Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold166
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: 2719372
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 17868 characters in sequence are not A, C, G, or T
File 11 of 18
Found at i:1908776 original size:208 final size:204
Alignment explanation
Indices: 1908385--1908838 Score: 622
Period size: 208 Copynumber: 2.2 Consensus size: 204
1908375 GATAAAGGGA
* * * * * *
1908385 CCAATACGCTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATAAAGGAGCTAA
1 CCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATAAGAAAAAGGATAAAAGAGCTAA
* * * *
1908450 TATGTGGCTAGCGATATTAGGCTCGAAGATCTGAAGAATGACAATGTGCTGATTCATGGCCAATG
66 TATGCGGCTAGCGATATTAGGCTCGAAGATCTAAAGAATAACAATGTGCTGATTCATGGCCAACG
* * * **
1908515 ACATTAGACTTGAAGAAGAATGCCAATGTTCTGAGACAAGGCCAATGACATTGGACTTGAAGAAG
131 ACATTAGACTTAAAGAAGAATGCCAATGTGCTAAGACAAGGCCAACAACATTGGAC--GAAG--G
1908580 AATGTTAAAGATG
192 AATGTTAAAGATG
* * *
1908593 CCAATATGCTAATTCAAGGCCGATGATATCGGACTTAAAGATAAGAAAAAGGATAAAAGAGCTAA
1 CCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATAAGAAAAAGGATAAAAGAGCTAA
* * *
1908658 TATGCGGCTAGCGATATTGGGCTCGAAGATGC-AAAGAATAACAATGTGCTGATTCATGGCTAGC
66 TATGCGGCTAGCGATATTAGGCTCGAAGAT-CTAAAGAATAACAATGTGCTGATTCATGGCCAAC
* *
1908722 GACATTAGACTTAAAGAAGAATGCCAATGTGCTAAGACAAGGCCAACAACATTGGGCGTAGGAAT
130 GACATTAGACTTAAAGAAGAATGCCAATGTGCTAAGACAAGGCCAACAACATTGGACGAAGGAAT
1908787 GTTAAAGATG
195 GTTAAAGATG
* * *
1908797 CCAATATACTGATTCAAGGCCAACGATATCGAATTTAAAGAT
1 CCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGAT
1908839 GAAGGTGCCA
Statistics
Matches: 216, Mismatches: 29, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
204 50 0.23
206 3 0.01
208 162 0.75
209 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (204 bp):
CCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATAAGAAAAAGGATAAAAGAGCTAA
TATGCGGCTAGCGATATTAGGCTCGAAGATCTAAAGAATAACAATGTGCTGATTCATGGCCAACG
ACATTAGACTTAAAGAAGAATGCCAATGTGCTAAGACAAGGCCAACAACATTGGACGAAGGAATG
TTAAAGATG
Found at i:1909001 original size:52 final size:49
Alignment explanation
Indices: 1908884--1909478 Score: 226
Period size: 49 Copynumber: 12.8 Consensus size: 49
1908874 TGGGGTTGTG
* * *
1908884 CCAATGTGCTGATTCAAGGCCAGCGACATGGGTCTTAGAGATGAAGATG
1 CCAATGTGCTGATTCAAGGCCAGCGACATGGGACTTAAAGATGAAGATA
* * * * *
1908933 CCAACGTGCTAATTCAAGG-CTGACGACATTGGACTTAAAGATGGTTAAGGTA
1 CCAATGTGCTGATTCAAGGCCAG-CGACATGGGACTTAAAGAT-G--AAGATA
** * ** * *
1908985 CCAATGTGCTGATTCAAGGCCAATGACATCGGTTTTAAAGATGAAGGTG
1 CCAATGTGCTGATTCAAGGCCAGCGACATGGGACTTAAAGATGAAGATA
* * * * *
1909034 CCAATATGTTGATTCGAGGCCAGCAATATTGGG-C-T-----T---G-TA
1 CCAATGTGCTGATTCAAGGCCAGCGACA-TGGGACTTAAAGATGAAGATA
* * * *
1909073 CCAATGTGCTGATTCAAGGCCAGCGACAT-TGATCTTAAAGA-CAAGGTG
1 CCAATGTGCTGATTCAAGGCCAGCGACATGGGA-CTTAAAGATGAAGATA
* * *
1909121 CCAATATGCTGATTCAAGGCCAGCAATATTGGG-CTT---G-T---G---
1 CCAATGTGCTGATTCAAGGCCAGCGACA-TGGGACTTAAAGATGAAGATA
* * * * * * *
1909160 CCAATGTACTGATTCAAGGCCAGCAACATTGGTCTTAAAGA-CAAGGTG
1 CCAATGTGCTGATTCAAGGCCAGCGACATGGGACTTAAAGATGAAGATA
* * * * * * *
1909208 CCAATATGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGA-CAAGGTG
1 CCAATGTGCTGATTCAAGGCCAGCGACATGGGACTTAAAGATGAAGATA
* * * * *
1909256 CCAATATGCTGATTTAAGGCCAGCGATATTGGACTT-AA-A-G--G-TG
1 CCAATGTGCTGATTCAAGGCCAGCGACATGGGACTTAAAGATGAAGATA
* * * * *
1909299 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTG
1 CCAATGTGCTGATTCAAGGCCAGCGACATGGGACTTAAAGATGAAGATA
* * ** *
1909348 CCAATATGCTGATTCAAGGCCAGCGATATTAGACTT-AA-A-G--G-TG
1 CCAATGTGCTGATTCAAGGCCAGCGACATGGGACTTAAAGATGAAGATA
* ** * * * * * * *
1909391 CC-ATATGCAAATTCAAGGCTAGCGACATTGGTCTTAAAGGTAAAGGTG
1 CCAATGTGCTGATTCAAGGCCAGCGACATGGGACTTAAAGATGAAGATA
* * *
1909439 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 CCAATGTGCTGATTCAAGGCCAGCGACATGGGACTTAAAG
1909479 GTGCCACAGA
Statistics
Matches: 429, Mismatches: 72, Indels: 90
0.73 0.12 0.15
Matches are distributed among these distances:
37 1 0.00
38 4 0.01
39 53 0.12
40 2 0.00
42 29 0.07
43 41 0.10
44 4 0.01
45 3 0.01
46 1 0.00
47 5 0.01
48 117 0.27
49 126 0.29
50 5 0.01
51 1 0.00
52 36 0.08
53 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (49 bp):
CCAATGTGCTGATTCAAGGCCAGCGACATGGGACTTAAAGATGAAGATA
Found at i:1909093 original size:39 final size:39
Alignment explanation
Indices: 1909031--1909322 Score: 143
Period size: 48 Copynumber: 6.7 Consensus size: 39
1909021 AAAGATGAAG
* *
1909031 GTGCCAATATGTTGATTCGAGGCCAGCAATATTGGGCTT
1 GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTT
* * * * **
1909070 GTACCAATGTGCTGATTCAAGGCCAGCGACATTGATCTTAAAGACAAG
1 GTGCCAATATGCTGATTCAAGGCCAGC-A-A-T-A--TT--GGGC-TT
1909118 GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTT
1 GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTT
* * * *
1909157 GTGCCAATGTACTGATTCAAGGCCAGCAACATTGGTCTT
1 GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTT
* *
1909196 AAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCAACATTGGTCTT
1 ---------GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTT
* * *
1909244 AAAGACAAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTT
1 ---------GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTT
*
1909292 AAAGGTGCCAATGTGCTGATTCAAGGCCAGC
1 ----GTGCCAATATGCTGATTCAAGGCCAGC
1909323 GACATTGGTC
Statistics
Matches: 208, Mismatches: 27, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
39 58 0.28
40 3 0.01
41 1 0.00
42 3 0.01
43 29 0.14
44 1 0.00
45 3 0.01
46 1 0.00
47 3 0.01
48 106 0.51
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (39 bp):
GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTT
Found at i:1909144 original size:48 final size:48
Alignment explanation
Indices: 1909073--1909478 Score: 392
Period size: 48 Copynumber: 8.8 Consensus size: 48
1909063 TGGGCTTGTA
*
1909073 CCAATGTGCTGATTCAAGGCCAGCGACATTGATCTTAAAGACAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGATCTTAAAGACAAGGTG
* * **
1909121 CCAATATGCTGATTCAAGGCCAGC-A-A-T-A--TT--GGGC-TTGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGATCTTAAAGACAAGGTG
* * * *
1909160 CCAATGTACTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGATCTTAAAGACAAGGTG
* *
1909208 CCAATATGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGATCTTAAAGACAAGGTG
* *
1909256 CCAATATGCTGATTTAAGGCCAGCGATATTGGA-CTT----A-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATT-GATCTTAAAGACAAGGTG
* * *
1909299 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGATCTTAAAGA-CAAGGTG
*
1909348 CCAATATGCTGATTCAAGGCCAGCGATATTAGA-CTT----A-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATT-GATCTTAAAGACAAGGTG
** * *
1909391 CC-ATATGCAAATTCAAGGCTAGCGACATTGGTCTTAAAGGTA-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGATCTTAAA-G-ACAAGGTG
*
1909439 CCAATATGCTGATTCAAGGCCAGCGATATTGGA-CTTAAAG
1 CCAATATGCTGATTCAAGGCCAGCGACATT-GATCTTAAAG
1909479 GTGCCACAGA
Statistics
Matches: 296, Mismatches: 35, Indels: 54
0.77 0.09 0.14
Matches are distributed among these distances:
39 25 0.08
40 3 0.01
41 2 0.01
42 30 0.10
43 44 0.15
44 2 0.01
45 4 0.01
46 1 0.00
47 4 0.01
48 112 0.38
49 67 0.23
50 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (48 bp):
CCAATATGCTGATTCAAGGCCAGCGACATTGATCTTAAAGACAAGGTG
Found at i:1909153 original size:87 final size:87
Alignment explanation
Indices: 1908982--1909239 Score: 399
Period size: 87 Copynumber: 3.0 Consensus size: 87
1908972 GATGGTTAAG
** * * * *
1908982 GTACCAATGTGCTGATTCAAGGCCAATGACATCGGTTTTAAAGATGAAGGTGCCAATATGTTGAT
1 GTACCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGAT
*
1909047 TCGAGGCCAGCAATATTGGGCTT
65 TCAAGGCCAGCAATATTGGGCTT
*
1909070 GTACCAATGTGCTGATTCAAGGCCAGCGACATTGATCTTAAAGACAAGGTGCCAATATGCTGATT
1 GTACCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
1909135 CAAGGCCAGCAATATTGGGCTT
66 CAAGGCCAGCAATATTGGGCTT
* * *
1909157 GTGCCAATGTACTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
1 GTACCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
*
1909222 CAAGGCCAGCAACATTGG
66 CAAGGCCAGCAATATTGG
1909240 TCTTAAAGAC
Statistics
Matches: 157, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
87 118 0.75
88 39 0.25
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (87 bp):
GTACCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
CAAGGCCAGCAATATTGGGCTT
Found at i:1909237 original size:135 final size:137
Alignment explanation
Indices: 1909073--1909371 Score: 476
Period size: 135 Copynumber: 2.2 Consensus size: 137
1909063 TGGGCTTGTA
* *
1909073 CCAATGTGCTGATTCAAGGCCAGCGACATTGATCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATATGCTGATTCAAGGCCAGCAACATTGATCTTAAAGACAAGGTGCCAATATGCTGATTCAA
*
1909138 GGCCAGCAATATTGGGCTT-GTGCCAATGTACTGATTCAAGGCCAGCAACATTGGTCTTAAAGA-
66 GGCCAGCAATATTGGACTTAGTGCCAATGTACTGATTCAAGGCCAGCAACATTGGTCTTAAAGAT
*
1909201 CAAGGTG
131 AAAGGTG
* *
1909208 CCAATATGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTTAA
1 CCAATATGCTGATTCAAGGCCAGCAACATTGATCTTAAAGACAAGGTGCCAATATGCTGATTCAA
* * *
1909273 GGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAA
66 GGCCAGCAATATTGGACTT--A-GTGCCAATGTACTGATTCAAGGCCAGCAACATTGGTCTTAAA
1909338 GATAAAGGTG
128 GATAAAGGTG
1909348 CCAATATGCTGATTCAAGGCCAGC
1 CCAATATGCTGATTCAAGGCCAGC
1909372 GATATTAGAC
Statistics
Matches: 150, Mismatches: 9, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
135 78 0.52
139 42 0.28
140 30 0.20
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (137 bp):
CCAATATGCTGATTCAAGGCCAGCAACATTGATCTTAAAGACAAGGTGCCAATATGCTGATTCAA
GGCCAGCAATATTGGACTTAGTGCCAATGTACTGATTCAAGGCCAGCAACATTGGTCTTAAAGAT
AAAGGTG
Found at i:1909329 original size:91 final size:90
Alignment explanation
Indices: 1909157--1909484 Score: 451
Period size: 91 Copynumber: 3.5 Consensus size: 90
1909147 TATTGGGCTT
* * * * *
1909157 GTGCCAATGTACTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-AAGGTGCCAATATGCTGATT
*
1909222 CAAGGCCAGCAACATTGGTCTTAAAGACAAG
61 CAAGGCCAGCGACATTGGTCTTAAAGA-AAG
* *
1909253 GTGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGG
1909318 CCAGCGACATTGGTCTTAAAGATAAAG
66 CCAGCGACATTGGTCTTAAAG--AAAG
* **
1909345 GTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAGGTGCC-ATATGCAAATTCAAGG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGG
*
1909409 CTAGCGACATTGGTCTTAAAGGTAAAG
66 CCAGCGACATTGGTCTTAAA-G-AAAG
1909436 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCA
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCA
1909485 CAGAGTTGTG
Statistics
Matches: 213, Mismatches: 15, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
91 128 0.60
92 51 0.24
93 1 0.00
96 33 0.15
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (90 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGG
CCAGCGACATTGGTCTTAAAGAAAG
Found at i:1909435 original size:140 final size:136
Alignment explanation
Indices: 1909073--1909478 Score: 423
Period size: 135 Copynumber: 2.9 Consensus size: 136
1909063 TGGGCTTGTA
* * **
1909073 CCAATGTGCTGATTCAAGGCCAGCGACATT-GATCTTAAAGACAAGGTGCCAATATGCTGATTCA
1 CCAATATGCTGATTCAAGGCCAGCAACATTAGA-CTT--A-ACAAGGTGCCAATATGCAAATTCA
* * * * *
1909137 AGGCCAGCAATATTGGGCTT----GTGCCAATGTACTGATTCAAGGCCAGCAACATTGGTCTTAA
62 AGGCCAGCGACATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAA
*
1909198 AGACAAGGTG
127 AGAAAAGGTG
* * ** *
1909208 CCAATATGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTTAA
1 CCAATATGCTGATTCAAGGCCAGCAACATTAGACTT--A-ACAAGGTGCCAATATGCAAATTCAA
*
1909273 GGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAA
63 GGCCAGCGACATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAA
1909338 GATAAAGGTG
128 GA-AAAGGTG
* *
1909348 CCAATATGCTGATTCAAGGCCAGCGATATTAGACTT-A-AAGGTGCC-ATATGCAAATTCAAGGC
1 CCAATATGCTGATTCAAGGCCAGCAACATTAGACTTAACAAGGTGCCAATATGCAAATTCAAGGC
* * * * *
1909410 TAGCGACATTGGTCTTAAAGGTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
66 CAGCGACATTGGAC-T-----TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
1909475 AAAG
125 AAAG
1909479 GTGCCACAGA
Statistics
Matches: 237, Mismatches: 22, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
134 25 0.11
135 85 0.36
136 2 0.01
139 42 0.18
140 83 0.35
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (136 bp):
CCAATATGCTGATTCAAGGCCAGCAACATTAGACTTAACAAGGTGCCAATATGCAAATTCAAGGC
CAGCGACATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAA
AAGGTG
Found at i:1909518 original size:34 final size:34
Alignment explanation
Indices: 1909478--1909817 Score: 252
Period size: 34 Copynumber: 10.6 Consensus size: 34
1909468 TGGACTTAAA
*
1909478 GGTGCCACAGAGTTGTGGACTT-ATAGGAAAAAG
1 GGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAG
* * * *
1909511 GGATGCCACAAAGGTGTGGGCTTAAAAGGGAAAAG
1 GG-TGCCACAGAGTTGTGGACTTAAAAGGAAAAAG
* ** *
1909546 GGTGCCACGGAAGTCATGGACTTAAAAAG-AAAA-
1 GGTGCCACAG-AGTTGTGGACTTAAAAGGAAAAAG
1909579 GGTGCCAC-GAAGTTGTGGACTTAAAAGGAACAAA-
1 GGTGCCACAG-AGTTGTGGACTTAAAAGGAA-AAAG
1909613 ------ACAGAGTTGTGGACTTAAAAGGAAAAA-
1 GGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAG
* *
1909640 GATGCCACGGAGTTGTGGACTT-------AAAAG
1 GGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAG
1909667 GGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAG
1 GGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAG
* * * *
1909701 AGTGCCATAGAGTTGTGGGCTTTAAAAAGAAAAA-
1 GGTGCCACAGAGTTGTGGAC-TTAAAAGGAAAAAG
**
1909735 GGTGCCATGGAGTTGTGGACTT-------AAAAG
1 GGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAG
*
1909762 GGTGCCACAGAGTTATGGACTTTGAAAA-GAAAAA-
1 GGTGCCACAGAGTTGTGGAC-TT-AAAAGGAAAAAG
1909796 GGTGCCACAGAGTTGTGGACTT
1 GGTGCCACAGAGTTGTGGACTT
1909818 TGGGAAGAGA
Statistics
Matches: 248, Mismatches: 29, Indels: 60
0.74 0.09 0.18
Matches are distributed among these distances:
26 8 0.03
27 40 0.16
28 24 0.10
29 1 0.00
32 17 0.07
33 30 0.12
34 88 0.35
35 40 0.16
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.20
Consensus pattern (34 bp):
GGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAG
Found at i:1909587 original size:33 final size:34
Alignment explanation
Indices: 1909531--1909605 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 34
1909521 AAGGTGTGGG
*
1909531 CTTAAAAGGGAAAAGGGTGCCACGGAAGTCATGGA
1 CTTAAAAGAGAAAAGGGTGCCAC-GAAGTCATGGA
**
1909566 CTTAAAA-AGAAAA-GGTGCCACGAAGTTGTGGA
1 CTTAAAAGAGAAAAGGGTGCCACGAAGTCATGGA
1909598 CTTAAAAG
1 CTTAAAAG
1909606 GAACAAAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 16 0.44
33 8 0.22
34 5 0.14
35 7 0.19
ACGTcount: A:0.40, C:0.13, G:0.29, T:0.17
Consensus pattern (34 bp):
CTTAAAAGAGAAAAGGGTGCCACGAAGTCATGGA
Found at i:1909622 original size:28 final size:28
Alignment explanation
Indices: 1909589--1909696 Score: 105
Period size: 28 Copynumber: 3.7 Consensus size: 28
1909579 GGTGCCACGA
1909589 AGTTGTGGACTTAAAAGGAACAAAACAG
1 AGTTGTGGACTTAAAAGGAACAAAACAG
1909617 AGTTGTGGACTTAAAAGGAA-AAAGATGCCACGG
1 AGTTGTGGACTTAAAAGGAACAAA-A---CA--G
** *
1909650 AGTTGTGGACTTAAAAGGGTGC--CACAG
1 AGTTGTGGACTTAAAA-GGAACAAAACAG
1909677 AGTTGTGGACTTAAAAGGAA
1 AGTTGTGGACTTAAAAGGAA
1909697 AAAGAGTGCC
Statistics
Matches: 67, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
26 2 0.03
27 20 0.30
28 21 0.31
29 2 0.03
31 2 0.03
32 1 0.01
33 17 0.25
34 2 0.03
ACGTcount: A:0.39, C:0.11, G:0.30, T:0.20
Consensus pattern (28 bp):
AGTTGTGGACTTAAAAGGAACAAAACAG
Found at i:1909627 original size:60 final size:60
Alignment explanation
Indices: 1909562--1909707 Score: 197
Period size: 60 Copynumber: 2.4 Consensus size: 60
1909552 ACGGAAGTCA
*
1909562 TGGACTTAAAAAG-AAAAGGTGCCACGAAGTTGTGGACTTAAAA-GGAACAAAACAGAGTTG
1 TGGACTTAAAAGGAAAAAGGTGCCACGAAGTTGTGGACTTAAAAGGGAAC--AACAGAGTTG
* * ** *
1909622 TGGACTTAAAAGGAAAAAGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTG
1 TGGACTTAAAAGGAAAAAGGTGCCACGAAGTTGTGGACTTAAAAGGGAACAACAGAGTTG
1909682 TGGACTTAAAAGGAAAAAGAGTGCCA
1 TGGACTTAAAAGGAAAAAG-GTGCCA
1909708 TAGAGTTGTG
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
60 40 0.53
61 33 0.43
62 3 0.04
ACGTcount: A:0.40, C:0.12, G:0.29, T:0.18
Consensus pattern (60 bp):
TGGACTTAAAAGGAAAAAGGTGCCACGAAGTTGTGGACTTAAAAGGGAACAACAGAGTTG
Found at i:1909659 original size:61 final size:60
Alignment explanation
Indices: 1909562--1909727 Score: 201
Period size: 61 Copynumber: 2.7 Consensus size: 60
1909552 ACGGAAGTCA
* * *
1909562 TGGACTTAAAAAG-AAAAGGTGCCACGAAGTTGTGGACTTAAAA-GGAACAAAACAGAGTTG
1 TGGACTTAAAAGGAAAAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAC--AACAGAGTTG
** *
1909622 TGGACTTAAAAGGAAAAAGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTG
1 TGGACTTAAAAGGAAAAAGATGCCACGGAGTTGTGGACTTAAAAGGGAACAACAGAGTTG
** *
1909682 TGGACTTAAAAGGAAAAAGAGTGCCATAGAGTTGTGGGCTTTAAAA
1 TGGACTTAAAAGGAAAAAGA-TGCCACGGAGTTGTGGAC-TTAAAA
1909728 AGAAAAAGGT
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
60 41 0.44
61 43 0.46
62 9 0.10
ACGTcount: A:0.39, C:0.11, G:0.29, T:0.20
Consensus pattern (60 bp):
TGGACTTAAAAGGAAAAAGATGCCACGGAGTTGTGGACTTAAAAGGGAACAACAGAGTTG
Found at i:1909747 original size:95 final size:94
Alignment explanation
Indices: 1909468--1909817 Score: 373
Period size: 95 Copynumber: 3.7 Consensus size: 94
1909458 CCAGCGATAT
* * * *
1909468 TGGACTT-AAA-GGTGCCACAGAGTTGTGGACTT-ATAGGAAAAAGGGATGCCACAAAGGTGTGG
1 TGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAG-TGCCACAGAGTTGTGG
* * **
1909530 GCTTAAAAGGGAAAAGGGTGCCACGGAAGTCA
65 ACTTAAAA-GGAAAAAGGTGCCACGG-AGTTG
*
1909562 TGGACTTAAAAAGAAAAGGTGCCAC-GAAGTTGTGGACTTAAAAGGAACAA-A-----ACAGAGT
1 TGGACTT-AAAAG----GGTGCCACAG-AGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGT
*
1909620 TGTGGACTTAAAAGGAAAAAGATGCCACGGAGTTG
60 TGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTG
* *
1909655 TGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCATAGAGTTGTGGG
1 TGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGA
* *
1909720 CTTTAAAAAGAAAAAGGTGCCATGGAGTTG
66 C-TTAAAAGGAAAAAGGTGCCACGGAGTTG
*
1909750 TGGACTTAAAAGGGTGCCACAGAGTTATGGACTTTGAAAA-GAAAAAG-GTGCCACAGAGTTGTG
1 TGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TT-AAAAGGAAAAAGAGTGCCACAGAGTTGTG
1909813 GACTT
64 GACTT
1909818 TGGGAAGAGA
Statistics
Matches: 218, Mismatches: 19, Indels: 38
0.79 0.07 0.14
Matches are distributed among these distances:
88 30 0.14
89 2 0.01
92 5 0.02
93 10 0.05
94 36 0.17
95 90 0.41
96 12 0.06
97 4 0.02
100 1 0.00
101 20 0.09
102 8 0.04
ACGTcount: A:0.37, C:0.12, G:0.31, T:0.20
Consensus pattern (94 bp):
TGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGA
CTTAAAAGGAAAAAGGTGCCACGGAGTTG
Found at i:1909761 original size:61 final size:61
Alignment explanation
Indices: 1909696--1909817 Score: 181
Period size: 61 Copynumber: 2.0 Consensus size: 61
1909686 CTTAAAAGGA
* * * **
1909696 AAAAGAGTGCCATAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCATGGAGTTGTGGACTT
1 AAAAGAGTGCCACAGAGTTATGGACTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTT
* *
1909757 AAAAGGGTGCCACAGAGTTATGGACTTTGAAAAGAAAAAGGTGCCACAGAGTTGTGGACTT
1 AAAAGAGTGCCACAGAGTTATGGACTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTT
1909818 TGGGAAGAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.35, C:0.11, G:0.30, T:0.23
Consensus pattern (61 bp):
AAAAGAGTGCCACAGAGTTATGGACTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTT
Found at i:1909924 original size:92 final size:92
Alignment explanation
Indices: 1909777--1910038 Score: 384
Period size: 93 Copynumber: 2.8 Consensus size: 92
1909767 CACAGAGTTA
* *
1909777 TGGACTTTGAAAAGAAAAAGGTGCCAC-AGAGTTGTGGACTTTGGGAAGAGATGCCACTAAGTCA
1 TGGACTTTG--AAGAAAAAGATGCCACTA-AGTTGTGGACTTTGGGAAGAGATGCCACTAAGTCG
*
1909841 TGAACTTTGAGAAGAGATTGCCACTGAGTCG
63 TGGACTTTGAGAAGAGA-TGCCACTGAGTCG
*
1909872 TGGACTTTGAAG-AAAAGATGCCACTAAGTCGTGGACTTTGGGAAGAGATGCCACTAAGTCGTGG
1 TGGACTTTGAAGAAAAAGATGCCACTAAGTTGTGGACTTTGGGAAGAGATGCCACTAAGTCGTGG
*
1909936 ACTTTGGGAAGAGATGCCACTGAGTCG
66 ACTTTGAGAAGAGATGCCACTGAGTCG
* * * *
1909963 TGGACTTTGAAGAAAAAAGATGCCACTGAGTTATGGACTTTGAGAAGAGATGCCACTGAGTCGTG
1 TGGACTTTGAAG-AAAAAGATGCCACTAAGTTGTGGACTTTGGGAAGAGATGCCACTAAGTCGTG
1910028 GACTTTGAGAA
65 GACTTTGAGAA
1910039 TAGAGATTTG
Statistics
Matches: 153, Mismatches: 11, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
91 25 0.16
92 59 0.39
93 60 0.39
95 9 0.06
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (92 bp):
TGGACTTTGAAGAAAAAGATGCCACTAAGTTGTGGACTTTGGGAAGAGATGCCACTAAGTCGTGG
ACTTTGAGAAGAGATGCCACTGAGTCG
Found at i:1910001 original size:63 final size:62
Alignment explanation
Indices: 1909777--1910035 Score: 301
Period size: 63 Copynumber: 4.2 Consensus size: 62
1909767 CACAGAGTTA
* * * * *
1909777 TGGACTTTGAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTTGGGAAGAGATGCCACTAAGTCA
1 TGGACTTTG--AAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGAAGAGATGCCACTAAGTCG
* * *
1909841 TGAACTTTG-AG-AAGAGATTGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTAAGTCG
1 TGGACTTTGAAGAAAAAGA-TGCCACTGAGTCGTGGACTTTG-AGAAGAGATGCCACTAAGTCG
* * * * *
1909903 TGGACTTTG--GGAAGAGATGCCACTAAGTCGTGGACTTTGGGAAGAGATGCCACTGAGTCG
1 TGGACTTTGAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGAAGAGATGCCACTAAGTCG
** *
1909963 TGGACTTTGAAGAAAAAAGATGCCACTGAGTTATGGACTTTGAGAAGAGATGCCACTGAGTCG
1 TGGACTTTGAAG-AAAAAGATGCCACTGAGTCGTGGACTTTGAGAAGAGATGCCACTAAGTCG
1910026 TGGACTTTGA
1 TGGACTTTGA
1910036 GAATAGAGAT
Statistics
Matches: 170, Mismatches: 19, Indels: 13
0.84 0.09 0.06
Matches are distributed among these distances:
60 31 0.18
61 44 0.26
62 33 0.19
63 54 0.32
64 8 0.05
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (62 bp):
TGGACTTTGAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGAAGAGATGCCACTAAGTCG
Found at i:1910025 original size:93 final size:94
Alignment explanation
Indices: 1909777--1910038 Score: 395
Period size: 92 Copynumber: 2.8 Consensus size: 94
1909767 CACAGAGTTA
* * * *
1909777 TGGACTTTGAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTTGGGAAGAGATGCCACTAAGTCAT
1 TGGACTTTGAAGA-AAAAAGATGCCACTGAGTTGTGGACTTTGGGAAGAGATGCCACTAAGTCGT
*
1909842 GAACTTTGAGAAGAGATTGCCACTGAGTCG
65 GGACTTTGAGAAGAGATTGCCACTGAGTCG
* *
1909872 TGGACTTTGAAG--AAAAGATGCCACTAAGTCGTGGACTTTGGGAAGAGATGCCACTAAGTCGTG
1 TGGACTTTGAAGAAAAAAGATGCCACTGAGTTGTGGACTTTGGGAAGAGATGCCACTAAGTCGTG
*
1909935 GACTTTGGGAAGAGA-TGCCACTGAGTCG
66 GACTTTGAGAAGAGATTGCCACTGAGTCG
* * *
1909963 TGGACTTTGAAGAAAAAAGATGCCACTGAGTTATGGACTTTGAGAAGAGATGCCACTGAGTCGTG
1 TGGACTTTGAAGAAAAAAGATGCCACTGAGTTGTGGACTTTGGGAAGAGATGCCACTAAGTCGTG
1910028 GACTTTGAGAA
66 GACTTTGAGAA
1910039 TAGAGATTTG
Statistics
Matches: 151, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
91 25 0.17
92 59 0.39
93 56 0.37
95 11 0.07
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (94 bp):
TGGACTTTGAAGAAAAAAGATGCCACTGAGTTGTGGACTTTGGGAAGAGATGCCACTAAGTCGTG
GACTTTGAGAAGAGATTGCCACTGAGTCG
Found at i:1910035 original size:30 final size:30
Alignment explanation
Indices: 1909798--1910038 Score: 311
Period size: 30 Copynumber: 7.9 Consensus size: 30
1909788 AAGAAAAAGG
* * *
1909798 TGCCACAGAGTTGTGGACTTTGGGAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGA
* * *
1909828 TGCCACTAAGTCATGAACTTTGAGAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGA
*
1909858 TTGCCACTGAGTCGTGGACTTTGAAGAAAAGA
1 -TGCCACTGAGTCGTGGACTTTG-AGAAGAGA
* *
1909890 TGCCACTAAGTCGTGGACTTTGGGAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGA
* *
1909920 TGCCACTAAGTCGTGGACTTTGGGAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGA
*
1909950 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTTG-AG--AAGAGA
**
1909983 TGCCACTGAGTTATGGACTTTGAGAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGA
1910013 TGCCACTGAGTCGTGGACTTTGAGAA
1 TGCCACTGAGTCGTGGACTTTGAGAA
1910039 TAGAGATTTG
Statistics
Matches: 185, Mismatches: 21, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
30 110 0.59
31 41 0.22
32 9 0.05
33 25 0.14
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (30 bp):
TGCCACTGAGTCGTGGACTTTGAGAAGAGA
Found at i:1911358 original size:14 final size:13
Alignment explanation
Indices: 1911323--1911366 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
1911313 CTTTGCACTC
*
1911323 TTTTTTTGTGTGT
1 TTTTTTTTTGTGT
1911336 ATTTTTTTTT-TGT
1 -TTTTTTTTTGTGT
1911349 TTTTTGTTTTGTGT
1 TTTTT-TTTTGTGT
1911363 TTTT
1 TTTT
1911367 ACTTTTGACT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 5 0.19
13 7 0.26
14 15 0.56
ACGTcount: A:0.02, C:0.00, G:0.16, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTGTGT
Found at i:1918453 original size:13 final size:13
Alignment explanation
Indices: 1918435--1918462 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1918425 ATATAAAGAT
1918435 CAATGTATCGATA
1 CAATGTATCGATA
1918448 CAATGTATCGATA
1 CAATGTATCGATA
1918461 CA
1 CA
1918463 TTGAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1918459 original size:33 final size:33
Alignment explanation
Indices: 1918417--1918482 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1918407 AAATTCCCAG
*
1918417 ATGTATCGATATAAAG-ATCAATGTATCGATACA
1 ATGTATCGATACAAAGAAT-AATGTATCGATACA
**
1918450 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
1918483 TTTCCTTGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCGATACA
Found at i:1918877 original size:33 final size:33
Alignment explanation
Indices: 1918839--1918918 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
1918829 GTCTACAAAC
1918839 ATGTATCGATACATAGTATCGATACAAAGCATG
1 ATGTATCGATACATAGTATCGATACAAAGCATG
*
1918872 ATGTATCGATACGTAGTATCGATACAAAGCATG
1 ATGTATCGATACATAGTATCGATACAAAGCATG
1918905 ATGTATCGATACAT
1 ATGTATCGATACAT
1918919 CCGGATATGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACATAGTATCGATACAAAGCATG
Found at i:1918879 original size:20 final size:20
Alignment explanation
Indices: 1918854--1918917 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1918844 TCGATACATA
1918854 GTATCGATACAAAGCATGAT
1 GTATCGATACAAAGCATGAT
1918874 GTATCGATAC---G--T-A-
1 GTATCGATACAAAGCATGAT
1918887 GTATCGATACAAAGCATGAT
1 GTATCGATACAAAGCATGAT
1918907 GTATCGATACA
1 GTATCGATACA
1918918 TCCGGATATG
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.27
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 1 0.03
20 21 0.57
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (20 bp):
GTATCGATACAAAGCATGAT
Found at i:1919299 original size:20 final size:20
Alignment explanation
Indices: 1919271--1919318 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1919261 GTATCGATAC
*
1919271 ATTGCATCGATACATGATGA
1 ATTGTATCGATACATGATGA
*
1919291 ATTGTATCGATACATGGTGA
1 ATTGTATCGATACATGATGA
1919311 ATTGTATC
1 ATTGTATC
1919319 AACAAATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
ATTGTATCGATACATGATGA
Found at i:1919835 original size:32 final size:35
Alignment explanation
Indices: 1919756--1919842 Score: 110
Period size: 32 Copynumber: 2.5 Consensus size: 35
1919746 TAAGTGATTA
**
1919756 AGAGG-TTCTATCTTAGCCTTTGAAAAAGATAGGG
1 AGAGGTTTCTATCTTAGCCCATGAAAAAGATAGGG
1919790 AGACAGGTTTCTATCTTAGCCCATG-AAAAGATA-GG
1 AG--AGGTTTCTATCTTAGCCCATGAAAAAGATAGGG
1919825 -GAGGTTTCTATCTTAGCC
1 AGAGGTTTCTATCTTAGCC
1919843 TTGAAAGATA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
32 17 0.35
34 3 0.06
35 2 0.04
36 11 0.23
37 15 0.31
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (35 bp):
AGAGGTTTCTATCTTAGCCCATGAAAAAGATAGGG
Found at i:1924072 original size:13 final size:12
Alignment explanation
Indices: 1924038--1924123 Score: 50
Period size: 11 Copynumber: 6.8 Consensus size: 12
1924028 AATTTTCAAC
1924038 ATAAAAAAATAA
1 ATAAAAAAATAA
* *
1924050 ATTAACAAA-AA
1 ATAAAAAAATAA
* *
1924061 ATCAAATAA-AA
1 ATAAAAAAATAA
1924072 ATAAAAAAATCAA
1 ATAAAAAAAT-AA
1924085 ATATCCAAAAAATAAAA
1 ATA---AAAAAAT--AA
*
1924102 ATAAAAAATATAT
1 ATAAAAAA-ATAA
1924115 ATAAAAAAA
1 ATAAAAAAA
1924124 GAAGAGAACG
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
11 17 0.29
12 8 0.14
13 14 0.24
14 5 0.09
15 2 0.03
16 7 0.12
17 5 0.09
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.19
Consensus pattern (12 bp):
ATAAAAAAATAA
Found at i:1924081 original size:34 final size:36
Alignment explanation
Indices: 1924038--1924108 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 36
1924028 AATTTTCAAC
*
1924038 ATAAAAAAAT-AAAT-TAACAAAAAAT-CAAATAAAA
1 ATAAAAAAATCAAATAT-ACAAAAAATAAAAATAAAA
*
1924072 ATAAAAAAATCAAATATCCAAAAAATAAAAATAAAA
1 ATAAAAAAATCAAATATACAAAAAATAAAAATAAAA
1924108 A
1 A
1924109 ATATATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 10 0.31
35 12 0.38
36 10 0.31
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (36 bp):
ATAAAAAAATCAAATATACAAAAAATAAAAATAAAA
Found at i:1924094 original size:35 final size:35
Alignment explanation
Indices: 1924038--1924108 Score: 92
Period size: 34 Copynumber: 2.0 Consensus size: 35
1924028 AATTTTCAAC
*
1924038 ATAAAAAAATAAATTAACAAAAAAT-CAAATAAAA
1 ATAAAAAAATAAATTAACAAAAAATAAAAATAAAA
*
1924072 ATAAAAAAATCAAA-TATCCAAAAAATAAAAATAAAA
1 ATAAAAAAAT-AAATTA-ACAAAAAATAAAAATAAAA
1924108 A
1 A
1924109 ATATATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 12 0.38
35 11 0.34
36 9 0.28
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (35 bp):
ATAAAAAAATAAATTAACAAAAAATAAAAATAAAA
Found at i:1924302 original size:33 final size:33
Alignment explanation
Indices: 1924256--1924336 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
1924246 GAAAGAAAGC
* *
1924256 AAAGCAACGTGAAGCAGCATGGAGTTGCAAATA
1 AAAGCAACATGAAGAAGCATGGAGTTGCAAATA
*
1924289 AAAGCAACATGAAGAAGCATGGAGTTGCAAATG
1 AAAGCAACATGAAGAAGCATGGAGTTGCAAATA
1924322 AAAGCAACATGAAGA
1 AAAGCAACATGAAGA
1924337 CCATTACACC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.14, G:0.26, T:0.14
Consensus pattern (33 bp):
AAAGCAACATGAAGAAGCATGGAGTTGCAAATA
Found at i:1924759 original size:46 final size:43
Alignment explanation
Indices: 1924656--1924749 Score: 170
Period size: 43 Copynumber: 2.2 Consensus size: 43
1924646 CATCGTGGAA
*
1924656 GGAAAGCACGAGCAATTAGCAGCAGCAAATGATGAAGAAGAAT
1 GGAAAGCACGAGCAATTAGCAGCAGCAAATGATGAAAAAGAAT
*
1924699 GGAAAGCACGAGCAATTGGCAGCAGCAAATGATGAAAAAGAAT
1 GGAAAGCACGAGCAATTAGCAGCAGCAAATGATGAAAAAGAAT
1924742 GGAAAGCA
1 GGAAAGCA
1924750 TGGGTAGCAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.47, C:0.14, G:0.29, T:0.11
Consensus pattern (43 bp):
GGAAAGCACGAGCAATTAGCAGCAGCAAATGATGAAAAAGAAT
Found at i:1924882 original size:22 final size:22
Alignment explanation
Indices: 1924855--1924896 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1924845 GAGAGGGAGC
*
1924855 GAGCAGCAAAGAGAGGAAGAAG
1 GAGCAGCAAAGAGAGAAAGAAG
1924877 GAGCAGCAAAGAGAGAAAGA
1 GAGCAGCAAAGAGAGAAAGA
1924897 TAGCAACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.10, G:0.38, T:0.00
Consensus pattern (22 bp):
GAGCAGCAAAGAGAGAAAGAAG
Found at i:1925491 original size:30 final size:30
Alignment explanation
Indices: 1925457--1925539 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
1925447 ATGCTTAGAC
* * *
1925457 TAAAATGCAAATATTGAAAGATTTAGGAAT
1 TAAAATGCAAACATGGAAAAATTTAGGAAT
* *
1925487 TAAAATGTAAACATGGAAAAATTTAGGGAT
1 TAAAATGCAAACATGGAAAAATTTAGGAAT
* *
1925517 TAAATTGCAAA-ATGCAAAAATTT
1 TAAAATGCAAACATGGAAAAATTT
1925540 TGATTCATGG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 11 0.24
30 34 0.76
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.29
Consensus pattern (30 bp):
TAAAATGCAAACATGGAAAAATTTAGGAAT
Found at i:1930545 original size:20 final size:20
Alignment explanation
Indices: 1930491--1930547 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1930481 AAAAACCTAG
* *
1930491 AATGTATCGATACAATGAGT
1 AATGTATCGATACATTTAGT
* *
1930511 AATGTATCAATACATTTATT
1 AATGTATCGATACATTTAGT
*
1930531 TATGTATCGATACATTT
1 AATGTATCGATACATTT
1930548 CTTTTCCAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTTAGT
Found at i:1937906 original size:32 final size:33
Alignment explanation
Indices: 1937825--1937916 Score: 107
Period size: 32 Copynumber: 2.7 Consensus size: 33
1937815 ATTGTTTACC
* *
1937825 TTTAAGGCTAAGGTATAACCT-TACACTCCTATCT
1 TTTAAGGCTAAGATAGAACCTCTACA--CCTATCT
1937859 TTTACAAAGGCTAAGATAGAACCTCTACA-CTATCT
1 TTT---AAGGCTAAGATAGAACCTCTACACCTATCT
1937894 TTTAAGGCTAAGATAGAACCTCT
1 TTTAAGGCTAAGATAGAACCTCT
1937917 TAATCACTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
32 20 0.38
34 3 0.06
35 9 0.17
37 16 0.31
38 4 0.08
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.32
Consensus pattern (33 bp):
TTTAAGGCTAAGATAGAACCTCTACACCTATCT
Found at i:1938406 original size:19 final size:20
Alignment explanation
Indices: 1938363--1938406 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1938353 CCGTTGGACT
* **
1938363 CAATGTATTGATACTATTCA
1 CAATGTATCGATACTATGAA
1938383 CAATGTATCGATAC-ATGAA
1 CAATGTATCGATACTATGAA
1938402 CAATG
1 CAATG
1938407 ATGAATAGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (20 bp):
CAATGTATCGATACTATGAA
Found at i:1938444 original size:52 final size:52
Alignment explanation
Indices: 1938365--1938470 Score: 158
Period size: 52 Copynumber: 2.0 Consensus size: 52
1938355 GTTGGACTCA
* * * *
1938365 ATGTATTGATACTATTCACAATGTATCGATACATGAACAATGATGAATAGTG
1 ATGTATCGATACTATTCACAATATATCGATACATGAACAATGATAAACAGTG
* *
1938417 ATGTATCGATACTATTCATAATATATCGATACATGAACAGTGATAAACAGTG
1 ATGTATCGATACTATTCACAATATATCGATACATGAACAATGATAAACAGTG
1938469 AT
1 AT
1938471 AAATAGTGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (52 bp):
ATGTATCGATACTATTCACAATATATCGATACATGAACAATGATAAACAGTG
Found at i:1938467 original size:10 final size:10
Alignment explanation
Indices: 1938452--1938486 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
1938442 TCGATACATG
1938452 AACAGTGATA
1 AACAGTGATA
1938462 AACAGTGATA
1 AACAGTGATA
*
1938472 AATAGTGATA
1 AACAGTGATA
1938482 AACAG
1 AACAG
1938487 CGAAAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.51, C:0.09, G:0.20, T:0.20
Consensus pattern (10 bp):
AACAGTGATA
Found at i:1938494 original size:20 final size:20
Alignment explanation
Indices: 1938455--1938494 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1938445 ATACATGAAC
* *
1938455 AGTGATAAACAGTGATAAAT
1 AGTGATAAACAGCGAAAAAT
1938475 AGTGATAAACAGCGAAAAAT
1 AGTGATAAACAGCGAAAAAT
1938495 GAGATTTAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (20 bp):
AGTGATAAACAGCGAAAAAT
Found at i:1941912 original size:52 final size:52
Alignment explanation
Indices: 1941820--1941999 Score: 290
Period size: 52 Copynumber: 3.5 Consensus size: 52
1941810 TGAAATATGA
* * *
1941820 AAATTTACCTGCATGTAT-GATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
*
1941871 AAATTTGCCTGCATGTATCAATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
* * *
1941923 AAAGTTGCCTGCATGTATCGATACATTTTATAATGTATCAATACATCTGGGA
1 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1941975 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1942000 AAGATCAGTG
Statistics
Matches: 119, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
51 17 0.14
52 102 0.86
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
Found at i:1942018 original size:104 final size:103
Alignment explanation
Indices: 1941827--1942019 Score: 280
Period size: 104 Copynumber: 1.9 Consensus size: 103
1941817 TGAAAATTTA
* * *
1941827 CCTGCATGTATGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCAA
1 CCTGCATGTATGATACATTTAATAATGTATCAATACATCTGGGAAAATTTGCCTGCATGTATCAA
***
1941892 TACATTTTATAATGTATCGATACATCTGGGCAAAGTTG
66 TACATAAGATAATGTATCGATACATCTGGGCAAAGTTG
* *
1941930 CCTGCATGTATCGATACATTTTATAATGTATCAATACATCTGGGAAAATTTGCCTGCATGTATCG
1 CCTGCATGTAT-GATACATTTAATAATGTATCAATACATCTGGGAAAATTTGCCTGCATGTATCA
*
1941995 ATACA-AAGATCAGTGTATCGATACA
65 ATACATAAGAT-AATGTATCGATACA
1942020 ATGTATCGAT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
103 13 0.16
104 66 0.84
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (103 bp):
CCTGCATGTATGATACATTTAATAATGTATCAATACATCTGGGAAAATTTGCCTGCATGTATCAA
TACATAAGATAATGTATCGATACATCTGGGCAAAGTTG
Found at i:1942026 original size:13 final size:13
Alignment explanation
Indices: 1942008--1942032 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1941998 CAAAGATCAG
1942008 TGTATCGATACAA
1 TGTATCGATACAA
1942021 TGTATCGATACA
1 TGTATCGATACA
1942033 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1943721 original size:34 final size:34
Alignment explanation
Indices: 1943683--1943747 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
1943673 ATAGATATAA
* *
1943683 AATATTAACTTCTTAGCTAGAGTCAAAAATAGAG
1 AATATTAACTTCTTAGCTAAAGTAAAAAATAGAG
1943717 AATATTAACTTCTTAGCTAAAGTAAAAAATA
1 AATATTAACTTCTTAGCTAAAGTAAAAAATA
1943748 AGGCTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.31
Consensus pattern (34 bp):
AATATTAACTTCTTAGCTAAAGTAAAAAATAGAG
Found at i:1947770 original size:2 final size:2
Alignment explanation
Indices: 1947763--1947789 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1947753 ATTAATGTGT
1947763 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1947790 GTTTTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1950080 original size:43 final size:43
Alignment explanation
Indices: 1950024--1950127 Score: 181
Period size: 43 Copynumber: 2.4 Consensus size: 43
1950014 CGACGTTTTT
*
1950024 AAAATAAATGCCACTAAATTTAAACATGTCACGACGTTTGCTA
1 AAAATAAATGCCACTAAATTTAAACATGTCACGACGTTTACTA
* *
1950067 AAAATAAATGCCACTAAATTTAAACATTTCATGACGTTTACTA
1 AAAATAAATGCCACTAAATTTAAACATGTCACGACGTTTACTA
1950110 AAAATAAATGCCACTAAA
1 AAAATAAATGCCACTAAA
1950128 ATATTGCCAC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (43 bp):
AAAATAAATGCCACTAAATTTAAACATGTCACGACGTTTACTA
Found at i:1960841 original size:13 final size:13
Alignment explanation
Indices: 1960823--1960847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1960813 ACATTGTTCA
1960823 TTGTATCGATACT
1 TTGTATCGATACT
1960836 TTGTATCGATAC
1 TTGTATCGATAC
1960848 ATTCTAGGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (13 bp):
TTGTATCGATACT
Found at i:1960891 original size:20 final size:20
Alignment explanation
Indices: 1960866--1960979 Score: 140
Period size: 20 Copynumber: 5.7 Consensus size: 20
1960856 TTTACCCAAA
*
1960866 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTTACAT
*
1960886 TGTATCGATACATTGCT-CAT
1 TGTATCGATACATT-TTACAT
*
1960906 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTTACAT
***
1960926 TGTATCGATACATTACCCAT
1 TGTATCGATACATTTTACAT
* *
1960946 TGTTTCGATACATTTTACAA
1 TGTATCGATACATTTTACAT
1960966 TGTATCGATACATT
1 TGTATCGATACATT
1960980 CTGGCATTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 1 0.01
20 77 0.97
21 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTTTACAT
Found at i:1960916 original size:40 final size:40
Alignment explanation
Indices: 1960857--1960979 Score: 183
Period size: 40 Copynumber: 3.0 Consensus size: 40
1960847 CATTCTAGGT
* * *
1960857 TTACCCAAATGTATCGATACATTTTGCATTGTATCGATACA
1 TTACCC-ATTGTATCGATACATTTTACAATGTATCGATACA
* *
1960898 TTGCTCATTGTATCGATACATTTTACAATGTATCGATACA
1 TTACCCATTGTATCGATACATTTTACAATGTATCGATACA
*
1960938 TTACCCATTGTTTCGATACATTTTACAATGTATCGATACA
1 TTACCCATTGTATCGATACATTTTACAATGTATCGATACA
1960978 TT
1 TT
1960980 CTGGCATTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 70 0.95
41 4 0.05
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (40 bp):
TTACCCATTGTATCGATACATTTTACAATGTATCGATACA
Found at i:1960947 original size:60 final size:60
Alignment explanation
Indices: 1960864--1960979 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
1960854 GGTTTACCCA
*** *
1960864 AATGTATCGATACATTTTGCATTGTATCGATACATTGCT-CATTGTATCGATACATTTTAC
1 AATGTATCGATACATTACCCATTGTATCGATACATT-CTACAATGTATCGATACATTTTAC
* *
1960924 AATGTATCGATACATTACCCATTGTTTCGATACATTTTACAATGTATCGATACATT
1 AATGTATCGATACATTACCCATTGTATCGATACATTCTACAATGTATCGATACATT
1960980 CTGGCATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 1 0.02
60 48 0.98
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (60 bp):
AATGTATCGATACATTACCCATTGTATCGATACATTCTACAATGTATCGATACATTTTAC
Found at i:1965618 original size:17 final size:17
Alignment explanation
Indices: 1965598--1965633 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1965588 GCAAAAGCAC
1965598 AAAAATGAGAAAC-ACA
1 AAAAATGAGAAACGACA
*
1965614 AAAAATGAGGAACGACA
1 AAAAATGAGAAACGACA
1965631 AAA
1 AAA
1965634 CCAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.67, C:0.11, G:0.17, T:0.06
Consensus pattern (17 bp):
AAAAATGAGAAACGACA
Found at i:1966943 original size:62 final size:62
Alignment explanation
Indices: 1966844--1967518 Score: 782
Period size: 62 Copynumber: 11.0 Consensus size: 62
1966834 CTCTTTTAGC
* * * * *
1966844 CCTTCCAGTCCTCAAAAAGTAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1966906 CCTTCTGGTCCTCAAAGAGCAGGATGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
** * * * *
1966967 TTTTCCAGTCCCTCAAAGAGTAGGACGCCTTCTCC--TTCAAAGCCCACACAAGCTGGTGGCA
1 CCTTCTAGT-CCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
1967028 TCTTC-AGTCCTCAAAGAGCAGGACGCC-TTCCCCTTTCAAAGCCCATACAAGCTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1967088 CCTTC-AGTCCTCAAAGAGCAAGACG-CTTTCTCC-TTTCGAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTT-TCCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
1967148 CTTTTCTAGTCCTCAAAGAGCAGGACACTTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 C-CTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
1967211 CC-TCTTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTTAAAGCCCACACAAGCTGGTGGTA
1 CCTTC-TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
* **
1967273 CCTTC-AGTCCTCAAAGAGCAGGACGCCTTCTCC-TTTCGGAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * * *
1967333 CTTTTCTAGTCCTTAAAGAGCAAGACACCTTTTTCTTTTCAAAGCACACACAAGTTGGTGGCA
1 C-CTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
1967396 CC-TCTTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGTCCACACGAGTTGGTAGCA
1 CCTTC-TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
1967458 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTT-CTTTTCAAAGCCTACGCGAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
1967519 TTTCATACTC
Statistics
Matches: 530, Mismatches: 66, Indels: 35
0.84 0.10 0.06
Matches are distributed among these distances:
58 3 0.01
59 19 0.04
60 103 0.19
61 116 0.22
62 231 0.44
63 58 0.11
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (62 bp):
CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:1967288 original size:185 final size:184
Alignment explanation
Indices: 1966850--1967518 Score: 882
Period size: 185 Copynumber: 3.6 Consensus size: 184
1966840 TAGCCCTTCC
* * * * * *
1966850 AGTCCTCAAAAAGTAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTGGT
1 AGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGCTGGTGGCACCTTC-AGT
* * *
1966915 CCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCC
65 CCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGT-CC
* * * * * *
1966979 TCAAAGAGTAGGACGCCTTCTC-CTTCAAAGCCCACACAAGCTGGTGGCA--TCTT
129 TCAAAGAGCAGGACACTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTCTT
* ** * *
1967032 CAGTCCTCAAAGAGCAGGACGCC-TTCCCCTTTCAAAGCCCATACAAGCTGGTGGCACCTTCAGT
1 -AGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGCTGGTGGCACCTTCAGT
* *
1967096 CCTCAAAGAGCAAGACG-CTTTCTCCTTTCGAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCC
65 CCTCAAAGAGCAGGACGCCTTT-TCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCC
1967160 TCAAAGAGCAGGACACTTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTCTT
129 TCAAAGAGCAGGACAC-TTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTCTT
* *
1967217 AGTCCTCAAAGAGCAGGACACCTTTTTCTTTTTAAAGCCCACACAAGCTGGTGGTACCTTCAGTC
1 AGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGCTGGTGGCACCTTCAGTC
* ** *
1967282 CTCAAAGAGCAGGACGCCTTCTCCTTTCGGAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTT
66 CTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTC
* *
1967347 AAAGAGCAAGACACCTTTTTCTTTTCAAAGCACACACAAGTTGGTGGCACCTCTT
131 AAAGAGCAGGACA-CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTCTT
* * * * *
1967402 AGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGTCCACACGAGTTGGTAGCACCTTTTAGT
1 AGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGCTGGTGGCACC-TTCAGT
* * * *
1967467 CCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCTACGCGAGTTGGTGGCA
65 CCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
1967519 TTTCATACTC
Statistics
Matches: 429, Mismatches: 47, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
180 4 0.01
181 61 0.14
182 44 0.10
183 45 0.10
184 21 0.05
185 200 0.47
186 54 0.13
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (184 bp):
AGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGCTGGTGGCACCTTCAGTC
CTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTC
AAAGAGCAGGACACTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTCTT
Found at i:1967632 original size:45 final size:44
Alignment explanation
Indices: 1967547--1967848 Score: 257
Period size: 45 Copynumber: 6.8 Consensus size: 44
1967537 TGATACGTTC
* *
1967547 CATTTCCTTATTTTCCCCTTTTTGTCCTCAAAAAGTAGGACACATTT
1 CATTTCCTT-TTTT-CCC-TTTTGTCCTCAAAGAGCAGGACACATTT
*
1967594 CATTTCCTTATTTTCCCTTTTGTCCTCAAAGAGCAGGACGCACTTT
1 CATTTCCTT-TTTTCCCTTTTGTCCTCAAAGAGCAGGACACA-TTT
* * * * * *
1967640 -ATTTTCC--TCTTCTCATTTGTCCTCAAAGAGTAGGACACGTTC
1 CA-TTTCCTTTTTTCCCTTTTGTCCTCAAAGAGCAGGACACATTT
* *
1967682 CATTTCCTTATTTTCCCCTTTTTGTCCTCAAAGAGCAGGACGCACTT
1 CATTTCCTT-TTTT-CCC-TTTTGTCCTCAAAGAGCAGGACACATTT
*
1967729 CCTTTCCTTCTTTTCCCTTTTGTCCTCAAAGAGCATGG-CACACTTT
1 CATTTCCTT-TTTTCCCTTTTGTCCTCAAAGAGCA-GGACACA-TTT
*
1967775 -ATTTTCC-TTTTT--CTTTTGTCCTCAAAGAGCAGGACGCATTT
1 CA-TTTCCTTTTTTCCCTTTTGTCCTCAAAGAGCAGGACACATTT
* *
1967816 CGTTTTTCTTTTTT-CC-TTTGTCCTCGAAA-AGCA
1 C-ATTTCCTTTTTTCCCTTTTGTCCTC-AAAGAGCA
1967849 AGACGCACTT
Statistics
Matches: 212, Mismatches: 26, Indels: 38
0.77 0.09 0.14
Matches are distributed among these distances:
41 5 0.02
42 33 0.16
43 45 0.21
44 8 0.04
45 48 0.23
46 25 0.12
47 48 0.23
ACGTcount: A:0.19, C:0.27, G:0.12, T:0.41
Consensus pattern (44 bp):
CATTTCCTTTTTTCCCTTTTGTCCTCAAAGAGCAGGACACATTT
Found at i:1967709 original size:135 final size:134
Alignment explanation
Indices: 1967532--1967809 Score: 423
Period size: 135 Copynumber: 2.1 Consensus size: 134
1967522 CATACTCGAC
* * * *
1967532 GAGCATGATACGTTCCATTTCCTTATTTTCCCCTTTTTGTCCTCAAAAAGTAGGACACATTTCAT
1 GAGCAGGACACGTTCCATTTCCTTATTTTCCCCTTTTTGTCCTCAAAAAGCAGGACACACTTCAT
*
1967597 TTCCTTATTTTCCCTTTTGTCCTCAAAGAGCA-GGACGCACTTTATTTTCCTCTTCTCATTTGTC
66 TTCCTTATTTTCCCTTTTGTCCTCAAAGAGCATGG-CACACTTTATTTTCCT-TTCTCATTTGTC
1967661 CTCAAA
129 CTCAAA
* * * *
1967667 GAGTAGGACACGTTCCATTTCCTTATTTTCCCCTTTTTGTCCTCAAAGAGCAGGACGCACTTCCT
1 GAGCAGGACACGTTCCATTTCCTTATTTTCCCCTTTTTGTCCTCAAAAAGCAGGACACACTTCAT
* * *
1967732 TTCCTTCTTTTCCCTTTTGTCCTCAAAGAGCATGGCACACTTTATTTTCCTTTTTCTTTTGTCCT
66 TTCCTTATTTTCCCTTTTGTCCTCAAAGAGCATGGCACACTTTATTTTCCTTTCTCATTTGTCCT
1967797 CAAA
131 CAAA
1967801 GAGCAGGAC
1 GAGCAGGAC
1967810 GCATTTCGTT
Statistics
Matches: 129, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
134 24 0.19
135 103 0.80
136 2 0.02
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (134 bp):
GAGCAGGACACGTTCCATTTCCTTATTTTCCCCTTTTTGTCCTCAAAAAGCAGGACACACTTCAT
TTCCTTATTTTCCCTTTTGTCCTCAAAGAGCATGGCACACTTTATTTTCCTTTCTCATTTGTCCT
CAAA
Found at i:1967712 original size:47 final size:44
Alignment explanation
Indices: 1967655--1967809 Score: 160
Period size: 47 Copynumber: 3.5 Consensus size: 44
1967645 CCTCTTCTCA
*
1967655 TTTGTCCTCAAAGAGTAGGA-CACGTTCCATTTCCTTATTTTCCCCTT
1 TTTGTCCTCAAAGAGCAGGACCAC-TTCC-TTTCCTTATTTT-CCC-T
*
1967702 TTTGTCCTCAAAGAGCAGGACGCACTTCCTTTCCTTCTTTTCCCT
1 TTTGTCCTCAAAGAGCAGGAC-CACTTCCTTTCCTTATTTTCCCT
**
1967747 TTTGTCCTCAAAGAGCATGG-CACACTTTATTTTCC-T-TTTT--CT
1 TTTGTCCTCAAAGAGCA-GGAC-CAC-TTCCTTTCCTTATTTTCCCT
1967789 TTTGTCCTCAAAGAGCAGGAC
1 TTTGTCCTCAAAGAGCAGGAC
1967810 GCATTTCGTT
Statistics
Matches: 98, Mismatches: 5, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
41 2 0.02
42 20 0.20
44 4 0.04
45 23 0.23
46 12 0.12
47 30 0.31
48 4 0.04
49 3 0.03
ACGTcount: A:0.19, C:0.28, G:0.14, T:0.39
Consensus pattern (44 bp):
TTTGTCCTCAAAGAGCAGGACCACTTCCTTTCCTTATTTTCCCT
Found at i:1967800 original size:42 final size:45
Alignment explanation
Indices: 1967566--1967864 Score: 234
Period size: 43 Copynumber: 6.8 Consensus size: 45
1967556 ATTTTCCCCT
* * *
1967566 TTTTGTCCTCAAAAAGTAGGACACA-TTTCA-TTTCCTTATTTTCCC
1 TTTTGTCCTCAAAGAGCAGGACACACTTT-ATTTTCCTTCTTTT-CC
* *
1967611 TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCC-TCTTCT-C
1 TTTTGTCCTCAAAGAGCAGGACACACTTTATTTTCCTTCTTTTCC
* * * * *
1967654 ATTTGTCCTCAAAGAGTAGGACAC-GTTCCA-TTTCCTTATTTTCCCC
1 TTTTGTCCTCAAAGAGCAGGACACACTT-TATTTTCCTTCTTTT--CC
* **
1967700 TTTTTGTCCTCAAAGAGCAGGACGCAC-TTCCTTTCCTTCTTTTCCC
1 -TTTTGTCCTCAAAGAGCAGGACACACTTTATTTTCCTTCTTTT-CC
1967746 TTTTGTCCTCAAAGAGCATGG-CACACTTTATTTTCC-T-TTTT-C
1 TTTTGTCCTCAAAGAGCA-GGACACACTTTATTTTCCTTCTTTTCC
* * *
1967788 TTTTGTCCTCAAAGAGCAGGACGCA-TTTCGTTTTTCTT-TTTTCC
1 TTTTGTCCTCAAAGAGCAGGACACACTTT-ATTTTCCTTCTTTTCC
* *
1967832 -TTTGTCCTCGAAA-AGCAAGACGCACTTT-TTTTC
1 TTTTGTCCTC-AAAGAGCAGGACACACTTTATTTTC
1967865 ACCTTGTCCT
Statistics
Matches: 209, Mismatches: 27, Indels: 39
0.76 0.10 0.14
Matches are distributed among these distances:
41 5 0.02
42 38 0.18
43 51 0.24
44 11 0.05
45 50 0.24
46 21 0.10
47 33 0.16
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.41
Consensus pattern (45 bp):
TTTTGTCCTCAAAGAGCAGGACACACTTTATTTTCCTTCTTTTCC
Found at i:1967911 original size:39 final size:39
Alignment explanation
Indices: 1967856--1967957 Score: 170
Period size: 39 Copynumber: 2.6 Consensus size: 39
1967846 GCAAGACGCA
*
1967856 CTTTT-TTTCACCTTGTCCTCAAGAAGCAGGACACTTTC
1 CTTTTCTTTCACTTTGTCCTCAAGAAGCAGGACACTTTC
1967894 CTTTTCTTTCACTTTGTCCTCAAGAAGCAGGACACTTTC
1 CTTTTCTTTCACTTTGTCCTCAAGAAGCAGGACACTTTC
*
1967933 CTTTTCTTTTCCCTTTGTCCTCAAG
1 CTTTTC-TTTCACTTTGTCCTCAAG
1967958 GAGCGAGACC
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
38 5 0.08
39 38 0.63
40 17 0.28
ACGTcount: A:0.18, C:0.29, G:0.12, T:0.41
Consensus pattern (39 bp):
CTTTTCTTTCACTTTGTCCTCAAGAAGCAGGACACTTTC
Found at i:1968644 original size:20 final size:20
Alignment explanation
Indices: 1968593--1968649 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1968583 TTTTCACAAT
*
1968593 TTGTATCGATACATTGTTCA
1 TTGTATCAATACATTGTTCA
*
1968613 TTGCAT-AGATACATTGTTCA
1 TTGTATCA-ATACATTGTTCA
*
1968633 TTGTATCAATACTTTGT
1 TTGTATCAATACATTGT
1968650 ATCGATACGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (20 bp):
TTGTATCAATACATTGTTCA
Found at i:1971564 original size:17 final size:16
Alignment explanation
Indices: 1971529--1971577 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 16
1971519 CGTCTTCCGC
*
1971529 AAAAAAAAAAGAGACAAG
1 AAAAAAAAAA-A-AAAAG
1971547 AAAAAAAAACAAAAAAG
1 AAAAAAAAA-AAAAAAG
1971564 AAAAAGAAAAAAAA
1 AAAAA-AAAAAAAA
1971578 CAACAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 13 0.46
18 14 0.50
19 1 0.04
ACGTcount: A:0.86, C:0.04, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAG
Found at i:1971587 original size:24 final size:24
Alignment explanation
Indices: 1971529--1971586 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
1971519 CGTCTTCCGC
*
1971529 AAAA-AAAAAAGAGACAAGAAAAA
1 AAAACAAAAAAGAGAAAAGAAAAA
1971552 AAAACAAAAAAGA-AAAAGAAAAAA
1 AAAACAAAAAAGAGAAAAG-AAAAA
1971576 AACAACAAAAA
1 AA-AACAAAAA
1971587 GGGTCCGGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 8 0.26
24 15 0.48
25 8 0.26
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (24 bp):
AAAACAAAAAAGAGAAAAGAAAAA
Found at i:1972650 original size:37 final size:37
Alignment explanation
Indices: 1972609--1972691 Score: 139
Period size: 37 Copynumber: 2.2 Consensus size: 37
1972599 TGCCACAATC
*
1972609 ATGCATTTGGGACATTCATAACATTTCATTTTGCATG
1 ATGCATTTGGAACATTCATAACATTTCATTTTGCATG
* *
1972646 ATGCATTTGTAAGATTCATAACATTTCATTTTGCATG
1 ATGCATTTGGAACATTCATAACATTTCATTTTGCATG
1972683 ATGCATTTG
1 ATGCATTTG
1972692 TGCTTCATCT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (37 bp):
ATGCATTTGGAACATTCATAACATTTCATTTTGCATG
Found at i:1972692 original size:37 final size:37
Alignment explanation
Indices: 1972622--1972692 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
1972612 CATTTGGGAC
1972622 ATTCATAACATTTCATTTTGCATGATGCATTTGTAAG
1 ATTCATAACATTTCATTTTGCATGATGCATTTGTAAG
1972659 ATTCATAACATTTCATTTTGCATGATGCATTTGT
1 ATTCATAACATTTCATTTTGCATGATGCATTTGT
1972693 GCTTCATCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (37 bp):
ATTCATAACATTTCATTTTGCATGATGCATTTGTAAG
Found at i:1973099 original size:29 final size:29
Alignment explanation
Indices: 1973059--1973353 Score: 293
Period size: 29 Copynumber: 10.3 Consensus size: 29
1973049 CTCACCTTCC
*
1973059 AAAGCCCACAAGTTAGTGGCATCTTTTCA
1 AAAGCCCACAAGTTAGTGGCAACTTTTCA
* *
1973088 AAAGCTCACAAGTCAGTGGC-ACTTTTTCA
1 AAAGCCCACAAGTTAGTGGCAAC-TTTTCA
* *
1973117 AAAGCCCACAAGTCAGTGGCACCTTTTC-
1 AAAGCCCACAAGTTAGTGGCAACTTTTCA
* *
1973145 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
1 AAAGCCCACAAGTTAGTGGCAACTTTTCA
* * ** * *
1973173 GAAGCCCATAAGTCGGTGGCACCCCTTTC-
1 AAAGCCCACAAGTTAGTGGCA-ACTTTTCA
*
1973202 AAAGCCCACAAGTTAGTGGCAAC-CTTCA
1 AAAGCCCACAAGTTAGTGGCAACTTTTCA
* *
1973230 AAAGCCCACAAGTCAGTGGCATCTTTTCA
1 AAAGCCCACAAGTTAGTGGCAACTTTTCA
1973259 AAAGCCCACAAGTTAGTGGC-ACATTTTC-
1 AAAGCCCACAAGTTAGTGGCAAC-TTTTCA
* *
1973287 AAAGCCCACAAGGTAGTGGCAAC-CTTCA
1 AAAGCCCACAAGTTAGTGGCAACTTTTCA
* * * *
1973315 AAAGCACACAGGTTGGT-GCAACCCTTTCA
1 AAAGCCCACAAGTTAGTGGCAA-CTTTTCA
1973344 AAAGCCCACA
1 AAAGCCCACA
1973354 CAAGTTGGTG
Statistics
Matches: 223, Mismatches: 31, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
27 13 0.06
28 97 0.43
29 109 0.49
30 4 0.02
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.21
Consensus pattern (29 bp):
AAAGCCCACAAGTTAGTGGCAACTTTTCA
Found at i:1973202 original size:57 final size:57
Alignment explanation
Indices: 1973052--1973353 Score: 314
Period size: 57 Copynumber: 5.3 Consensus size: 57
1973042 GATATTCCTC
* * * *
1973052 ACCTTCCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAAGCTCACAAGTCAGTGGC-
1 ACCTTCAAAAGCCCACAAGTCAGTGGCACCTTTTCAAAAGCCCACAAGTCAGTGGCA
*
1973108 ACTTTTTCAAAAGCCCACAAGTCAGTGGCACCTTTTC-AAAGCCCACAAGTCAGTGGCA
1 AC--CTTCAAAAGCCCACAAGTCAGTGGCACCTTTTCAAAAGCCCACAAGTCAGTGGCA
* * * * *
1973166 ACCTTCAGAAGCCCATAAGTCGGTGGCACCCCTTTC-AAAGCCCACAAGTTAGTGGCA
1 ACCTTCAAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAAGCCCACAAGTCAGTGGCA
* *
1973223 ACCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTTAGTGGCA
1 ACCTTCAAAAGCCCACAAGTCAGTGGCACCTTTTCAAAAGCCCACAAGTCAGTGGCA
** * * **
1973280 CATTTTC-AAAGCCCACAAGGT-AGTGGCAACC--TTCAAAAGCACACAGGTTGGT-GCA
1 -ACCTTCAAAAGCCCACAA-GTCAGTGGC-ACCTTTTCAAAAGCCCACAAGTCAGTGGCA
1973335 ACCCTTTCAAAAGCCCACA
1 A-CC-TTCAAAAGCCCACA
1973354 CAAGTTGGTG
Statistics
Matches: 211, Mismatches: 24, Indels: 21
0.82 0.09 0.08
Matches are distributed among these distances:
54 1 0.00
55 3 0.01
56 50 0.24
57 118 0.56
58 39 0.18
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.21
Consensus pattern (57 bp):
ACCTTCAAAAGCCCACAAGTCAGTGGCACCTTTTCAAAAGCCCACAAGTCAGTGGCA
Found at i:1973313 original size:85 final size:85
Alignment explanation
Indices: 1973052--1973324 Score: 347
Period size: 85 Copynumber: 3.2 Consensus size: 85
1973042 GATATTCCTC
* * * *
1973052 ACCTTCCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAAGCTCACAAGTCAGTGGCACTTTTTCA
1 ACCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCACATTTTC-
1973117 AAAGCCCACAA-GTCAGTGGC-
65 AAAGCCCACAAGGT-AGTGGCA
* * * * * **
1973137 ACCTTTTC-AAAGCCCACAAGTCAGTGGCAAC-CTTCAGAAGCCCATAAGTCGGTGGCACCCCTT
1 ACC--TTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCA-CATTT
*
1973200 TCAAAGCCCACAAGTTAGTGGCA
63 TCAAAGCCCACAAGGTAGTGGCA
*
1973223 ACCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTTAGTGGCACATTTTCA
1 ACCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCACATTTTCA
1973288 AAGCCCACAAGGTAGTGGCA
66 AAGCCCACAAGGTAGTGGCA
*
1973308 ACCTTCAAAAGCACACA
1 ACCTTCAAAAGCCCACA
1973325 GGTTGGTGCA
Statistics
Matches: 161, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
84 3 0.02
85 104 0.65
86 51 0.32
87 3 0.02
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (85 bp):
ACCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCACATTTTCA
AAGCCCACAAGGTAGTGGCA
Found at i:1973534 original size:39 final size:39
Alignment explanation
Indices: 1973480--1973631 Score: 169
Period size: 39 Copynumber: 3.7 Consensus size: 39
1973470 GTCCAAAATT
*
1973480 GCTGGCCTTGAATCAGCACATTGGCATGAGCCCAATATC
1 GCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATC
* * *
1973519 GCTGGCCTTGAATCAGCATATTGGCACCTTTTCTTTAAGACCAATGTC
1 GCTGGCCTTGAATCAGCACATTGGCA---------TAAGCCCAATATC
*
1973567 GCTGGCTTTGAATCAGCACATTGGCATAAGCCCAATATC
1 GCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATC
*
1973606 GCTGGCCTTGAATCAGCATATTGGCA
1 GCTGGCCTTGAATCAGCACATTGGCA
1973632 CCTTGTCTTT
Statistics
Matches: 94, Mismatches: 10, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
39 60 0.64
48 34 0.36
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.28
Consensus pattern (39 bp):
GCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATC
Found at i:1973582 original size:48 final size:47
Alignment explanation
Indices: 1973511--1973680 Score: 203
Period size: 48 Copynumber: 3.7 Consensus size: 47
1973501 TGGCATGAGC
1973511 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTTCTTTAAGA
* * * *
1973559 CCAATGTCGCTGGCTTTGAATCAGCACATTGGCA--------TAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCTTTAAGA
1973598 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-TCTTTAAGA
* * *
1973646 CCAATGTTGCTGGCCTTGAATCAGCATATTAGCAC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1973681 AAGTCCAATG
Statistics
Matches: 102, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
39 35 0.34
48 67 0.66
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (47 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCTTTAAGA
Found at i:1973589 original size:87 final size:87
Alignment explanation
Indices: 1973388--1973722 Score: 402
Period size: 87 Copynumber: 3.8 Consensus size: 87
1973378 GTCTAATATC
* * * * *
1973388 GCTGGCCTTGAATCAGCATC-TTGGCACCTCTAAGTCCAATCTTGCTGGTCTTGAATAAGCACAT
1 GCTGGCCTTGAATCAGCA-CATTGGCA----TAAGCCCAATATCGCTGGCCTTGAATCAGCACAT
* * **
1973452 TGGCACCTTTACCTTTAAGTCCAAAATT
61 TGGCACCTTT-TCTTTAAGACCAATGTT
* *
1973480 GCTGGCCTTGAATCAGCACATTGGCATGAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1 GCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCA
*
1973545 CCTTTTCTTTAAGACCAATGTC
66 CCTTTTCTTTAAGACCAATGTT
* *
1973567 GCTGGCTTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1 GCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCA
*
1973632 CCTTGTCTTTAAGACCAATGTT
66 CCTTTTCTTTAAGACCAATGTT
* * * * * * * *
1973654 GCTGGCCTTGAATCAGCATATTAGCACAAGTCCAATGTCGTTGGCCTTAAATCAGCACATTAGCA
1 GCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCA
1973719 CCTT
66 CCTT
1973723 CACCTCTAAG
Statistics
Matches: 216, Mismatches: 26, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
87 154 0.71
88 37 0.17
91 1 0.00
92 24 0.11
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (87 bp):
GCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCA
CCTTTTCTTTAAGACCAATGTT
Found at i:1978393 original size:21 final size:21
Alignment explanation
Indices: 1978360--1978402 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1978350 CTAAGTAAAA
1978360 ATACGTATTGTATCAATACAC
1 ATACGTATTGTATCAATACAC
*
1978381 ATAC-TATTGGTATTAATACAC
1 ATACGTATT-GTATCAATACAC
1978402 A
1 A
1978403 AGGTTAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAC
Found at i:1978466 original size:21 final size:20
Alignment explanation
Indices: 1978437--1978493 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
1978427 AAAACCCTGA
**
1978437 AAAGTATCGATACACATTTT
1 AAAGTATCGATACACATTGC
*
1978457 AAATGTATCGATACAGATTGC
1 AAA-GTATCGATACACATTGC
*
1978478 ATAGTATCGATACACA
1 AAAGTATCGATACACA
1978494 CAAATATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (20 bp):
AAAGTATCGATACACATTGC
Found at i:1978607 original size:10 final size:10
Alignment explanation
Indices: 1978588--1978618 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1978578 AATCTCATTT
1978588 TCACTGTTCA
1 TCACTGTTCA
*
1978598 TCACTATTCA
1 TCACTGTTCA
1978608 TCACTGTTCA
1 TCACTGTTCA
1978618 T
1 T
1978619 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:1978679 original size:10 final size:10
Alignment explanation
Indices: 1978664--1978696 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
1978654 AATATCGATA
1978664 CATCACTGTT
1 CATCACTGTT
*
1978674 CATCACTATT
1 CATCACTGTT
1978684 CATCACTGTT
1 CATCACTGTT
1978694 CAT
1 CAT
1978697 GTATCGATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.24, C:0.30, G:0.06, T:0.39
Consensus pattern (10 bp):
CATCACTGTT
Found at i:1978712 original size:22 final size:22
Alignment explanation
Indices: 1978656--1978739 Score: 120
Period size: 22 Copynumber: 4.0 Consensus size: 22
1978646 TATTCATAAA
1978656 TATCGATACATCACTGTTCAT-
1 TATCGATACATCACTGTTCATG
* * *
1978677 CA-CTATTCATCACTGTTCATG
1 TATCGATACATCACTGTTCATG
1978698 TATCGATACATCACTGTTCATG
1 TATCGATACATCACTGTTCATG
1978720 TATCGATACATCACT-TTCAT
1 TATCGATACATCACTGTTCAT
1978740 AAATATCACT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
20 16 0.29
21 7 0.13
22 32 0.58
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (22 bp):
TATCGATACATCACTGTTCATG
Found at i:1978830 original size:13 final size:13
Alignment explanation
Indices: 1978812--1978850 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1978802 TCACTATTCA
1978812 TGTATCGATACAT
1 TGTATCGATACAT
*
1978825 TGTATCGATACAG
1 TGTATCGATACAT
1978838 TGTATCGATACAT
1 TGTATCGATACAT
1978851 CATAAATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1980507 original size:21 final size:21
Alignment explanation
Indices: 1980481--1980522 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1980471 AATCAACCAT
* *
1980481 TCAAGATGATGATGAAGATGA
1 TCAAGAGGATGATGAAAATGA
*
1980502 TCAAGAGGTTGATGAAAATGA
1 TCAAGAGGATGATGAAAATGA
1980523 AGAAATGGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.24
Consensus pattern (21 bp):
TCAAGAGGATGATGAAAATGA
Found at i:1982623 original size:13 final size:13
Alignment explanation
Indices: 1982605--1982629 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1982595 TTTTCTAGAT
1982605 TGTATCGATACAA
1 TGTATCGATACAA
1982618 TGTATCGATACA
1 TGTATCGATACA
1982630 TTGCTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1986275 original size:17 final size:17
Alignment explanation
Indices: 1986253--1986295 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
1986243 TAATTCATTA
1986253 TTTATCCATTTTTTGTT
1 TTTATCCATTTTTTGTT
1986270 TTTATCCATTTTTTGTT
1 TTTATCCATTTTTTGTT
1986287 TTTATCCAT
1 TTTATCCAT
1986296 ATATTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.14, C:0.14, G:0.05, T:0.67
Consensus pattern (17 bp):
TTTATCCATTTTTTGTT
Found at i:1986750 original size:31 final size:31
Alignment explanation
Indices: 1986712--1986777 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
1986702 TGCATGCAAG
*
1986712 GCAATGTAGCATGCAATCATGGGAGACACAT
1 GCAATGTAGCATGCAATCATGGGAGACACAA
*
1986743 GCAATGTAGCATGCAATCATGGGGGACACAA
1 GCAATGTAGCATGCAATCATGGGAGACACAA
1986774 GCAA
1 GCAA
1986778 ATGGAAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.17
Consensus pattern (31 bp):
GCAATGTAGCATGCAATCATGGGAGACACAA
Found at i:1987363 original size:31 final size:31
Alignment explanation
Indices: 1987320--1987412 Score: 141
Period size: 31 Copynumber: 3.0 Consensus size: 31
1987310 GCACTCGAAA
* * *
1987320 CCAGCAGCTCGAGCTTCTCCCAGCTTCCACG
1 CCAGTAGCTCGAGCCTCTTCCAGCTTCCACG
1987351 CCAGTAGCTCGAGCCTCTTCCAGCTTCCACG
1 CCAGTAGCTCGAGCCTCTTCCAGCTTCCACG
* *
1987382 GCAGTAGCTCAAGCCTCTTCCAGCTTCCACG
1 CCAGTAGCTCGAGCCTCTTCCAGCTTCCACG
1987413 AACACAGCAG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.17, C:0.42, G:0.19, T:0.22
Consensus pattern (31 bp):
CCAGTAGCTCGAGCCTCTTCCAGCTTCCACG
Found at i:1987822 original size:13 final size:13
Alignment explanation
Indices: 1987804--1987828 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1987794 TTTCATTCTA
1987804 TTATTGCTTGTTT
1 TTATTGCTTGTTT
1987817 TTATTGCTTGTT
1 TTATTGCTTGTT
1987829 GTTCTTTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.08, G:0.16, T:0.68
Consensus pattern (13 bp):
TTATTGCTTGTTT
Found at i:1988349 original size:13 final size:13
Alignment explanation
Indices: 1988331--1988378 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
1988321 AAGTAAAATT
1988331 TAAAAAAATATAA
1 TAAAAAAATATAA
1988344 T-AAAAAATAATAA
1 TAAAAAAAT-ATAA
*
1988357 CAAAATAAA-ATAA
1 TAAAA-AAATATAA
1988370 TAAAAAAAT
1 TAAAAAAAT
1988379 TCCTTTCATC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 10 0.34
13 13 0.45
14 3 0.10
15 3 0.10
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (13 bp):
TAAAAAAATATAA
Found at i:1988368 original size:16 final size:16
Alignment explanation
Indices: 1988347--1988378 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1988337 AATATAATAA
*
1988347 AAAATAATAACAAAAT
1 AAAATAATAAAAAAAT
1988363 AAAATAATAAAAAAAT
1 AAAATAATAAAAAAAT
1988379 TCCTTTCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAATAATAAAAAAAT
Found at i:1990718 original size:21 final size:21
Alignment explanation
Indices: 1990689--1990733 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1990679 AAGTTTTCAT
*
1990689 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1990709 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1990731 TTT
1 TTT
1990734 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1992970 original size:13 final size:13
Alignment explanation
Indices: 1992952--1992977 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1992942 CAATTTTTTG
1992952 TGTATCGATACAT
1 TGTATCGATACAT
1992965 TGTATCGATACAT
1 TGTATCGATACAT
1992978 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1994901 original size:42 final size:42
Alignment explanation
Indices: 1994854--1995329 Score: 625
Period size: 42 Copynumber: 11.4 Consensus size: 42
1994844 AAACTTCTGA
* * * *
1994854 AGACTTTCCTTCCCTTAGTCTACTTATTGGCTTTGACCCTAG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* *
1994896 AGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* *
1994938 ATACTTT-CTTCCCTTAGTCTGCTTGTCGGCTTTGACCCTAG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
*
1994979 AGACTTTCC-TACCTTAGTCTGCCTGTCGGCTTTGACCCTAG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * * * *
1995020 AGACTTTTCTTCCCTTAGTCTTCCTATTGGTTTTGACCCTAA
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * *
1995062 AGACTTTCCTTCCCTTAGTCTGCCTATCGGCTTTGACCATGG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * *
1995104 AGACTTTCCTTCCCTTAGTCTGCTTGTTGGCTTTGAACCT-G
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * * * *
1995145 AAGACTTTTCTACCCTTAGTCTACCTGTCGACTTTGACCCTGG
1 -AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* * *
1995188 AGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCTTGG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
* *
1995230 AGACTTTCCTTCCCTTAGTCTGCCTGTTGGCTTTGACCCTAA
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
*
1995272 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGG
1 AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
*
1995314 AGACTTTCCTACCCTT
1 AGACTTTCCTTCCCTT
1995330 CTTGTTTTAT
Statistics
Matches: 379, Mismatches: 51, Indels: 8
0.87 0.12 0.02
Matches are distributed among these distances:
41 77 0.20
42 301 0.79
43 1 0.00
ACGTcount: A:0.14, C:0.30, G:0.18, T:0.38
Consensus pattern (42 bp):
AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAG
Found at i:1995165 original size:126 final size:126
Alignment explanation
Indices: 1994854--1995329 Score: 688
Period size: 126 Copynumber: 3.8 Consensus size: 126
1994844 AAACTTCTGA
* * *
1994854 AGACTTTCCTTCCCTTAGTCTACTTATTGGCTTTGACCCTAGAGACTTTTCTTCCCTTAGTCTGC
1 AGACTTTCCTTCCCTTAGTCTGCCTGTTGGCTTTGACCCTAGAGACTTTTCTTCCCTTAGTCTGC
* * * * *
1994919 CTGTCGGCTTTGACCCTGGATACTTT-CTTCCCTTAGTCTGCTTGTCGGCTTTGACCCTAG
66 CTGTCGGCTTTGACCCTGGAGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCATGG
* * *
1994979 AGACTTTCC-TACCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTTCCCTTAGTCTTC
1 AGACTTTCCTTCCCTTAGTCTGCCTGTTGGCTTTGACCCTAGAGACTTTTCTTCCCTTAGTCTGC
* * * ** * *
1995043 CTATTGGTTTTGACCCTAAAGACTTTCCTTCCCTTAGTCTGCCTATCGGCTTTGACCATGG
66 CTGTCGGCTTTGACCCTGGAGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCATGG
* * * *
1995104 AGACTTTCCTTCCCTTAGTCTGCTTGTTGGCTTTGAACCT-GAAGACTTTTCTACCCTTAGTCTA
1 AGACTTTCCTTCCCTTAGTCTGCCTGTTGGCTTTGACCCTAG-AGACTTTTCTTCCCTTAGTCTG
* *
1995168 CCTGTCGACTTTGACCCTGGAGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCTTGG
65 CCTGTCGGCTTTGACCCTGGAGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCATGG
* *
1995230 AGACTTTCCTTCCCTTAGTCTGCCTGTTGGCTTTGACCCTAAAGACTTTCCTTCCCTTAGTCTGC
1 AGACTTTCCTTCCCTTAGTCTGCCTGTTGGCTTTGACCCTAGAGACTTTTCTTCCCTTAGTCTGC
1995295 CTGTCGGCTTTGACCCTGGAGACTTTCCTACCCTT
66 CTGTCGGCTTTGACCCTGGAGACTTTCCTACCCTT
1995330 CTTGTTTTAT
Statistics
Matches: 309, Mismatches: 38, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
124 69 0.22
125 49 0.16
126 191 0.62
ACGTcount: A:0.14, C:0.30, G:0.18, T:0.38
Consensus pattern (126 bp):
AGACTTTCCTTCCCTTAGTCTGCCTGTTGGCTTTGACCCTAGAGACTTTTCTTCCCTTAGTCTGC
CTGTCGGCTTTGACCCTGGAGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCATGG
Found at i:1996458 original size:31 final size:31
Alignment explanation
Indices: 1996419--1996507 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 31
1996409 TCGAATCCAG
* *
1996419 CAGCTCGAGCTTCTTCCAGCTTCCACGCCAA
1 CAGCTCGAGCATCTTCTAGCTTCCACGCCAA
* * * * *
1996450 TAGCTCGAGCCTCTTCTAGTTTCCACGGCAG
1 CAGCTCGAGCATCTTCTAGCTTCCACGCCAA
*
1996481 CAGCTTGAGCATCTTCTAGCTTCCACG
1 CAGCTCGAGCATCTTCTAGCTTCCACG
1996508 AACACAGCAG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.18, C:0.36, G:0.19, T:0.27
Consensus pattern (31 bp):
CAGCTCGAGCATCTTCTAGCTTCCACGCCAA
Found at i:1996528 original size:21 final size:21
Alignment explanation
Indices: 1996502--1996566 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 21
1996492 TCTTCTAGCT
1996502 TCCACGAACACAGCAGCAGCA
1 TCCACGAACACAGCAGCAGCA
1996523 TCCACGAACACGGCAGCAGCAGCA
1 TCCACGAACA---CAGCAGCAGCA
1996547 TCCACGAACAC-GACAGCAGC
1 TCCACGAACACAG-CAGCAGC
1996567 TCGAGCCTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
20 1 0.03
21 18 0.45
24 21 0.52
ACGTcount: A:0.35, C:0.38, G:0.22, T:0.05
Consensus pattern (21 bp):
TCCACGAACACAGCAGCAGCA
Found at i:1996544 original size:24 final size:24
Alignment explanation
Indices: 1996511--1996566 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
1996501 TTCCACGAAC
1996511 ACAGCAGCAGCATCCACGAACACG
1 ACAGCAGCAGCATCCACGAACACG
*
1996535 GCAGCAGCAGCATCCACGAACACG
1 ACAGCAGCAGCATCCACGAACACG
1996559 ACAGCAGC
1 ACAGCAGC
1996567 TCGAGCCTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.36, C:0.38, G:0.23, T:0.04
Consensus pattern (24 bp):
ACAGCAGCAGCATCCACGAACACG
Found at i:1997468 original size:12 final size:11
Alignment explanation
Indices: 1997451--1997493 Score: 59
Period size: 12 Copynumber: 3.7 Consensus size: 11
1997441 GTAAAATTTA
1997451 AAAAAATATAAT
1 AAAAAA-ATAAT
*
1997463 AAAAAAATAAC
1 AAAAAAATAAT
1997474 AAATAAAATAAT
1 AAA-AAAATAAT
1997486 AAAAAAAT
1 AAAAAAAT
1997494 CTTTTCATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 12 0.43
12 16 0.57
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAAAAATAAT
Found at i:2002094 original size:29 final size:29
Alignment explanation
Indices: 2002027--2002125 Score: 85
Period size: 31 Copynumber: 3.3 Consensus size: 29
2002017 AAAAAAGCCT
* *
2002027 TTAACCTTTATTATT-TATTTAGATAAGTTT
1 TTAA-CTTT-TTATTATATTTAAATAAGTTA
*
2002057 TTATA-TTTTTATTATATTTAAATAAGTTC
1 TTA-ACTTTTTATTATATTTAAATAAGTTA
* * *
2002086 TTAACTTTTTAAATTATACTCAAATAAGTAA
1 TTAACTTTTT--ATTATATTTAAATAAGTTA
2002117 TTAACTTTT
1 TTAACTTTT
2002126 AAATTTACTA
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
28 6 0.10
29 24 0.41
30 3 0.05
31 25 0.43
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (29 bp):
TTAACTTTTTATTATATTTAAATAAGTTA
Found at i:2002111 original size:31 final size:29
Alignment explanation
Indices: 2002075--2002142 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
2002065 TTATTATATT
**
2002075 TAAATAAGTTCTTAACTTTTTAAATTATAC
1 TAAATAAGTAATTAAC-TTTTAAATTATAC
2002105 TCAAATAAGTAATTAACTTTTAAATT-TAC
1 T-AAATAAGTAATTAACTTTTAAATTATAC
*
2002134 TAATTAAGT
1 TAAATAAGT
2002143 GTCTAATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.21
29 4 0.12
30 10 0.29
31 13 0.38
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (29 bp):
TAAATAAGTAATTAACTTTTAAATTATAC
Found at i:2006199 original size:24 final size:24
Alignment explanation
Indices: 2006172--2006231 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
2006162 GATTATGATT
*
2006172 TTCTAAGATATTATTTCACAAATC
1 TTCTAAGATATCATTTCACAAATC
2006196 TTCTAAGATATCATTTCACAAATC
1 TTCTAAGATATCATTTCACAAATC
2006220 TTCTAAGATATC
1 TTCTAAGATATC
2006232 GTCAATATGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (24 bp):
TTCTAAGATATCATTTCACAAATC
Found at i:2006584 original size:108 final size:108
Alignment explanation
Indices: 2006395--2006604 Score: 411
Period size: 108 Copynumber: 1.9 Consensus size: 108
2006385 GACTGACTGT
*
2006395 GCCATTGTCAATTTCAGACTTTGTGAAGTTCCTGTCGATTCTAACATGCTTCATCCTATCATGTT
1 GCCATTGTCAATTTCAGACTTTATGAAGTTCCTGTCGATTCTAACATGCTTCATCCTATCATGTT
2006460 GAATAGGATTATGAACAATGCTGATAGCTGACTTGTTGTTCGC
66 GAATAGGATTATGAACAATGCTGATAGCTGACTTGTTGTTCGC
2006503 GCCATTGTCAATTTCAGACTTTATGAAGTTCCTGTCGATTCTAACATGCTTCATCCTATCATGTT
1 GCCATTGTCAATTTCAGACTTTATGAAGTTCCTGTCGATTCTAACATGCTTCATCCTATCATGTT
2006568 GAATAGGATTATGAACAATGCTGATAGCTGACTTGTT
66 GAATAGGATTATGAACAATGCTGATAGCTGACTTGTT
2006605 ATCCGCGAAC
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 101 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (108 bp):
GCCATTGTCAATTTCAGACTTTATGAAGTTCCTGTCGATTCTAACATGCTTCATCCTATCATGTT
GAATAGGATTATGAACAATGCTGATAGCTGACTTGTTGTTCGC
Found at i:2011007 original size:24 final size:24
Alignment explanation
Indices: 2010980--2011043 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
2010970 TAGGGATTAT
*
2010980 AATTTTCTAAGATATTATTTCACA
1 AATTTTCTAAGATATCATTTCACA
2011004 AATTTTCTAAGATATCATTTCACA
1 AATTTTCTAAGATATCATTTCACA
*
2011028 AATCTTCTAAGATATC
1 AATTTTCTAAGATATC
2011044 GTCAATATGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.42
Consensus pattern (24 bp):
AATTTTCTAAGATATCATTTCACA
Found at i:2013609 original size:106 final size:106
Alignment explanation
Indices: 2013424--2013633 Score: 393
Period size: 106 Copynumber: 2.0 Consensus size: 106
2013414 ATTTTGACTG
*
2013424 TGTCAATGTCATATGTAATTAAAGTTGTATTTTCTCTATGTGCATGCAAGTAAATCTTCTATGTT
1 TGTCAATGTCATATGTAATTAAAGTTGTATTTTCTCTATCTGCATGCAAGTAAATCTTCTATGTT
2013489 TTTGTGTATGCTTATGGGTTTAGAAGAGGAGGTTGGAAGTC
66 TTTGTGTATGCTTATGGGTTTAGAAGAGGAGGTTGGAAGTC
* *
2013530 TGTCAATGTCGTATGTAATTAAAGTTTTATTTTCTCTATCTGCATGCAAGTAAATCTTCTATGTT
1 TGTCAATGTCATATGTAATTAAAGTTGTATTTTCTCTATCTGCATGCAAGTAAATCTTCTATGTT
2013595 TTTGTGTATGCTTATGGGTTTAGAAGAGGAGGTTGGAAG
66 TTTGTGTATGCTTATGGGTTTAGAAGAGGAGGTTGGAAG
2013634 CTTGTTTGTA
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 101 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (106 bp):
TGTCAATGTCATATGTAATTAAAGTTGTATTTTCTCTATCTGCATGCAAGTAAATCTTCTATGTT
TTTGTGTATGCTTATGGGTTTAGAAGAGGAGGTTGGAAGTC
Found at i:2015498 original size:14 final size:14
Alignment explanation
Indices: 2015477--2015505 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2015467 CTTAATTCAA
2015477 AATTTTTTT-TTTT
1 AATTTTTTTATTTT
2015490 AATTTTTTTATTTT
1 AATTTTTTTATTTT
2015504 AA
1 AA
2015506 GTTAAAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
AATTTTTTTATTTT
Found at i:2015643 original size:14 final size:15
Alignment explanation
Indices: 2015613--2015649 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
2015603 AAAGGTTCCC
*
2015613 GTTGGAACTGGAGCT
1 GTTGGAACTGGAACT
2015628 GTTGGAA-TGGAACT
1 GTTGGAACTGGAACT
2015642 GTTGGAAC
1 GTTGGAAC
2015650 GTTGCTCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.24, C:0.11, G:0.38, T:0.27
Consensus pattern (15 bp):
GTTGGAACTGGAACT
Found at i:2017614 original size:46 final size:46
Alignment explanation
Indices: 2017547--2017637 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
2017537 TTTATGAGAT
2017547 AACCTAACTCCTTTGCCACCTATTTTTTTACAGTGTATCCTACATC
1 AACCTAACTCCTTTGCCACCTATTTTTTTACAGTGTATCCTACATC
2017593 AACCTAACTCCTTTGCCACCTATTTTTTTACAGTGTATCCTACAT
1 AACCTAACTCCTTTGCCACCTATTTTTTTACAGTGTATCCTACAT
2017638 AGCAGTAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.24, C:0.30, G:0.07, T:0.40
Consensus pattern (46 bp):
AACCTAACTCCTTTGCCACCTATTTTTTTACAGTGTATCCTACATC
Found at i:2022223 original size:13 final size:13
Alignment explanation
Indices: 2022205--2022230 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2022195 AATTTTTTTG
2022205 TGTATCGATACAT
1 TGTATCGATACAT
2022218 TGTATCGATACAT
1 TGTATCGATACAT
2022231 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2024806 original size:13 final size:13
Alignment explanation
Indices: 2024788--2024825 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2024778 ATAATCCCCC
*
2024788 TGTATCGATATAG
1 TGTATCGATACAG
*
2024801 TGTATCGATACAT
1 TGTATCGATACAG
2024814 TGTATCGATACA
1 TGTATCGATACA
2024826 AAGAAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2028457 original size:19 final size:19
Alignment explanation
Indices: 2028433--2028497 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
2028423 TAGCCAAACT
2028433 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
2028452 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
2028465 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
2028486 TGTATCGATACA
1 TGTATCGATACA
2028498 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:2028469 original size:13 final size:13
Alignment explanation
Indices: 2028451--2028476 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2028441 TACACAAAAT
2028451 ATGTATCGATACA
1 ATGTATCGATACA
2028464 ATGTATCGATACA
1 ATGTATCGATACA
2028477 CAAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2028474 original size:32 final size:33
Alignment explanation
Indices: 2028433--2028497 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
2028423 TAGCCAAACT
2028433 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
2028465 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
2028498 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:2033639 original size:13 final size:13
Alignment explanation
Indices: 2033621--2033658 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2033611 CATTTTTCTT
2033621 TGTATCGATACAA
1 TGTATCGATACAA
*
2033634 TGTATCGATACAC
1 TGTATCGATACAA
*
2033647 TGTATTGATACA
1 TGTATCGATACA
2033659 GGGGGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2033813 original size:20 final size:20
Alignment explanation
Indices: 2033770--2033815 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2033760 AAATCTTTTG
2033770 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
2033791 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
2033811 CAAAA
1 CAAAA
2033816 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:2036222 original size:32 final size:33
Alignment explanation
Indices: 2036181--2036243 Score: 110
Period size: 34 Copynumber: 1.9 Consensus size: 33
2036171 TAGCCAAACT
2036181 TGTATCGATACAC-AAAATATGTATCGATATAA
1 TGTATCGATACACAAAAATATGTATCGATATAA
2036213 TGTATCGATACACAAAAAATATGTATCGATA
1 TGTATCGATACAC-AAAAATATGTATCGATA
2036244 CATTGGCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.45
34 16 0.55
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATATAA
Found at i:2037344 original size:21 final size:21
Alignment explanation
Indices: 2037315--2037359 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2037305 AAGTTTTTAT
*
2037315 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2037335 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2037357 TTT
1 TTT
2037360 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2039599 original size:13 final size:13
Alignment explanation
Indices: 2039581--2039605 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2039571 AATTTTTTTG
2039581 TGTATCGATACAA
1 TGTATCGATACAA
2039594 TGTATCGATACA
1 TGTATCGATACA
2039606 TACTTGGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2039621 original size:32 final size:34
Alignment explanation
Indices: 2039557--2039625 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 34
2039547 CGTTACAAGC
** *
2039557 CAATGTATCGATACAATTTTTTTGTGTATCGATA
1 CAATGTATCGATACAATTACTTGGTGTATCGATA
2039591 CAATGTATCGATAC-A-TACTTGGTGTATCGATA
1 CAATGTATCGATACAATTACTTGGTGTATCGATA
2039623 CAA
1 CAA
2039626 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 17 0.53
33 1 0.03
34 14 0.44
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (34 bp):
CAATGTATCGATACAATTACTTGGTGTATCGATA
Found at i:2040182 original size:14 final size:14
Alignment explanation
Indices: 2040165--2040191 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2040155 CGTGACGATA
2040165 ATTTCTTGACAACC
1 ATTTCTTGACAACC
2040179 ATTTCTTGACAAC
1 ATTTCTTGACAAC
2040192 TGGCAAATTG
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:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (14 bp):
ATTTCTTGACAACC
Found at i:2047375 original size:15 final size:15
Alignment explanation
Indices: 2047336--2047380 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
2047326 GTGTATCAAC
*
2047336 AATTTTGTGGTGGGT
1 AATTTTGTGGTGGAT
**
2047351 AATTAGGTGGTGGAT
1 AATTTTGTGGTGGAT
*
2047366 GATTTTGTGGTGGAT
1 AATTTTGTGGTGGAT
2047381 TTGGCGGAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.18, C:0.00, G:0.40, T:0.42
Consensus pattern (15 bp):
AATTTTGTGGTGGAT
Found at i:2053215 original size:13 final size:13
Alignment explanation
Indices: 2053197--2053221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2053187 ATTACTCACA
2053197 TGTATCGATACAT
1 TGTATCGATACAT
2053210 TGTATCGATACA
1 TGTATCGATACA
2053222 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2053273 original size:52 final size:50
Alignment explanation
Indices: 2053210--2053350 Score: 201
Period size: 52 Copynumber: 2.7 Consensus size: 50
2053200 ATCGATACAT
*
2053210 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
2053262 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
2053314 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1 TGTATCGATACACTATT--ATGTATCGATACATGCAG
2053351 ATAAATTTTC
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
51 2 0.03
52 78 0.98
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:2053358 original size:52 final size:52
Alignment explanation
Indices: 2053230--2053350 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
2053220 CACTGATCTT
*
2053230 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2053282 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2053334 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
2053351 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2059798 original size:20 final size:20
Alignment explanation
Indices: 2059773--2059847 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
2059763 AAAAAAATAC
* *
2059773 ATTGTATCGATACCTTGAAA
1 ATTGTATCAATACATTGAAA
* *
2059793 ATTGTATCAATACATTCATAC
1 ATTGTATCAATACATTGA-AA
*
2059814 A-TGTATCGATACATTGAAA
1 ATTGTATCAATACATTGAAA
*
2059833 AATGTATCAATACAT
1 ATTGTATCAATACAT
2059848 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 41 0.91
21 2 0.04
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (20 bp):
ATTGTATCAATACATTGAAA
Found at i:2059825 original size:40 final size:41
Alignment explanation
Indices: 2059769--2059847 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 41
2059759 AGCTAAAAAA
* *
2059769 ATACATTGTATCGATACCTTGAAAATTGTATCAATACATTC
1 ATACATTGTATCGATACATTGAAAAATGTATCAATACATTC
2059810 ATACA-TGTATCGATACATTGAAAAATGTATCAATACAT
1 ATACATTGTATCGATACATTGAAAAATGTATCAATACAT
2059848 CTGGGTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 31 0.86
41 5 0.14
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (41 bp):
ATACATTGTATCGATACATTGAAAAATGTATCAATACATTC
Found at i:2064190 original size:21 final size:20
Alignment explanation
Indices: 2064150--2064188 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
2064140 TTAAGTATAA
2064150 ATATTTTTCAAGCATTAAATC
1 ATATTTTTCAA-CATTAAATC
2064171 ATATGTTTTCAA-ATTAAA
1 ATAT-TTTTCAACATTAAA
2064189 ATAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 4 0.24
22 7 0.41
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (20 bp):
ATATTTTTCAACATTAAATC
Found at i:2066474 original size:16 final size:15
Alignment explanation
Indices: 2066425--2066466 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
2066415 AAATAAATAA
* *
2066425 AAAATTGTTGAGAAT
1 AAAATTGTTGAAAAG
*
2066440 AAAATTTTTGAAAAG
1 AAAATTGTTGAAAAG
2066455 AAAATTGTTGAA
1 AAAATTGTTGAA
2066467 CTAGAAAAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (15 bp):
AAAATTGTTGAAAAG
Found at i:2068245 original size:18 final size:19
Alignment explanation
Indices: 2068219--2068256 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2068209 TGTTCATCAC
2068219 TATTCA-TGTATCGATACA
1 TATTCAGTGTATCGATACA
*
2068237 TATTTATGTGTATCGATACA
1 TATTCA-GTGTATCGATACA
2068257 GTGTATCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
20 12 0.71
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (19 bp):
TATTCAGTGTATCGATACA
Done.