGGGGTTAAAA-TTAATTTTTTA
1 AGGGATTAAAATTTAATTTTTTA
2109409 AGG
1 AGG
2109412 AAATAGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (23 bp):
AGGGATTAAAATTTAATTTTTTA
Found at i:2109767 original size:152 final size:153
Alignment explanation
Indices: 2109487--2109788 Score: 439
Period size: 152 Copynumber: 2.0 Consensus size: 153
2109477 ATGAAAATAG
* * * *
2109487 TGAAAGTGAGCTATAAAAGTATTATCTAGTTAATGTGGGAGTAAAATTAACTTTTTAAATGAAAA
1 TGAAAGCGAGCTATAAAAGTATTATCTAGTCAATATGAGAGTAAAATTAACTTTTTAAATGAAAA
* * * * * **
2109552 TAGTGAAGAAATTGTCACTTATTTATAAGGTAAATATGAGATATGGGAGTATTCTCCGGTCAAT-
66 CAGTAAAGAAATTGTCACTTATTTATAACGTAAATATGAGATACGAGAGTATTCTCCCATCAATG
2109616 ATGGAATTAAAATTAACTTTTTTA
131 ATGG-ATTAAAATTAACTTTTTTA
2109640 TGAAAGCGAGCTATAAAAGTATTATCTAGTCAATATGAGA-TAAAAATTAACTTTTT-AATGAAA
1 TGAAAGCGAGCTATAAAAGTATTATCTAGTCAATATGAGAGT-AAAATTAACTTTTTAAATGAAA
* *
2109703 ACAGTAAAGAAGTTGTCACTTATTTATAACGTAAATGTGAGATACGAGAGTATTCTCCCATCAAT
65 ACAGTAAAGAAATTGTCACTTATTTATAACGTAAATATGAGATACGAGAGTATTCTCCCATCAAT
*
2109768 GTTGGATTAAAATTAACTTTT
130 GATGGATTAAAATTAACTTTT
2109789 AACCTTTTAA
Statistics
Matches: 133, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
152 80 0.60
153 53 0.40
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.35
Consensus pattern (153 bp):
TGAAAGCGAGCTATAAAAGTATTATCTAGTCAATATGAGAGTAAAATTAACTTTTTAAATGAAAA
CAGTAAAGAAATTGTCACTTATTTATAACGTAAATATGAGATACGAGAGTATTCTCCCATCAATG
ATGGATTAAAATTAACTTTTTTA
Found at i:2115375 original size:21 final size:21
Alignment explanation
Indices: 2115351--2115391 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2115341 ATCTGCTCAA
* *
2115351 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2115372 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2115392 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2120805 original size:13 final size:13
Alignment explanation
Indices: 2120780--2120820 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2120770 GTGTATGGTG
2120780 TTTAAATATTATTT
1 TTTAAA-ATTATTT
*
2120794 TTTAAAATTATTC
1 TTTAAAATTATTT
2120807 TTT-AAA-TATTT
1 TTTAAAATTATTT
2120818 TTT
1 TTT
2120821 TACTAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 7 0.28
12 3 0.12
13 9 0.36
14 6 0.24
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTAAAATTATTT
Found at i:2120946 original size:16 final size:15
Alignment explanation
Indices: 2120925--2120957 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
2120915 CCATCTTGTA
2120925 TAAATTAATTTATTTT
1 TAAATTAATTT-TTTT
2120941 TAAATTAATTTTTTT
1 TAAATTAATTTTTTT
2120956 TA
1 TA
2120958 TTTTGATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TAAATTAATTTTTTT
Found at i:2124451 original size:31 final size:31
Alignment explanation
Indices: 2124413--2124476 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
2124403 AAAACTATAG
2124413 ACCAAGCAATATCATATACAACACGGTACTA
1 ACCAAGCAATATCATATACAACACGGTACTA
2124444 ACCAAGCAATATCATATACAACACGGTACTA
1 ACCAAGCAATATCATATACAACACGGTACTA
2124475 AC
1 AC
2124477 ATGACACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.45, C:0.27, G:0.09, T:0.19
Consensus pattern (31 bp):
ACCAAGCAATATCATATACAACACGGTACTA
Found at i:2129532 original size:12 final size:12
Alignment explanation
Indices: 2129515--2129540 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2129505 TGTCACAAAA
2129515 ATTTAGTAGCAT
1 ATTTAGTAGCAT
2129527 ATTTAGTAGCAT
1 ATTTAGTAGCAT
2129539 AT
1 AT
2129541 GCTCTTAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATTTAGTAGCAT
Found at i:2132551 original size:2 final size:2
Alignment explanation
Indices: 2132539--2132574 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2132529 GCCAGATCCT
2132539 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2132575 AATTATTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Done.