Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 91 of 203
Found at i:28702721 original size:42 final size:42
Alignment explanation
Indices: 28702627--28702794 Score: 246
Period size: 42 Copynumber: 4.0 Consensus size: 42
28702617 CAAACAAAAA
*
28702627 CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTTTTACAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTTTTACAAG
* *
28702670 CGCCACTAAAGAACATGTTCTTTAGCGGCGTTTTTCTACAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACAAG
* *
28702712 CGCCGCTAAAGAACATGTTCTTTAGCGGCATTTTTTTACAAA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACAAG
* * * *
28702754 CGCCGCGAAAGAACATGTTCTTTAGTGGCGCTTTTATACAA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACAA
28702795 AAACGCCACC
Statistics
Matches: 113, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
42 85 0.75
43 28 0.25
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACAAG
Found at i:28702877 original size:14 final size:14
Alignment explanation
Indices: 28702854--28702887 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
28702844 GCCCTCCTGT
*
28702854 AGCAAAAATTCAAA
1 AGCAACAATTCAAA
28702868 AGCAACAATTCAAA
1 AGCAACAATTCAAA
28702882 AGCAAC
1 AGCAAC
28702888 CAATAGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.21, G:0.09, T:0.12
Consensus pattern (14 bp):
AGCAACAATTCAAA
Found at i:28703137 original size:21 final size:21
Alignment explanation
Indices: 28703111--28703181 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
28703101 TTTTGCTCTG
* *
28703111 CTCTGCTTCTCTCACTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
28703132 CTCTGCTTCCCTCGCTGCAG-
1 CTCTGCTTCCCTCGCTGCAGC
* *
28703152 CTGCTGCTTCCCTCGCTTCTGC
1 CT-CTGCTTCCCTCGCTGCAGC
28703174 CTCTGCTT
1 CTCTGCTT
28703182 TAAGTTGTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.05
21 40 0.91
22 2 0.05
ACGTcount: A:0.04, C:0.44, G:0.17, T:0.35
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:28708669 original size:11 final size:9
Alignment explanation
Indices: 28708621--28708785 Score: 69
Period size: 7 Copynumber: 19.0 Consensus size: 9
28708611 AATTGCAATG
28708621 GTAAGTTAT
1 GTAAGTTAT
28708630 GTAAGTTAT
1 GTAAGTTAT
28708639 GTAAGTTAAAT
1 GTAAGTT--AT
28708650 GT-A-TTAT
1 GTAAGTTAT
28708657 GTAAGTTAAAT
1 GTAAGTT--AT
28708668 GTAAG-T-T
1 GTAAGTTAT
28708675 GTAAGTTAT
1 GTAAGTTAT
*
28708684 -TATGTATTAT
1 GTAAG--TTAT
28708694 GTAAG-T-T
1 GTAAGTTAT
28708701 GTAAGTTAAAT
1 GTAAGTT--AT
*
28708712 GT-A-TTGT
1 GTAAGTTAT
28708719 GTAAG-T-T
1 GTAAGTTAT
28708726 GTAAGTTAAAT
1 GTAAGTT--AT
28708737 GT-A-TTAT
1 GTAAGTTAT
28708744 GTAAG-T-T
1 GTAAGTTAT
28708751 GTAAGTTAT
1 GTAAGTTAT
*
28708760 -TATGTATTAT
1 GTAAG--TTAT
28708770 GTAAG-T-T
1 GTAAGTTAT
28708777 GTAAGTTAT
1 GTAAGTTAT
28708786 TATGTATTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 60
0.65 0.03 0.32
Matches are distributed among these distances:
7 41 0.34
8 18 0.15
9 27 0.22
10 12 0.10
11 23 0.19
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:28708696 original size:19 final size:19
Alignment explanation
Indices: 28708635--28709052 Score: 82
Period size: 18 Copynumber: 21.6 Consensus size: 19
28708625 GTTATGTAAG
*
28708635 TTATGTAAGTTA-AATGTA
1 TTATGTAAGTTATTATGTA
*
28708653 TTATGTAAGTTA-AATGTAA
1 TTATGTAAGTTATTATGT-A
*
28708672 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
28708690 TTATGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAG-T-T-A-TT--ATGTA
*
28708715 TTGTGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAG-T-T-A-TT--ATGTA
* *
28708740 TTATGTAAGTT-GTAAG--
1 TTATGTAAGTTATTATGTA
*
28708756 TTAT-TATG-TATTATGTAA
1 TTATGTAAGTTATTATGT-A
*
28708774 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
*
28708792 TTGTGTAAGTTGCAAGTTAAATGTA
1 TTATGTAAGTT---A-TT--ATGTA
* *
28708817 TTATGTAAGTT-GTAAG--
1 TTATGTAAGTTATTATGTA
*
28708833 TTAT-TATG-TATTATGTAA
1 TTATGTAAGTTATTATGT-A
*
28708851 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
* * *
28708869 TTGTGTAAGTT-GTAAG--
1 TTATGTAAGTTATTATGTA
*
28708885 TTAT-TATG-TATTATGTAA
1 TTATGTAAGTTATTATGT-A
*
28708903 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
*
28708921 TTGTGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAG-T-T-A-TT--ATGTA
* * *
28708946 TTATGTCAGTCA-AATGTA
1 TTATGTAAGTTATTATGTA
28708964 TTATGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAG-T-T-A-TT--ATGTA
* *
28708989 TTATGTAAGTT-GTAAGTTA
1 TTATGTAAGTTATTATG-TA
*
28709008 TTATGT-A-TTATGTAAGTA
1 TTATGTAAGTTAT-TATGTA
*
28709026 --ATGTAAGTTA-AATGTA
1 TTATGTAAGTTATTATGTA
28709042 TTATGTAAGTT
1 TTATGTAAGTT
28709053 GTAAGTTATT
Statistics
Matches: 301, Mismatches: 43, Indels: 112
0.66 0.09 0.25
Matches are distributed among these distances:
14 3 0.01
15 18 0.06
16 19 0.06
17 6 0.02
18 83 0.28
19 71 0.24
20 5 0.02
21 3 0.01
22 4 0.01
23 8 0.03
24 3 0.01
25 78 0.26
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (19 bp):
TTATGTAAGTTATTATGTA
Found at i:28708700 original size:26 final size:26
Alignment explanation
Indices: 28708666--28709071 Score: 579
Period size: 26 Copynumber: 16.1 Consensus size: 26
28708656 TGTAAGTTAA
28708666 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
28708692 ATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
28708717 GTGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
28708742 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
28708768 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* * *
28708794 GTGTAAGTTGCAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
28708819 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
28708845 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
28708871 GTGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
28708897 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
28708923 GTGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
28708948 ATGTCA---GTCA---A--ATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
28708966 ATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
28708991 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
28709017 ATGTAAGTAATGTAAGTTA-AATGTATT
1 ATGTAAGT--TGTAAGTTATTATGTATT
28709044 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
28709070 AT
1 AT
28709072 TTAATAAAAT
Statistics
Matches: 345, Mismatches: 22, Indels: 26
0.88 0.06 0.07
Matches are distributed among these distances:
18 12 0.03
19 1 0.00
21 3 0.01
22 3 0.01
24 1 0.00
25 113 0.33
26 188 0.54
27 15 0.04
28 9 0.03
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (26 bp):
ATGTAAGTTGTAAGTTATTATGTATT
Found at i:28709041 original size:53 final size:51
Alignment explanation
Indices: 28708666--28709071 Score: 571
Period size: 51 Copynumber: 8.0 Consensus size: 51
28708656 TGTAAGTTAA
* *
28708666 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTATTATGTATT
*
28708717 GTGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
* * * *
28708768 ATGTAAGTTGTAAGTTATTATGTATTGTGTAAGTTGCAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTATTATGTATT
*
28708819 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTATTATGTATT
* *
28708871 GTGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTATTATGTATT
* * *
28708923 GTGTAAGTTGTAAGTTAAATGTATTATGTCA---GTCA---A--ATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
28708966 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
28709017 ATGTAAGTAATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGT--TGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
28709070 AT
1 AT
28709072 TTAATAAAAT
Statistics
Matches: 324, Mismatches: 18, Indels: 24
0.89 0.05 0.07
Matches are distributed among these distances:
43 36 0.11
45 1 0.00
46 3 0.01
48 3 0.01
49 1 0.00
50 24 0.07
51 114 0.35
52 97 0.30
53 45 0.14
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (51 bp):
ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
Found at i:28709064 original size:19 final size:19
Alignment explanation
Indices: 28708841--28709067 Score: 100
Period size: 19 Copynumber: 12.5 Consensus size: 19
28708831 AGTTATTATG
28708841 TATTATGTAAGTTGTAAGT
1 TATTATGTAAGTTGTAAGT
28708860 TATTATGT-A-TTGT--GT
1 TATTATGTAAGTTGTAAGT
* * * *
28708875 AAGT-TGTAAGTTATTA-T
1 TATTATGTAAGTTGTAAGT
28708892 GTATTATGTAAGTTGTAAGT
1 -TATTATGTAAGTTGTAAGT
28708912 TATTATGT-A-TTGT--GT
1 TATTATGTAAGTTGTAAGT
* * *
28708927 AAGT-TGTAAG-T-TAAAT
1 TATTATGTAAGTTGTAAGT
* * *
28708943 GTATTATGTCAG-T-CAAAT
1 -TATTATGTAAGTTGTAAGT
28708961 GTATTATGTAAGTTGTAAGTTAAAT
1 -TATTATGTAAGTTGTAAG-----T
28708986 GTATTATGTAAGTTGTAAGT
1 -TATTATGTAAGTTGTAAGT
*
28709006 TATTATGT-ATTATGTAAG-
1 TATTATGTAAGT-TGTAAGT
*
28709024 TA--ATGTAAG-T-TAAAT
1 TATTATGTAAGTTGTAAGT
28709039 GTATTATGTAAGTTGTAAGT
1 -TATTATGTAAGTTGTAAGT
28709059 TATTATGTA
1 TATTATGTA
28709068 TTATTTAATA
Statistics
Matches: 159, Mismatches: 21, Indels: 56
0.67 0.09 0.24
Matches are distributed among these distances:
14 10 0.06
15 12 0.08
16 10 0.06
17 12 0.08
18 36 0.23
19 51 0.32
20 8 0.05
25 20 0.13
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.47
Consensus pattern (19 bp):
TATTATGTAAGTTGTAAGT
Found at i:28709265 original size:74 final size:74
Alignment explanation
Indices: 28709108--28709255 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
28709098 ACATTACTAA
28709108 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
28709173 TATTTTTTT
66 TATTTTTTT
28709182 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
28709247 TATTTTTTT
66 TATTTTTTT
28709256 ATATTTTATT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (74 bp):
TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
TATTTTTTT
Found at i:28709423 original size:13 final size:13
Alignment explanation
Indices: 28709405--28709475 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
28709395 ATTTATAATT
28709405 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
28709418 ATTTAAGTAACAT
1 ATTTAAGTAATAA
28709431 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
28709444 ATTTAAGTAACAT
1 ATTTAAGTAATAA
28709457 ATTTAAGTAATAA
1 ATTTAAGTAATAA
28709470 ATTTAA
1 ATTTAA
28709476 ACAAATTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAAGTAATAA
Found at i:28709434 original size:26 final size:26
Alignment explanation
Indices: 28709404--28709475 Score: 144
Period size: 26 Copynumber: 2.8 Consensus size: 26
28709394 TATTTATAAT
28709404 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
28709430 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
28709456 TATTTAAGTAATAAATTTAA
1 TATTTAAGTAATAAATTTAA
28709476 ACAAATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (26 bp):
TATTTAAGTAATAAATTTAAGTAACA
Found at i:28709502 original size:17 final size:17
Alignment explanation
Indices: 28709480--28709738 Score: 178
Period size: 17 Copynumber: 14.6 Consensus size: 17
28709470 ATTTAAACAA
28709480 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
28709497 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
*
28709514 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
28709531 AAACAAATTTTAGTAAGTAATGT
1 ------ATTTTAGTAAGTAATGT
* * *
28709554 ATTTAAGTAATTAAT-A
1 ATTTTAGTAAGTAATGT
* *
28709570 AATTTA--AA-CAA---
1 ATTTTAGTAAGTAATGT
28709581 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
28709598 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
*
28709615 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
28709632 AAACAAATTTTAGTAAGTAATGT
1 ------ATTTTAGTAAGTAATGT
28709655 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
*
28709672 ATTTTAGTAA-TAAATTT
1 ATTTTAGTAAGT-AATGT
*
28709689 AAACAAATTTTAGTAAGTAATTT
1 ------ATTTTAGTAAGTAATGT
28709712 ATTTTAGTAAGTAATGT
1 ATTTTAGTAAGTAATGT
28709729 ATTTTAGTAA
1 ATTTTAGTAA
28709739 TAAATTTAAC
Statistics
Matches: 198, Mismatches: 14, Indels: 60
0.73 0.05 0.22
Matches are distributed among these distances:
11 5 0.03
13 4 0.02
14 4 0.02
16 7 0.04
17 132 0.67
23 43 0.22
24 3 0.02
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (17 bp):
ATTTTAGTAAGTAATGT
Found at i:28709526 original size:57 final size:57
Alignment explanation
Indices: 28709447--28709747 Score: 432
Period size: 57 Copynumber: 5.5 Consensus size: 57
28709437 GTAATAAATT
** *
28709447 TAAGTAACATATTTAAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
28709504 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTA--TT--
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
* * *
28709557 TAAGTAAT-TA----A-T-A-AATTTAAACA-AATTTT-AGTAAGTAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAA-ACAAATTTTAGTAAGTAATGTATTTTAG
28709605 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
*
28709662 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATTTATTTTAG
1 TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
28709719 TAAGTAATGTATTTTAGTAATAAATTTAA
1 TAAGTAATGTATTTTAGTAATAAATTTAA
28709748 CATTCAATCG
Statistics
Matches: 219, Mismatches: 10, Indels: 30
0.85 0.04 0.12
Matches are distributed among these distances:
44 13 0.06
45 11 0.05
46 4 0.02
47 1 0.00
48 9 0.04
49 2 0.01
52 2 0.01
53 9 0.04
54 1 0.00
55 4 0.02
56 11 0.05
57 152 0.69
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (57 bp):
TAAGTAATGTATTTTAGTAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAG
Found at i:28709541 original size:40 final size:40
Alignment explanation
Indices: 28709497--28709721 Score: 199
Period size: 40 Copynumber: 5.7 Consensus size: 40
28709487 TAAGTAATGT
28709497 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
*
28709537 ATTTTAGTAAGTAATGTATTTAAGTAATTAATAAATTTAAACAA
1 ATTTTAGTAAGTAATGTATTT---T-AGTAATAAATTTAAACAA
*
28709581 ATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAA
1 ATTTTAGTAAGTAATGTATTTTAGTAA-TAA---A-TTTA--AACAA
* *
28709628 A-TTTA--AA-CAA---ATTTTAGTAAGT-AATGT------
1 ATTTTAGTAAGTAATGTATTTTAGTAA-TAAATTTAAACAA
28709655 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
1 ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
*
28709695 ATTTTAGTAAGTAATTTATTTTAGTAA
1 ATTTTAGTAAGTAATGTATTTTAGTAA
28709722 GTAATGTATT
Statistics
Matches: 152, Mismatches: 8, Indels: 50
0.72 0.04 0.24
Matches are distributed among these distances:
27 1 0.01
28 4 0.03
30 2 0.01
31 2 0.01
33 1 0.01
34 14 0.09
35 2 0.01
36 1 0.01
39 1 0.01
40 63 0.41
41 4 0.03
43 3 0.02
44 41 0.27
45 4 0.03
46 4 0.03
47 5 0.03
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.44
Consensus pattern (40 bp):
ATTTTAGTAAGTAATGTATTTTAGTAATAAATTTAAACAA
Found at i:28709550 original size:44 final size:44
Alignment explanation
Indices: 28709497--28709612 Score: 159
Period size: 44 Copynumber: 2.7 Consensus size: 44
28709487 TAAGTAATGT
*
28709497 ATTTTAGTAAGTAATGTAT-T---TTAGTAATAAATTTAAACAA
1 ATTTTAGTAAGTAATGTATGTAAGTAAGTAATAAATTTAAACAA
* *
28709537 ATTTTAGTAAGTAATGTATTTAAGTAATTAATAAATTTAAACAA
1 ATTTTAGTAAGTAATGTATGTAAGTAAGTAATAAATTTAAACAA
* *
28709581 ATTTTAGTAAGTAATGTATTTTAGTAAGTAAT
1 ATTTTAGTAAGTAATGTATGTAAGTAAGTAAT
28709613 GTATTTTAGT
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
40 19 0.28
41 1 0.01
44 48 0.71
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (44 bp):
ATTTTAGTAAGTAATGTATGTAAGTAAGTAATAAATTTAAACAA
Found at i:28709583 original size:101 final size:107
Alignment explanation
Indices: 28709464--28709747 Score: 454
Period size: 101 Copynumber: 2.6 Consensus size: 107
28709454 CATATTTAAG
28709464 TAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAAT
1 TAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAAT
28709529 TTAAACAAATTTTAGTAAGTAATGTA-TT-TAAGT-A-A-T-
66 TTAAACAAATTTTAGTAAGTAATGTATTTATAAGTAATATTA
28709565 TAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAAT
1 TAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAAT
28709630 TTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTA
66 TTAAACAAATTTTAGTAAGTAATGTA-TTTA-TAAGTAA--TA--TTA
*
28709678 GTAATAAATTTAAACAAATTTTAGTAAGTAATTTATTTTAGTAAGTAATGTATTTTAGTAATAAA
1 -TAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAA
28709743 TTTAA
65 TTTAA
28709748 CATTCAATCG
Statistics
Matches: 169, Mismatches: 1, Indels: 13
0.92 0.01 0.07
Matches are distributed among these distances:
101 91 0.54
103 2 0.01
105 5 0.03
106 1 0.01
109 1 0.01
112 1 0.01
114 68 0.40
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.44
Consensus pattern (107 bp):
TAATAAATTTAAACAAATTTTAGTAAGTAATGTATTTTAGTAAGTAATGTATTTTAGTAATAAAT
TTAAACAAATTTTAGTAAGTAATGTATTTATAAGTAATATTA
Found at i:28711982 original size:84 final size:84
Alignment explanation
Indices: 28711869--28712305 Score: 694
Period size: 84 Copynumber: 5.1 Consensus size: 84
28711859 CCACATTTCC
*
28711869 GGCGTTTTCCTAAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCATTTTCGTGG
1 GGCGTTTTCCT-AAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTTCGTGG
28711934 TCTGGAATTGCATTATTTGT
65 TCTGGAATTGCATTATTTGT
* * * *
28711954 GGCATTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACAACACCATTTTCGTAGT
1 GGCGTTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTTCGTGGT
28712019 CTGGAATTGCATTATTTGT
66 CTGGAATTGCATTATTTGT
*
28712038 GGCGTTTTCCTAAAAACGCCACTAAATATTACAGTTGTGAACAGAAACGACACCGTTTTGCGTGG
1 GGCGTTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTT-CGTGG
28712103 TCTGGAATAATTGCATTATTTGT
65 TCTGG---AATTGCATTATTTGT
* *
28712126 GGCGTTTTCCTAAAAACGCCACTAAATATTACAACTGTGAACAGAAACGACACCGTTTTTGTGGT
1 GGCGTTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTTCGTGGT
28712191 CTGGAATTGCATTATTTGT
66 CTGGAATTGCATTATTTGT
*
28712210 GGCGTTTTCCTAAAAACGCCACTAGATATTACAGCTGTGAACAGAAACGACACCGTTTTGCGTGG
1 GGCGTTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTT-CGTGG
*
28712275 TCTGGAATAATTGCATTATTTCT
65 TCTGG---AATTGCATTATTTGT
*
28712298 GGCATTTT
1 GGCGTTTT
28712306 AAGCACAAAT
Statistics
Matches: 328, Mismatches: 16, Indels: 13
0.92 0.04 0.04
Matches are distributed among these distances:
84 198 0.60
85 28 0.09
87 9 0.03
88 93 0.28
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (84 bp):
GGCGTTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTTCGTGGT
CTGGAATTGCATTATTTGT
Found at i:28712153 original size:172 final size:172
Alignment explanation
Indices: 28711869--28712305 Score: 747
Period size: 172 Copynumber: 2.6 Consensus size: 172
28711859 CCACATTTCC
*
28711869 GGCGTTTTCCTAAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCATTTT-CGTG
1 GGCGTTTTCCT-AAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTTGCGTG
*
28711933 GTCTGG---AATTGCATTATTTGTGGCATTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAA
65 GTCTGGAATAATTGCATTATTTGTGGCATTTTCCTAAAAACGCCACTAAATATTACAACTGTGAA
28711995 CAGAAACAACACCATTTTCGTAGTCTGGAATTGCATTATTTGT
130 CAGAAACAACACCATTTTCGTAGTCTGGAATTGCATTATTTGT
*
28712038 GGCGTTTTCCTAAAAACGCCACTAAATATTACAGTTGTGAACAGAAACGACACCGTTTTGCGTGG
1 GGCGTTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTTGCGTGG
*
28712103 TCTGGAATAATTGCATTATTTGTGGCGTTTTCCTAAAAACGCCACTAAATATTACAACTGTGAAC
66 TCTGGAATAATTGCATTATTTGTGGCATTTTCCTAAAAACGCCACTAAATATTACAACTGTGAAC
* * * *
28712168 AGAAACGACACCGTTTTTGTGGTCTGGAATTGCATTATTTGT
131 AGAAACAACACCATTTTCGTAGTCTGGAATTGCATTATTTGT
*
28712210 GGCGTTTTCCTAAAAACGCCACTAGATATTACAGCTGTGAACAGAAACGACACCGTTTTGCGTGG
1 GGCGTTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTTGCGTGG
*
28712275 TCTGGAATAATTGCATTATTTCTGGCATTTT
66 TCTGGAATAATTGCATTATTTGTGGCATTTT
28712306 AAGCACAAAT
Statistics
Matches: 252, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
168 46 0.18
169 21 0.08
172 185 0.73
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (172 bp):
GGCGTTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTTGCGTGG
TCTGGAATAATTGCATTATTTGTGGCATTTTCCTAAAAACGCCACTAAATATTACAACTGTGAAC
AGAAACAACACCATTTTCGTAGTCTGGAATTGCATTATTTGT
Found at i:28715053 original size:112 final size:112
Alignment explanation
Indices: 28714818--28715072 Score: 420
Period size: 112 Copynumber: 2.3 Consensus size: 112
28714808 AACACCTAGA
* *
28714818 TTAGAGGCGCTGTACAAAAAACGCCACTAATTCCCCCCCAAAGGACACAAAACAGCACCGTCTGG
1 TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGACACAAAACAGCACCGTCTGG
28714883 GTGTATTATTTGCAGCGTTTTTTATAAACGCTGCTAATGTTCACTCT
66 GTGTATTATTTGCAGCGTTTTTTATAAACGCTGCTAATGTTCACTCT
* *
28714930 TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGG
1 TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGACACAAAACAGCACCGTCTGG
* *
28714995 GTGTATTATTTGCGGCTTTTTTTATAAACGCTGCTAATGTTCACTCT
66 GTGTATTATTTGCAGCGTTTTTTATAAACGCTGCTAATGTTCACTCT
* ***
28715042 TTAGCGGCGCTTTTCCTTAAACGCCACTAAT
1 TTAGCGGCGCTTTACAAAAAACGCCACTAAT
28715073 GCTCACTCTT
Statistics
Matches: 133, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 133 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (112 bp):
TTAGCGGCGCTTTACAAAAAACGCCACTAATTCCCCCCCAAAGGACACAAAACAGCACCGTCTGG
GTGTATTATTTGCAGCGTTTTTTATAAACGCTGCTAATGTTCACTCT
Found at i:28715065 original size:40 final size:40
Alignment explanation
Indices: 28715019--28715152 Score: 196
Period size: 40 Copynumber: 3.3 Consensus size: 40
28715009 GCTTTTTTTA
* *
28715019 TAAACGCTGCTAATGTTCACTCTTTAGCGGCGCTTTTCCT
1 TAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTTCCT
*
28715059 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTCCT
1 TAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTTCCT
* * *
28715099 TAAACGCCGCTAATGCTCACTCTTTAGCAGCGTTTTTGCT
1 TAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTTCCT
*
28715139 CCAAACGCCGCTAA
1 -TAAACGCCGCTAA
28715153 AAGTGCCGCT
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 73 0.86
41 12 0.14
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.32
Consensus pattern (40 bp):
TAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTTCCT
Found at i:28715454 original size:18 final size:18
Alignment explanation
Indices: 28715423--28715457 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28715413 ATATGTAGAA
28715423 AAATATATAAACTAATAT
1 AAATATATAAACTAATAT
28715441 AAATA-ATAATACTAATA
1 AAATATATAA-ACTAATA
28715458 ATAATGATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATATATAAACTAATAT
Found at i:28717061 original size:44 final size:44
Alignment explanation
Indices: 28716934--28717311 Score: 169
Period size: 44 Copynumber: 8.6 Consensus size: 44
28716924 GATGCGATCC
* * * * * * * *
28716934 ACTCTACTACAACTTCAGAGAGATAAGATCTATTACTTTAATCC
1 ACTCCACTGCAACCTCAGGGAGATAAGATTTGTTACTTCAATCT
* * * *
28716978 GCTCCACTACAACCTCAAGGAGATAGGATTATCG--ACTTCAATCT
1 ACTCCACTGCAACCTCAGGGAGATAAGATT-T-GTTACTTCAATCT
** * *
28717022 GGTCCACTGCAACCTCAGGGAGATAAGATTTGTTTCTTCAGTCT
1 ACTCCACTGCAACCTCAGGGAGATAAGATTTGTTACTTCAATCT
* ** * * * * *
28717066 ACCCCACTGTGACTTCAGGGGGATAAGACTTGTT-TTCTCAGTCT
1 ACTCCACTGCAACCTCAGGGAGATAAGATTTGTTACT-TCAATCT
** * * *
28717110 ACTCCACTGCAACCTCAGGGAGATAAGACCTG--A-TGCGATCC
1 ACTCCACTGCAACCTCAGGGAGATAAGATTTGTTACTTCAATCT
* ** ** * * * *
28717151 ACTCTACTGCAAATTCAAAGAGATAAGATCTATTACTTTAATCC
1 ACTCCACTGCAACCTCAGGGAGATAAGATTTGTTACTTCAATCT
* * * * * *
28717195 GCTCCACTACAACTTCAGGGAGATAGGATTATCG--ACTTTAATTT
1 ACTCCACTGCAACCTCAGGGAGATAAGATT-T-GTTACTTCAATCT
* * * * *
28717239 GCTCCACTGTAACTTCAGGGAGATAAGATTTGTCATCTTCGATCT
1 ACTCCACTGCAACCTCAGGGAGATAAGATTTGTTA-CTTCAATCT
* * * *
28717284 GCCCCACTGCAACTTCAGGGGGATAAGA
1 ACTCCACTGCAACCTCAGGGAGATAAGA
28717312 CCTGCTTACT
Statistics
Matches: 255, Mismatches: 65, Indels: 27
0.73 0.19 0.08
Matches are distributed among these distances:
41 28 0.11
42 3 0.01
43 4 0.02
44 187 0.73
45 33 0.13
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (44 bp):
ACTCCACTGCAACCTCAGGGAGATAAGATTTGTTACTTCAATCT
Found at i:28717406 original size:218 final size:217
Alignment explanation
Indices: 28716917--28717459 Score: 791
Period size: 218 Copynumber: 2.5 Consensus size: 217
28716907 TCTAGTCGGC
* *
28716917 AAGACTTGATGCGATCCACTCTACTACAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
1 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
* * *
28716982 CACTACAACCTCAAGGAGATAGGATTATCGACTTCAATCTGGTCCACTGCAACCTCAGGGAGATA
66 CACTACAACTTCAGGGAGATAGGATTATCGACTTCAATCTGCTCCACTGCAACCTCAGGGAGATA
* ** * * *
28717047 AGATTTGTTTCTTCAGTCTACCCCACTGTGACTTCAGGGGGATAAGACTTGTTTTCTCAGTCTAC
131 AGATTTGTATCTTCAGTCTACCCCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTAC
28717112 TCCACTGCAACCTCAGGGAGAT
196 TCCACTGCAACCTCAGGGAGAT
* *
28717134 AAGACCTGATGCGATCCACTCTACTGCAAATTCAAAGAGATAAGATCTATTACTTTAATCCGCTC
1 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
* * * *
28717199 CACTACAACTTCAGGGAGATAGGATTATCGACTTTAATTTGCTCCACTGTAACTTCAGGGAGATA
66 CACTACAACTTCAGGGAGATAGGATTATCGACTTCAATCTGCTCCACTGCAACCTCAGGGAGATA
* *
28717264 AGATTTGTCATCTTC-GATCTGCCCCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTGT
131 AGATTTGT-ATCTTCAG-TCTACCCCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCT
* *** *
28717328 GCTTTGCTGCAACTTCAGGGAGAT
194 ACTCCACTGCAACCTCAGGGAGAT
* * * *
28717352 AAGACCTGATGCGATCCACTCTATTGCAACTTTAGAGAGATAAGAACTATTACTTTAATCCACTC
1 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
* *
28717417 CACTACAACTTCAGGGAGATAGGCTTATCGGCTTCAATCTGCT
66 CACTACAACTTCAGGGAGATAGGATTATCGACTTCAATCTGCT
28717460 TCCTTACACT
Statistics
Matches: 290, Mismatches: 34, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
217 128 0.44
218 162 0.56
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (217 bp):
AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
CACTACAACTTCAGGGAGATAGGATTATCGACTTCAATCTGCTCCACTGCAACCTCAGGGAGATA
AGATTTGTATCTTCAGTCTACCCCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTAC
TCCACTGCAACCTCAGGGAGAT
Found at i:28717739 original size:129 final size:128
Alignment explanation
Indices: 28717428--28717947 Score: 844
Period size: 128 Copynumber: 4.0 Consensus size: 128
28717418 ACTACAACTT
* * * *
28717428 CAGGGAGATAGG-CTTATCGGCTTCAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCATCTT
1 CAGGGACATAGGACTTGT-GGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTT
* * *
28717492 TGATCTGCTCTGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGAC
65 TGATCTACTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTACTCCACTGCTGAC
*
28717556 CAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTT
1 CAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTT
* *
28717621 GATCTACTCTGCTACTGCTTAAGGAGACAAGATCTGTAATTTCTCAACCTACTCCACTGCTGAC
66 GATCTACTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTC-CAACCTACTCCACTGCTGAC
* *
28717685 CAGAGACATAGGACTTGTGGTTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTT
1 CAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTT
* * * *
28717750 GATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTCCAACCTATTCCACTGCTGAA
66 GATCTACTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTACTCCACTGCTGAC
*
28717813 CAGGGACATAGGACTTGTGGCCTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTT
1 CAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTT
*
28717878 GATCTACTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTACTCCAATGCTGAC
66 GATCTACTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT-CCAACCTACTCCACTGCTGAC
28717942 CAGGGA
1 CAGGGA
28717948 GCTAGGTTTT
Statistics
Matches: 364, Mismatches: 25, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
128 216 0.59
129 148 0.41
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (128 bp):
CAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTT
GATCTACTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTACTCCACTGCTGAC
Found at i:28717766 original size:257 final size:257
Alignment explanation
Indices: 28717452--28717944 Score: 896
Period size: 257 Copynumber: 1.9 Consensus size: 257
28717442 TATCGGCTTC
*
28717452 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCATCTTTGATCTGCTCTGCTACTGCTTAGGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCATCTTTGATCTGCTCCGCTACTGCTTAGGG
* *
28717517 AGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAA
66 AGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGAACAGGGACATAGGACTTGTGGCCTAAA
*
28717582 TCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTTGATCTACTCTGCTACTGCTTAAGGAG
131 TCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTTGATCTACTCCGCTACTGCTTAAGGAG
* *
28717647 ACAAGATCTGTAATTTCTCAACCTACTCCACTGCTGACCAGAGACATAGGACTTGTGGTTTA
196 ACAAGATCTGTAATTTCCCAACCTACTCCAATGCTGACCAGAGACATAGGACTTGTGGTTTA
*
28717709 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTTGATCTGCTCCGCTACTGCTTAGGG
1 AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCATCTTTGATCTGCTCCGCTACTGCTTAGGG
*
28717774 AGACAAGATTTGTAATTTCCAACCTATTCCACTGCTGAACAGGGACATAGGACTTGTGGCCTAAA
66 AGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGAACAGGGACATAGGACTTGTGGCCTAAA
* *
28717839 TCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTTGATCTACTCCGCTACTGCTTAGGGAG
131 TCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTTGATCTACTCCGCTACTGCTTAAGGAG
28717904 ACAAGATCTGTAATTTCCCAACCTACTCCAATGCTGACCAG
196 ACAAGATCTGTAATTTCCCAACCTACTCCAATGCTGACCAG
28717945 GGAGCTAGGT
Statistics
Matches: 226, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
257 226 1.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (257 bp):
AATCTGCTTCCTTACACTTGAAGATAAGATTCGCCATCTTTGATCTGCTCCGCTACTGCTTAGGG
AGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGAACAGGGACATAGGACTTGTGGCCTAAA
TCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTTGATCTACTCCGCTACTGCTTAAGGAG
ACAAGATCTGTAATTTCCCAACCTACTCCAATGCTGACCAGAGACATAGGACTTGTGGTTTA
Found at i:28719342 original size:14 final size:15
Alignment explanation
Indices: 28719323--28719367 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
28719313 GCCTCTCCAT
28719323 TTTTTTA-TTTTTCA
1 TTTTTTATTTTTTCA
28719337 TTTTTTATTTTTTCA
1 TTTTTTATTTTTTCA
28719352 TTTTTCATATTTTTTC
1 TTTTT--TATTTTTTC
28719368 TGACTCAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.25
15 12 0.43
17 9 0.32
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTATTTTTTCA
Found at i:28719346 original size:22 final size:23
Alignment explanation
Indices: 28719321--28719365 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
28719311 TAGCCTCTCC
*
28719321 ATTTTTTTATTTTTCAT-TTTTT
1 ATTTTTTCATTTTTCATATTTTT
28719343 ATTTTTTCATTTTTCATATTTTT
1 ATTTTTTCATTTTTCATATTTTT
28719366 TCTGACTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (23 bp):
ATTTTTTCATTTTTCATATTTTT
Found at i:28722312 original size:25 final size:25
Alignment explanation
Indices: 28722284--28722334 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
28722274 GGAGTACTAA
28722284 GTCTGGAACCAAGCTCAGATCTTTT
1 GTCTGGAACCAAGCTCAGATCTTTT
28722309 GTCTGGAACCAAGCTCAGATCTTTT
1 GTCTGGAACCAAGCTCAGATCTTTT
28722334 G
1 G
28722335 CATCGATTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (25 bp):
GTCTGGAACCAAGCTCAGATCTTTT
Found at i:28726660 original size:90 final size:90
Alignment explanation
Indices: 28726543--28726729 Score: 268
Period size: 90 Copynumber: 2.1 Consensus size: 90
28726533 AATAGTTTTT
* * *
28726543 GAGAAATCTTGTCGATAAGAAGTTCAAAAAAAGAAGTCTAGAGAAATGTCGAGAAAAATAGCAAT
1 GAGAAATCTTGTCGATAAGAAGTTCAAAAAAAGAAGTCTAAAGAAATGTCGAGAAAAACAACAAT
* * *
28726608 TGAATAGCAACAATCAAAAATTGTC
66 TGAATACCAACAACCAAAAATTGTA
* *
28726633 GAGAAATCTTG-CTGATAAGAAGTTCAAAAAAATAAGTTTAAAGAAATGTCGAGAAAAACAACAA
1 GAGAAATCTTGTC-GATAAGAAGTTCAAAAAAAGAAGTCTAAAGAAATGTCGAGAAAAACAACAA
* *
28726697 TTGAATACCAACAACCAACAGTTGTA
65 TTGAATACCAACAACCAAAAATTGTA
28726723 GAGAAAT
1 GAGAAAT
28726730 TTTTAATTAG
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
89 1 0.01
90 85 0.99
ACGTcount: A:0.50, C:0.12, G:0.18, T:0.21
Consensus pattern (90 bp):
GAGAAATCTTGTCGATAAGAAGTTCAAAAAAAGAAGTCTAAAGAAATGTCGAGAAAAACAACAAT
TGAATACCAACAACCAAAAATTGTA
Found at i:28734161 original size:49 final size:49
Alignment explanation
Indices: 28734105--28734202 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 49
28734095 TATGGAAAAC
* **
28734105 AATTCTCAAGAAGAAAACACTCATATATAATATGCATTTGCTTTGTGTA
1 AATTCTCAAAAAGAAAACACTCATATATAATACACATTTGCTTTGTGTA
*
28734154 AATTCTCAAAAAGAAAACACTCATATATAATACACATTTGTTTTGTGTA
1 AATTCTCAAAAAGAAAACACTCATATATAATACACATTTGCTTTGTGTA
28734203 TCTATAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (49 bp):
AATTCTCAAAAAGAAAACACTCATATATAATACACATTTGCTTTGTGTA
Found at i:28737639 original size:125 final size:124
Alignment explanation
Indices: 28737341--28737747 Score: 602
Period size: 124 Copynumber: 3.3 Consensus size: 124
28737331 ATTTATTAAG
* * * * *
28737341 GAAATCACTCCCACGA-GGACGCGTTTTTGATACAGTAGGTCCTGAAAAAATAATTTTGAGTTGA
1 GAAATCGCTCCCAC-ATGGACGCGCTTTTGCTACAGGAAGTCCTGAAAAAATAATTTTGAGTTGA
* * * *
28737405 TGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAACAGAATGCTTTATCAGAAGAATTTCT
65 CGTTTCTGAGCAAATAGTAT-AAAAACGCTTCAAGCAGAATGCTTTATCAAAAGAATTTTT
** *
28737466 GAAATCGCTCTTACGTGGACGCGCTTTTGCTACAGGAAGTCCTGAAAAAATAATTTTGAGTTGAC
1 GAAATCGCTCCCACATGGACGCGCTTTTGCTACAGGAAGTCCTGAAAAAATAATTTTGAGTTGAC
28737531 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGAATGCTTTATCAAAAGAATTTTT
66 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGAATGCTTTATCAAAAGAATTTTT
* *
28737590 GAAATCGCTCCCACATGGACGCGCTTTTGCTACAGGAAGTCCTGAAAAAATAATTTCGAGTTAAC
1 GAAATCGCTCCCACATGGACGCGCTTTTGCTACAGGAAGTCCTGAAAAAATAATTTTGAGTTGAC
* * * *
28737655 GTTTCTGAACAAATAGTATAAAAACGCTTCAAGCAGGATGTTTTAGT-GAAAGAATTTTT
66 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGAATGCTTTA-TCAAAAGAATTTTT
*
28737714 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACA
1 GAAATCGCTCCCACATGGACGCGCTTTTGCTACA
28737748 ATAGAATGTT
Statistics
Matches: 258, Mismatches: 22, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
124 183 0.71
125 75 0.29
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (124 bp):
GAAATCGCTCCCACATGGACGCGCTTTTGCTACAGGAAGTCCTGAAAAAATAATTTTGAGTTGAC
GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGAATGCTTTATCAAAAGAATTTTT
Found at i:28740355 original size:14 final size:14
Alignment explanation
Indices: 28740336--28740371 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
28740326 TATTGTGTAC
28740336 ACTTGCGAAATAAG
1 ACTTGCGAAATAAG
*
28740350 ACTTGCGAAATAGG
1 ACTTGCGAAATAAG
28740364 ACTTGCGA
1 ACTTGCGA
28740372 CTATGGGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (14 bp):
ACTTGCGAAATAAG
Found at i:28741343 original size:18 final size:18
Alignment explanation
Indices: 28741317--28741359 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
28741307 GACTAGAAAA
* *
28741317 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGTT
28741335 AGGATACATAAAAGGGTT
1 AGGATACATAAAAGGGTT
28741353 AGGATAC
1 AGGATAC
28741360 GCACATGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.44, C:0.07, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATAAAAGGGTT
Found at i:28743189 original size:11 final size:11
Alignment explanation
Indices: 28743159--28743183 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28743149 GAGAAATTTA
28743159 AGAGCAAATTG
1 AGAGCAAATTG
28743170 AGAGCAAATTG
1 AGAGCAAATTG
28743181 AGA
1 AGA
28743184 TTAAATATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.28, T:0.16
Consensus pattern (11 bp):
AGAGCAAATTG
Found at i:28743208 original size:11 final size:12
Alignment explanation
Indices: 28743194--28743256 Score: 66
Period size: 11 Copynumber: 5.7 Consensus size: 12
28743184 TTAAATATGG
28743194 ATTTGAGA-GAA
1 ATTTGAGAGGAA
28743205 ATTTG-GAAGGAA
1 ATTTGAG-AGGAA
*
28743217 A-TTGAGA-GCA
1 ATTTGAGAGGAA
28743227 ATTTGAGAGGAA
1 ATTTGAGAGGAA
28743239 A-TTGAGAGGAA
1 ATTTGAGAGGAA
28743250 A-TTGAGA
1 ATTTGAGA
28743257 AAATAATTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
10 4 0.09
11 33 0.73
12 8 0.18
ACGTcount: A:0.43, C:0.02, G:0.32, T:0.24
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:28743221 original size:22 final size:22
Alignment explanation
Indices: 28743196--28743256 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
28743186 AAATATGGAT
28743196 TTGAGAGAAATTTG-GAAGGAAA
1 TTGAGAGAAATTTGAG-AGGAAA
*
28743218 TTGAGAGCAATTTGAGAGGAAA
1 TTGAGAGAAATTTGAGAGGAAA
28743240 TTGAGAGGAAA-TTGAGA
1 TTGAGA-GAAATTTGAGA
28743257 AAATAATTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 31 0.89
23 4 0.11
ACGTcount: A:0.43, C:0.02, G:0.33, T:0.23
Consensus pattern (22 bp):
TTGAGAGAAATTTGAGAGGAAA
Found at i:28743231 original size:33 final size:33
Alignment explanation
Indices: 28743194--28743256 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
28743184 TTAAATATGG
28743194 ATTTGAGA-GAAATTTG-GAAGGAAATTGAGAGCA
1 ATTTGAGAGGAAA-TTGAG-AGGAAATTGAGAGCA
28743227 ATTTGAGAGGAAATTGAGAGGAAATTGAGA
1 ATTTGAGAGGAAATTGAGAGGAAATTGAGA
28743257 AAATAATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 23 0.82
34 5 0.18
ACGTcount: A:0.43, C:0.02, G:0.32, T:0.24
Consensus pattern (33 bp):
ATTTGAGAGGAAATTGAGAGGAAATTGAGAGCA
Found at i:28743264 original size:23 final size:22
Alignment explanation
Indices: 28743215--28743268 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
28743205 ATTTGGAAGG
* **
28743215 AAATTGAGAGCAATTTGAGAGG
1 AAATTGAGAGCAAATTGAGAAA
*
28743237 AAATTGAGAGGAAATTGAGAAA
1 AAATTGAGAGCAAATTGAGAAA
28743259 ATAATTGAGA
1 A-AATTGAGA
28743269 AAAGGATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.48, C:0.02, G:0.28, T:0.22
Consensus pattern (22 bp):
AAATTGAGAGCAAATTGAGAAA
Found at i:28744016 original size:30 final size:29
Alignment explanation
Indices: 28743940--28744016 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
28743930 ATAATTATGG
* *
28743940 AAAAAAATTTCTTATATTATAAATTCTAA
1 AAAAAAATTTATTATTTTATAAATTCTAA
* *
28743969 AAAATAATTTTTGTATTTTATAAATT-TATA
1 AAAAAAATTTAT-TATTTTATAAATTCTA-A
28743999 AAAAAAATTATATTATTT
1 AAAAAAATT-TATTATTT
28744017 AAATCTTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 12 0.30
30 26 0.65
31 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (29 bp):
AAAAAAATTTATTATTTTATAAATTCTAA
Found at i:28765157 original size:13 final size:13
Alignment explanation
Indices: 28765139--28765168 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28765129 ACATATATTG
28765139 TAATATTTATTAA
1 TAATATTTATTAA
*
28765152 TAATATTTATTCA
1 TAATATTTATTAA
28765165 TAAT
1 TAAT
28765169 CTTAATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
TAATATTTATTAA
Found at i:28767387 original size:23 final size:24
Alignment explanation
Indices: 28767360--28767412 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
28767350 TCTTTCTAGA
* *
28767360 ATATTTAGTATTTA-TAGTATAAT
1 ATATTTAGCATTTATTAGCATAAT
28767383 ATATTTAGCATTTATTAGCATAAT
1 ATATTTAGCATTTATTAGCATAAT
*
28767407 TTATTT
1 ATATTT
28767413 GACTTACTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.53
Consensus pattern (24 bp):
ATATTTAGCATTTATTAGCATAAT
Found at i:28771992 original size:23 final size:24
Alignment explanation
Indices: 28771965--28772017 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
28771955 TCTTTCTAGA
* *
28771965 ATATTTAGTATTTA-TAGTATAAT
1 ATATTTAGCATTTATTAGCATAAT
28771988 ATATTTAGCATTTATTAGCATAAT
1 ATATTTAGCATTTATTAGCATAAT
*
28772012 TTATTT
1 ATATTT
28772018 GACTTACTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.53
Consensus pattern (24 bp):
ATATTTAGCATTTATTAGCATAAT
Found at i:28797482 original size:24 final size:24
Alignment explanation
Indices: 28797451--28797521 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
28797441 AAGAATTTAG
* *
28797451 TCAAGATCATTCATATATTTTCAA
1 TCAAGATCATTCATGTATATTCAA
28797475 TCAAGATCATTCATGTATATTCAA
1 TCAAGATCATTCATGTATATTCAA
*
28797499 TCAAAATCATTCATGTATATTCA
1 TCAAGATCATTCATGTATATTCA
28797522 CATAATTCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (24 bp):
TCAAGATCATTCATGTATATTCAA
Found at i:28797704 original size:32 final size:30
Alignment explanation
Indices: 28797668--28797731 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
28797658 AAGCAGAGGC
* *
28797668 ACGATTGTGCAATCAGAGGCACCAGAGTGCAA
1 ACGATTGTG--ATCAAAGGCACCAAAGTGCAA
*
28797700 ACGATTGTGATGAAAGGCACCAAAGTGCAA
1 ACGATTGTGATCAAAGGCACCAAAGTGCAA
28797730 AC
1 AC
28797732 CCGTACAAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 20 0.69
32 9 0.31
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.16
Consensus pattern (30 bp):
ACGATTGTGATCAAAGGCACCAAAGTGCAA
Found at i:28803315 original size:17 final size:17
Alignment explanation
Indices: 28803293--28803392 Score: 65
Period size: 17 Copynumber: 5.5 Consensus size: 17
28803283 AATATTAAAG
28803293 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
* ***
28803310 AATTATGTAGTGATTCAA
1 AATTATGTAATG-TTTTT
*
28803328 AGACTTATGTAATATTTTT
1 A-A-TTATGTAATGTTTTT
* * *
28803347 AATTATGTAGTGATTCTA
1 AATTATGTAATG-TTTTT
*
28803365 AGATTTATGTAATTTTTTT
1 A-A-TTATGTAATGTTTTT
28803384 AATTATGTA
1 AATTATGTA
28803393 GTGATTCAAT
Statistics
Matches: 60, Mismatches: 17, Indels: 12
0.67 0.19 0.13
Matches are distributed among these distances:
17 26 0.43
18 9 0.15
19 9 0.15
20 16 0.27
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:28803339 original size:37 final size:37
Alignment explanation
Indices: 28803289--28803401 Score: 181
Period size: 37 Copynumber: 3.1 Consensus size: 37
28803279 GGAGAATATT
*
28803289 AAAGAATTATGTAATGTTTTTAATTATGTAGTGATTC
1 AAAGAATTATGTAATATTTTTAATTATGTAGTGATTC
*
28803326 AAAGACTTATGTAATATTTTTAATTATGTAGTGATTC
1 AAAGAATTATGTAATATTTTTAATTATGTAGTGATTC
* * *
28803363 TAAGATTTATGTAATTTTTTTAATTATGTAGTGATTC
1 AAAGAATTATGTAATATTTTTAATTATGTAGTGATTC
28803400 AA
1 AA
28803402 TTTGGGTAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.48
Consensus pattern (37 bp):
AAAGAATTATGTAATATTTTTAATTATGTAGTGATTC
Found at i:28803374 original size:20 final size:19
Alignment explanation
Indices: 28803311--28803375 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
28803301 AATGTTTTTA
*
28803311 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCTAAG
* * *
28803330 ACTTATGTAAT-ATTTTTA-
1 A-TTATGTAGTGATTCTAAG
28803348 ATTATGTAGTGATTCTAAG
1 ATTATGTAGTGATTCTAAG
28803367 ATTTATGTA
1 A-TTATGTA
28803376 ATTTTTTTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
17 8 0.23
18 6 0.17
19 6 0.17
20 15 0.43
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (19 bp):
ATTATGTAGTGATTCTAAG
Found at i:28803417 original size:9 final size:9
Alignment explanation
Indices: 28803400--28803439 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
28803390 GTAGTGATTC
*
28803400 AATTTGGGT
1 AATTCGGGT
28803409 AATTCGGGT
1 AATTCGGGT
*
28803418 AATTCTGGT
1 AATTCGGGT
28803427 AATTCGGGT
1 AATTCGGGT
28803436 AATT
1 AATT
28803440 TTTAACCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.25, C:0.07, G:0.28, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:28804419 original size:25 final size:27
Alignment explanation
Indices: 28804390--28804451 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 27
28804380 ATGTGAAAAG
28804390 TTTAAATATATT-TTGATTTAAA-TAT
1 TTTAAATATATTATTGATTTAAATTAT
*
28804415 TTTAAATA-ATTATTTATTTAAATTTAT
1 TTTAAATATATTATTGATTTAAA-TTAT
*
28804442 TTTTAATATA
1 TTTAAATATA
28804452 AAGAAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 3 0.10
25 17 0.55
27 10 0.32
28 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTAAATATATTATTGATTTAAATTAT
Found at i:28809745 original size:9 final size:9
Alignment explanation
Indices: 28809707--28809929 Score: 69
Period size: 10 Copynumber: 22.9 Consensus size: 9
28809697 AAATAACAAA
28809707 AATTTTCTAT
1 AATTTT-TAT
28809717 AA-TTTTATT
1 AATTTTTA-T
*
28809726 ACATATTTAT
1 A-ATTTTTAT
28809736 AATTTTTAT
1 AATTTTTAT
28809745 AACTTTTTAAT
1 AA-TTTTT-AT
* *
28809756 ACTTTTAAT
1 AATTTTTAT
28809765 AAGTTTTTAT
1 AA-TTTTTAT
28809775 AACTTTTTAAAAT
1 AA-TTTTT---AT
*
28809788 AAATTTATAT
1 -AATTTTTAT
*
28809798 ATTTTTATAT
1 AATTTT-TAT
28809808 AATTTCTTAT
1 AATTT-TTAT
28809818 --TGTTTTAT
1 AAT-TTTTAT
*
28809826 -TTTTTTAT
1 AATTTTTAT
* *
28809834 AAGTTCTAT
1 AATTTTTAT
28809843 AATTTTATAT
1 AATTTT-TAT
* *
28809853 TATTTATAT
1 AATTTTTAT
*
28809862 AATAGTTTGAT
1 AAT--TTTTAT
*
28809873 ATCTTTTTCAT
1 A-ATTTTT-AT
* *
28809884 AACATATTAAT
1 -A-ATTTTTAT
*
28809895 GATATTTTAT
1 AAT-TTTTAT
28809905 AATTTTTAT
1 AATTTTTAT
28809914 AATTTTT-T
1 AATTTTTAT
*
28809922 AATATTTA
1 AATTTTTA
28809930 ATAACAATTT
Statistics
Matches: 158, Mismatches: 32, Indels: 47
0.67 0.14 0.20
Matches are distributed among these distances:
8 20 0.13
9 53 0.34
10 55 0.35
11 17 0.11
12 5 0.03
13 6 0.04
14 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (9 bp):
AATTTTTAT
Found at i:28812622 original size:16 final size:16
Alignment explanation
Indices: 28812597--28812652 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
28812587 TTATTTATAT
*
28812597 TTATTCATATAATAAA
1 TTATTAATATAATAAA
*
28812613 TTATTAATATAATTAA
1 TTATTAATATAATAAA
28812629 TTATT--T-TAATAAA
1 TTATTAATATAATAAA
28812642 TTATTTAATAT
1 TTA-TTAATAT
28812653 TTAAATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 9 0.27
14 3 0.09
16 20 0.61
17 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTAATATAATAAA
Found at i:28812754 original size:15 final size:15
Alignment explanation
Indices: 28812734--28812790 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
28812724 ATTCAATATG
28812734 AATATTTTAATAATA
1 AATATTTTAATAATA
*
28812749 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
28812768 AATATATTAATAATA
1 AATATTTTAATAATA
*
28812783 AATGTTTT
1 AATATTTT
28812791 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:28818336 original size:37 final size:37
Alignment explanation
Indices: 28818275--28818420 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
28818265 TACGTATGAT
* *
28818275 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
28818310 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
28818347 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
28818384 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
28818421 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:28818437 original size:46 final size:46
Alignment explanation
Indices: 28818384--28818652 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
28818374 TAAGTGTAGC
* **
28818384 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
28818430 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
28818476 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
28818528 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
28818574 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
28818626 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
28818653 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:28818503 original size:52 final size:52
Alignment explanation
Indices: 28818427--28818646 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
28818417 TAGCTAAAGC
* *
28818427 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
28818480 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
28818532 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
28818578 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
28818630 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
28818647 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:28818549 original size:98 final size:98
Alignment explanation
Indices: 28818384--28818652 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
28818374 TAAGTGTAGC
* * *
28818384 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
28818449 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
28818483 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
28818548 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
28818581 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
28818646 GATCAGA
66 GATCAGA
28818653 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:28822708 original size:14 final size:14
Alignment explanation
Indices: 28822689--28822727 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
28822679 TTAATACTTG
28822689 CAACTTTAACTAAC
1 CAACTTTAACTAAC
*
28822703 CAACTTCAACTAAC
1 CAACTTTAACTAAC
*
28822717 CAACTGTAACT
1 CAACTTTAACT
28822728 GAAAATACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.31, G:0.03, T:0.26
Consensus pattern (14 bp):
CAACTTTAACTAAC
Found at i:28823715 original size:18 final size:20
Alignment explanation
Indices: 28823675--28823719 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
28823665 CTGAATTTTG
*
28823675 TATTTTTTTCATTTTCTCCC
1 TATTTTTTTCATTTTCTACC
*
28823695 TATTTTTTT-ATTTT-TATC
1 TATTTTTTTCATTTTCTACC
28823713 TATTTTT
1 TATTTTT
28823720 GAAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 9 0.39
19 5 0.22
20 9 0.39
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (20 bp):
TATTTTTTTCATTTTCTACC
Found at i:28829457 original size:20 final size:20
Alignment explanation
Indices: 28829412--28829492 Score: 53
Period size: 20 Copynumber: 4.0 Consensus size: 20
28829402 GCTAGTACAG
* *
28829412 GATTGCACTTCGGTGCCTCT
1 GATTGAACTTCGATGCCTCT
*
28829432 -ATTTGAACTTCGATGTCTCT
1 GA-TTGAACTTCGATGCCTCT
28829452 GATTGAA-TAATCG-TGCCTCT
1 GATTGAACT--TCGATGCCTCT
* *
28829472 -ATCTGTACTTCGATACCTCT
1 GAT-TGAACTTCGATGCCTCT
28829492 G
1 G
28829493 TTACGCATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 15
0.69 0.09 0.22
Matches are distributed among these distances:
19 7 0.15
20 35 0.74
21 5 0.11
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (20 bp):
GATTGAACTTCGATGCCTCT
Found at i:28835169 original size:8 final size:8
Alignment explanation
Indices: 28835147--28835184 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
28835137 AAATTAGCCA
28835147 AATTTTA-
1 AATTTTAT
*
28835154 ACTTTTAT
1 AATTTTAT
28835162 AATTTTAT
1 AATTTTAT
28835170 AATTTTTAT
1 AA-TTTTAT
28835179 AATTTT
1 AATTTT
28835185 TGAATATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
7 6 0.22
8 13 0.48
9 8 0.30
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (8 bp):
AATTTTAT
Found at i:28835178 original size:9 final size:9
Alignment explanation
Indices: 28835156--28835185 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28835146 AAATTTTAAC
28835156 TTTTATAA-
1 TTTTATAAT
28835164 TTTTATAAT
1 TTTTATAAT
28835173 TTTTATAAT
1 TTTTATAAT
28835182 TTTT
1 TTTT
28835186 GAATATGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTATAAT
Found at i:28835264 original size:19 final size:19
Alignment explanation
Indices: 28835240--28835303 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
28835230 CACATTTAAT
28835240 TTTTCTAAAATTTTAATAA
1 TTTTCTAAAATTTTAATAA
* *
28835259 TTTTCTATAATAATT-ATAA
1 TTTTCTAAAAT-TTTAATAA
*
28835278 ATTTCTAATAATTTTATTATAA
1 TTTTCTAA-AATTTTA--ATAA
28835300 TTTT
1 TTTT
28835304 TATAATTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
19 22 0.65
20 5 0.15
22 7 0.21
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTCTAAAATTTTAATAA
Found at i:28838001 original size:110 final size:110
Alignment explanation
Indices: 28837806--28838008 Score: 354
Period size: 110 Copynumber: 1.8 Consensus size: 110
28837796 TAAATTCAAT
*
28837806 AGGATATTTGACAATTTGGTTAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
1 AGGATATTTGACAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
28837871 TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTTAAA
66 TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTTAAA
* *
28837916 AGGATATTT-AGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
1 AGGATATTTGA-CAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGA
*
28837980 ATTTCCAAACGCAAAATATTGCCTTATTT
65 ATTTCCAAACGCAAAACATTGCCTTATTT
28838009 GGAAATATTT
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
109 1 0.01
110 87 0.99
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (110 bp):
AGGATATTTGACAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAA
TTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTTTTTTAAA
Found at i:28849237 original size:14 final size:14
Alignment explanation
Indices: 28849218--28849253 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
28849208 AAACAAAATG
28849218 ATAAAATATATTTT
1 ATAAAATATATTTT
*
28849232 ATAAAAAATATTTT
1 ATAAAATATATTTT
*
28849246 AAAAAATA
1 ATAAAATA
28849254 ACAATAACAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAAAATATATTTT
Found at i:28849750 original size:14 final size:14
Alignment explanation
Indices: 28849731--28849757 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28849721 ATAACGAAAT
28849731 AAATATTTAATTTG
1 AAATATTTAATTTG
28849745 AAATATTTAATTT
1 AAATATTTAATTT
28849758 TTAGGGTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (14 bp):
AAATATTTAATTTG
Found at i:28850969 original size:2 final size:2
Alignment explanation
Indices: 28850908--28850950 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
28850898 GAGTGTAAAT
28850908 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28850950 A
1 A
28850951 AATGAAGAAA
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28853125 original size:21 final size:21
Alignment explanation
Indices: 28853085--28853126 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28853075 TGTTTGATAT
*
28853085 ATTTTAAAAAAGTATTTATTA
1 ATTTTAAAAAAGAATTTATTA
28853106 ATTTTAAAAAA-AATTGTATTA
1 ATTTTAAAAAAGAATT-TATTA
28853127 GCTTTGTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
ATTTTAAAAAAGAATTTATTA
Found at i:28861959 original size:148 final size:148
Alignment explanation
Indices: 28861736--28862046 Score: 622
Period size: 148 Copynumber: 2.1 Consensus size: 148
28861726 TGAGTATAAG
28861736 TATGAAATTATATATATATGTTAAATTCGAATATGTATGAGTATATAGGTATATGTTCTTGTTTC
1 TATGAAATTATATATATATGTTAAATTCGAATATGTATGAGTATATAGGTATATGTTCTTGTTTC
28861801 GAATATAAGTATAGAGTAATATATGTTTGTTAGATTTGAATAAGTATATATGTATATGTATAAGA
66 GAATATAAGTATAGAGTAATATATGTTTGTTAGATTTGAATAAGTATATATGTATATGTATAAGA
28861866 TCTTGTATTGAAATGGTA
131 TCTTGTATTGAAATGGTA
28861884 TATGAAATTATATATATATGTTAAATTCGAATATGTATGAGTATATAGGTATATGTTCTTGTTTC
1 TATGAAATTATATATATATGTTAAATTCGAATATGTATGAGTATATAGGTATATGTTCTTGTTTC
28861949 GAATATAAGTATAGAGTAATATATGTTTGTTAGATTTGAATAAGTATATATGTATATGTATAAGA
66 GAATATAAGTATAGAGTAATATATGTTTGTTAGATTTGAATAAGTATATATGTATATGTATAAGA
28862014 TCTTGTATTGAAATGGTA
131 TCTTGTATTGAAATGGTA
28862032 TATGAAATTATATAT
1 TATGAAATTATATAT
28862047 GTATATATGG
Statistics
Matches: 163, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
148 163 1.00
ACGTcount: A:0.37, C:0.03, G:0.17, T:0.43
Consensus pattern (148 bp):
TATGAAATTATATATATATGTTAAATTCGAATATGTATGAGTATATAGGTATATGTTCTTGTTTC
GAATATAAGTATAGAGTAATATATGTTTGTTAGATTTGAATAAGTATATATGTATATGTATAAGA
TCTTGTATTGAAATGGTA
Found at i:28861971 original size:74 final size:74
Alignment explanation
Indices: 28861745--28861995 Score: 278
Period size: 74 Copynumber: 3.4 Consensus size: 74
28861735 GTATGAAATT
*
28861745 ATATATATATGTTAAATTCGAATATGTATGAGTATATAGGTATATGTTCTTGTTTCGAATATAAG
1 ATATATATATGTTAAATTCGAATAAGTATGAGTATATAGGTATATGTTCTTGTTTCGAATATAAG
28861810 TATAGAGTA
66 TATAGAGTA
* * * * * * *
28861819 ATATATGTTTGTTAGATTTGAATAAGTAT-A-TATGTATATGTATAAGATCTTGTATT-GAA-AT
1 ATATATATATGTTAAATTCGAATAAGTATGAGTA--TATAGGTATATGTTCTTGT-TTCGAATAT
* * *
28861880 -GGTATATGAAATT
63 AAGTATA-G-AGTA
*
28861893 ATATATATATGTTAAATTCGAATATGTATGAGTATATAGGTATATGTTCTTGTTTCGAATATAAG
1 ATATATATATGTTAAATTCGAATAAGTATGAGTATATAGGTATATGTTCTTGTTTCGAATATAAG
28861958 TATAGAGTA
66 TATAGAGTA
* * * *
28861967 ATATATGTTTGTTAGATTTGAATAAGTAT
1 ATATATATATGTTAAATTCGAATAAGTAT
28861996 ATATGTATAT
Statistics
Matches: 140, Mismatches: 27, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
72 7 0.05
73 6 0.04
74 114 0.81
75 6 0.04
76 7 0.05
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.43
Consensus pattern (74 bp):
ATATATATATGTTAAATTCGAATAAGTATGAGTATATAGGTATATGTTCTTGTTTCGAATATAAG
TATAGAGTA
Found at i:28862045 original size:74 final size:74
Alignment explanation
Indices: 28861819--28862048 Score: 281
Period size: 74 Copynumber: 3.1 Consensus size: 74
28861809 GTATAGAGTA
28861819 ATATATGTTTGTTAGATTTGAATAAGTATATATGTATATGTATAAGATCTTGTATTGAAATGGTA
1 ATATATGTTTGTTAGATTTGAATAAGTATATATGTATATGTATAAGATCTTGTATTGAAATGGTA
28861884 TATGAAATT
66 TATGAAATT
* * * * * * * *
28861893 ATATATATATGTTAAATTCGAATATGTATGAGTA--TATAGGTATATGTTCTTGT-TTCGAATAT
1 ATATATGTTTGTTAGATTTGAATAAGTAT-A-TATGTATATGTATAAGATCTTGTATT-GAA-AT
* * *
28861955 AAGTATA-G-AGTA
62 -GGTATATGAAATT
28861967 ATATATGTTTGTTAGATTTGAATAAGTATATATGTATATGTATAAGATCTTGTATTGAAATGGTA
1 ATATATGTTTGTTAGATTTGAATAAGTATATATGTATATGTATAAGATCTTGTATTGAAATGGTA
28862032 TATGAAATT
66 TATGAAATT
28862041 ATATATGT
1 ATATATGT
28862049 ATATATGGAA
Statistics
Matches: 124, Mismatches: 22, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
72 7 0.06
73 6 0.05
74 98 0.79
75 6 0.05
76 7 0.06
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (74 bp):
ATATATGTTTGTTAGATTTGAATAAGTATATATGTATATGTATAAGATCTTGTATTGAAATGGTA
TATGAAATT
Found at i:28862393 original size:41 final size:41
Alignment explanation
Indices: 28862331--28862439 Score: 155
Period size: 41 Copynumber: 2.6 Consensus size: 41
28862321 GACTATACGT
* * *
28862331 CTAGCAGGCTAAGTGCCGGTGATCTGAGTCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAAGCTATAAAC
* *
28862372 CTAGCAGGCTAAGTGCTGGTGATCTGAATCAAGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAAGCTATAAAC
*
28862413 CTAGCAGGCCAAGTGCCGGTGAATCTG
1 CTAGCAGGCTAAGTGCCGGTG-ATCTG
28862440 TTAAATTAAG
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
41 55 0.92
42 5 0.08
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAAGCTATAAAC
Found at i:28865045 original size:24 final size:24
Alignment explanation
Indices: 28865018--28865080 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
28865008 CAGCTCGAAA
28865018 GAGCATCCCGTTATTAGCTCTCAT
1 GAGCATCCCGTTATTAGCTCTCAT
* *
28865042 GAGCATCCCGATATTTGGCTCTCAT
1 GAGCATCCCGTTA-TTAGCTCTCAT
**
28865067 GAGTTTCCCGTTAT
1 GAGCATCCCGTTAT
28865081 ATGGTTATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
24 13 0.39
25 20 0.61
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (24 bp):
GAGCATCCCGTTATTAGCTCTCAT
Found at i:28865291 original size:24 final size:23
Alignment explanation
Indices: 28865225--28865341 Score: 90
Period size: 24 Copynumber: 4.8 Consensus size: 23
28865215 CTCTTTCATA
*
28865225 AGCTTCCCGATTAATGGCTCTCTGG
1 AGCTTCCCG-TTAATGGCTCTAT-G
* * *
28865250 AGCTTCCTGATATTGGCTCGTATG
1 AGCTTCCCGTTAATGGCTC-TATG
* **
28865274 AGCTTCCCGTTAAAGGCTCTCCGG
1 AGCTTCCCGTTAATGGCTCT-ATG
* *
28865298 AGCTTCCTGTTACATGGATCATATG
1 AGCTTCCCGTTA-ATGGCTC-TATG
28865323 AGCTTCCCGTTATATGGCT
1 AGCTTCCCGTTA-ATGGCT
28865342 TGAGAGAGAG
Statistics
Matches: 70, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
23 1 0.01
24 36 0.51
25 32 0.46
26 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (23 bp):
AGCTTCCCGTTAATGGCTCTATG
Found at i:28865300 original size:48 final size:49
Alignment explanation
Indices: 28865225--28865334 Score: 150
Period size: 49 Copynumber: 2.2 Consensus size: 49
28865215 CTCTTTCATA
* * * * *
28865225 AGCTTCCCGATTAATGGCTCTCTGGAGCTTCCTGATA-TTGGCTCGTATG
1 AGCTTCCCG-TTAAAGGCTCTCCGGAGCTTCCTGATACATGGATCATATG
*
28865274 AGCTTCCCGTTAAAGGCTCTCCGGAGCTTCCTGTTACATGGATCATATG
1 AGCTTCCCGTTAAAGGCTCTCCGGAGCTTCCTGATACATGGATCATATG
28865323 AGCTTCCCGTTA
1 AGCTTCCCGTTA
28865335 TATGGCTTGA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
48 24 0.44
49 30 0.56
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (49 bp):
AGCTTCCCGTTAAAGGCTCTCCGGAGCTTCCTGATACATGGATCATATG
Found at i:28871595 original size:24 final size:24
Alignment explanation
Indices: 28871568--28871630 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 24
28871558 CAGCTCAAAA
*
28871568 GAGCGTCCCGTTATTAGCTCTCAT
1 GAGCATCCCGTTATTAGCTCTCAT
* * *
28871592 GAGCATCCTGATATTTGGCTCTCAT
1 GAGCATCCCGTTA-TTAGCTCTCAT
* *
28871617 GAACTTCCCGTTAT
1 GAGCATCCCGTTAT
28871631 ACGGTTCTTG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
24 11 0.37
25 19 0.63
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (24 bp):
GAGCATCCCGTTATTAGCTCTCAT
Found at i:28871758 original size:25 final size:25
Alignment explanation
Indices: 28871730--28871853 Score: 60
Period size: 24 Copynumber: 4.9 Consensus size: 25
28871720 ATGAGCGTCA
28871730 TGATATATGGCTCTCTGGAGCTTCT
1 TGATATATGGCTCTCTGGAGCTTCT
* * *
28871755 TGATTAGAAGGCTCTTTCATGG-GCTTCC
1 TGA-TATATGGCTC--TC-TGGAGCTTCT
* * *
28871783 TGAT-TATTGCCTCTCCGTAGCTTCT
1 TGATATA-TGGCTCTCTGGAGCTTCT
* * *
28871808 TGATAT-TGGCTCGCTTGAACTTCT
1 TGATATATGGCTCTCTGGAGCTTCT
**
28871832 CCATAT-TGGCTCGTCT-GAGCTT
1 TGATATATGGCTC-TCTGGAGCTT
28871854 TCCGTTAAAG
Statistics
Matches: 72, Mismatches: 19, Indels: 17
0.67 0.18 0.16
Matches are distributed among these distances:
24 28 0.39
25 16 0.22
26 10 0.14
27 5 0.07
28 10 0.14
29 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.22, T:0.40
Consensus pattern (25 bp):
TGATATATGGCTCTCTGGAGCTTCT
Found at i:28876442 original size:35 final size:36
Alignment explanation
Indices: 28876382--28876458 Score: 129
Period size: 35 Copynumber: 2.1 Consensus size: 36
28876372 TTGTGAATAA
*
28876382 TACATATGTTAGTTTTATCTGTATTTGTTATTGTACG
1 TACA-ATGTTAGTTTTATCTATATTTGTTATTGTACG
28876419 TACAATG-TAGTTTTATCTATATTTGTTATTGTACG
1 TACAATGTTAGTTTTATCTATATTTGTTATTGTACG
28876454 TACAA
1 TACAA
28876459 CGTGCCTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
35 32 0.82
36 3 0.08
37 4 0.10
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (36 bp):
TACAATGTTAGTTTTATCTATATTTGTTATTGTACG
Found at i:28889936 original size:14 final size:14
Alignment explanation
Indices: 28889917--28889954 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
28889907 TATTAACATG
*
28889917 AAAGAAACTAAAAA
1 AAAGAAAATAAAAA
*
28889931 AAAGAAAATAGAAA
1 AAAGAAAATAAAAA
28889945 AAAGAAAATA
1 AAAGAAAATA
28889955 TATGTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.79, C:0.03, G:0.11, T:0.08
Consensus pattern (14 bp):
AAAGAAAATAAAAA
Found at i:28893743 original size:84 final size:86
Alignment explanation
Indices: 28893649--28893868 Score: 247
Period size: 84 Copynumber: 2.6 Consensus size: 86
28893639 AAAGTATTAT
* *
28893649 CAGTTTGTTTAATCTACAAATATGTTGTGCACTCACAAAAAGTTAG-AGTAATTG-GAATATGTG
1 CAGTTTGTTTAATCTACAAATATGTTGTGCACTCACAAAAAGTTAGCAGTAACTGAAAATATGTG
* **
28893712 GTTCAATCACAAACTGAGTTG-
66 GTTAAATCACAAACCAAG-TGA
** * * *
28893733 CAGTTTGTTTAATCTGTAAATATATTGTGCACTCACAACAAG-TGGCAGTAACTGAAAATATGTG
1 CAGTTTGTTTAATCTACAAATATGTTGTGCACTCACAAAAAGTTAGCAGTAACTGAAAATATGTG
28893797 GTTAAATCACAAACCAAGTGA
66 GTTAAATCACAAACCAAGTGA
* ** *
28893818 CAGTTTGTTT-GTCTACAAATATGTCATGCACTCA-AAAGAAG-TGGCAGTAAC
1 CAGTTTGTTTAATCTACAAATATGTTGTGCACTCACAAA-AAGTTAGCAGTAAC
28893869 CACAATCAGT
Statistics
Matches: 115, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
83 4 0.03
84 78 0.68
85 33 0.29
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (86 bp):
CAGTTTGTTTAATCTACAAATATGTTGTGCACTCACAAAAAGTTAGCAGTAACTGAAAATATGTG
GTTAAATCACAAACCAAGTGA
Found at i:28896068 original size:19 final size:20
Alignment explanation
Indices: 28896044--28896093 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
28896034 GCTTAACATT
*
28896044 AGTTAATTAAAATTAA-ATA
1 AGTTAATTAAAATTAATAAA
**
28896063 AGTTAATTGTAATTAATTAAA
1 AGTTAATTAAAATTAA-TAAA
28896084 AGTTAATTAA
1 AGTTAATTAA
28896094 CCTATAAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 14 0.58
21 10 0.42
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (20 bp):
AGTTAATTAAAATTAATAAA
Found at i:28898540 original size:24 final size:24
Alignment explanation
Indices: 28898508--28898556 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
28898498 TGGTTTGTTT
28898508 TCTCCATGGGCAAGTTAGATTTAA
1 TCTCCATGGGCAAGTTAGATTTAA
28898532 TCTCCATGGGCAAGTTAGATTTAA
1 TCTCCATGGGCAAGTTAGATTTAA
28898556 T
1 T
28898557 TTTAGATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (24 bp):
TCTCCATGGGCAAGTTAGATTTAA
Found at i:28920529 original size:31 final size:32
Alignment explanation
Indices: 28920491--28920570 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 32
28920481 AAGCTTGTTT
* *
28920491 TATTTTTAATTAATAAATAT-ATTTTTTTCAA
1 TATTTTTAATTAATAAATATCATCTTTTTAAA
* *
28920522 TTTTTTTAATT--TTAAT-TCATCTTTTTAAA
1 TATTTTTAATTAATAAATATCATCTTTTTAAA
28920551 TATTTTTAATTAATAAATAT
1 TATTTTTAATTAATAAATAT
28920571 TTTATTCATA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
28 1 0.03
29 23 0.59
31 14 0.36
32 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (32 bp):
TATTTTTAATTAATAAATATCATCTTTTTAAA
Found at i:28922456 original size:104 final size:105
Alignment explanation
Indices: 28922287--28922480 Score: 239
Period size: 104 Copynumber: 1.9 Consensus size: 105
28922277 AATAACATGC
* *
28922287 CACACGGCCGGGTCACACGCCTATGTCCTCTGCCCGTGTGGTTCCGAAGCATAAACAGTAAGTTA
1 CACACGGCCGGGTCACACGCCTATGTCCTCTGCCCGTGTGGTTCCGAACCACAAACAGTAAGTTA
**
28922352 CACGGCCTGGACACACGCCCGTGTCCTTGCCCGTGTGATT
66 CACGGCCCAGACACACGCCCGTGTCCTTGCCCGTGTGATT
* ** ** * * *
28922392 CACACGGCCTGGG-CACACGCCTGTGTCC-CTGGTCGTGTGGTTTTGTACCACAAATAGTGAGTT
1 CACACGGCC-GGGTCACACGCCTATGTCCTCTGCCCGTGTGGTTCCGAACCACAAACAGTAAGTT
* *
28922455 ACACGGCCCAGACACATGCCTGTGTC
65 ACACGGCCCAGACACACGCCCGTGTC
28922481 TGTTCCGTGT
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
104 48 0.65
105 23 0.31
106 3 0.04
ACGTcount: A:0.19, C:0.32, G:0.26, T:0.23
Consensus pattern (105 bp):
CACACGGCCGGGTCACACGCCTATGTCCTCTGCCCGTGTGGTTCCGAACCACAAACAGTAAGTTA
CACGGCCCAGACACACGCCCGTGTCCTTGCCCGTGTGATT
Found at i:28931413 original size:23 final size:23
Alignment explanation
Indices: 28931377--28931422 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28931367 TTAGGGGAGT
* *
28931377 TTGGATGAACGAATTGCCTAAGG
1 TTGGACGAACGAATCGCCTAAGG
* *
28931400 TTGGACGAATGAATCGCGTAAGG
1 TTGGACGAACGAATCGCCTAAGG
28931423 CCACACGGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.13, G:0.33, T:0.24
Consensus pattern (23 bp):
TTGGACGAACGAATCGCCTAAGG
Found at i:28931916 original size:16 final size:15
Alignment explanation
Indices: 28931895--28931924 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28931885 TGCACATAAA
28931895 AAATGTTTTATTTTTG
1 AAATGTTTT-TTTTTG
28931911 AAATGTTTTTTTTT
1 AAATGTTTTTTTTT
28931925 ATTTACCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (15 bp):
AAATGTTTTTTTTTG
Found at i:28932253 original size:113 final size:113
Alignment explanation
Indices: 28932055--28932278 Score: 403
Period size: 113 Copynumber: 2.0 Consensus size: 113
28932045 ATTTCCTTGT
* *
28932055 TTGTGAAAGTTGAAACTAACTTTAACATTTTGGATCTTTCGAATGTTATGTTTTAAAAAACAATA
1 TTGTGAAAGTTGAAACTAACTTCAACATTTTGGATCTTTCGAATGTCATGTTTTAAAAAACAATA
28932120 CAAAAGTTTTAGTTAAACTTGAACTCAATGCATTTTATGTGCATAACC
66 CAAAAGTTTTAGTTAAACTTGAACTCAATGCATTTTATGTGCATAACC
* *
28932168 TTGTGAAAGTTGAAACTAACTTCAACATTTTGGATCTTTTGAATGTCATGTTTTAAAAGACAATA
1 TTGTGAAAGTTGAAACTAACTTCAACATTTTGGATCTTTCGAATGTCATGTTTTAAAAAACAATA
*
28932233 CAAAAGTTTTAGTTAAACTTGAACTCACTGCATTTTATGTGCATAA
66 CAAAAGTTTTAGTTAAACTTGAACTCAATGCATTTTATGTGCATAA
28932279 ACTTTCAACC
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 106 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (113 bp):
TTGTGAAAGTTGAAACTAACTTCAACATTTTGGATCTTTCGAATGTCATGTTTTAAAAAACAATA
CAAAAGTTTTAGTTAAACTTGAACTCAATGCATTTTATGTGCATAACC
Found at i:28936257 original size:57 final size:57
Alignment explanation
Indices: 28936118--28936259 Score: 198
Period size: 57 Copynumber: 2.5 Consensus size: 57
28936108 TTTTTAATTC
*
28936118 ATAT-TTTAATAATAATTATATTAAGAATATTATTAAATTATATATTATTTTATTAAA
1 ATATATTTAATAATAATTATATTAA-AATATGATTAAATTATATATTATTTTATTAAA
* * * * *
28936175 TTGTATTTAACAATAATTATGTTAAAATATGATTAAATTATTTATTATTTTATTAAA
1 ATATATTTAATAATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAA
28936232 ATATATTTAATAATAATCT-TATTAAAAT
1 ATATATTTAATAATAAT-TATATTAAAAT
28936260 TTAATAACAA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
57 54 0.74
58 19 0.26
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (57 bp):
ATATATTTAATAATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAA
Found at i:28937610 original size:11 final size:11
Alignment explanation
Indices: 28937594--28937625 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
28937584 CTCTAATATT
28937594 CTCACAAATTC
1 CTCACAAATTC
28937605 CTCACAAATTC
1 CTCACAAATTC
*
28937616 CTCTCAAATT
1 CTCACAAATT
28937626 TCTATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (11 bp):
CTCACAAATTC
Found at i:28939475 original size:18 final size:18
Alignment explanation
Indices: 28939452--28939494 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
28939442 TGCCAGGTGC
* *
28939452 GTATCCTAGCCCTTCTAT
1 GTATCCTAACCCTTATAT
28939470 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
28939488 GTTTCCT
1 GTATCCT
28939495 TTTTCTAGTC
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:0.19, C:0.30, G:0.09, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:28939750 original size:14 final size:14
Alignment explanation
Indices: 28939731--28939758 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28939721 TTATTTTTAA
28939731 TATTTTGAATATTT
1 TATTTTGAATATTT
28939745 TATTTTGAATATTT
1 TATTTTGAATATTT
28939759 GATATTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (14 bp):
TATTTTGAATATTT
Found at i:28939758 original size:9 final size:9
Alignment explanation
Indices: 28939697--28939745 Score: 64
Period size: 9 Copynumber: 5.3 Consensus size: 9
28939687 CTCCACATTA
28939697 TTTGAATAT
1 TTTGAATAT
28939706 TTTG-ATAT
1 TTTGAATAT
28939714 TTTGATATTAT
1 TTTGA-A-TAT
*
28939725 TTTTAATAT
1 TTTGAATAT
28939734 TTTGAATAT
1 TTTGAATAT
28939743 TTT
1 TTT
28939746 ATTTTGAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 8 0.23
9 18 0.51
10 2 0.06
11 7 0.20
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (9 bp):
TTTGAATAT
Found at i:28939820 original size:49 final size:49
Alignment explanation
Indices: 28939738--28940035 Score: 517
Period size: 49 Copynumber: 6.1 Consensus size: 49
28939728 TAATATTTTG
*
28939738 AATATTTTATTTTGAAT-ATTTGATATTATTTGATGTAATAAAATACAA
1 AATAGTTTATTTTGAATAATTTGATATTATTTGATGTAATAAAATACAA
*
28939786 AATAGTTTATTTTGAATATTTTGATATTATTTGATGTAATAAAATACAA
1 AATAGTTTATTTTGAATAATTTGATATTATTTGATGTAATAAAATACAA
28939835 AATAGTTTATTTTGAATAATTTGATATTATTTGATGTAATAAAATACAA
1 AATAGTTTATTTTGAATAATTTGATATTATTTGATGTAATAAAATACAA
28939884 AATAGTTTATTTTGAATAATTTGATATTATTTGATGTAATAAAATACAA
1 AATAGTTTATTTTGAATAATTTGATATTATTTGATGTAATAAAATACAA
* *
28939933 AATAGTTTATTTTGAATAATTTGATATTATTTCATTTAATAAAATACAA
1 AATAGTTTATTTTGAATAATTTGATATTATTTGATGTAATAAAATACAA
* * * *
28939982 AATAGTTTATTTTGAATATTTTGATATTATTTCATTTAACAAAATACAA
1 AATAGTTTATTTTGAATAATTTGATATTATTTGATGTAATAAAATACAA
28940031 AATAG
1 AATAG
28940036 CTAATATTCT
Statistics
Matches: 242, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
48 16 0.07
49 226 0.93
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (49 bp):
AATAGTTTATTTTGAATAATTTGATATTATTTGATGTAATAAAATACAA
Found at i:28943468 original size:124 final size:124
Alignment explanation
Indices: 28943243--28943528 Score: 430
Period size: 124 Copynumber: 2.3 Consensus size: 124
28943233 CCCAAACATG
* *
28943243 CTACTGTAGCAAAAGCGCGTTCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTAC
* * **
28943308 TTGAAGCGTTTTTATACAATATTCTCAGAAATGTCAACTTGAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTATACAATATTCTCACAAACGTCAACTCAAAATTATTTTTTCAGGAC
* * * *
28943367 CTATTGTAGCAAAAGTGCGTCCACGTGGGAGCGATTTTAGAAATTCTTCTGATAAAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTAC
* *
28943432 TTGAAGCGTTTTTATACTAT-TTGCTCACAAACGTCAACTCAAAATTATTTTTTTAGGAC
66 TTGAAGCGTTTTTATACAATATT-CTCACAAACGTCAACTCAAAATTATTTTTTCAGGAC
* *
28943491 CTACTGTAGGAAAAGCGCGTCCACGTGGGATCGATTTC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
28943529 CTTAATAAAT
Statistics
Matches: 144, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
123 2 0.01
124 142 0.99
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTAC
TTGAAGCGTTTTTATACAATATTCTCACAAACGTCAACTCAAAATTATTTTTTCAGGAC
Found at i:28943743 original size:12 final size:12
Alignment explanation
Indices: 28943715--28943753 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
28943705 AAATCCTAAA
*
28943715 AACCTTAAACTCT
1 AACCTT-AACCCT
28943728 AACCTTAACCCT
1 AACCTTAACCCT
*
28943740 AACCCTAACCCT
1 AACCTTAACCCT
28943752 AA
1 AA
28943754 AAACCCTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 18 0.75
13 6 0.25
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (12 bp):
AACCTTAACCCT
Found at i:28944594 original size:19 final size:20
Alignment explanation
Indices: 28944553--28944603 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
28944543 ATGTTGGATG
28944553 AAAATTTTATATAATAAATTT
1 AAAATTTTATATAAT-AATTT
28944574 AAAATTTTAGTATAAT-A-TT
1 AAAATTTTA-TATAATAATTT
*
28944593 AAAATATTATA
1 AAAATTTTATA
28944604 AATTTTAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.07
19 10 0.36
20 1 0.04
21 9 0.32
22 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AAAATTTTATATAATAATTT
Found at i:28946122 original size:21 final size:19
Alignment explanation
Indices: 28946084--28946122 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
28946074 AATCTATATT
*
28946084 TCTCTTTATTTTATAATAA
1 TCTCTTTATTTAATAATAA
28946103 TCTCATTTATATTAATAATA
1 TCTC-TTTAT-TTAATAATA
28946123 TTGAATGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 5 0.29
21 8 0.47
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (19 bp):
TCTCTTTATTTAATAATAA
Found at i:28947457 original size:3 final size:3
Alignment explanation
Indices: 28947445--28947476 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
28947435 TTTATTTTTT
*
28947445 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28947477 TCTTTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:28950223 original size:23 final size:23
Alignment explanation
Indices: 28950197--28950242 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
28950187 TATAACATAC
*
28950197 ATATATATAAATAAGTTATAAAT
1 ATATATATAAATAAATTATAAAT
**
28950220 ATATATATATGTAAATTATAAAT
1 ATATATATAAATAAATTATAAAT
28950243 GAAAAATATA
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:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (23 bp):
ATATATATAAATAAATTATAAAT
Found at i:28950612 original size:3 final size:3
Alignment explanation
Indices: 28950567--28950593 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
28950557 AACTAATACG
28950567 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
28950594 CAAGATTAAT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28951862 original size:16 final size:17
Alignment explanation
Indices: 28951843--28951881 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
28951833 GCCTTTTGGG
*
28951843 TTGTTT-TTTTTTTTGT
1 TTGTTTGTTTTTTATGT
28951859 TTGTTTGTTTTTTAT-T
1 TTGTTTGTTTTTTATGT
28951875 TTGTTTG
1 TTGTTTG
28951882 GGTTCATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (17 bp):
TTGTTTGTTTTTTATGT
Found at i:28951868 original size:20 final size:20
Alignment explanation
Indices: 28951843--28951881 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28951833 GCCTTTTGGG
*
28951843 TTGTTTTTTTTTTTGTTTGT
1 TTGTTTTTTATTTTGTTTGT
28951863 TTGTTTTTTATTTTGTTTG
1 TTGTTTTTTATTTTGTTTG
28951882 GGTTCATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (20 bp):
TTGTTTTTTATTTTGTTTGT
Found at i:28952220 original size:37 final size:38
Alignment explanation
Indices: 28952169--28952245 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 38
28952159 CACAATGGAG
28952169 AAAAAATATTTTTTTAATAGGTGGTCGATGTGTCAAGT
1 AAAAAATATTTTTTTAATAGGTGGTCGATGTGTCAAGT
*
28952207 AAAAAATA-TTTTTTAATAGGTGGTCGGTGTGTCAAGT
1 AAAAAATATTTTTTTAATAGGTGGTCGATGTGTCAAGT
28952244 AA
1 AA
28952246 CATTGGTGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 30 0.79
38 8 0.21
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (38 bp):
AAAAAATATTTTTTTAATAGGTGGTCGATGTGTCAAGT
Found at i:28954021 original size:20 final size:20
Alignment explanation
Indices: 28953972--28954012 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
28953962 TCTAGCCTAA
*
28953972 ACATCAACCAAACCACTCCC
1 ACATCAAACAAACCACTCCC
28953992 ACATCAAACAAACCACTCCC
1 ACATCAAACAAACCACTCCC
28954012 A
1 A
28954013 TATTAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.46, G:0.00, T:0.10
Consensus pattern (20 bp):
ACATCAAACAAACCACTCCC
Found at i:28957679 original size:21 final size:23
Alignment explanation
Indices: 28957655--28957707 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 23
28957645 ATAAAAAAAC
28957655 AAAATAATACAT-TATG-AAA-TT
1 AAAATAATA-ATATATGAAAACTT
28957676 AAAAT-ATAATATATGAAAAACTT
1 AAAATAATAATATATG-AAAACTT
28957699 AAAATAATA
1 AAAATAATA
28957708 TTACATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 2 0.07
20 7 0.26
21 5 0.19
22 3 0.11
23 7 0.26
24 3 0.11
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (23 bp):
AAAATAATAATATATGAAAACTT
Found at i:28958838 original size:19 final size:18
Alignment explanation
Indices: 28958797--28958838 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
28958787 TGGACTTTTA
28958797 TTTTTTTATTTTTATTTGG
1 TTTTTTTATTTTTATTT-G
*
28958816 TTTTTTGATTTTT-TTGTG
1 TTTTTTTATTTTTATT-TG
28958834 TTTTT
1 TTTTT
28958839 GGGCCCGCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.07, C:0.00, G:0.12, T:0.81
Consensus pattern (18 bp):
TTTTTTTATTTTTATTTG
Found at i:28959939 original size:20 final size:20
Alignment explanation
Indices: 28959914--28959968 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
28959904 TGTGGTTCAA
*
28959914 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
28959934 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
28959954 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
28959969 TTTAACTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:28961079 original size:15 final size:15
Alignment explanation
Indices: 28961045--28961082 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
28961035 TCAGTATTGG
28961045 AAAAAAAAGAGAAAT
1 AAAAAAAAGAGAAAT
*
28961060 TAAAAAAAGAAGAAA-
1 AAAAAAAAG-AGAAAT
28961075 AAAAAAAA
1 AAAAAAAA
28961083 TGTTTCAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (15 bp):
AAAAAAAAGAGAAAT
Found at i:28962016 original size:17 final size:15
Alignment explanation
Indices: 28961996--28962034 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
28961986 GCGAGCGAGA
28961996 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
28962013 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
28962028 AAGATGA
1 AA-ATGA
28962035 GTGTGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:28972955 original size:42 final size:42
Alignment explanation
Indices: 28972893--28972983 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
28972883 TTATTTTGTC
*
28972893 CACACGGGCAGAGACACGGGCATGTGTCTCAGCCATGTGTGA
1 CACACGGGCAGAGACACGGGCATGTATCTCAGCCATGTGTGA
* * *
28972935 CATACGGGCAGAGACACGGGCGTGTATCTCAGCCGTGTGTGA
1 CACACGGGCAGAGACACGGGCATGTATCTCAGCCATGTGTGA
28972977 CACACGG
1 CACACGG
28972984 CCATGTGCAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.23, C:0.26, G:0.34, T:0.16
Consensus pattern (42 bp):
CACACGGGCAGAGACACGGGCATGTATCTCAGCCATGTGTGA
Found at i:28972995 original size:42 final size:42
Alignment explanation
Indices: 28972893--28973001 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 42
28972883 TTATTTTGTC
* * *
28972893 CACACGGGCAGAGACACGGGCATGTGTCTCAGCCATGTGTGA
1 CACACGGCCAGAGACACGGGCGTGTATCTCAGCCATGTGTGA
* * *
28972935 CATACGGGCAGAGACACGGGCGTGTATCTCAGCCGTGTGTGA
1 CACACGGCCAGAGACACGGGCGTGTATCTCAGCCATGTGTGA
*
28972977 CACACGGCCATGTG-CACGGGCGTGT
1 CACACGGCCA-GAGACACGGGCGTGT
28973002 GGTTTGGCCG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 57 0.97
43 2 0.03
ACGTcount: A:0.21, C:0.27, G:0.35, T:0.17
Consensus pattern (42 bp):
CACACGGCCAGAGACACGGGCGTGTATCTCAGCCATGTGTGA
Found at i:28975908 original size:20 final size:20
Alignment explanation
Indices: 28975883--28975926 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
28975873 TCTAGCCTAA
* *
28975883 ACATCAACCAAATCACTCCC
1 ACATCAAACAAACCACTCCC
*
28975903 ACATCAAACAAACCACTCTC
1 ACATCAAACAAACCACTCCC
28975923 ACAT
1 ACAT
28975927 TAAATATTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.41, G:0.00, T:0.16
Consensus pattern (20 bp):
ACATCAAACAAACCACTCCC
Found at i:28998221 original size:24 final size:22
Alignment explanation
Indices: 28998180--28998244 Score: 77
Period size: 21 Copynumber: 3.1 Consensus size: 22
28998170 ATTCTTCAAG
28998180 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
*
28998199 GATATGCAATCTTAG-ATATGAT
1 GATATGCAATCTTAGAAGAT-AT
28998221 -ATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
28998242 GAT
1 GAT
28998245 TTTGTAATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
19 13 0.33
21 19 0.49
22 7 0.18
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.35
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:28998226 original size:21 final size:19
Alignment explanation
Indices: 28998180--28998235 Score: 94
Period size: 19 Copynumber: 2.8 Consensus size: 19
28998170 ATTCTTCAAG
28998180 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28998199 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28998218 GATATATGCAATCTTAGA
1 G--ATATGCAATCTTAGA
28998236 AGATATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 20 0.57
21 15 0.43
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:28998300 original size:16 final size:16
Alignment explanation
Indices: 28998279--28998343 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
28998269 TTCGCTGTAT
28998279 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
28998295 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
28998311 TGGAATAGAGACGTAA
1 TGGAATAGAGGCGTAA
28998327 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
28998343 T
1 T
28998344 AGCAAATCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.38, C:0.06, G:0.35, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:29001992 original size:36 final size:36
Alignment explanation
Indices: 29001917--29001992 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
29001907 TATACATACG
*
29001917 TTTTATAATATATACATATACGTACACATTTTTTAAT
1 TTTTATAATATATACATATACG-ACACATTTTATAAT
* *
29001954 TTTTATAA-ATATATATATAC-ACATACTTTTATATAT
1 TTTTATAATATATACATATACGACACA-TTTTATA-AT
29001990 TTT
1 TTT
29001993 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 4 0.12
35 6 0.18
36 16 0.47
37 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.51
Consensus pattern (36 bp):
TTTTATAATATATACATATACGACACATTTTATAAT
Found at i:29002114 original size:23 final size:22
Alignment explanation
Indices: 29002085--29002127 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
29002075 TAATTCACAC
*
29002085 ACATATATATTTTTCTTATATGT
1 ACATATATATGTTT-TTATATGT
29002108 ACATATATATGTTTTTATAT
1 ACATATATATGTTTTTATAT
29002128 TTTATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (22 bp):
ACATATATATGTTTTTATATGT
Found at i:29007072 original size:12 final size:12
Alignment explanation
Indices: 29007038--29007066 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
29007028 TTGGGCCTCG
29007038 AGGGATCATATA
1 AGGGATCATATA
29007050 AGGGATCATATA
1 AGGGATCATATA
29007062 AGGGA
1 AGGGA
29007067 CAATATGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.31, T:0.21
Consensus pattern (12 bp):
AGGGATCATATA
Found at i:29018314 original size:30 final size:29
Alignment explanation
Indices: 29018280--29018393 Score: 103
Period size: 29 Copynumber: 3.9 Consensus size: 29
29018270 CATTCTTTCG
*
29018280 ATAGAGACTGCAACAATGGCTTCCTTTTTA
1 ATAGAGA-TGCAACAAAGGCTTCCTTTTTA
29018310 ATAGAGAT-CACCACAAAGGCTTCC-TTTTA
1 ATAGAGATGCA--ACAAAGGCTTCCTTTTTA
* *
29018339 ATAAAGATAGCCACAAAGGCTTCC--TTTA
1 ATAGAGAT-GCAACAAAGGCTTCCTTTTTA
*
29018367 ACAGAGATAGGC-ACAAAGGCTTCCTTT
1 ATAGAGAT--GCAACAAAGGCTTCCTTT
29018394 AACAGAGATA
Statistics
Matches: 71, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
28 24 0.34
29 27 0.38
30 19 0.27
31 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (29 bp):
ATAGAGATGCAACAAAGGCTTCCTTTTTA
Found at i:29018375 original size:28 final size:28
Alignment explanation
Indices: 29018292--29018440 Score: 165
Period size: 28 Copynumber: 5.2 Consensus size: 28
29018282 AGAGACTGCA
*
29018292 ACAATGGCTTCCTTTTTAATAGAGATCA-CC
1 ACAAAGGCTTCC--TTTAATAGAGAT-AGCC
*
29018322 ACAAAGGCTTCCTTTTAATAAAGATAGCC
1 ACAAAGGCTTCC-TTTAATAGAGATAGCC
* *
29018351 ACAAAGGCTTCCTTTAACAGAGATAGGC
1 ACAAAGGCTTCCTTTAATAGAGATAGCC
* **
29018379 ACAAAGGCTTCCTTTAACAGAGATATTC
1 ACAAAGGCTTCCTTTAATAGAGATAGCC
* * *
29018407 ATAAAGGCTTCCTTTAATAAATATAGCC
1 ACAAAGGCTTCCTTTAATAGAGATAGCC
29018435 ACAAAG
1 ACAAAG
29018441 ACTTACCTAT
Statistics
Matches: 104, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
28 67 0.64
29 26 0.25
30 11 0.11
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.28
Consensus pattern (28 bp):
ACAAAGGCTTCCTTTAATAGAGATAGCC
Found at i:29020952 original size:22 final size:22
Alignment explanation
Indices: 29020895--29020952 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
29020885 TGCATTGCGA
*
29020895 ATGAACCACCAGTAATTTGTAG
1 ATGAACCACCAGTAAGTTGTAG
* ** * *
29020917 ATAAACTGCTAGTAAGTTGTGG
1 ATGAACCACCAGTAAGTTGTAG
29020939 ATGAACCACCAGTA
1 ATGAACCACCAGTA
29020953 TTTGTATATT
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (22 bp):
ATGAACCACCAGTAAGTTGTAG
Done.