Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397268.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_81.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6219335
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 77647 characters in sequence are not A, C, G, or T
File 2 of 13
Found at i:749819 original size:24 final size:23
Alignment explanation
Indices: 749785--749852 Score: 86
Period size: 24 Copynumber: 3.0 Consensus size: 23
749775 TTTATTTTTA
749785 TTTATTA-TAATAATTTTATATAT
1 TTTATTATTAAT-ATTTTATATAT
* *
749808 TTTATTTTTAATATATTTATATTT
1 TTTATTATTAATAT-TTTATATAT
749832 TTTATTATTAAT-TTTTATATA
1 TTTATTATTAATATTTTATATA
749853 ATATGATCTC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
22 7 0.18
23 9 0.23
24 23 0.59
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATTATTAATATTTTATATAT
Found at i:749837 original size:114 final size:114
Alignment explanation
Indices: 749700--749929 Score: 397
Period size: 114 Copynumber: 2.0 Consensus size: 114
749690 AAAATATAAG
*
749700 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTGTAA
* * *
749765 TGTCATTTATTTTATTTTTATTTATTATAATAATTTTATATATTTTATT
66 TGTCATATATTTTATTTTCATTTATTATAATAATTGTATATATTTTATT
*
749814 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATGATCTCTTAAATATATTTGTAA
1 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTGTAA
* *
749879 TGTCATATATTTTATTTTCATTTATTATTATAGTTGTATATATTTTATT
66 TGTCATATATTTTATTTTCATTTATTATAATAATTGTATATATTTTATT
749928 TT
1 TT
749930 CATTTTTTAA
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 109 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (114 bp):
TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTGTAA
TGTCATATATTTTATTTTCATTTATTATAATAATTGTATATATTTTATT
Found at i:749892 original size:57 final size:57
Alignment explanation
Indices: 749712--749894 Score: 176
Period size: 57 Copynumber: 3.2 Consensus size: 57
749702 TAATATATTT
* *
749712 ATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAATGTC
1 ATATATTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTATAATGTC
* * * * * * * * *
749769 ATTTATTTTATT-TTTATTTATTATAATAATTTTATATATT--TTATTTTTAATATAT-TT
1 ATATATTTTATTATTAATTT-TTAT-ATAATATCATCTCTTAAATATATTT-ATA-ATGTC
* * *
749826 ATATTTTTTATTATTAATTTTTATATAATATGATCTCTTAAATATATTTGTAATGTC
1 ATATATTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTATAATGTC
749883 ATATATTTTATT
1 ATATATTTTATT
749895 TTCATTTATT
Statistics
Matches: 95, Mismatches: 23, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
56 25 0.26
57 45 0.47
58 25 0.26
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (57 bp):
ATATATTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTATAATGTC
Found at i:749929 original size:5 final size:5
Alignment explanation
Indices: 749919--750073 Score: 52
Period size: 5 Copynumber: 30.4 Consensus size: 5
749909 TAGTTGTATA
* * *
749919 TATTT TATTT TCATTT T-TTAA TATATT T-TTT TATAT TA-TA TATTT
1 TATTT TATTT T-ATTT TATT-T TAT-TT TATTT TATTT TATTT TATTT
* ** * * * *
749964 TATTT TAATT TATTT TA-CC TATAT TATATA AATTT TAATTT T-TTA TATTT
1 TATTT TATTT TATTT TATTT TATTT TAT-TT TATTT T-ATTT TATTT TATTT
* * * * *
750014 TATTT TGTTT TAATTTT TGATTAT TATAT TA-TA TATTT TATTT TAATA
1 TATTT TATTT T-A-TTT T-ATT-T TATTT TATTT TATTT TATTT TATTT
750062 TATTT TATTT TA
1 TATTT TATTT TA
750074 ATTATAATAT
Statistics
Matches: 106, Mismatches: 30, Indels: 28
0.65 0.18 0.17
Matches are distributed among these distances:
4 14 0.13
5 66 0.62
6 18 0.17
7 8 0.08
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (5 bp):
TATTT
Found at i:749954 original size:33 final size:33
Alignment explanation
Indices: 749883--749969 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 33
749873 TTGTAATGTC
* *
749883 ATATATTTTATTTTCATTTATTATTATAGTTGT
1 ATATATTTTATTTTCATTTTTTAATATAGTTGT
* *
749916 ATATATTTTATTTTCATTTTTTAATATATTTTT
1 ATATATTTTATTTTCATTTTTTAATATAGTTGT
*
749949 TTATATTATATATTTT-ATTTT
1 ATATATT-T-TATTTTCATTTT
749970 AATTTATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
33 35 0.74
34 6 0.13
35 6 0.13
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (33 bp):
ATATATTTTATTTTCATTTTTTAATATAGTTGT
Found at i:750013 original size:35 final size:32
Alignment explanation
Indices: 749950--750015 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 32
749940 TATATTTTTT
749950 TATATTATATATTTTATTTTAATTTATTTTACC
1 TATATTATATATTTTATTTT-ATTTATTTTACC
749983 TATATTATATAAATTTTAATTTT-TTATATTTTA
1 TATATTATAT--ATTTT-ATTTTATT-TATTTTA
750016 TTTTGTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
33 10 0.34
34 2 0.07
35 12 0.41
36 5 0.17
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (32 bp):
TATATTATATATTTTATTTTATTTATTTTACC
Found at i:750064 original size:15 final size:15
Alignment explanation
Indices: 750044--750075 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
750034 TTATTATATT
750044 ATATATTTTATTTTA
1 ATATATTTTATTTTA
750059 ATATATTTTATTTTA
1 ATATATTTTATTTTA
750074 AT
1 AT
750076 TATAATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATATATTTTATTTTA
Found at i:751691 original size:15 final size:15
Alignment explanation
Indices: 751673--751702 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
751663 ATGTCAAAAC
751673 CCCCCATGGTGGAAG
1 CCCCCATGGTGGAAG
751688 CCCCCATGGTGGAAG
1 CCCCCATGGTGGAAG
751703 GCATGGAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.33, G:0.33, T:0.13
Consensus pattern (15 bp):
CCCCCATGGTGGAAG
Found at i:760559 original size:22 final size:20
Alignment explanation
Indices: 760534--760583 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
760524 TAATAATATT
* *
760534 ATAATATTTGATATATAAATAA
1 ATAATATTTAAAATAT-AA-AA
*
760556 ATAATAATTAAAATATAAAA
1 ATAATATTTAAAATATAAAA
760576 ATAATATT
1 ATAATATT
760584 ATAATATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 9 0.38
21 2 0.08
22 13 0.54
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
ATAATATTTAAAATATAAAA
Found at i:760733 original size:16 final size:15
Alignment explanation
Indices: 760673--760736 Score: 55
Period size: 16 Copynumber: 4.3 Consensus size: 15
760663 TTAATATATT
*
760673 TATATTTTT-TATTA
1 TATATTTTTATATAA
760687 T-TAATTTTTATATAA
1 TAT-ATTTTTATATAA
*
760702 TATCATCTTT-TA-AA
1 TAT-ATTTTTATATAA
760716 TATATTTTTAATATAA
1 TATATTTTT-ATATAA
760732 TATAT
1 TATAT
760737 ATTATTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
13 6 0.15
14 12 0.30
15 9 0.22
16 13 0.32
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
TATATTTTTATATAA
Found at i:760791 original size:16 final size:17
Alignment explanation
Indices: 760677--760804 Score: 62
Period size: 14 Copynumber: 7.9 Consensus size: 17
760667 TATATTTATA
760677 TTTTT-TATTAT-TAA-
1 TTTTTATATTATATAAT
* *
760691 TTTTTATATAATATCAT
1 TTTTTATATTATATAAT
*
760708 CTTTTA-A--ATAT-AT
1 TTTTTATATTATATAAT
* *
760721 TTTTAATATAATATATATT
1 TTTT--TATATTATATAAT
*
760740 ATTTTTATTTTTATTATAAT
1 -TTTTTA-TATTA-TATAAT
**
760760 TTTAAATATT-T-T-AT
1 TTTTTATATTATATAAT
760774 TTTTTAT-TTATATAAT
1 TTTTTATATTATATAAT
760790 TTTTTATATTATATA
1 TTTTTATATTATATA
760805 TGTTATTTAA
Statistics
Matches: 85, Mismatches: 13, Indels: 29
0.67 0.10 0.23
Matches are distributed among these distances:
13 7 0.08
14 17 0.20
15 9 0.11
16 14 0.16
17 12 0.14
18 9 0.11
19 8 0.09
20 9 0.11
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTATATTATATAAT
Found at i:760795 original size:32 final size:32
Alignment explanation
Indices: 760733--760792 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
760723 TTAATATAAT
*
760733 ATATATTATTTTTATTTTTATTATAATTTTAA
1 ATATATTATTTTTATATTTATTATAATTTTAA
*
760765 ATATTTTATTTTT-TATTTA-TATAATTTT
1 ATATATTATTTTTATATTTATTATAATTTT
760793 TTATATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 9 0.35
31 5 0.19
32 12 0.46
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (32 bp):
ATATATTATTTTTATATTTATTATAATTTTAA
Found at i:760799 original size:30 final size:30
Alignment explanation
Indices: 760732--760822 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 30
760722 TTTAATATAA
* * *
760732 TATATATTATTTTTATTTTTATTATAATTTTA
1 TATATTTTATTTTT-TATTTA-TATAATTTTT
*
760764 AATATTTTATTTTTTATTTATATAATTTTT
1 TATATTTTATTTTTTATTTATATAATTTTT
* * * *
760794 TATATTATATATGTTATTTAAAT-ATTTTT
1 TATATTTTATTTTTTATTTATATAATTTTT
760823 CCTTAAAGAC
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
29 6 0.12
30 27 0.54
31 5 0.10
32 12 0.24
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (30 bp):
TATATTTTATTTTTTATTTATATAATTTTT
Found at i:771115 original size:4 final size:4
Alignment explanation
Indices: 771108--771133 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
771098 CTTCTTTTTT
771108 TTGG TTGG TTGG TTGG TTGG TTGG TT
1 TTGG TTGG TTGG TTGG TTGG TTGG TT
771134 TGTTTTACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (4 bp):
TTGG
Found at i:800109 original size:73 final size:72
Alignment explanation
Indices: 800023--800169 Score: 269
Period size: 73 Copynumber: 2.0 Consensus size: 72
800013 TTTTTTTTTT
800023 TTTCGGTTGTTGTGTATTCTTTTATCATTTATTGGTAGGTTTCGGGTG-ATTTAACTTAAACATG
1 TTTCGGTTGTTGTGTATTCTTTTATCATTTATTGGTAGGTTTC-GGTGAATTT-ACTTAAACATG
800087 GCCAAAGGA
64 GCCAAAGGA
800096 TTTCGGTTGTTGTGTATTCTTTTATCATTTATTGGTAGGTTTCGGTGAATTTACTTAAACATGGC
1 TTTCGGTTGTTGTGTATTCTTTTATCATTTATTGGTAGGTTTCGGTGAATTTACTTAAACATGGC
800161 CAAAGGA
66 CAAAGGA
800168 TT
1 TT
800170 AATAAGGCAA
Statistics
Matches: 73, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
72 26 0.36
73 47 0.64
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.45
Consensus pattern (72 bp):
TTTCGGTTGTTGTGTATTCTTTTATCATTTATTGGTAGGTTTCGGTGAATTTACTTAAACATGGC
CAAAGGA
Found at i:802410 original size:21 final size:20
Alignment explanation
Indices: 802384--802448 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
802374 AAGCCCTCAC
802384 CATCTGCGACTAAGCCTGTGA
1 CATCTGC-ACTAAGCCTGTGA
* *
802405 CTTCTGCAGCAAAGCCTGTGA
1 CATCTGCA-CTAAGCCTGTGA
*
802426 CATCTGCAACTAAGCCTGCGA
1 CATCTGC-ACTAAGCCTGTGA
802447 CA
1 CA
802449 AGGCCTGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.03
21 35 0.95
22 1 0.03
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.22
Consensus pattern (20 bp):
CATCTGCACTAAGCCTGTGA
Found at i:812493 original size:87 final size:86
Alignment explanation
Indices: 812347--812514 Score: 291
Period size: 87 Copynumber: 1.9 Consensus size: 86
812337 TTTGATTGGG
*
812347 ACTGCCTACCTTCTTCAACAATAGAAGACATGGAAGAGTTTCAAAAGTTCTACAGTTTATAGTTT
1 ACTGCCTACCTTCTTCAACAATAGAAGACATGGAAGAGTTTCAAAAGTTCTACACTTTATAGTTT
812412 GAATCTTTTTTTTCTGCCAGGA
66 GAATC-TTTTTTTCTGCCAGGA
** *
812434 ACTGCCTACCTTCTTTGACAATAGAAGACATGGAAGAGTTTCAAAAGTTCTACACTTTATATTTT
1 ACTGCCTACCTTCTTCAACAATAGAAGACATGGAAGAGTTTCAAAAGTTCTACACTTTATAGTTT
812499 GAATCTTTTTTTCTGC
66 GAATCTTTTTTTCTGC
812515 TCAGCCAATA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
86 11 0.14
87 66 0.86
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (86 bp):
ACTGCCTACCTTCTTCAACAATAGAAGACATGGAAGAGTTTCAAAAGTTCTACACTTTATAGTTT
GAATCTTTTTTTCTGCCAGGA
Found at i:838107 original size:16 final size:17
Alignment explanation
Indices: 838082--838115 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
838072 CTTTAATAAT
838082 AAATTATTAAATTATTA
1 AAATTATTAAATTATTA
*
838099 AAATT-TTAAATTTTTA
1 AAATTATTAAATTATTA
838115 A
1 A
838116 TGAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTATTAAATTATTA
Found at i:838369 original size:15 final size:15
Alignment explanation
Indices: 838342--838395 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
838332 GATAAATTGA
838342 TAATATTTAAAATTTT
1 TAATATTT-AAATTTT
*
838358 TAATATTTAAATTAT
1 TAATATTTAAATTTT
*
838373 TAAT-TATTAATTTTT
1 TAATAT-TTAAATTTT
838388 TAAATATT
1 T-AATATT
838396 ATAGAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 1 0.03
15 18 0.56
16 12 0.38
17 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATATTTAAATTTT
Found at i:838377 original size:22 final size:22
Alignment explanation
Indices: 838352--838396 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
838342 TAATATTTAA
*
838352 AATTTTTAA-TATTTAAATTATT
1 AATTATTAATTATTTAAA-TATT
*
838374 AATTATTAATTTTTTAAATATT
1 AATTATTAATTATTTAAATATT
838396 A
1 A
838397 TAGAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AATTATTAATTATTTAAATATT
Found at i:849556 original size:37 final size:37
Alignment explanation
Indices: 849506--849579 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
849496 CTATATTGAG
849506 TTAGCAAGTAGTTCATGTAATATTGGTACAATGATGA
1 TTAGCAAGTAGTTCATGTAATATTGGTACAATGATGA
849543 TTAGCAAGTAGTTCATGTAATATTGGTACAATGATGA
1 TTAGCAAGTAGTTCATGTAATATTGGTACAATGATGA
849580 CCAAAGAGCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (37 bp):
TTAGCAAGTAGTTCATGTAATATTGGTACAATGATGA
Found at i:869369 original size:33 final size:33
Alignment explanation
Indices: 869332--869396 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
869322 ATATTAAATT
869332 AACATATCACATCATCATCAATTATAATATATC
1 AACATATCACATCATCATCAATTATAATATATC
* * *
869365 AACATATCATATTATGATCAATTATAATATAT
1 AACATATCACATCATCATCAATTATAATATAT
869397 TAGCATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (33 bp):
AACATATCACATCATCATCAATTATAATATATC
Found at i:873985 original size:124 final size:125
Alignment explanation
Indices: 873708--873999 Score: 383
Period size: 125 Copynumber: 2.3 Consensus size: 125
873698 TTTAATTTTT
* * ** *
873708 AAGACTACTTGTTTGCCCCAGCTGGAAATTTCTTCCATGAGAGCGGAATTGAATTGGGCAACACG
1 AAGACTACTTGTTTGCCCCAGCTGGAAATTTCATCCATGAGAGAGGAATTGAATTGGAAAACAAG
* * * *
873773 CAAGTTTAACCATCCATGTCCTCCCAAATTGGTTGACGATGGGCCTAATCATTATATTGG
66 CAAGTTTAACCATCCATGTCCACCCAAATTGGTTGACGATAGGCCTAATAATTATACTGG
* * *
873833 AAGACTGCTTGTTTGCCCTAGCTGGAAATTTCATCCATGAGAGAGGAATTGACTTGGAAAACAAG
1 AAGACTACTTGTTTGCCCCAGCTGGAAATTTCATCCATGAGAGAGGAATTGAATTGGAAAACAAG
* * * *
873898 C-AGTTTTAAGCGTCCATGTCCACCC-AATTGGTTGGCTATAGGCCTAATAATTATAGCT-G
66 CAAG-TTTAACCATCCATGTCCACCCAAATTGGTTGACGATAGGCCTAATAATTATA-CTGG
* *
873957 AAGACTACTAGTTTGCCCCAGTTGGAAATTTCATCCATGAGAG
1 AAGACTACTTGTTTGCCCCAGCTGGAAATTTCATCCATGAGAG
874000 CTGTACGTAT
Statistics
Matches: 145, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
124 68 0.47
125 77 0.53
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (125 bp):
AAGACTACTTGTTTGCCCCAGCTGGAAATTTCATCCATGAGAGAGGAATTGAATTGGAAAACAAG
CAAGTTTAACCATCCATGTCCACCCAAATTGGTTGACGATAGGCCTAATAATTATACTGG
Found at i:876189 original size:17 final size:18
Alignment explanation
Indices: 876143--876189 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
876133 TCACCAGCTG
876143 CTGTTAAAATACCTTGACT
1 CTGTTAAAATACCTT-ACT
* *
876162 CGTGTTCAAATACCTT-TT
1 C-TGTTAAAATACCTTACT
876180 CTGTTAAAAT
1 CTGTTAAAAT
876190 GGAGTTACGA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 8 0.33
18 2 0.08
19 1 0.04
20 13 0.54
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (18 bp):
CTGTTAAAATACCTTACT
Found at i:877407 original size:21 final size:21
Alignment explanation
Indices: 877378--877419 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
877368 ATAGTTGAGA
877378 CTTGAGATTTGGCAACTTATT
1 CTTGAGATTTGGCAACTTATT
* * *
877399 CTTGTGATTTTGCAAGTTATT
1 CTTGAGATTTGGCAACTTATT
877420 AAATAGGAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (21 bp):
CTTGAGATTTGGCAACTTATT
Found at i:880868 original size:108 final size:108
Alignment explanation
Indices: 880738--880954 Score: 328
Period size: 108 Copynumber: 2.0 Consensus size: 108
880728 AGTTAAGACA
* * * *
880738 AAAACAACAAAAATTGGAGTTGACAAAAGGAGTCTGAACTCTG-ACCGGCTTTCCTTGGCAGTCT
1 AAAACAACAAAAATTAGAGTTGACAAAACGAGTCTGAACTCTGAAGC-GCTTTCCTTGGCAGTAT
* *
880802 TCTGCCTTAATGTCACCTTCGAAATAACTAGAAAATGATTGGCC
65 TCGGCCTTAATGTCACCTTCGAAATAACTAGAAAATGATTAGCC
* *
880846 AAAACAACAAAAATTAGAGTTGACAAAACGAGTCTGAACTTTGAAGCTCTTTCCTTGGCAGTATT
1 AAAACAACAAAAATTAGAGTTGACAAAACGAGTCTGAACTCTGAAGCGCTTTCCTTGGCAGTATT
* *
880911 CGGCCTTAATGTCACCTTTGAAGTAACTAGAAAATGATTAGCC
66 CGGCCTTAATGTCACCTTCGAAATAACTAGAAAATGATTAGCC
880954 A
1 A
880955 TAATTAATAA
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
108 96 0.98
109 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (108 bp):
AAAACAACAAAAATTAGAGTTGACAAAACGAGTCTGAACTCTGAAGCGCTTTCCTTGGCAGTATT
CGGCCTTAATGTCACCTTCGAAATAACTAGAAAATGATTAGCC
Found at i:884373 original size:51 final size:51
Alignment explanation
Indices: 884285--884397 Score: 165
Period size: 51 Copynumber: 2.2 Consensus size: 51
884275 CAAATCAAAG
* *
884285 CAACCAATCAAGAAATATCACTAATTATCAAATAAGGCACAAAATTTGAAC
1 CAACCAATCAAGAAACATCACTAATGATCAAATAAGGCACAAAATTTGAAC
* *
884336 TAACCAATCAAGAAACATCACTAATGATCGAAA-AAGGCACGAAATTTGAAC
1 CAACCAATCAAGAAACATCACTAATGATC-AAATAAGGCACAAAATTTGAAC
*
884387 CAACCATTCAA
1 CAACCAATCAA
884398 CTAATGATCA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 52 0.95
52 3 0.05
ACGTcount: A:0.50, C:0.21, G:0.10, T:0.19
Consensus pattern (51 bp):
CAACCAATCAAGAAACATCACTAATGATCAAATAAGGCACAAAATTTGAAC
Found at i:887450 original size:23 final size:23
Alignment explanation
Indices: 887411--887456 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
887401 ATTGAAAATT
*
887411 GACAATTGTGTTCGTTAAAAACA
1 GACAATTGTCTTCGTTAAAAACA
* *
887434 GACAATTGTCTTTGTTAGAAACA
1 GACAATTGTCTTCGTTAAAAACA
887457 ATATCTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (23 bp):
GACAATTGTCTTCGTTAAAAACA
Found at i:891924 original size:26 final size:26
Alignment explanation
Indices: 891888--891941 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
891878 GTATGGTTTC
891888 AAGACAAAAGGTAGGTCGACAGAGAA
1 AAGACAAAAGGTAGGTCGACAGAGAA
891914 AAGACAAAAGGTAGGTCGACAGAGAA
1 AAGACAAAAGGTAGGTCGACAGAGAA
891940 AA
1 AA
891942 TAACAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.52, C:0.11, G:0.30, T:0.07
Consensus pattern (26 bp):
AAGACAAAAGGTAGGTCGACAGAGAA
Found at i:900242 original size:93 final size:93
Alignment explanation
Indices: 900126--900399 Score: 460
Period size: 93 Copynumber: 2.9 Consensus size: 93
900116 CCTCATTAGT
*
900126 CTCTGATGCAGGGTCCAAGCCATTGCTGACCTGCAACGCGATGTTGGGAGGATTCACATCAGAGC
1 CTCTGATGCAGGGTCCAAGCCATTGCTGACCTGCAACGCGGTGTTGGGAGGATTCACATCAGAGC
900191 ATGCAAGTGCAAGAGTCCCACCACAGGC
66 ATGCAAGTGCAAGAGTCCCACCACAGGC
*
900219 CTCTGATGCAGGGTCCAAGCCATTGCTGACCTGCAATGCGGTGTTGGGAGGATTCACATCAGAGC
1 CTCTGATGCAGGGTCCAAGCCATTGCTGACCTGCAACGCGGTGTTGGGAGGATTCACATCAGAGC
*
900284 ATGCAAGTGCAAGAGTCCCACCACAGGT
66 ATGCAAGTGCAAGAGTCCCACCACAGGC
* * * *
900312 CTCTGATGCAGGGTCCAAGTCATTGCCGATCTGCAATC-CGGTGTTGGGAGGGTTCACATCAGAG
1 CTCTGATGCAGGGTCCAAGCCATTGCTGACCTGCAA-CGCGGTGTTGGGAGGATTCACATCAGAG
*
900376 CATGCAAGTGAAAGAGTCCCACCA
65 CATGCAAGTGCAAGAGTCCCACCA
900400 GAAGTCTCAG
Statistics
Matches: 171, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
93 171 1.00
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.20
Consensus pattern (93 bp):
CTCTGATGCAGGGTCCAAGCCATTGCTGACCTGCAACGCGGTGTTGGGAGGATTCACATCAGAGC
ATGCAAGTGCAAGAGTCCCACCACAGGC
Found at i:913473 original size:2 final size:2
Alignment explanation
Indices: 913468--913493 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
913458 AAAAAAAAAA
913468 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
913494 GTACACGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:946194 original size:30 final size:30
Alignment explanation
Indices: 946154--946217 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
946144 AGATTAAAAA
* *
946154 ACTTTTTTTTATATTATTTATTTTATTTGC
1 ACTTTCTTTTATAATATTTATTTTATTTGC
946184 ACTTTCTTTTATAATATTTATTTTATTTGC
1 ACTTTCTTTTATAATATTTATTTTATTTGC
946214 ACTT
1 ACTT
946218 CAAGCAAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.22, C:0.09, G:0.03, T:0.66
Consensus pattern (30 bp):
ACTTTCTTTTATAATATTTATTTTATTTGC
Found at i:950153 original size:27 final size:27
Alignment explanation
Indices: 950111--950162 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
950101 NNNNNNNNAA
*
950111 TAAATAAATCATCAATTATTAATATTT
1 TAAATAAATCACCAATTATTAATATTT
*
950138 TAAATAAATTACCAATTATTAATAT
1 TAAATAAATCACCAATTATTAATAT
950163 GTAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAATAAATCACCAATTATTAATATTT
Found at i:951285 original size:2 final size:2
Alignment explanation
Indices: 951280--951322 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
951270 TGTGTGTGTG
951280 TA TA TA TA TA 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 TA TA TA TA TA
951322 T
1 T
951323 GTCTTCATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:954507 original size:33 final size:32
Alignment explanation
Indices: 954440--954519 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
954430 AAAAAAATTT
*
954440 AATATTTTTTATTATTTAGATAAATTGTTGAA
1 AATATTTTTTATTATTTAGATAAATTGGTGAA
* * * *
954472 AATGTTTTTTATTGTTTAGATCATTTGGTGAAA
1 AATATTTTTTATTATTTAGATAAATTGGTG-AA
*
954505 AATATTTTCTATTAT
1 AATATTTTTTATTAT
954520 AGTGGAATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 25 0.64
33 14 0.36
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.54
Consensus pattern (32 bp):
AATATTTTTTATTATTTAGATAAATTGGTGAA
Found at i:954861 original size:76 final size:74
Alignment explanation
Indices: 954778--954919 Score: 185
Period size: 76 Copynumber: 1.9 Consensus size: 74
954768 ACTTATACTT
* * ** * *
954778 ATAAATATATATTTATTAAATAAAAATTGTTGGAATATTTTTTATTATATAATTATTAGTAAGTT
1 ATAAATATATATTCATCAAATAAAAATCATTGAAATATTTTTTA-T-TATAATTATTAGTAAGAT
954843 TTAAATTTATC
64 TTAAATTTATC
* * *
954854 ATAAATATGTATTCATCAAATGAAGATCATTGAAATATTTTTTATTATAATTATTAGTAAGATTT
1 ATAAATATATATTCATCAAATAAAAATCATTGAAATATTTTTTATTATAATTATTAGTAAGATTT
954919 A
66 A
954920 TTTCATTTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
74 20 0.35
75 1 0.02
76 36 0.63
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (74 bp):
ATAAATATATATTCATCAAATAAAAATCATTGAAATATTTTTTATTATAATTATTAGTAAGATTT
AAATTTATC
Found at i:962258 original size:2 final size:2
Alignment explanation
Indices: 962251--962275 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
962241 AGATAATTAC
962251 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
962276 CTAAAAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:965454 original size:28 final size:29
Alignment explanation
Indices: 965414--965488 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 29
965404 GATATTGAAT
*
965414 TTTATTATATTTGA-TAAATATTATGATA
1 TTTATAATATTTGATTAAATATTATGATA
*
965442 TTTATAATTTTTGATTGTAAATATTATGATA
1 TTTATAATATTTGA-T-TAAATATTATGATA
*
965473 TTTATGATATTATGAT
1 TTTATAATATT-TGAT
965489 ATCTCTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
28 12 0.31
31 24 0.62
32 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (29 bp):
TTTATAATATTTGATTAAATATTATGATA
Found at i:965484 original size:17 final size:17
Alignment explanation
Indices: 965415--965490 Score: 77
Period size: 17 Copynumber: 4.5 Consensus size: 17
965405 ATATTGAATT
*
965415 TTATTATATTTGATAAATA
1 TTATGATATTT-AT-AATA
965434 TTATGATATTTATAAT-
1 TTATGATATTTATAATA
* *
965450 TTTTGAT-TGTA-AATA
1 TTATGATATTTATAATA
*
965465 TTATGATATTTATGATA
1 TTATGATATTTATAATA
965482 TTATGATAT
1 TTATGATAT
965491 CTCTTTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
14 3 0.06
15 9 0.19
16 9 0.19
17 15 0.31
18 2 0.04
19 10 0.21
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (17 bp):
TTATGATATTTATAATA
Found at i:966039 original size:4 final size:4
Alignment explanation
Indices: 966030--966057 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
966020 AATAATAACT
966030 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
966058 TATATACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:967380 original size:14 final size:13
Alignment explanation
Indices: 967357--967421 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 13
967347 TATTTTTATT
*
967357 TAAATTTAAAATA
1 TAAATATAAAATA
967370 CTAAATATAAAATTA
1 -TAAATATAAAA-TA
*
967385 TAATGTATAAAATA
1 TAA-ATATAAAATA
*
967399 TAAATAGTTAAATA
1 TAAATA-TAAAATA
967413 TAATATATA
1 TAA-ATATA
967422 GAATCTTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
13 2 0.05
14 28 0.67
15 12 0.29
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (13 bp):
TAAATATAAAATA
Found at i:967880 original size:51 final size:50
Alignment explanation
Indices: 967762--967897 Score: 136
Period size: 50 Copynumber: 2.7 Consensus size: 50
967752 ATAAAATATT
* *
967762 ATTTT-GAGAGAACCATTAAAAAAATATATAATAAATAAATAATTCCGTAA
1 ATTTTGGAGAGAACCATT-AAAAAATATATAATAAATAAAAAATTCAGTAA
* * *
967812 ATTTT-GAAAGTGACCATTAAAAAATCTATAATAAATAAAAAATTCTAAG-AA
1 ATTTTGGAGAG-AACCATTAAAAAATATATAATAAATAAAAAATTC--AGTAA
* *
967863 ATTTTGGAG-GAAGCCATTAATATATATATAATAAA
1 ATTTTGGAGAGAA-CCATTAAAAAATATATAATAAA
967898 AATTTTTAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
50 35 0.49
51 33 0.46
52 3 0.04
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (50 bp):
ATTTTGGAGAGAACCATTAAAAAATATATAATAAATAAAAAATTCAGTAA
Found at i:976333 original size:22 final size:22
Alignment explanation
Indices: 976308--976353 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
976298 TGTATATATC
976308 TTTAAGATTCTAGCATAATTAA
1 TTTAAGATTCTAGCATAATTAA
976330 TTTAAGATTCTAGCATAATTAA
1 TTTAAGATTCTAGCATAATTAA
976352 TT
1 TT
976354 AATCGTGTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (22 bp):
TTTAAGATTCTAGCATAATTAA
Found at i:978412 original size:12 final size:12
Alignment explanation
Indices: 978395--978431 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
978385 CAGGAACACG
978395 AATCTTCAAAAT
1 AATCTTCAAAAT
*
978407 AATCTTCAAAAC
1 AATCTTCAAAAT
978419 AA--TTCAAAAT
1 AATCTTCAAAAT
978429 AAT
1 AAT
978432 TGAACGGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (12 bp):
AATCTTCAAAAT
Found at i:1004140 original size:2 final size:2
Alignment explanation
Indices: 1004133--1004163 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1004123 NNNNNNNNNN
1004133 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
1004164 CTATCTTCAC
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:1006153 original size:2 final size:2
Alignment explanation
Indices: 1006146--1006179 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1006136 CAAACCGAAG
1006146 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1006180 TAGTGATAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1008401 original size:20 final size:19
Alignment explanation
Indices: 1008371--1008408 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1008361 TGTTTTCTTT
1008371 AAATTATTAATAAATAAAA
1 AAATTATTAATAAATAAAA
*
1008390 AAATTAATTAATTAATAAA
1 AAATT-ATTAATAAATAAA
1008409 TTTGTCGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATTATTAATAAATAAAA
Found at i:1009035 original size:21 final size:22
Alignment explanation
Indices: 1009006--1009048 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1008996 AAAAGAAAAA
*
1009006 TATTATTAAATTA-TAATTTTT
1 TATTATTAAAATATTAATTTTT
*
1009027 TATTTTTAAAATATTAATTTTT
1 TATTATTAAAATATTAATTTTT
1009049 AATCAATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTATTAAAATATTAATTTTT
Found at i:1016896 original size:39 final size:38
Alignment explanation
Indices: 1016826--1016905 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 38
1016816 GTACGACGGT
1016826 GGAGGAGGAGGAGAGGCTGACGGTTGGGGAGGCGGCGGG
1 GGAGGAGGAGGAGAGGCTGACGGTTGGGGAGGCGG-GGG
* * * *
1016865 GGAGGAGGAGGAGATGCTGCCTG-TGGAGGAGGTGGGGG
1 GGAGGAGGAGGAGAGGCTGACGGTTGG-GGAGGCGGGGG
1016903 GGA
1 GGA
1016906 AGAGACACGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 9 0.25
39 27 0.75
ACGTcount: A:0.19, C:0.09, G:0.62, T:0.10
Consensus pattern (38 bp):
GGAGGAGGAGGAGAGGCTGACGGTTGGGGAGGCGGGGG
Found at i:1020727 original size:18 final size:18
Alignment explanation
Indices: 1020700--1020735 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1020690 TTTAGGACCT
*
1020700 TAATTGATTTTTTAAATA
1 TAATTGATTTTTAAAATA
*
1020718 TAATTTATTTTTAAAATA
1 TAATTGATTTTTAAAATA
1020736 GTACTCTCTA
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:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TAATTGATTTTTAAAATA
Found at i:1022057 original size:22 final size:21
Alignment explanation
Indices: 1022024--1022065 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1022014 GTAAGATTCT
1022024 CTTTTTTCTTTTCTTTTATTTC
1 CTTTTTTCTTTTC-TTTATTTC
1022046 CTTTTTAT-TTTTCTTTATTT
1 CTTTTT-TCTTTTCTTTATTT
1022066 TTCATGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 11 0.58
23 1 0.05
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (21 bp):
CTTTTTTCTTTTCTTTATTTC
Found at i:1111140 original size:5 final size:5
Alignment explanation
Indices: 1111130--1111158 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1111120 TCCTATCAAA
1111130 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1111159 AGTAGGAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1113256 original size:26 final size:24
Alignment explanation
Indices: 1113227--1113274 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
1113217 CTTATAAACT
1113227 TTATCTATAATTATAAAATATATGAA
1 TTATCTATAA--ATAAAATATATGAA
* *
1113253 TTATGTATAAATTAAATATATG
1 TTATCTATAAATAAAATATATG
1113275 TATTTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.55
26 9 0.45
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (24 bp):
TTATCTATAAATAAAATATATGAA
Found at i:1113287 original size:17 final size:17
Alignment explanation
Indices: 1113267--1113308 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1113257 GTATAAATTA
1113267 AATATATGTA-TTTATAT
1 AATATATGTACTTTAT-T
1113284 AATATAT-TACTTTATT
1 AATATATGTACTTTATT
1113300 ATATATATG
1 A-ATATATG
1113309 AAATTAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (17 bp):
AATATATGTACTTTATT
Found at i:1113579 original size:219 final size:218
Alignment explanation
Indices: 1113252--1113710 Score: 554
Period size: 219 Copynumber: 2.1 Consensus size: 218
1113242 AAATATATGA
* *
1113252 ATTATGTATAAATTAAATATATGTATTTATATAATATATTACTTTATTATATATATGAAATTAAT
1 ATTATGTATAAATTAAATATATGTATTTATATAATAGATTACTTTATTATATATATAAAATTAAT
* * *
1113317 GACACAATTTATATATTATAATATTTTAATTTTATGTCAAAGTTTGTATAAATAATAACTAATTA
66 GACACAACTTATATATTATAATA-TTT-ATTTTATATCAAAGTTTATATAAATAATAACTAATTA
* *
1113382 TAAATAACATGTTATAAAAATTAAGACGATAACTAATAA-ATTATTAAGTGCAATGATATAAA-T
129 TAAATAACATGTTATAAAAACTAAGACGATAACTAATAAGATTATTAAGTGCAATCATATAAATT
* *
1113445 AAAGTCTATTATAAGTTACAGTAAT-
194 AAA-TCTATTACAAGTTACACTAATG
1113470 ACTTATGTATAAATTAAATATATGTGTATATATATATAATAGATTACTTTATTATGTATATATAA
1 A-TTATGTATAAATTAAATATA--TGTAT-T-TATATAATAGATTACTTTATTA--TATATATAA
* *
1113535 AATTAATGACATAACTTATATATTAT-A-A-TT-TTTTATATCAAAGTTTATATAAATAATAATT
59 AATTAATGACACAACTTATATATTATAATATTTATTTTATATCAAAGTTTATATAAATAATAACT
* ** *** ** * **
1113596 GATTATAAATAATTTGTTATAAAAACTAAGGTTATAGTTAATAAGGTTATTAAGTTTAATCATAT
124 AATTATAAATAACATGTTATAAAAACTAAGACGATAACTAATAAGATTATTAAGTGCAATCATAT
* *
1113661 AAATTAAATTTATTACAAGTTATACTAATG
189 AAATTAAATCTATTACAAGTTACACTAATG
*
1113691 ATTATATATAAATTAAATAT
1 ATTATGTATAAATTAAATAT
1113711 GTATAATCTA
Statistics
Matches: 206, Mismatches: 25, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
218 1 0.00
219 83 0.40
220 54 0.26
221 12 0.06
222 1 0.00
223 22 0.11
224 1 0.00
225 32 0.16
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (218 bp):
ATTATGTATAAATTAAATATATGTATTTATATAATAGATTACTTTATTATATATATAAAATTAAT
GACACAACTTATATATTATAATATTTATTTTATATCAAAGTTTATATAAATAATAACTAATTATA
AATAACATGTTATAAAAACTAAGACGATAACTAATAAGATTATTAAGTGCAATCATATAAATTAA
ATCTATTACAAGTTACACTAATG
Found at i:1114388 original size:82 final size:82
Alignment explanation
Indices: 1114288--1114441 Score: 227
Period size: 82 Copynumber: 1.9 Consensus size: 82
1114278 ACGTTAAGTT
* *
1114288 AAAAAAAAATACTATTGTTACACATCATATACCAAAATATGTTACACGTCATGATTAAAAAAAGT
1 AAAAAAAAATACTATTGTTACACACCATATACAAAAATATGTTACACGTCATGATTAAAAAAAGT
1114353 TATTACATGCCATGTTC
66 TATTACATGCCATGTTC
* * ** * *
1114370 AAAAAAAAATACTGTTGTTGCATGCCATGTACAAAAATATGTTACACGTCATGGTTAAAAAAAGT
1 AAAAAAAAATACTATTGTTACACACCATATACAAAAATATGTTACACGTCATGATTAAAAAAAGT
*
1114435 TGTTACA
66 TATTACA
1114442 CATCATATTC
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 63 1.00
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (82 bp):
AAAAAAAAATACTATTGTTACACACCATATACAAAAATATGTTACACGTCATGATTAAAAAAAGT
TATTACATGCCATGTTC
Found at i:1117683 original size:2 final size:2
Alignment explanation
Indices: 1117676--1117703 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1117666 TTTACTTAAA
1117676 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
1117704 TCAACTTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1121168 original size:2 final size:2
Alignment explanation
Indices: 1121163--1121190 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1121153 TATATGTGTG
1121163 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
1121191 ATTAATATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1127139 original size:13 final size:13
Alignment explanation
Indices: 1127121--1127156 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
1127111 AGAAAGACAA
1127121 TGGAAAGGACTTG
1 TGGAAAGGACTTG
1127134 TGGAAAGGACTTG
1 TGGAAAGGACTTG
1127147 TGGAAAGGAC
1 TGGAAAGGAC
1127157 CTATTGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.39, T:0.19
Consensus pattern (13 bp):
TGGAAAGGACTTG
Found at i:1136297 original size:16 final size:16
Alignment explanation
Indices: 1136276--1136309 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1136266 TCTTAATTTT
1136276 TATATAACAAA-TATTA
1 TATATAA-AAATTATTA
1136292 TATATAAAAATTATTA
1 TATATAAAAATTATTA
1136308 TA
1 TA
1136310 AAAATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATAAAAATTATTA
Found at i:1136558 original size:27 final size:27
Alignment explanation
Indices: 1136518--1136569 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1136508 TACCATATTC
*
1136518 TATAAATAACAAAAAAAAAACAAAATT
1 TATAAAAAACAAAAAAAAAACAAAATT
* * *
1136545 TATAAAAAATAAAAAATAAATAAAA
1 TATAAAAAACAAAAAAAAAACAAAA
1136570 ATGGGTCTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (27 bp):
TATAAAAAACAAAAAAAAAACAAAATT
Found at i:1137442 original size:21 final size:22
Alignment explanation
Indices: 1137399--1137449 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1137389 TTTTAAATTT
*
1137399 TAAATCTTGTGTCTTACTGTATA
1 TAAAT-TTGTGTCTGACTGTATA
*
1137422 TAAATTTG-GTCTGACTTTATA
1 TAAATTTGTGTCTGACTGTATA
*
1137443 TTAATTT
1 TAAATTT
1137450 ATTTCGGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 17 0.68
22 3 0.12
23 5 0.20
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (22 bp):
TAAATTTGTGTCTGACTGTATA
Found at i:1139541 original size:2 final size:2
Alignment explanation
Indices: 1139534--1139560 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1139524 TATATTTCTT
1139534 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 T
1139561 TTTTTAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1140663 original size:2 final size:2
Alignment explanation
Indices: 1140656--1140684 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1140646 AATTTATTGG
1140656 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 T
1140685 GTATTTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1149542 original size:23 final size:22
Alignment explanation
Indices: 1149516--1149586 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 22
1149506 TAAATTTTTA
1149516 ATTTACTTAAT-TAATTATATTAT
1 ATTTA-TTAATATAATTA-ATTAT
*
1149539 ATTTATTCATATAATTAATTAT
1 ATTTATTAATATAATTAATTAT
*
1149561 ATCTTATTTAAACATAATATAATTAT
1 AT-TTA-TT-AATATAAT-TAATTAT
1149587 GACACAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 11 0.28
23 14 0.35
24 2 0.05
25 6 0.15
26 7 0.17
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTATTAATATAATTAATTAT
Found at i:1149576 original size:27 final size:27
Alignment explanation
Indices: 1149523--1149576 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1149513 TTAATTTACT
**
1149523 TAATTAATTATATTATATTTATTCATA
1 TAATTAATTATATTATATTTAAACATA
1149550 TAATTAATTATATCT-TATTTAAACATA
1 TAATTAATTATAT-TATATTTAAACATA
1149577 ATATAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.52
Consensus pattern (27 bp):
TAATTAATTATATTATATTTAAACATA
Found at i:1149717 original size:2 final size:2
Alignment explanation
Indices: 1149710--1149737 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1149700 TTCAAAATTG
1149710 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1149738 GTTTACTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1151737 original size:149 final size:150
Alignment explanation
Indices: 1151445--1151842 Score: 446
Period size: 150 Copynumber: 2.7 Consensus size: 150
1151435 TTGAAAATCA
* * * *
1151445 TTACCATTTAATACTTACATATAATGTGTAACAAATAATCGAGACGTGGAGTAATGATTTCATTC
1 TTACCATTTAATACTTACATATAATGTGTAACAAAGAATTGAGACGTGGAGTAATGGTTCCATTC
* * * * * *
1151510 AAATCATGGCACGTAATTACGTTTT-TAAAAAATTAATTATTTATTCCAAAACTCATTAATATGA
66 AAATCATGACACATAATCACGTTTTAAAAAAAATCAATTATTTATTCCAAAACTCATTAACATGA
*
1151574 GCTCAACCCAAAACAAATAT
131 ACTCAACCCAAAACAAATAT
* ** * *
1151594 TTACCGTTTAATACTTGTATATAATGTGTAACAAAGAATTGAGATGTGGAGTAACGGTTCCATTC
1 TTACCATTTAATACTTACATATAATGTGTAACAAAGAATTGAGACGTGGAGTAATGGTTCCATTC
* * * * * *
1151659 AAATCATGATACACAATCACGTTTTAAAAAAAATCAATTTTTCTTTTCGAAAA-TCGTTAACATG
66 AAATCATGACACATAATCACGTTTTAAAAAAAATCAATTATT-TATTCCAAAACTCATTAACATG
** *
1151723 TAAC-C-GGCCGAAACAAATAT
130 -AACTCAACCCAAAACAAATAT
* * * * *
1151743 TTACCCACTTAATACTTACATATAATGTGTAACAAATG-ATTGAGACATGGAGCAATTGTTCTAT
1 TTA-CCATTTAATACTTACATATAATGTGTAACAAA-GAATTGAGACGTGGAGTAATGGTTCCAT
1151807 TCAAATCATGACACATAATCACGTTTCTAAAAAAAA
64 TCAAATCATGACACATAATCACGTTT-TAAAAAAAA
1151843 AAGGTTAATT
Statistics
Matches: 206, Mismatches: 37, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
149 91 0.44
150 95 0.46
151 20 0.10
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (150 bp):
TTACCATTTAATACTTACATATAATGTGTAACAAAGAATTGAGACGTGGAGTAATGGTTCCATTC
AAATCATGACACATAATCACGTTTTAAAAAAAATCAATTATTTATTCCAAAACTCATTAACATGA
ACTCAACCCAAAACAAATAT
Found at i:1156751 original size:19 final size:20
Alignment explanation
Indices: 1156708--1156752 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1156698 AATCAATTCG
1156708 TGTGTTATTCTCATGATAAA
1 TGTGTTATTCTCATGATAAA
* * *
1156728 TGTGTTGTTC-CATTATATA
1 TGTGTTATTCTCATGATAAA
1156747 TGTGTT
1 TGTGTT
1156753 TTTTTCCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.22, C:0.09, G:0.18, T:0.51
Consensus pattern (20 bp):
TGTGTTATTCTCATGATAAA
Found at i:1158900 original size:21 final size:21
Alignment explanation
Indices: 1158863--1158903 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1158853 CTGAAGACCC
*
1158863 ACAGTAAAAACACAACCACAT
1 ACAGTAAAAACAAAACCACAT
1158884 ACAG-AAAAACGAAAACCACA
1 ACAGTAAAAAC-AAAACCACA
1158904 AGCTTATCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.61, C:0.27, G:0.07, T:0.05
Consensus pattern (21 bp):
ACAGTAAAAACAAAACCACAT
Found at i:1159339 original size:31 final size:31
Alignment explanation
Indices: 1159301--1159392 Score: 130
Period size: 31 Copynumber: 3.0 Consensus size: 31
1159291 TTTTAGCTAT
*
1159301 TTGTTTCAGTATAAATTGTCCAGAAGTGTCA
1 TTGTTTCAGTATAAGTTGTCCAGAAGTGTCA
** *
1159332 TTGTTTCAGTATAAGTCATCGAGAAGTGTCA
1 TTGTTTCAGTATAAGTTGTCCAGAAGTGTCA
* *
1159363 TTGCTTCAGTTTAAGTTGTCCAGAAGTGTC
1 TTGTTTCAGTATAAGTTGTCCAGAAGTGTC
1159393 CCTGAATTGC
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (31 bp):
TTGTTTCAGTATAAGTTGTCCAGAAGTGTCA
Found at i:1166835 original size:24 final size:24
Alignment explanation
Indices: 1166806--1166853 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1166796 ACGTAATTTC
1166806 AAGATTTGAATTTGAAACTTTCAA
1 AAGATTTGAATTTGAAACTTTCAA
1166830 AAGATTTGAATTTGAAACTTTCAA
1 AAGATTTGAATTTGAAACTTTCAA
1166854 GATAAACAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (24 bp):
AAGATTTGAATTTGAAACTTTCAA
Found at i:1168666 original size:2 final size:2
Alignment explanation
Indices: 1168661--1168690 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1168651 TTTTTTCCAA
1168661 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
1168691 TACAACTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1187715 original size:54 final size:52
Alignment explanation
Indices: 1187631--1187764 Score: 169
Period size: 54 Copynumber: 2.5 Consensus size: 52
1187621 AACCGGTCAA
* * * *
1187631 GGTGACCAGGGCTTTATGCCGCCAGAGTTTACCTCAAACGGTCCAGGTGACCAT
1 GGTGACCAGGGCTTTGTGCTGCCA-AGTTTACC-CAAACGGTCAAGGTGACCAG
1187685 GGTGACCAGGGCTTTGTGCTGCCAATGTTTAACCCAAACGGTCAAGGTGACCAG
1 GGTGACCAGGGCTTTGTGCTGCCAA-GTTT-ACCCAAACGGTCAAGGTGACCAG
* * *
1187739 GGCGACCAGGCCTTTGTGCTACCAAG
1 GGTGACCAGGGCTTTGTGCTGCCAAG
1187765 GAATACCCCA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
53 2 0.03
54 66 0.93
55 3 0.04
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.22
Consensus pattern (52 bp):
GGTGACCAGGGCTTTGTGCTGCCAAGTTTACCCAAACGGTCAAGGTGACCAG
Found at i:1187775 original size:54 final size:54
Alignment explanation
Indices: 1187660--1187781 Score: 154
Period size: 54 Copynumber: 2.3 Consensus size: 54
1187650 CGCCAGAGTT
* * * * * * * **
1187660 TACCTCAAACGGTCCAGGTGACCATGGTGACCAGGGCTTTGTGCTGCCAATGTT
1 TACCCCAAACGGTCAAGGTGACCAGGGCGACCAGGCCTTTGTGCTACCAAGGAA
*
1187714 TAACCCAAACGGTCAAGGTGACCAGGGCGACCAGGCCTTTGTGCTACCAAGGAA
1 TACCCCAAACGGTCAAGGTGACCAGGGCGACCAGGCCTTTGTGCTACCAAGGAA
1187768 TACCCCAAACGGTC
1 TACCCCAAACGGTC
1187782 TTGTGATCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.25, C:0.29, G:0.26, T:0.20
Consensus pattern (54 bp):
TACCCCAAACGGTCAAGGTGACCAGGGCGACCAGGCCTTTGTGCTACCAAGGAA
Found at i:1189121 original size:54 final size:52
Alignment explanation
Indices: 1189028--1189288 Score: 375
Period size: 54 Copynumber: 5.0 Consensus size: 52
1189018 CAAACTTGTC
** * *
1189028 CAATGCCTCCTTACGTTGCATATC-CTGATTCAACATCTGTACTTCCAGGGT
1 CAATGCCTCCTTACAATGCATATCTCTGATTCAACATCTGGACTTCCAAGGT
* * *
1189079 CGATTCCTCCTTACAATGCATATGCTGCTGATTCAACATCTGTACTTCCAAGGT
1 CAATGCCTCCTTACAATGCATAT-CT-CTGATTCAACATCTGGACTTCCAAGGT
1189133 CAATGCCTCCTTACAATGCATATGCTGCTGATTCAACATCTGGACTTCCAAGGT
1 CAATGCCTCCTTACAATGCATAT-CT-CTGATTCAACATCTGGACTTCCAAGGT
*
1189187 CAATGCCTCCTTACAATGCATAT-TCTGATTCAACATCTGGACTTCCAAGTT
1 CAATGCCTCCTTACAATGCATATCTCTGATTCAACATCTGGACTTCCAAGGT
* *
1189238 CAATGCCTCCTTACAATGCCTATCT-TGATTCACCATCTGGACTTCCAAGGT
1 CAATGCCTCCTTACAATGCATATCTCTGATTCAACATCTGGACTTCCAAGGT
1189289 TTCCTGAATC
Statistics
Matches: 194, Mismatches: 12, Indels: 8
0.91 0.06 0.04
Matches are distributed among these distances:
51 91 0.47
52 3 0.02
54 100 0.52
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.32
Consensus pattern (52 bp):
CAATGCCTCCTTACAATGCATATCTCTGATTCAACATCTGGACTTCCAAGGT
Found at i:1189231 original size:105 final size:105
Alignment explanation
Indices: 1189028--1189288 Score: 377
Period size: 105 Copynumber: 2.5 Consensus size: 105
1189018 CAAACTTGTC
** * * * *
1189028 CAATGCCTCCTTACGTTGCATATC-CTGATTCAACATCTGTACTTCCAGGGTCGATTCCTCCTTA
1 CAATGCCTCCTTACAATGCATATCTCTGATTCAACATCTGGACTTCCAAGGTCAATGCCTCCTTA
*
1189092 CAATGCATATGCTGCTGATTCAACATCTGTACTTCCAAGGT
66 CAATGCATAT-CTGCTGATTCAACATCTGGACTTCCAAGGT
1189133 CAATGCCTCCTTACAATGCATATGCTGCTGATTCAACATCTGGACTTCCAAGGTCAATGCCTCCT
1 CAATGCCTCCTTACAATGCATAT-CT-CTGATTCAACATCTGGACTTCCAAGGTCAATGCCTCCT
*
1189198 TACAATGCATAT-T-CTGATTCAACATCTGGACTTCCAAGTT
64 TACAATGCATATCTGCTGATTCAACATCTGGACTTCCAAGGT
* *
1189238 CAATGCCTCCTTACAATGCCTATCT-TGATTCACCATCTGGACTTCCAAGGT
1 CAATGCCTCCTTACAATGCATATCTCTGATTCAACATCTGGACTTCCAAGGT
1189289 TTCCTGAATC
Statistics
Matches: 143, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
102 25 0.17
104 2 0.01
105 68 0.48
106 2 0.01
108 46 0.32
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.32
Consensus pattern (105 bp):
CAATGCCTCCTTACAATGCATATCTCTGATTCAACATCTGGACTTCCAAGGTCAATGCCTCCTTA
CAATGCATATCTGCTGATTCAACATCTGGACTTCCAAGGT
Found at i:1198102 original size:42 final size:42
Alignment explanation
Indices: 1198029--1198110 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
1198019 AAACTTGGAC
* *
1198029 ATAATCATCAGTCTTCTCCCAAATTTGTATATTCTAGAAGAA
1 ATAATCATCAGTCTTCTCCCAAATGTATATATTCTAGAAGAA
* *
1198071 ATAATCATCAGTCTTCTTCGAAATGTATATATTCTAGAAG
1 ATAATCATCAGTCTTCTCCCAAATGTATATATTCTAGAAG
1198111 TGGAAAGTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (42 bp):
ATAATCATCAGTCTTCTCCCAAATGTATATATTCTAGAAGAA
Found at i:1246446 original size:13 final size:14
Alignment explanation
Indices: 1246416--1246448 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1246406 AAATAAAAAT
1246416 AAAGAAAAGAAGAA
1 AAAGAAAAGAAGAA
*
1246430 AAAGAAAAGGA-AA
1 AAAGAAAAGAAGAA
1246443 AAAGAA
1 AAAGAA
1246449 CAAATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:1278592 original size:178 final size:182
Alignment explanation
Indices: 1278250--1278683 Score: 522
Period size: 178 Copynumber: 2.4 Consensus size: 182
1278240 TGTAACTGAT
* *
1278250 AGGAAATTTGAAGGAAGCTAAGCTAAGATGAAACATATTCCAAGTATTATTATTTTATACAACAT
1 AGGAAATTTGGAGG-AGC-AAGCTAACATGAAACATATTCCAAGTATTATTATTTTATAC-ACAT
* * ** * ** *
1278315 TAGTGATCATGATTGTGGTGTGGGCAGGCACTCCCATTTCATTTTTTTTTTAAAAAAAAACAATA
63 TAGTGATCATCATTGTAGTGTAAGCAGG-ACTCCCACTTCACCTTTTTTTAAAAAAAAAACAATA
* * * **
1278380 TTATGGTCAACATAGAAGATTAAATTAAAAAGAATACTAGCTTTTGTGAAACCGAG
127 ATATGGCCAAAATAGAAGATTAAATTAAAAAGAATACTAGCTTTTGTGAAACAAAG
* *
1278436 AGGAAATTTGGA-G-G-AAGCTAACATGAAACATCTTCCAAGTATTATTACTTTATACACTATTA
1 AGGAAATTTGGAGGAGCAAGCTAACATGAAACATATTCCAAGTATTATTATTTTATACAC-ATTA
*
1278498 -TGGGTCATCATTGTAGTGTAAGC-GG-CTCCCACTTC-CCTTTTTTTAAAAAAAAAATCAATAA
65 GT-GATCATCATTGTAGTGTAAGCAGGACTCCCACTTCACCTTTTTTTAAAAAAAAAA-CAATAA
** * *
1278559 TATGGCCAAAATAGATTATTAAATTAAAAAGAATACTAGTTTTTGTGAAGCAAAG
128 TATGGCCAAAATAGAAGATTAAATTAAAAAGAATACTAGCTTTTGTGAAACAAAG
*
1278614 AGGAAATTTGGAGGAAGCTAAGCTAACATGAAACATGTTCCAAGTATTATTATTTTATACACCAT
1 AGGAAATTTGGAGG-AGC-AAGCTAACATGAAACATATTCCAAGTATTATTATTTTATACA-CAT
1278679 TAGTG
63 TAGTG
1278684 GACATGATTG
Statistics
Matches: 214, Mismatches: 24, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
177 16 0.07
178 73 0.34
179 1 0.00
180 5 0.02
181 59 0.28
183 46 0.21
184 2 0.01
185 1 0.00
186 11 0.05
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (182 bp):
AGGAAATTTGGAGGAGCAAGCTAACATGAAACATATTCCAAGTATTATTATTTTATACACATTAG
TGATCATCATTGTAGTGTAAGCAGGACTCCCACTTCACCTTTTTTTAAAAAAAAAACAATAATAT
GGCCAAAATAGAAGATTAAATTAAAAAGAATACTAGCTTTTGTGAAACAAAG
Found at i:1279049 original size:15 final size:16
Alignment explanation
Indices: 1279029--1279061 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1279019 GTAAAAATAA
*
1279029 TAAGAAA-TCATAATG
1 TAAGAAATTAATAATG
1279044 TAAGAAATTAATAATG
1 TAAGAAATTAATAATG
1279060 TA
1 TA
1279062 TTATTCATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (16 bp):
TAAGAAATTAATAATG
Found at i:1286047 original size:92 final size:93
Alignment explanation
Indices: 1285930--1286204 Score: 358
Period size: 92 Copynumber: 3.0 Consensus size: 93
1285920 ACTCATATAA
* * ** *
1285930 TTTTTCAGTGTTAAGTGTAACTAATGTAAATTGATATATATCAACTCGCTAAA-ATAAGGTTTTG
1 TTTTTAAGTGTTAAGTGTAACTAATGTAAAGTGATGCATATCAACTAGCTAAAGATAAGGTTTTG
1285994 AGAGAAATTGAGTTACTACATATTCTAT
66 AGAGAAATTGAGTTACTACATATTCTAT
* * * *
1286022 TTTTTAAGTGTTAAGTGTAATTAATGTAAAGTGGTGCATATCAATTAGCTAAAGATAGGGTTTTG
1 TTTTTAAGTGTTAAGTGTAACTAATGTAAAGTGATGCATATCAACTAGCTAAAGATAAGGTTTTG
*
1286087 AGAGAGATTGAGTTACTACATATTCTAT
66 AGAGAAATTGAGTTACTACATATTCTAT
* * * ** *
1286115 TTTTCAA-TGTTAAATGTAACTAATG-AAAGTGATGCAGATCAACTAGCTAAAGATAAAATTTTA
1 TTTTTAAGTGTTAAGTGTAACTAATGTAAAGTGATGCATATCAACTAGCTAAAGATAAGGTTTTG
* * *
1286178 AAAAAAATTGAGTTATTACATATTCTA
66 AGAGAAATTGAGTTACTACATATTCTA
1286205 CTATAAGTTT
Statistics
Matches: 158, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
91 54 0.34
92 61 0.39
93 43 0.27
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.37
Consensus pattern (93 bp):
TTTTTAAGTGTTAAGTGTAACTAATGTAAAGTGATGCATATCAACTAGCTAAAGATAAGGTTTTG
AGAGAAATTGAGTTACTACATATTCTAT
Found at i:1286188 original size:91 final size:92
Alignment explanation
Indices: 1285929--1286204 Score: 358
Period size: 91 Copynumber: 3.0 Consensus size: 92
1285919 TACTCATATA
* * ** *
1285929 ATTTTTCAGTGTTAAGTGTAACTAATGTAAATTGATATATATCAACTCGCTAAA-ATAAGGTTTT
1 ATTTTTCAATGTTAAGTGTAACTAATGTAAAGTGATGCATATCAACTAGCTAAAGATAAGGTTTT
1285993 GAGAGAAATTGAGTTACTACATATTCT
66 GAGAGAAATTGAGTTACTACATATTCT
* * * * *
1286020 ATTTTTTAAGTGTTAAGTGTAATTAATGTAAAGTGGTGCATATCAATTAGCTAAAGATAGGGTTT
1 ATTTTTCAA-TGTTAAGTGTAACTAATGTAAAGTGATGCATATCAACTAGCTAAAGATAAGGTTT
*
1286085 TGAGAGAGATTGAGTTACTACATATTCT
65 TGAGAGAAATTGAGTTACTACATATTCT
* * **
1286113 ATTTTTCAATGTTAAATGTAACTAATG-AAAGTGATGCAGATCAACTAGCTAAAGATAAAATTTT
1 ATTTTTCAATGTTAAGTGTAACTAATGTAAAGTGATGCATATCAACTAGCTAAAGATAAGGTTTT
* * * *
1286177 AAAAAAAATTGAGTTATTACATATTCT
66 GAGAGAAATTGAGTTACTACATATTCT
1286204 A
1 A
1286205 CTATAAGTTT
Statistics
Matches: 158, Mismatches: 25, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
91 61 0.39
92 54 0.34
93 43 0.27
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.37
Consensus pattern (92 bp):
ATTTTTCAATGTTAAGTGTAACTAATGTAAAGTGATGCATATCAACTAGCTAAAGATAAGGTTTT
GAGAGAAATTGAGTTACTACATATTCT
Found at i:1304898 original size:30 final size:29
Alignment explanation
Indices: 1304830--1304900 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
1304820 AAATACTTAA
*
1304830 AAATAAAAT-TTATATTTTTATTGTTTTC
1 AAATAAAATCTTATATTTTTATTGTTATC
*
1304858 -TATCAAAATCTTATATTTTTATT-TTGAATC
1 AAAT-AAAATCTTATATTTTTATTGTT--ATC
1304888 AAATAAAATCTTA
1 AAATAAAATCTTA
1304901 ACTAATGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
27 2 0.06
28 7 0.20
29 13 0.37
30 11 0.31
31 2 0.06
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (29 bp):
AAATAAAATCTTATATTTTTATTGTTATC
Found at i:1305120 original size:23 final size:22
Alignment explanation
Indices: 1305062--1305120 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
1305052 TAGTTAATCA
* *
1305062 TTAAGTATAAAAACTTATTTAAT
1 TTAA-TATAAAAATTTAATTAAT
*
1305085 TTAAAATAAAAATTTAATTAAT
1 TTAATATAAAAATTTAATTAAT
1305107 TATAATATAAAAAT
1 T-TAATATAAAAAT
1305121 AAATACTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 16 0.52
23 15 0.48
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
TTAATATAAAAATTTAATTAAT
Found at i:1311364 original size:2 final size:2
Alignment explanation
Indices: 1311357--1311387 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1311347 CCCTGCTCTC
1311357 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 A
1311388 ATAGCATCAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1319374 original size:20 final size:21
Alignment explanation
Indices: 1319346--1319385 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1319336 GAGAAGCTAT
1319346 AACTCCTTCA-TTCTTCAATG
1 AACTCCTTCAGTTCTTCAATG
*
1319366 AACTTCTTCAGGTTCTTCAA
1 AACTCCTTCA-GTTCTTCAA
1319386 CCACCTAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.25, C:0.28, G:0.07, T:0.40
Consensus pattern (21 bp):
AACTCCTTCAGTTCTTCAATG
Found at i:1320997 original size:19 final size:18
Alignment explanation
Indices: 1320973--1321022 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 18
1320963 AATCAAAATT
1320973 AAATTTAAAATATATAAAA
1 AAATTTAAAATATA-AAAA
1320992 AAATTT--AATGATAAAAA
1 AAATTTAAAAT-ATAAAAA
1321009 AAATTTATAAATAT
1 AAATTTA-AAATAT
1321023 CAAATTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 13 0.48
18 3 0.11
19 8 0.30
20 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
AAATTTAAAATATAAAAA
Found at i:1330485 original size:37 final size:37
Alignment explanation
Indices: 1330444--1330517 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
1330434 TTTATGCTCA
**
1330444 GTTTAAATGAATTTTCTTTGCTTTTTAATGAGATTTT
1 GTTTAAATGAATTTTCTTTGCTTTTTAACCAGATTTT
*
1330481 GTTTAACTGAATTTTCTTTGCTTTTTAACCAGATTTT
1 GTTTAAATGAATTTTCTTTGCTTTTTAACCAGATTTT
1330518 AAATTCAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.23, C:0.09, G:0.12, T:0.55
Consensus pattern (37 bp):
GTTTAAATGAATTTTCTTTGCTTTTTAACCAGATTTT
Found at i:1330696 original size:17 final size:18
Alignment explanation
Indices: 1330674--1330712 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1330664 TCAATTTTTA
*
1330674 AAAAATAT-AATTTATAT
1 AAAAATATGAAATTATAT
*
1330691 AAAAATATGAAATTATGT
1 AAAAATATGAAATTATAT
1330709 AAAA
1 AAAA
1330713 TTTAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
AAAAATATGAAATTATAT
Found at i:1330704 original size:89 final size:88
Alignment explanation
Indices: 1330574--1330790 Score: 303
Period size: 88 Copynumber: 2.5 Consensus size: 88
1330564 GATTTTATAG
* * * * * *
1330574 TCAAAATTCAAAATATATAAATTCTATA-AAAAATATGAAATTATGTGAAATTTAATAATTGTCT
1 TCAAATTTTAAAAAATAT-AATT-TATATAAAAATATGAAATTATGTAAAATTTAAAAATTGTCC
*
1330638 CATATTCAAATAAAAATTACTTAAAA
64 CATATACAAAT-AAAATTACTTAAAA
*
1330664 TCAATTTTTAAAAAATATAATTTATATAAAAATATGAAATTATGTAAAATTTAAAAATTGTCCCA
1 TCAAATTTTAAAAAATATAATTTATATAAAAATATGAAATTATGTAAAATTTAAAAATTGTCCCA
*
1330729 TATACAAATAAAATTACTTATAA
66 TATACAAATAAAATTACTTAAAA
*
1330752 TCAAATTTTAAAAAATATAAATTATATAAAAA-ATGAAAT
1 TCAAATTTTAAAAAATATAATTTATATAAAAATATGAAAT
1330791 AAAAATTGTG
Statistics
Matches: 115, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
87 7 0.06
88 47 0.41
89 47 0.41
90 14 0.12
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (88 bp):
TCAAATTTTAAAAAATATAATTTATATAAAAATATGAAATTATGTAAAATTTAAAAATTGTCCCA
TATACAAATAAAATTACTTAAAA
Found at i:1360632 original size:15 final size:16
Alignment explanation
Indices: 1360614--1360656 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1360604 TAACTTTCCC
1360614 TCTTCTTCTTTT-TTA
1 TCTTCTTCTTTTATTA
*
1360629 TCTT-TTATTTTATTA
1 TCTTCTTCTTTTATTA
1360644 TCTTCCTTCTTTT
1 TCTT-CTTCTTTT
1360657 GAATTTTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 6 0.26
15 11 0.48
17 6 0.26
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (16 bp):
TCTTCTTCTTTTATTA
Found at i:1399211 original size:11 final size:11
Alignment explanation
Indices: 1399191--1399223 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1399181 AAATTTTACA
1399191 TAAAAAGTAAT
1 TAAAAAGTAAT
*
1399202 TAAAATGTAAT
1 TAAAAAGTAAT
1399213 TAAAAAGTAAT
1 TAAAAAGTAAT
1399224 CATATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (11 bp):
TAAAAAGTAAT
Found at i:1404989 original size:27 final size:28
Alignment explanation
Indices: 1404948--1405004 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
1404938 TTAAATCGAT
*
1404948 TAAATATTTAGATATTTGATTT-AATAA
1 TAAATATATAGATATTTGATTTAAATAA
* *
1404975 TAAATATATATATATTTTATTTAAATAA
1 TAAATATATAGATATTTGATTTAAATAA
1405003 TA
1 TA
1405005 TGATTTCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (28 bp):
TAAATATATAGATATTTGATTTAAATAA
Found at i:1405041 original size:2 final size:2
Alignment explanation
Indices: 1405034--1405073 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1405024 TTTAAATTCA
1405034 AT 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 AT
1405074 CAAGCTATAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1405964 original size:2 final size:2
Alignment explanation
Indices: 1405957--1405990 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1405947 AACATAATAC
* *
1405957 AT AT AT AT AT AT AT AT GT AC 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
1405991 TTCCAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1408537 original size:16 final size:16
Alignment explanation
Indices: 1408516--1408548 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1408506 GAACTTGTTA
1408516 AAGAGTTCATGGAATT
1 AAGAGTTCATGGAATT
1408532 AAGAGTTCATGGAATT
1 AAGAGTTCATGGAATT
1408548 A
1 A
1408549 TGTATGTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.30
Consensus pattern (16 bp):
AAGAGTTCATGGAATT
Found at i:1432724 original size:18 final size:19
Alignment explanation
Indices: 1432703--1432738 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1432693 TTAATTTAAA
*
1432703 ATTTTTAA-ATAATTTTTT
1 ATTTTTAATAAAATTTTTT
1432721 ATTTTTAATAAAATTTTT
1 ATTTTTAATAAAATTTTT
1432739 ATAATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTTAATAAAATTTTTT
Found at i:1447051 original size:20 final size:18
Alignment explanation
Indices: 1447028--1447067 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
1447018 TTTAAAAAAA
1447028 TTAAATAATATTTTTTATAT
1 TTAAATAA-A-TTTTTATAT
*
1447048 TTAATTAAATTTTTATAT
1 TTAAATAAATTTTTATAT
1447066 TT
1 TT
1447068 TTATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 1 0.05
20 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAAATAAATTTTTATAT
Found at i:1452397 original size:39 final size:39
Alignment explanation
Indices: 1452343--1452424 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
1452333 CATGGCATTA
* * * *
1452343 TGCATCACTTGTCTTGTGTGGAGAGTCCATAGCAAAATG
1 TGCATCAATTGTCTTGTGTAGAGACTCCAGAGCAAAATG
1452382 TGCATCAATTGTCTTGTGTAGAGACTCCAGAGCAAAATG
1 TGCATCAATTGTCTTGTGTAGAGACTCCAGAGCAAAATG
1452421 -GCAT
1 TGCAT
1452425 AGTAGAAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 4 0.10
39 35 0.90
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (39 bp):
TGCATCAATTGTCTTGTGTAGAGACTCCAGAGCAAAATG
Found at i:1463270 original size:28 final size:30
Alignment explanation
Indices: 1463239--1463296 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 30
1463229 TTAATAATTG
1463239 TTCTTTA-TTTT-AAAAAATTATAATTTTA
1 TTCTTTATTTTTAAAAAAATTATAATTTTA
1463267 TTCTTTATTTTTTAAAAAAAATTATAATTT
1 TTCTTTA-TTTTT-AAAAAAATTATAATTT
1463297 CACCCCAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 7 0.27
30 4 0.15
32 15 0.58
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (30 bp):
TTCTTTATTTTTAAAAAAATTATAATTTTA
Found at i:1465472 original size:13 final size:14
Alignment explanation
Indices: 1465454--1465496 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
1465444 TATTACTATA
1465454 ATTTATA-AATTTT
1 ATTTATATAATTTT
* *
1465467 ATTTATATGATTAT
1 ATTTATATAATTTT
1465481 ATTTA-ATAATTTT
1 ATTTATATAATTTT
1465494 ATT
1 ATT
1465497 AATTATCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTTATATAATTTT
Found at i:1465501 original size:22 final size:20
Alignment explanation
Indices: 1465476--1465535 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 20
1465466 TATTTATATG
1465476 ATTATATTTAATAATTTTATTA
1 ATTATATTT-ATAATTTTA-TA
1465498 ATTATCATCTTA-AATTTTATA
1 ATTAT-AT-TTATAATTTTATA
1465519 ATATATTATTTATAATT
1 AT-TA-TATTTATAATT
1465536 AGTTATGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
21 7 0.21
22 20 0.61
23 4 0.12
24 2 0.06
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTATATTTATAATTTTATA
Found at i:1466746 original size:13 final size:14
Alignment explanation
Indices: 1466722--1466761 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
1466712 TAGCCTTACT
*
1466722 TAAATAATTTTAAA
1 TAAATTATTTTAAA
1466736 T-AATTATTTT-AA
1 TAAATTATTTTAAA
1466748 TAAATT-TTTTAAA
1 TAAATTATTTTAAA
1466761 T
1 T
1466762 TTTATAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
12 7 0.30
13 15 0.65
14 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAAATTATTTTAAA
Found at i:1468711 original size:21 final size:22
Alignment explanation
Indices: 1468690--1468734 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 22
1468680 AATAAAAAAC
1468690 AAAATAAAAGAAAATCTCAACAATT
1 AAAA-AAAA-AAAATCTCAACAA-T
1468715 AAAAAAAAAAAATCTCAACA
1 AAAAAAAAAAAATCTCAACA
1468735 TGAGATCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 12 0.60
24 4 0.20
25 4 0.20
ACGTcount: A:0.69, C:0.13, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAAAAAAAAAATCTCAACAAT
Found at i:1472651 original size:18 final size:18
Alignment explanation
Indices: 1472628--1472662 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1472618 GCAAGGAGGG
1472628 AATGGGAATAATGGGAAC
1 AATGGGAATAATGGGAAC
* *
1472646 AATGGGAGTGATGGGAA
1 AATGGGAATAATGGGAA
1472663 TAGGTCACTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.40, T:0.17
Consensus pattern (18 bp):
AATGGGAATAATGGGAAC
Found at i:1473714 original size:64 final size:64
Alignment explanation
Indices: 1473613--1473740 Score: 211
Period size: 64 Copynumber: 2.0 Consensus size: 64
1473603 TAATTTAATC
* *
1473613 ATGGTTGTAATTAATGTGGCATTGAGGGTCAAATTATTTTAATTTCTTCTGCATAGTTGGGAAG
1 ATGGTTGTAATTAATGTGGCATTGAGGGTCAAATTATTTTAACTTCTACTGCATAGTTGGGAAG
* * *
1473677 ATGGTTGTAATTAATGTGGCATTGAGGGTCAAATTATTTTCACTTCTACTGCTTATTTGGGAAG
1 ATGGTTGTAATTAATGTGGCATTGAGGGTCAAATTATTTTAACTTCTACTGCATAGTTGGGAAG
1473741 TTTCATTAGT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (64 bp):
ATGGTTGTAATTAATGTGGCATTGAGGGTCAAATTATTTTAACTTCTACTGCATAGTTGGGAAG
Found at i:1491249 original size:62 final size:61
Alignment explanation
Indices: 1491134--1491249 Score: 151
Period size: 62 Copynumber: 1.9 Consensus size: 61
1491124 AACAATTTCC
* * *
1491134 AAATTTTTCTAATTTATTTTTATTTTTTAAAATTTAATAATTTTACCCTTACAAAATTTTA
1 AAATTTTTCTAACTTATTTTGATTTTTTAAAATTTAATAATTTTACCCGTACAAAATTTTA
* * * **
1491195 AAATTTTTTTAACTTATTTTGATTTTTTTAGAATTTTATAATTTTATTCGTACAA
1 AAATTTTTCTAACTTATTTTGA-TTTTTTAAAATTTAATAATTTTACCCGTACAA
1491250 TAATATTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
61 19 0.41
62 27 0.59
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.57
Consensus pattern (61 bp):
AAATTTTTCTAACTTATTTTGATTTTTTAAAATTTAATAATTTTACCCGTACAAAATTTTA
Found at i:1498026 original size:2 final size:2
Alignment explanation
Indices: 1498019--1498048 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1498009 CAGAAACCTG
1498019 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
1498049 GAGACATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1508896 original size:24 final size:24
Alignment explanation
Indices: 1508868--1508929 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
1508858 AATATTTTGA
**
1508868 TTTATTTATT-ATATTTTTAAATTT
1 TTTA-TTATTAATATTAATAAATTT
1508892 TTTATTATTAATATTAATAAATTT
1 TTTATTATTAATATTAATAAATTT
*
1508916 TATT-TAATTAATAT
1 T-TTATTATTAATAT
1508930 ATATATATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 5 0.15
24 26 0.79
25 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTATTATTAATATTAATAAATTT
Found at i:1521975 original size:2 final size:2
Alignment explanation
Indices: 1521968--1521992 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1521958 ATTTGGAATC
1521968 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1521993 CTCCCACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1524109 original size:21 final size:21
Alignment explanation
Indices: 1524083--1524123 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1524073 AAGAGATATC
*
1524083 AACTTAATAGTAAGTATGAGG
1 AACTTAACAGTAAGTATGAGG
1524104 AACTTAACAGTAAGTATGAG
1 AACTTAACAGTAAGTATGAG
1524124 AAATCAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (21 bp):
AACTTAACAGTAAGTATGAGG
Found at i:1524132 original size:25 final size:24
Alignment explanation
Indices: 1524075--1524135 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 24
1524065 AAACTAAAAA
*
1524075 GAGATATCAACTTAATAGTAAGTAT
1 GAGA-ATCAACTTAACAGTAAGTAT
*
1524100 GAG---GAACTTAACAGTAAGTAT
1 GAGAATCAACTTAACAGTAAGTAT
1524121 GAGAAATCAACTTAA
1 GAG-AATCAACTTAA
1524136 TACAAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
21 19 0.66
25 10 0.34
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (24 bp):
GAGAATCAACTTAACAGTAAGTAT
Found at i:1534965 original size:7 final size:7
Alignment explanation
Indices: 1534956--1534987 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1534946 AAACTTTTTC
*
1534956 CTGCTTC
1 CTGCTTT
1534963 CTGCTTT
1 CTGCTTT
1534970 CTGCTTT
1 CTGCTTT
1534977 CTGCTTT
1 CTGCTTT
1534984 CTGC
1 CTGC
1534988 AATGCTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.34, G:0.16, T:0.50
Consensus pattern (7 bp):
CTGCTTT
Found at i:1551986 original size:33 final size:31
Alignment explanation
Indices: 1551921--1551986 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1551911 GTTTTTTTAT
**
1551921 AAAAATAAAAATATATAAATTTAATTTCATA
1 AAAAATAAAAATATATAAATTTAATTAAATA
*
1551952 AAAAATAAAAATATATTTAAATTTTATTAAATA
1 AAAAATAAAAATATA--TAAATTTAATTAAATA
1551985 AA
1 AA
1551987 TTAATGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 15 0.50
33 15 0.50
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (31 bp):
AAAAATAAAAATATATAAATTTAATTAAATA
Found at i:1559396 original size:2 final size:2
Alignment explanation
Indices: 1559389--1559414 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1559379 CCAATTTCTG
1559389 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
1559415 GCGCTGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1575648 original size:26 final size:26
Alignment explanation
Indices: 1575551--1575662 Score: 70
Period size: 26 Copynumber: 4.3 Consensus size: 26
1575541 CTTTGGGTGG
* * * **
1575551 TAAAATAATCCATCTATTTCTAGTGG
1 TAAAATTATTCATCCATTTCTAGTAA
* *
1575577 TAAAATTATTTAACCACTTT-TAGTGAA
1 TAAAATTATTCATCCA-TTTCTAGT-AA
* **
1575604 -AAAATTATTCTTTGA-TTCTAGTAA
1 TAAAATTATTCATCCATTTCTAGTAA
*
1575628 TAAAATTATTCATCCATTTCT-GATGA
1 TAAAATTATTCATCCATTTCTAG-TAA
1575654 TAAAATTAT
1 TAAAATTAT
1575663 CCTTAATTAA
Statistics
Matches: 64, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
24 4 0.06
25 17 0.27
26 40 0.62
27 3 0.05
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
TAAAATTATTCATCCATTTCTAGTAA
Found at i:1575711 original size:57 final size:60
Alignment explanation
Indices: 1575645--1575762 Score: 152
Period size: 66 Copynumber: 1.9 Consensus size: 60
1575635 ATTCATCCAT
*
1575645 TTCTGATGATAAAATTAT-C-C-TTAATTAAAATAGTGATAGTGTAAATTATTATAGAGA
1 TTCTAATGATAAAATTATCCACATTAATTAAAATAGTGATAGTGTAAATTATTATAGAGA
1575702 TTCTAATGATAAAATTATCCATCAATTTATTAATTAAAATAGTGATAGTGTAAATTATTAT
1 TTCTAATGATAAAATTATCCA-C-----ATTAATTAAAATAGTGATAGTGTAAATTATTAT
1575763 GGCCATCATA
Statistics
Matches: 51, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
57 17 0.33
58 1 0.02
60 1 0.02
66 32 0.63
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (60 bp):
TTCTAATGATAAAATTATCCACATTAATTAAAATAGTGATAGTGTAAATTATTATAGAGA
Found at i:1576324 original size:10 final size:12
Alignment explanation
Indices: 1576297--1576329 Score: 52
Period size: 10 Copynumber: 2.9 Consensus size: 12
1576287 AAATAAATCT
1576297 TATAAAAATAAC
1 TATAAAAATAAC
1576309 TATAAAAA-AA-
1 TATAAAAATAAC
1576319 TATAAAAATAA
1 TATAAAAATAA
1576330 GTATTTAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.40
11 4 0.20
12 8 0.40
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (12 bp):
TATAAAAATAAC
Found at i:1581988 original size:65 final size:65
Alignment explanation
Indices: 1581872--1581999 Score: 213
Period size: 65 Copynumber: 2.0 Consensus size: 65
1581862 TTTTAACCTA
*
1581872 AAGATTCCATATGAAATAGGGATTATAATCAATATCTTGTAATTAGGTATCTTGTATTATTCACT
1 AAGATTCCATATGAAATAGGGATTATAATCAATATCTTATAATTAGGTATCTTGTATTATTCACT
* *
1581937 AAGATTCCATATGAAATAGGGATTATAATTAATATCTTATAA-TCGGATATCTTGTATTATTCA
1 AAGATTCCATATGAAATAGGGATTATAATCAATATCTTATAATTAGG-TATCTTGTATTATTCA
1582000 ATTTAAGTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
64 3 0.05
65 56 0.95
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (65 bp):
AAGATTCCATATGAAATAGGGATTATAATCAATATCTTATAATTAGGTATCTTGTATTATTCACT
Done.