Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008617.1 Hibiscus syriacus cultivar Beakdansim tig00111575_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 526994
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:253438 original size:105 final size:103
Alignment explanation
Indices: 252435--253438 Score: 703
Period size: 105 Copynumber: 9.6 Consensus size: 103
252425 GTCGTGGTCG
* * * *
252435 TGGAATAAATCGCAA-CGAATTTGGAATAAATCGCAACGCGAACTT-CACTATCGCAACGAACTT
1 TGGAATAAATCGCAAGCGAACTTCGACT--ATCGCAA-GCGAACTTGGACTATCGCAACGAACTT
*
252498 GGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATT
63 GGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATT
* * * * * *
252539 TGGAATAAATCACAACGCGAACTTCGACTATCGCAA-CCAATTTGGAATAAATCGCAACCAATTT
1 TGGAATAAATCGCAA-GCGAACTTCGACTATCGCAAGCGAACTTGGACT--ATCGCAACGAACTT
* * *
252603 GGAATAAATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACT
63 GGAATAAATCGCAACGCGAACTTGGACT--ATCGCAA--CGAATT
* * * ** *
252646 TCGACT--ATCGCAA-CGAA-TTTGAAAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTG
1 TGGAATAAATCGCAAGCGAACTTCG-ACTATCGCAA-GCGAACTTGGACTATCGCAACGAACTTG
252707 GAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATT
64 GAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATT
* * *
252747 TGGAATAAATCGCAACGCGAACTTCGACTATCGCAA-CGAAGTTGGAATAAATCACAACGCGAAC
1 TGGAATAAATCGCAA-GCGAACTTCGACTATCGCAAGCGAACTTGGACT--ATCGCAA--CGAAC
* * * * *
252811 TTCGACT--ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACT
61 TTGGAATAAATCGCAACGCGAACTTGGACT--ATCGCAA--CGAATT
* * * * *
252854 TCGACT--ATCGCAA-CGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAAC
1 TGGAATAAATCGCAAGCGAACTTCGACT--ATCGCAA-GCGAACTTGGACTATCGCAA--CGAAC
* * * * *
252916 TTGGACT--ATCGCAA--CGAATTTGGAATAAATCACAACGCGAACT
61 TTGGAATAAATCGCAACGCGAACTTGGACT--ATCGCAA--CGAATT
* * * * * * * *
252959 TCGACT--ATCGCAA-CGAATTTGGAATAAATCGCAACGCGAAGTTCGACTATCGCAACGAATTT
1 TGGAATAAATCGCAAGCGAACTTCGACT--ATCGCAA-GCGAACTTGGACTATCGCAACGAACTT
*
253021 GG-A-AAATCGCAACGCGAACTTGGACTACCGCAA-GAATT
63 GGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATT
* * *
253059 TGG-A-AAATCGCAATGCGAACTTGGACTATCGCAA-CGAATTTGGAATAAATCGCAACGCGAAC
1 TGGAATAAATCGCAA-GCGAACTTCGACTATCGCAAGCGAACTTGGACT--ATCGCAA--CGAAC
* * * *
253121 TTCGACT--ATCGCAACGCGAACTTCGACTATCGCAATGCGAACT
61 TTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA--CGAATT
* * * * * *
253164 TGGACT--ATCGCAA-CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTT
1 TGGAATAAATCGCAAGCGAACTTCGACT--ATCGCAA-GCGAACTTGGACTATCGCAACGAACTT
* *
253226 TGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATT
63 GGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATT
*
253267 TGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAACGAATTTG
1 TGGAATAAATCGCAA-GCGAACTTCGACTATCGCAA-GCGAACTTGGACTATCGCAACGAACTTG
* *
253332 GAATAAATCACAACGCGAACTTCGACTATCGCAACGAATT
64 GAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATT
* * **
253372 TGGAATAAATCGCAACGCGAACTTCGACTATCACAA-CGAATTTGGAAAATCGCAACGCGAACTT
1 TGGAATAAATCGCAA-GCGAACTTCGACTATCGCAAGCGAACTTGGACTATCGCAA--CGAACTT
253436 GGA
63 GGA
253439 CTATCGCAAT
Statistics
Matches: 741, Mismatches: 97, Indels: 123
0.77 0.10 0.13
Matches are distributed among these distances:
98 9 0.01
100 27 0.04
101 9 0.01
102 51 0.07
103 159 0.21
104 21 0.03
105 399 0.54
106 12 0.02
107 54 0.07
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (103 bp):
TGGAATAAATCGCAAGCGAACTTCGACTATCGCAAGCGAACTTGGACTATCGCAACGAACTTGGA
ATAAATCGCAACGCGAACTTGGACTATCGCAACGAATT
Found at i:253454 original size:42 final size:42
Alignment explanation
Indices: 252443--253447 Score: 775
Period size: 42 Copynumber: 24.2 Consensus size: 42
252433 CGTGGAATAA
*
252443 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTT-CACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
* *
252484 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
* *
252526 ATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
* * *
252568 ATCGCAACCAATTTGGAATAAATCGCAAC-C-AATTTGGAAT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
*
252608 AAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
252652 ATCGCAACGAATTT-GAA-AAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
252692 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
*
252734 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
* * *
252776 ATCGCAACGAAGTTGGAATAAATCACAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
*
252818 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
* *
252860 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
* * * *
252902 ATCGCAATGCGAACTTGGACT--ATCGCAA--CGAATTTGGAAT
1 ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTGGACT
* * * * * *
252942 AAATCACAACGCGAACTTCGACT--ATCGCAA--CGAATTTGGAAT
1 --ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTGGACT
* * * * **
252984 AAATCGCAACGCGAAGTTCGACT--ATCGCAA--CGAATTTGGAAA
1 --ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTGGACT
* * * * **
253026 ATCGCAACGCGAACTTGGACT--ACCGCAA---GAATTTGGAAA
1 ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTGGACT
* * * *
253065 ATCGCAATGCGAACTTGGACT--ATCGCAA--CGAATTTGGAAT
1 ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTGGACT
* * * *
253105 AAATCGCAACGCGAACTTCGACT--ATCGCAACGCGAACTTCGACT
1 --ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTGGACT
* * * *
253149 ATCGCAATGCGAACTTGGACT--ATCGCAA--CGAATTTGGAAT
1 ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTGGACT
* * * * * *
253189 AAATCGCAACGCGAACTTCGACT--ATCGCAA--CGAATTTTGAAT
1 --ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTGGACT
* * * * *
253231 AAATCGCAACGCGAACTTCGACT--ATCGCAA--CGAATTTGGAAT
1 --ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTGGACT
* * * *
253273 AAATCGCAACGCGAACTTCGACT--ATCGCAATGCGAACTTGGACT
1 --ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTGGACT
* *
253317 ATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
*
253359 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
*
253401 ATCACAACGAATTTGG-A-AAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
253441 ATCGCAA
1 ATCGCAA
253448 TACGAATATG
Statistics
Matches: 880, Mismatches: 62, Indels: 45
0.89 0.06 0.05
Matches are distributed among these distances:
39 37 0.04
40 133 0.15
41 44 0.05
42 628 0.71
43 1 0.00
44 37 0.04
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
Found at i:255466 original size:27 final size:26
Alignment explanation
Indices: 255435--255515 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 26
255425 AGATAATAAC
255435 AAAAAACATTTTTAAGTTAATAAAAG
1 AAAAAACATTTTTAAGTTAATAAAAG
* * * * *
255461 ATAAAATATATTTTTTGGAGTTAAGATAAT
1 A-AAAA-ACA-TTTTT-AAGTTAATAAAAG
255491 AAAAAACTATTTTTAAGTTAATAAA
1 AAAAAAC-ATTTTTAAGTTAATAAA
255516 GTAATAAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 9
0.69 0.15 0.15
Matches are distributed among these distances:
26 1 0.02
27 12 0.29
28 8 0.20
29 10 0.24
30 10 0.24
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37
Consensus pattern (26 bp):
AAAAAACATTTTTAAGTTAATAAAAG
Found at i:255523 original size:30 final size:28
Alignment explanation
Indices: 255442--255654 Score: 146
Period size: 30 Copynumber: 7.3 Consensus size: 28
255432 AACAAAAAAC
255442 ATTTTTAAGTTAATAAA-AGATAAAATAT
1 ATTTTTAAGTTAATAAATA-ATAAAATAT
* * *
255470 ATTTTTTGGAGTTAAGATAATAA-AAAA-CT
1 A-TTTTT-AAGTTAATA-AATAATAAAATAT
255499 ATTTTTAAGTTAATAAAGTAATAAAATAT
1 ATTTTTAAGTTAATAAA-TAATAAAATAT
* * *
255528 ATTATTTGAATTTAAGATAATAACAAAATAT
1 ATT-TTT-AAGTTAATA-AATAATAAAATAT
*
255559 ATTTTTTAAGTTAATAAAAGAATAAAATAT
1 A-TTTTTAAGTTAAT-AAATAATAAAATAT
* * * * *
255589 ATTATTTGA-TATAAGATAATAACATAATAC
1 ATT-TTTAAGT-TAATA-AATAATAAAATAT
* *
255619 ATTTTTAAGTTAATAAAAAATTAAATAT
1 ATTTTTAAGTTAATAAATAATAAAATAT
*
255647 AATTTTAA
1 ATTTTTAA
255655 AAGTAAATAT
Statistics
Matches: 142, Mismatches: 27, Indels: 32
0.71 0.13 0.16
Matches are distributed among these distances:
26 2 0.01
27 10 0.07
28 25 0.18
29 23 0.16
30 52 0.37
31 25 0.18
32 5 0.04
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (28 bp):
ATTTTTAAGTTAATAAATAATAAAATAT
Found at i:255548 original size:58 final size:57
Alignment explanation
Indices: 255413--255647 Score: 287
Period size: 58 Copynumber: 4.0 Consensus size: 57
255403 CTTTAAAATG
255413 TATTTGAATTTAAGATAATAACAAAAAACATTTTTAAGTTAATAAA-AGATAAAATATAT
1 TATTTGAATTTAAGATAATAAC--AAAACATTTTTAAGTTAATAAAGA-ATAAAATATAT
* * *
255472 TTTTTGGAGTTAAGATAATAA-AAAACTATTTTTAAGTTAATAAAGTAATAAAATATAT
1 TATTTGAATTTAAGATAATAACAAAAC-ATTTTTAAGTTAATAAAG-AATAAAATATAT
*
255530 TATTTGAATTTAAGATAATAACAAAATATATTTTTTAAGTTAATAAAAGAATAAAATATAT
1 TATTTGAATTTAAGATAATAAC-AAA-ACA-TTTTTAAGTTAAT-AAAGAATAAAATATAT
* * *
255591 TATTTG-ATATAAGATAATAACATAATACATTTTTAAGTTAATAAAAAATTAAATATA
1 TATTTGAATTTAAGATAATAACA-AA-ACATTTTTAAGTTAATAAAGAATAAAATATA
255648 ATTTTAAAAG
Statistics
Matches: 156, Mismatches: 11, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
56 5 0.03
57 17 0.11
58 42 0.27
59 33 0.21
60 23 0.15
61 32 0.21
62 4 0.03
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (57 bp):
TATTTGAATTTAAGATAATAACAAAACATTTTTAAGTTAATAAAGAATAAAATATAT
Found at i:258880 original size:3 final size:3
Alignment explanation
Indices: 258874--258906 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
258864 TAAAAAAATA
*
258874 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
258907 AATTTACATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:259403 original size:4 final size:4
Alignment explanation
Indices: 259394--259421 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
259384 GATAAAAACG
259394 AAGA AAGA AAGA AAGA AAGA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA
259422 GGGATGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:260482 original size:28 final size:28
Alignment explanation
Indices: 260434--260494 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
260424 ATCATGTATG
** * *
260434 TATATTTATATATGTTTTTATGTAAGTA
1 TATATTTATATATCATATTATATAAGTA
*
260462 TATATTTATATATCATATTATATATGTA
1 TATATTTATATATCATATTATATAAGTA
260490 TATAT
1 TATAT
260495 CTATTAAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (28 bp):
TATATTTATATATCATATTATATAAGTA
Found at i:260483 original size:20 final size:19
Alignment explanation
Indices: 260460--260500 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
260450 TTTATGTAAG
*
260460 TATATATTTATATATCATAT
1 TATATATGTATATATC-TAT
260480 TATATATGTATATATCTAT
1 TATATATGTATATATCTAT
260499 TA
1 TA
260501 AATGTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (19 bp):
TATATATGTATATATCTAT
Found at i:265288 original size:32 final size:32
Alignment explanation
Indices: 265243--265337 Score: 127
Period size: 32 Copynumber: 3.0 Consensus size: 32
265233 AAGAAATAAT
* * *
265243 GAATGATGGGGCATATTTGGAGATTTAACATC
1 GAATGTTGGGGCATCTTTGGAGATTAAACATC
*
265275 GAATGTTGTGGCATCTTTGGAGATTAAACATC
1 GAATGTTGGGGCATCTTTGGAGATTAAACATC
* * *
265307 AAATGTTGGGGAATCTTTGGAGATTCAACAT
1 GAATGTTGGGGCATCTTTGGAGATTAAACAT
265338 TCTGAAGTGA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.33
Consensus pattern (32 bp):
GAATGTTGGGGCATCTTTGGAGATTAAACATC
Found at i:265541 original size:36 final size:35
Alignment explanation
Indices: 265440--265571 Score: 138
Period size: 36 Copynumber: 3.7 Consensus size: 35
265430 ACAAAAGGTC
265440 GTCTCACTTGAGACAAGTTTTCTTAAAAACAAAATTTA
1 GTCTCACTTGAGACAA-TTTTCTT-AAAAC-AAATTTA
** * * * *
265478 GTCTTGCTTGAGATAGTTTTCTGAAAACAAATTTT
1 GTCTCACTTGAGACAATTTTCTTAAAACAAATTTA
* *
265513 GTCTCACTTGAGACAATTTATCTTAAAACCAATTTC
1 GTCTCACTTGAGACAATTT-TCTTAAAACAAATTTA
* *
265549 GTCTCGCTTGAGACATTTTTCTT
1 GTCTCACTTGAGACAATTTTCTT
265572 TTGAGATACA
Statistics
Matches: 78, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
35 25 0.32
36 35 0.45
37 6 0.08
38 12 0.15
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (35 bp):
GTCTCACTTGAGACAATTTTCTTAAAACAAATTTA
Found at i:265633 original size:36 final size:36
Alignment explanation
Indices: 265586--265683 Score: 101
Period size: 36 Copynumber: 2.7 Consensus size: 36
265576 GATACAAATT
* *
265586 TTGAGTTTGTTTCACTTGAAACAAA-GTTGATCTCAC
1 TTGAGATTGTTTCACTTAAAACAAACGTTG-TCTCAC
** *
265622 TTGAGATTGTTTTTCTTAAAACAAACTTTGTCTCAC
1 TTGAGATTGTTTCACTTAAAACAAACGTTGTCTCAC
* *
265658 TTGAGATAGTCTTC-CTTAAGACAAAC
1 TTGAGATTGT-TTCACTTAAAACAAAC
265684 TTTGAAATTG
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
36 47 0.90
37 5 0.10
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (36 bp):
TTGAGATTGTTTCACTTAAAACAAACGTTGTCTCAC
Found at i:265684 original size:36 final size:36
Alignment explanation
Indices: 265616--265687 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
265606 ACAAAGTTGA
* * *
265616 TCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTG
1 TCTCACTTGAGATAGTCTTCCTTAAAACAAACTTTG
*
265652 TCTCACTTGAGATAGTCTTCCTTAAGACAAACTTTG
1 TCTCACTTGAGATAGTCTTCCTTAAAACAAACTTTG
265688 AAATTGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (36 bp):
TCTCACTTGAGATAGTCTTCCTTAAAACAAACTTTG
Found at i:266267 original size:134 final size:130
Alignment explanation
Indices: 265965--266311 Score: 392
Period size: 134 Copynumber: 2.6 Consensus size: 130
265955 ATGGCATGTT
* * * * *
265965 GTCCTCATCGTGTAGGAACCGTGTCATCCACCGACCATACCTCCTCATCACGTAAGAGCCGTATC
1 GTCCTCATCGCGTAGGAACCGTGTCATCCACCAACCAAACCTCCTCATCACGTAAGAGACGTGTC
* * * *
266030 ACCCCCTAGATAACCAGTCGTCCTCATCACGTAGAAATCGTGTTATCATCCATAAAGATGGCCTG
66 A--CCCTAGATAACCAGCCATCCTCATCACGTAGAAATCGTGTTATCATCCATAAAGATAGCCAG
266095 CC
129 CC
* *
266097 ATCCTCATCACGTAGGAACCGTGTCATCCACCAACCAAACCTCCTCATCACGTAAGAGACGTGTC
1 GTCCTCATCGCGTAGGAACCGTGTCATCCACCAACCAAACCTCCTCATCACGTAAGAGACGTGTC
* * *
266162 ACTCCTAGATAACCAGCCATTCTCATCGCGTAGGAA-CTGTGTTATCACCCTTCC-TAAAGATAG
66 AC-CCTAGATAACCAGCCATCCTCATCACGTAGAAATC-GTGTTATCA----TCCATAAAGATAG
*
266225 CCAGGC
125 CCAGCC
* * * * * * *
266231 GTCCTTATCGCGTAGGAACCGTGTTATCCACCAACCAGATCTCCTTATCACGTAGGAGTCGTGTC
1 GTCCTCATCGCGTAGGAACCGTGTCATCCACCAACCAAACCTCCTCATCACGTAAGAGACGTGTC
*
266296 ACCCTTAGATGACCAG
66 ACCC-TAGATAACCAG
266312 AACTCTTCAT
Statistics
Matches: 183, Mismatches: 25, Indels: 12
0.83 0.11 0.05
Matches are distributed among these distances:
130 2 0.01
131 37 0.20
132 59 0.32
133 2 0.01
134 80 0.44
135 3 0.02
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (130 bp):
GTCCTCATCGCGTAGGAACCGTGTCATCCACCAACCAAACCTCCTCATCACGTAAGAGACGTGTC
ACCCTAGATAACCAGCCATCCTCATCACGTAGAAATCGTGTTATCATCCATAAAGATAGCCAGCC
Found at i:268882 original size:20 final size:22
Alignment explanation
Indices: 268857--268904 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
268847 TTTTTTAAAA
*
268857 TAAAAATCATAATT-ATT-TTT
1 TAAAAATAATAATTAATTATTT
*
268877 TAAAAATAATATTTAATTATTT
1 TAAAAATAATAATTAATTATTT
268899 TAAAAA
1 TAAAAA
268905 AATGGTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.50
21 3 0.12
22 9 0.38
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TAAAAATAATAATTAATTATTT
Found at i:270449 original size:2 final size:2
Alignment explanation
Indices: 270442--270470 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
270432 CCTTCTCTAT
270442 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
270471 TTGGCCCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:270800 original size:33 final size:33
Alignment explanation
Indices: 270758--270826 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
270748 GACACATTAC
*
270758 ATGATTAAGTGCTTTAGTCTTTCTGATATTCTT
1 ATGATTAAGTGCTTAAGTCTTTCTGATATTCTT
270791 ATGATTAAGTGCTTAAGTCTTTCTGATATTCTT
1 ATGATTAAGTGCTTAAGTCTTTCTGATATTCTT
270824 ATG
1 ATG
270827 TCTTTGAGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.23, C:0.12, G:0.16, T:0.49
Consensus pattern (33 bp):
ATGATTAAGTGCTTAAGTCTTTCTGATATTCTT
Found at i:274220 original size:34 final size:36
Alignment explanation
Indices: 274181--274346 Score: 143
Period size: 34 Copynumber: 4.6 Consensus size: 36
274171 TTTGAAAATA
274181 TTTTTGAAAACATATAATATATAGTTT-AAAAACGG
1 TTTTTGAAAACATATAATATATAGTTTAAAAAACGG
* * **
274216 -TTTTGAAAATATATAACATATAGTTT---TTACGG
1 TTTTTGAAAACATATAATATATAGTTTAAAAAACGG
274248 TTTTTGAAAACATATAATATATAGCTTTTTAAAAAACGG
1 TTTTTGAAAACATATAATATATAG---TTTAAAAAACGG
* *
274287 TTTTTGAAAACGAATATAATATA-ATTTTGAAAATA---
1 TTTTTGAAAAC--ATATAATATATAGTTT-AAAAAACGG
274322 TATTTTGAAAACATATATATATATA
1 T-TTTTGAAAACATATA-ATATATA
274347 TATATATATA
Statistics
Matches: 108, Mismatches: 10, Indels: 25
0.76 0.07 0.17
Matches are distributed among these distances:
32 4 0.04
33 21 0.19
34 29 0.27
35 6 0.06
36 14 0.13
37 3 0.03
38 5 0.05
39 15 0.14
40 1 0.01
41 10 0.09
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (36 bp):
TTTTTGAAAACATATAATATATAGTTTAAAAAACGG
Found at i:274328 original size:13 final size:13
Alignment explanation
Indices: 274304--274337 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
274294 AAACGAATAT
274304 AATATAATTTTGAA
1 AATAT-ATTTTGAA
274318 AATATATTTTGAA
1 AATATATTTTGAA
*
274331 AACATAT
1 AATATAT
274338 ATATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (13 bp):
AATATATTTTGAA
Found at i:274339 original size:2 final size:2
Alignment explanation
Indices: 274334--274368 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
274324 TTTTGAAAAC
274334 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
274369 GTTTTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:274444 original size:20 final size:21
Alignment explanation
Indices: 274411--274449 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
274401 TATATATAAC
*
274411 TTTTGGAAACATATTATATAG
1 TTTTGGAAACATATAATATAG
*
274432 TTTTTGAAA-ATATAATAT
1 TTTTGGAAACATATAATAT
274450 GTTATATAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (21 bp):
TTTTGGAAACATATAATATAG
Found at i:274496 original size:12 final size:11
Alignment explanation
Indices: 274481--274532 Score: 65
Period size: 12 Copynumber: 4.8 Consensus size: 11
274471 TATATAGTAC
274481 ATATTATATTAT
1 ATATTAT-TTAT
274493 ATATTATTTAT
1 ATATTATTTAT
274504 AGTATTATTTAT
1 A-TATTATTTAT
274516 -TATT-TTTA-
1 ATATTATTTAT
274524 ATATTATTT
1 ATATTATTT
274533 TTCGGTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
9 8 0.22
10 7 0.19
11 5 0.14
12 17 0.46
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
ATATTATTTAT
Found at i:274531 original size:19 final size:19
Alignment explanation
Indices: 274486--274532 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
274476 AGTACATATT
*
274486 ATATTATATATTATTTATA
1 ATATTATTTATTATTTATA
* *
274505 GTATTATTTATTATTTTTA
1 ATATTATTTATTATTTATA
274524 ATATTATTT
1 ATATTATTT
274533 TTCGGTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATATTATTTATTATTTATA
Found at i:278017 original size:110 final size:112
Alignment explanation
Indices: 277865--278066 Score: 291
Period size: 110 Copynumber: 1.8 Consensus size: 112
277855 TTCAAAAAAG
* * * *
277865 TATCGATCATTTTTATAAAAAATATCTATACTTTCAACATATCAGGTAAATTTTATCGGTTTTGT
1 TATCGATCACTTTTATAAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGT
* **
277930 CATAATTAAACTGGTTTTGTCATATTTATACTTGTTATATTGTAAGA
66 CATAATGAAACTAATTTTGTCATATTTATACTTGTTATATTGTAAGA
* * * *
277977 TATCGATC-CTTTTAT-AAAAGGATCGATACTTTTAACATATCAGGTATATTTTACCGTTTTTGT
1 TATCGATCACTTTTATAAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGT
278040 CATAATGAAACTAATTTTGTCATATTT
66 CATAATGAAACTAATTTTGTCATATTT
278067 TTACCTGCCA
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
110 65 0.82
111 6 0.08
112 8 0.10
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (112 bp):
TATCGATCACTTTTATAAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGT
CATAATGAAACTAATTTTGTCATATTTATACTTGTTATATTGTAAGA
Found at i:278684 original size:23 final size:23
Alignment explanation
Indices: 278649--278715 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
278639 CTAGTAATTA
**
278649 ACCTATTTTATTATATAAGCACT
1 ACCTATTACATTATATAAGCACT
* *
278672 ACTTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCACT
278695 ACCTATTACATTATATAAGCA
1 ACCTATTACATTATATAAGCA
278716 ATACATAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCACT
Found at i:278766 original size:110 final size:110
Alignment explanation
Indices: 278573--278802 Score: 363
Period size: 110 Copynumber: 2.1 Consensus size: 110
278563 TCTATTTTAA
* * * *
278573 TATATAATCGCTACCTATTACGTTATATAAGAGCTACTTAATATGTTATTGTGCATGATAATGTT
1 TATATAAGCGCTACCTATTACATTATATAAGAGATACATAATATGTTATTGTGCATGATAATGTT
*
278638 TCTAGTAATTAACCTATTTTATTATATAAGCACTACTTATTACAT
66 TCTAGTAATTAACCTATTTTATTATATAAGCACTACCTATTACAT
*
278683 TATATAAGCGCTACCTATTACATTATATAAGCA-ATACATAATATGTTATTGTGCTTGATAATGT
1 TATATAAGCGCTACCTATTACATTATATAAG-AGATACATAATATGTTATTGTGCATGATAATGT
* * *
278747 TTCTAGTAATTAATCTATTTTATTATATAAGCGCTACCTGTTACAT
65 TTCTAGTAATTAACCTATTTTATTATATAAGCACTACCTATTACAT
278793 TATATAAGCG
1 TATATAAGCG
278803 GTACTTAATA
Statistics
Matches: 110, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
110 109 0.99
111 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (110 bp):
TATATAAGCGCTACCTATTACATTATATAAGAGATACATAATATGTTATTGTGCATGATAATGTT
TCTAGTAATTAACCTATTTTATTATATAAGCACTACCTATTACAT
Found at i:281018 original size:29 final size:29
Alignment explanation
Indices: 280976--281034 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
280966 GCAACGACTC
* *
280976 AAGGTTTCATTCTCCCTTTAGTGAGCTGA
1 AAGGTTTCAGTCTCCCTTTAATGAGCTGA
*
281005 AAGGTTTCAGTCTCCTTTTAATGAGCTGA
1 AAGGTTTCAGTCTCCCTTTAATGAGCTGA
281034 A
1 A
281035 CTATCAAGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (29 bp):
AAGGTTTCAGTCTCCCTTTAATGAGCTGA
Found at i:287054 original size:90 final size:90
Alignment explanation
Indices: 286894--287081 Score: 362
Period size: 90 Copynumber: 2.1 Consensus size: 90
286884 ATGTCAAGAG
286894 AAGAAAA--ATACAAGAGGAGTCCTCCTGGACAACATTATTACTAACCTTAATCCTTAGTATCTA
1 AAGAAAACTATACAAGAGGAGTCCTCCTGGACAACATTATTACTAACCTTAATCCTTAGTATCTA
286957 TTATAAAACAAATACTTGATTACAA
66 TTATAAAACAAATACTTGATTACAA
286982 AAGAAAACTATACAAGAGGAGTCCTCCTGGACAACATTATTACTAACCTTAATCCTTAGTATCTA
1 AAGAAAACTATACAAGAGGAGTCCTCCTGGACAACATTATTACTAACCTTAATCCTTAGTATCTA
287047 TTATAAAACAAATACTTGATTACAA
66 TTATAAAACAAATACTTGATTACAA
287072 AAGAAAACTA
1 AAGAAAACTA
287082 AATAAAATAA
Statistics
Matches: 98, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
88 7 0.07
90 91 0.93
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (90 bp):
AAGAAAACTATACAAGAGGAGTCCTCCTGGACAACATTATTACTAACCTTAATCCTTAGTATCTA
TTATAAAACAAATACTTGATTACAA
Found at i:288160 original size:31 final size:31
Alignment explanation
Indices: 288122--288246 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
288112 CCCGAAGGAC
* * *
288122 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
288153 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
288184 AAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
288215 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
288246 C
1 C
288247 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:292528 original size:31 final size:31
Alignment explanation
Indices: 292505--292643 Score: 224
Period size: 31 Copynumber: 4.5 Consensus size: 31
292495 CATAGATTCT
* *
292505 GAAGAACCTAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
**
292536 GAAGAACATAGGTAAACAACCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
292567 GAAAGAACATAGGTAAACAGTCCATAAGTCCC
1 G-AAGAACATAGGTAAACAGTCCATATGTCCC
292599 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
292630 GAAGAACATAGGTA
1 GAAGAACATAGGTA
292644 GACCCTCGAC
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 71 0.72
32 28 0.28
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.18
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:292605 original size:63 final size:62
Alignment explanation
Indices: 292505--292643 Score: 224
Period size: 63 Copynumber: 2.2 Consensus size: 62
292495 CATAGATTCT
* * *
292505 GAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAACAACCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATAAGTCCCGAAGAACATAGGTAAACAACCCATATGTCCC
**
292567 GAAAGAACATAGGTAAACAGTCCATAAGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCC
1 G-AAGAACATAGGTAAACAGTCCATAAGTCCCGAAGAACATAGGTAAACAACCCATATGTCCC
292630 GAAGAACATAGGTA
1 GAAGAACATAGGTA
292644 GACCCTCGAC
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 14 0.20
63 57 0.80
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.18
Consensus pattern (62 bp):
GAAGAACATAGGTAAACAGTCCATAAGTCCCGAAGAACATAGGTAAACAACCCATATGTCCC
Found at i:298731 original size:2 final size:2
Alignment explanation
Indices: 298724--298759 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
298714 GGTTTGCCGA
298724 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
298760 GTGCACGCGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:298842 original size:2 final size:2
Alignment explanation
Indices: 298835--298897 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
298825 TTCGATTGTT
298835 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
298877 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
298898 GTCAATGCCA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:302769 original size:18 final size:18
Alignment explanation
Indices: 302746--302788 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
302736 GTATACCTCG
*
302746 AGAAGAAGGAC-GAGACAA
1 AGAAGAA-GACGGAGAAAA
302764 AGAAGAAGACGGAGAAAA
1 AGAAGAAGACGGAGAAAA
302782 AGAAGAA
1 AGAAGAA
302789 CGTATGAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.60, C:0.07, G:0.33, T:0.00
Consensus pattern (18 bp):
AGAAGAAGACGGAGAAAA
Found at i:303321 original size:21 final size:20
Alignment explanation
Indices: 303296--303357 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
303286 CCAATACCAA
303296 CAATGATATTGAAAGTAAAAT
1 CAATGATATTGAAA-TAAAAT
*
303317 TAATGA-ATTGCAAATCAAAAT
1 CAATGATATTG-AAAT-AAAAT
*
303338 CAATGATTTTGAAAATAAAA
1 CAATGATATTG-AAATAAAA
303358 ATTCTGATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 5 0.15
21 22 0.65
22 7 0.21
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.29
Consensus pattern (20 bp):
CAATGATATTGAAATAAAAT
Found at i:305576 original size:65 final size:65
Alignment explanation
Indices: 305456--305581 Score: 157
Period size: 65 Copynumber: 1.9 Consensus size: 65
305446 TCAAAGAGAT
* * * **
305456 GTACCGATGCACTAGTCTATGCATCAATGCACTCTCAATTAAATTGAATTTCGAATGCATTTAGA
1 GTACCGATGCACTACTCTATGCATCAATGCACTCTCAATCAAATAGAACATCGAATGCATTTAGA
* *
305521 GTACCGATGCACT-CTCTATGCATCGATGCACTCTTGAA-CAAATAGAAACATCGAATGCATT
1 GTACCGATGCACTACTCTATGCATCAATGCACTC-TCAATCAAATAG-AACATCGAATGCATT
305582 CAATGAACCG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
64 23 0.44
65 29 0.56
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (65 bp):
GTACCGATGCACTACTCTATGCATCAATGCACTCTCAATCAAATAGAACATCGAATGCATTTAGA
Found at i:305592 original size:65 final size:65
Alignment explanation
Indices: 305458--305597 Score: 151
Period size: 65 Copynumber: 2.2 Consensus size: 65
305448 AAAGAGATGT
* * * ** * *
305458 ACCGATGCACTAGTCTATGCATCAATGCACTCTCAATTAAATTGAATTTCGAATGCATTTAGAGT
1 ACCGATGCACTACTCTATGCATCAATGCACTCTCAATCAAATAGAACATCGAATGCATTCAGAGA
* *
305523 ACCGATGCACT-CTCTATGCATCGATGCACTCTTGAA-CAAATAGAAACATCGAATGCATTCA-A
1 ACCGATGCACTACTCTATGCATCAATGCACTC-TCAATCAAATAG-AACATCGAATGCATTCAGA
305585 TGA
64 -GA
305588 ACCGATGCAC
1 ACCGATGCAC
305598 AAGCCATGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
64 24 0.38
65 39 0.62
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (65 bp):
ACCGATGCACTACTCTATGCATCAATGCACTCTCAATCAAATAGAACATCGAATGCATTCAGAGA
Found at i:315488 original size:23 final size:23
Alignment explanation
Indices: 315454--315505 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
315444 AGAATCAATA
315454 CCCCCT-TAAAGGGGAACCGATT
1 CCCCCTATAAAGGGGAACCGATT
*
315476 CCCCCTATGAAGGGGAACCGATT
1 CCCCCTATAAAGGGGAACCGATT
315499 CCCCCTA
1 CCCCCTA
315506 GGGGAATCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 6 0.21
23 22 0.79
ACGTcount: A:0.25, C:0.37, G:0.21, T:0.17
Consensus pattern (23 bp):
CCCCCTATAAAGGGGAACCGATT
Found at i:315510 original size:19 final size:19
Alignment explanation
Indices: 315463--315527 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 19
315453 ACCCCCTTAA
315463 AGGGGAACCGATTCCCCCTAT
1 AGGGGAACCGATTCCCCC--T
315484 GAAGGGGAACCGATTCCCCCT
1 --AGGGGAACCGATTCCCCCT
* *
315505 AGGGGAATCGATACCCCCT
1 AGGGGAACCGATTCCCCCT
315524 -GGGG
1 AGGGG
315528 TTCTGTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.10
19 17 0.43
21 1 0.03
23 18 0.45
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (19 bp):
AGGGGAACCGATTCCCCCT
Found at i:317758 original size:25 final size:25
Alignment explanation
Indices: 317691--317748 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
317681 CAATTGGCTT
*
317691 ACGTTTTTCAAAAATCTTGTTTAAA
1 ACGTTTTTCAAAAGTCTTGTTTAAA
317716 ACGTTTTTCAAAAGTCTTGTTTAAA
1 ACGTTTTTCAAAAGTCTTGTTTAAA
317741 ACGTTTTT
1 ACGTTTTT
317749 ATAGGGTCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (25 bp):
ACGTTTTTCAAAAGTCTTGTTTAAA
Found at i:328753 original size:20 final size:19
Alignment explanation
Indices: 328724--328761 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
328714 TATGCTCGGA
328724 GGGAACCGATTCCCCCCAG
1 GGGAACCGATTCCCCCCAG
328743 GGGATACCGATTCCCCCCA
1 GGGA-ACCGATTCCCCCCA
328762 CTGTTCAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.21, C:0.42, G:0.24, T:0.13
Consensus pattern (19 bp):
GGGAACCGATTCCCCCCAG
Found at i:332957 original size:65 final size:65
Alignment explanation
Indices: 332837--332997 Score: 166
Period size: 65 Copynumber: 2.5 Consensus size: 65
332827 TTCAAAGAGA
* * * **
332837 TGTACCGATGCACTAGTCCATGCATCGATGCACTCTCAATTAAATTGAATTTCGAATGCATTTAG
1 TGTACCGATGCACTACTCCATGCATCGATGCACTCTCAATCAAATAGAACATCGAATGCATTTAG
* * *
332902 TGTACCGATGCACT-CTCTATGCATCGATGCACTCTTGAA-CAAATAGAAACATCGAATGCATTC
1 TGTACCGATGCACTACTCCATGCATCGATGCACTC-TCAATCAAATAG-AACATCGAATGCATTT
*
332965 AA
64 AG
* * **
332967 TGCACCGATGTAC-AAGCCATGCATCGATGCA
1 TGTACCGATGCACTACTCCATGCATCGATGCA
332998 TCCAGGATTT
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
64 23 0.29
65 56 0.71
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (65 bp):
TGTACCGATGCACTACTCCATGCATCGATGCACTCTCAATCAAATAGAACATCGAATGCATTTAG
Found at i:337311 original size:11 final size:12
Alignment explanation
Indices: 337267--337312 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
337257 GGGGAGTAAT
*
337267 TTTTCAAAATTG
1 TTTTCAAAAATG
*
337279 ATTTCAAAAATG
1 TTTTCAAAAATG
337291 TTTTCAAAAATG
1 TTTTCAAAAATG
*
337303 TTTTTAAAAA
1 TTTTCAAAAA
337313 AAAATCTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (12 bp):
TTTTCAAAAATG
Found at i:337427 original size:20 final size:19
Alignment explanation
Indices: 337399--337442 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
337389 AATAAAATAC
* *
337399 TATTAAATTTTAAGATTTTA
1 TATTAAA-TTCAAAATTTTA
*
337419 TATTCAATTCAAAATTTTA
1 TATTAAATTCAAAATTTTA
337438 TATTA
1 TATTA
337443 GATTAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (19 bp):
TATTAAATTCAAAATTTTA
Found at i:342823 original size:25 final size:24
Alignment explanation
Indices: 342755--342824 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
342745 AAACTTATTC
* *
342755 AAACATTTTTCAAAATTATTTCATG
1 AAACA-TTTTCAAAATTCTTTCATA
* *
342780 AAGCATTTTCCGAAATTCTTTCATA
1 AAACATTTT-CAAAATTCTTTCATA
342805 AAACATTTTCAAAACTTCTT
1 AAACATTTTCAAAA-TTCTT
342825 CAGTAAACTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
24 8 0.22
25 29 0.78
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.41
Consensus pattern (24 bp):
AAACATTTTCAAAATTCTTTCATA
Found at i:343206 original size:30 final size:30
Alignment explanation
Indices: 343170--343296 Score: 155
Period size: 30 Copynumber: 4.2 Consensus size: 30
343160 CTAAGTACCT
* *
343170 AATAGTACTGGGACTTGGCCACCAATGTTA
1 AATAGTACAGGGACTTGGCCACCAAGGTTA
* * *
343200 AATAGTACAAGGACTTGACCACCAAGGTTT
1 AATAGTACAGGGACTTGGCCACCAAGGTTA
* *
343230 AATAGTATAGGGACTTGGCCACAAAGGTTA
1 AATAGTACAGGGACTTGGCCACCAAGGTTA
* ** *
343260 AATAATACAGGGACTTGGTAACCAATGTTA
1 AATAGTACAGGGACTTGGCCACCAAGGTTA
343290 AATAGTA
1 AATAGTA
343297 TAAGGATCGA
Statistics
Matches: 80, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 80 1.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (30 bp):
AATAGTACAGGGACTTGGCCACCAAGGTTA
Found at i:345201 original size:30 final size:31
Alignment explanation
Indices: 345138--345220 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 31
345128 CCCAAAGGAC
*
345138 CTATCCAGAGGTCACAAAG-ACC-CCAGTAA
1 CTATCCAGAGGTCACAAAGAACCTCCAGCAA
* *
345167 CTATCCAGAGGTCATAAAGAACCTCGA-CAA
1 CTATCCAGAGGTCACAAAGAACCTCCAGCAA
* *
345197 CTATCCATAGGTCCCAAAGAACCT
1 CTATCCAGAGGTCACAAAGAACCT
345221 AGGTAAACTG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 18 0.39
30 26 0.57
31 2 0.04
ACGTcount: A:0.37, C:0.30, G:0.16, T:0.17
Consensus pattern (31 bp):
CTATCCAGAGGTCACAAAGAACCTCCAGCAA
Found at i:347588 original size:20 final size:19
Alignment explanation
Indices: 347549--347590 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
347539 GTAACTTCAA
*
347549 TCCATTTTCATTTCTTTAT
1 TCCATTTTCATTTATTTAT
*
347568 TCCATTCTTCCTTTATTTAT
1 TCCATT-TTCATTTATTTAT
347588 TCC
1 TCC
347591 TTATACACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.14, C:0.26, G:0.00, T:0.60
Consensus pattern (19 bp):
TCCATTTTCATTTATTTAT
Found at i:349661 original size:30 final size:31
Alignment explanation
Indices: 349622--349688 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
349612 CCGGTAGCTA
* * * *
349622 TCCAGAGGTCATAAAGAACCTCGG-CAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
*
349652 TCCATAGGTCCCAAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
349683 TCCATA
1 TCCATA
349689 TGTTCCTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGTAAACTG
Found at i:349685 original size:31 final size:31
Alignment explanation
Indices: 349647--349741 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
349637 GAACCTCGGC
* *
349647 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* ** *
349678 AACTGTCCATATGTTCCTTATAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
349709 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
349740 AA
1 AA
349742 ACCCTCGACT
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
31 48 0.96
32 2 0.04
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:360216 original size:3 final size:3
Alignment explanation
Indices: 360208--360240 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
360198 GATTGTAGCT
360208 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
360241 TAACTTTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:361531 original size:2 final size:2
Alignment explanation
Indices: 361524--361557 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
361514 AGGCAATAAC
361524 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
361558 CTAAAAAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:362446 original size:44 final size:43
Alignment explanation
Indices: 362391--362480 Score: 153
Period size: 44 Copynumber: 2.1 Consensus size: 43
362381 TTTTCAATAA
* *
362391 TATTTAACACATGAAATCTTAGTAACTTCATTTTTAAATATATT
1 TATTTAACACATGAAATCTTAATAACTTCATTTAT-AATATATT
362435 TATTTAACACATGAAATCTTAATAACTTCATTTATAATATATT
1 TATTTAACACATGAAATCTTAATAACTTCATTTATAATATATT
362478 TAT
1 TAT
362481 ATAAATGTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
43 11 0.25
44 33 0.75
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (43 bp):
TATTTAACACATGAAATCTTAATAACTTCATTTATAATATATT
Found at i:369114 original size:21 final size:21
Alignment explanation
Indices: 369088--369131 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
369078 GTGCCATTAT
*
369088 CTAGGTTTCTTATATCAACAG
1 CTAGGTTTCTCATATCAACAG
*
369109 CTAGGTTTCTCATATCAATAG
1 CTAGGTTTCTCATATCAACAG
369130 CT
1 CT
369132 CCATGAGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (21 bp):
CTAGGTTTCTCATATCAACAG
Found at i:369892 original size:17 final size:17
Alignment explanation
Indices: 369872--369914 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
369862 GGAAGAAGCG
*
369872 AATGAGCCCACGAAGTT
1 AATGACCCCACGAAGTT
* *
369889 AATGCCCCCACGAAGTC
1 AATGACCCCACGAAGTT
369906 AAT-ACCCCA
1 AATGACCCCA
369915 AACATCGAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.35, C:0.35, G:0.16, T:0.14
Consensus pattern (17 bp):
AATGACCCCACGAAGTT
Found at i:371361 original size:21 final size:21
Alignment explanation
Indices: 371315--371361 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
371305 CCATGAAGTT
* *
371315 CAAACAAAATATTCAAACCATT
1 CAAACAAAATATCCAAA-CATC
371337 CAAACAAATATATCCAAA-ATC
1 CAAACAAA-ATATCCAAACATC
371358 CAAA
1 CAAA
371362 ACACGCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 8 0.36
23 8 0.36
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.19
Consensus pattern (21 bp):
CAAACAAAATATCCAAACATC
Found at i:371373 original size:15 final size:15
Alignment explanation
Indices: 371353--371399 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
371343 AATATATCCA
**
371353 AAATCCAAAACACGC
1 AAATCCAAAACAAAC
371368 AAATCCAAAACAAAC
1 AAATCCAAAACAAAC
371383 AAATCCAAAACAAAC
1 AAATCCAAAACAAAC
371398 AA
1 AA
371400 GTTTAACATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.64, C:0.28, G:0.02, T:0.06
Consensus pattern (15 bp):
AAATCCAAAACAAAC
Found at i:372873 original size:12 final size:13
Alignment explanation
Indices: 372856--372888 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
372846 AATGGCAAAA
*
372856 TTTGAAAACTAT-
1 TTTGAAAACAATG
372868 TTTGAAAACAATG
1 TTTGAAAACAATG
372881 TTTGAAAA
1 TTTGAAAA
372889 ATCATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:378755 original size:19 final size:19
Alignment explanation
Indices: 378731--378791 Score: 79
Period size: 19 Copynumber: 3.1 Consensus size: 19
378721 ATCAGATTGT
378731 CCAGGGGGTACAGATTCCC
1 CCAGGGGGTACAGATTCCC
*
378750 CCAGGGGGAACAGATTCCCCC
1 CCAGGGGGTACAGATT--CCC
378771 CCAGGGGGTATC-GATTCCC
1 CCAGGGGGTA-CAGATTCCC
378790 CC
1 CC
378792 TGTCTAACGG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 20 0.54
21 16 0.43
22 1 0.03
ACGTcount: A:0.20, C:0.36, G:0.30, T:0.15
Consensus pattern (19 bp):
CCAGGGGGTACAGATTCCC
Found at i:378773 original size:21 final size:21
Alignment explanation
Indices: 378731--378791 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
378721 ATCAGATTGT
*
378731 CCAGGGGGTACAGATT--CCC
1 CCAGGGGGAACAGATTCCCCC
378750 CCAGGGGGAACAGATTCCCCC
1 CCAGGGGGAACAGATTCCCCC
*
378771 CCAGGGGGTATC-GATTCCCCC
1 CCAGGGGG-AACAGATTCCCCC
378792 TGTCTAACGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.41
21 20 0.54
22 2 0.05
ACGTcount: A:0.20, C:0.36, G:0.30, T:0.15
Consensus pattern (21 bp):
CCAGGGGGAACAGATTCCCCC
Found at i:380195 original size:3 final size:3
Alignment explanation
Indices: 380177--380214 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
380167 AAGAAAGGGA
* *
380177 AAG AAG AAA AAC AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
380215 TGAGGATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:383188 original size:14 final size:14
Alignment explanation
Indices: 383171--383205 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
383161 TAACAATCAA
* *
383171 GCCATAAATTATAG
1 GCCACAAATTACAG
383185 GCCACAAATTACAG
1 GCCACAAATTACAG
383199 GCCACAA
1 GCCACAA
383206 TAAAACAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.26, G:0.14, T:0.17
Consensus pattern (14 bp):
GCCACAAATTACAG
Found at i:395385 original size:21 final size:20
Alignment explanation
Indices: 395353--395404 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 20
395343 AAATTTAGGG
395353 GTATCGTACATCCCAAGAGT
1 GTATCGTACATCCCAAGAGT
395373 GTATCGATACATCCCAAGAGT
1 GTATCG-TACATCCCAAGAGT
395394 GTATCGGTACA
1 GTATC-GTACA
395405 CTCCTACCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.20
21 23 0.77
22 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (20 bp):
GTATCGTACATCCCAAGAGT
Found at i:406888 original size:20 final size:21
Alignment explanation
Indices: 406832--406889 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
406822 ATAGGGCAGA
*
406832 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCAT-AAG
*
406854 GGGAA-CTGATTCCCCCAT-AG
1 GGGAATC-GATACCCCCATAAG
406874 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
406890 CTGGGGTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 15 0.48
21 2 0.06
22 14 0.45
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.17
Consensus pattern (21 bp):
GGGAATCGATACCCCCATAAG
Found at i:412858 original size:2 final size:2
Alignment explanation
Indices: 412806--412839 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
412796 TATGGTATTT
412806 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
412840 TGTTTTGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:413190 original size:3 final size:3
Alignment explanation
Indices: 413169--413264 Score: 169
Period size: 3 Copynumber: 32.7 Consensus size: 3
413159 AATGTTTAAT
*
413169 TTA TT- TTA GTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
413215 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
413263 TT
1 TT
413265 GTTGTTGTTG
Statistics
Matches: 89, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
2 4 0.04
3 85 0.96
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:413288 original size:11 final size:11
Alignment explanation
Indices: 413263--413298 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
413253 ATTATTATTA
413263 TTGTTGTTGTTG
1 TTGTTGTT-TTG
413275 TTGTTGTTTTG
1 TTGTTGTTTTG
*
413286 TTGTAGTTTTG
1 TTGTTGTTTTG
413297 TT
1 TT
413299 TATTTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 15 0.65
12 8 0.35
ACGTcount: A:0.03, C:0.00, G:0.28, T:0.69
Consensus pattern (11 bp):
TTGTTGTTTTG
Found at i:423242 original size:7 final size:7
Alignment explanation
Indices: 423225--423272 Score: 57
Period size: 7 Copynumber: 7.0 Consensus size: 7
423215 GAATAAAGTG
423225 AAAATGAA
1 AAAATG-A
423233 AAAATGA
1 AAAATGA
423240 AAAA-GA
1 AAAATGA
423246 AAAATTGA
1 AAAA-TGA
423254 AAAA--A
1 AAAATGA
423259 AAAATGA
1 AAAATGA
423266 AAAATGA
1 AAAATGA
423273 TGAAAAAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
6 6 0.17
7 13 0.36
8 12 0.33
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAATGA
Found at i:423242 original size:14 final size:13
Alignment explanation
Indices: 423223--423268 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
423213 AGGAATAAAG
423223 TGAAAATGAAAAAA
1 TGAAAA-GAAAAAA
*
423237 TGAAAAAGAAAAAT
1 TG-AAAAGAAAAAA
423251 TGAAAA-AAAAAA
1 TGAAAAGAAAAAA
423263 TGAAAA
1 TGAAAA
423269 ATGATGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 11 0.38
13 4 0.14
14 10 0.34
15 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (13 bp):
TGAAAAGAAAAAA
Found at i:423244 original size:22 final size:23
Alignment explanation
Indices: 423209--423289 Score: 64
Period size: 22 Copynumber: 3.6 Consensus size: 23
423199 ACACATGAAG
*
423209 AAAAAGGAATAAAGTGAAAA-TGA
1 AAAAAGGAATAAAG-AAAAATTGA
*
423232 AAAAATGAA-AAAGAAAAATTGA
1 AAAAAGGAATAAAGAAAAATTGA
*
423254 AAAAA--AA-AATGAAAAATGATGAA
1 AAAAAGGAATAAAGAAAAAT--TG-A
423277 AAAAAGGAATAAA
1 AAAAAGGAATAAA
423290 AATGGGTTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
20 11 0.23
21 4 0.09
22 14 0.30
23 14 0.30
25 2 0.04
26 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (23 bp):
AAAAAGGAATAAAGAAAAATTGA
Found at i:423291 original size:33 final size:31
Alignment explanation
Indices: 423203--423291 Score: 72
Period size: 33 Copynumber: 2.6 Consensus size: 31
423193 GATACTACAC
**
423203 ATGAAGAAAAAGGAATAAAGTGAAAATGAAAAA
1 ATGAA-AAAAAGGAATAAA-AAAAAATGAAAAA
*
423236 ATGAAAAAGAA-AAATTGAAAAAAAAAATGAAAAA
1 ATGAAAAA-AAGGAA-T--AAAAAAAAATGAAAAA
423270 TGATGAAAAAAAGGAATAAAAA
1 --ATGAAAAAAAGGAATAAAAA
423292 TGGGTTCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
32 5 0.11
33 13 0.29
34 11 0.24
35 6 0.13
36 10 0.22
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (31 bp):
ATGAAAAAAAGGAATAAAAAAAAATGAAAAA
Found at i:423293 original size:22 final size:22
Alignment explanation
Indices: 423228--423281 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
423218 TAAAGTGAAA
*
423228 ATGAAAAAATGAAAAAGAAAAAT-
1 ATGAAAAAA--AAAATGAAAAATG
423251 -TGAAAAAAAAAATGAAAAATG
1 ATGAAAAAAAAAATGAAAAATG
423272 ATGAAAAAAA
1 ATGAAAAAAA
423282 GGAATAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 11 0.39
22 17 0.61
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (22 bp):
ATGAAAAAAAAAATGAAAAATG
Found at i:427196 original size:21 final size:21
Alignment explanation
Indices: 427172--427212 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
427162 TAAGGTACTT
*
427172 TAGTTCAATGCTAATGCACTC
1 TAGTACAATGCTAATGCACTC
*
427193 TAGTACAATGCTAATTCACT
1 TAGTACAATGCTAATGCACT
427213 TTAGATGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (21 bp):
TAGTACAATGCTAATGCACTC
Found at i:433047 original size:14 final size:14
Alignment explanation
Indices: 433028--433059 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
433018 AGAGAATGAT
*
433028 AGTTCTACAAGTGC
1 AGTTCTACAAGTGA
433042 AGTTCTACAAGTGA
1 AGTTCTACAAGTGA
433056 AGTT
1 AGTT
433060 GTTGATGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (14 bp):
AGTTCTACAAGTGA
Found at i:437182 original size:16 final size:16
Alignment explanation
Indices: 437161--437192 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
437151 TTTATCTATA
437161 TAAATGTCATGAAAAG
1 TAAATGTCATGAAAAG
*
437177 TAAATGTCATGGAAAG
1 TAAATGTCATGAAAAG
437193 CTTGACTGAA
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:0.47, C:0.06, G:0.22, T:0.25
Consensus pattern (16 bp):
TAAATGTCATGAAAAG
Found at i:442031 original size:59 final size:59
Alignment explanation
Indices: 441937--442403 Score: 711
Period size: 59 Copynumber: 7.9 Consensus size: 59
441927 AAATTCAATA
* * *
441937 GGAAATTCATACACTTAGTATGATTTCCTTTTCATTTTCGCACACTTTGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCCCTATCT
441996 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCCCTATCT
* * *
442055 GGAAATTCATACACTTAGTATGATTTGCTTATCATTTTAGCACACTTAGTACCCTATTT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCCCTATCT
*
442114 AGAAATTCATACACTTAGTATGATTTCCTTAT-ATTTTAGCACACTTAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCCCTATCT
**
442172 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGGAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCCCTATCT
* * * * * *
442231 GGAAATTAATACACTTAGTATGTTTTTCTTATCATCTTAGCACACTTAGTGTCGTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCCCTATCT
* * * **
442290 GGAAATTCATACACTTACTATAATTTCTTTATCATTTTAGCACACGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCCCTATCT
* * **
442349 TGAAATTCATAAACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCCCT
442404 TTTGGTAATC
Statistics
Matches: 370, Mismatches: 37, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
58 55 0.15
59 315 0.85
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCCCTATCT
Found at i:442247 original size:235 final size:236
Alignment explanation
Indices: 441937--442403 Score: 724
Period size: 235 Copynumber: 2.0 Consensus size: 236
441927 AAATTCAATA
* * ***
441937 GGAAATTCATACACTTAGTATGATTTCCTTTTCATTTTCGCACACTTTGTGCCCTATCTGGAAAT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGGAGTGCCCTATCTGGAAAT
* *
442002 TCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCCCTATCTGGAAATTCATAC
66 TAATACACTTAGTATGATTTCCTTATCATCTTAGCACACTTAGTGCCCTATCTGGAAATTCATAC
* * ** *
442067 ACTTAGTATGATTTGC-TTATCATTTTAGCACACTTAGTACCCTAT-TTAGAAATTCATACACTT
131 ACTTACTATAATTT-CTTTATCATTTTAGCACACGAAGTACCCTATCTT-GAAATTCATAAACTT
**
442130 AGTATGATTTCCTTAT-ATTTTAGCACACTTAGTGCCCTATCT
194 AGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
442172 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGGAGTGCCCTATCTGGAAAT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGGAGTGCCCTATCTGGAAAT
* * * *
442237 TAATACACTTAGTATGTTTTTCTTATCATCTTAGCACACTTAGTGTCGTATCTGGAAATTCATAC
66 TAATACACTTAGTATGATTTCCTTATCATCTTAGCACACTTAGTGCCCTATCTGGAAATTCATAC
*
442302 ACTTACTATAATTTCTTTATCATTTTAGCACACGAAGTGCCCTATCTTGAAATTCATAAACTTAG
131 ACTTACTATAATTTCTTTATCATTTTAGCACACGAAGTACCCTATCTTGAAATTCATAAACTTAG
442367 TATGATTTCCTTATCATTTTAGCACACGAAGTGCCCT
196 TATGATTTCCTTATCATTTTAGCACACGAAGTGCCCT
442404 TTTGGTAATC
Statistics
Matches: 210, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
234 1 0.00
235 187 0.89
236 22 0.10
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (236 bp):
GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGGAGTGCCCTATCTGGAAAT
TAATACACTTAGTATGATTTCCTTATCATCTTAGCACACTTAGTGCCCTATCTGGAAATTCATAC
ACTTACTATAATTTCTTTATCATTTTAGCACACGAAGTACCCTATCTTGAAATTCATAAACTTAG
TATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
Found at i:443029 original size:19 final size:21
Alignment explanation
Indices: 442990--443031 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
442980 CCTCCTCACA
442990 AAGTGTCATCATTTGATTTTC
1 AAGTGTCATCATTTGATTTTC
*
443011 AAGTG-CATC-TTTTATTTTC
1 AAGTGTCATCATTTGATTTTC
443030 AA
1 AA
443032 TGACTGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 4 0.20
21 5 0.25
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (21 bp):
AAGTGTCATCATTTGATTTTC
Found at i:447152 original size:25 final size:25
Alignment explanation
Indices: 447123--447170 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
447113 AATTTATAAC
447123 TTATTTATAGTATTA-TTTTATTTCT
1 TTATTTATAGTA-TAGTTTTATTTCT
* *
447148 TTATTTTTTGTATAGTTTTATTT
1 TTATTTATAGTATAGTTTTATTT
447171 GTTAGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATAGTATAGTTTTATTTCT
Found at i:447178 original size:13 final size:13
Alignment explanation
Indices: 447151--447184 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
447141 TATTTCTTTA
447151 TTTTTTGTATAGT
1 TTTTTTGTATAGT
447164 TTTATTTGT-TAGT
1 TTT-TTTGTATAGT
447177 TTTTTTGT
1 TTTTTTGT
447185 CTTTTTTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 10 0.50
14 5 0.25
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.74
Consensus pattern (13 bp):
TTTTTTGTATAGT
Found at i:457394 original size:31 final size:32
Alignment explanation
Indices: 457318--457394 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 32
457308 TAAAGTGCCC
457318 CTTGGGTAGGCTCTGAGAACCCGATAAACTTT
1 CTTGGGTAGGCTCTGAGAACCCGATAAACTTT
* * *
457350 CTTGAGTAAGCTCTGAGGACCCGATAAAC-TT
1 CTTGGGTAGGCTCTGAGAACCCGATAAACTTT
457381 CTTGGGTAGGCTCT
1 CTTGGGTAGGCTCT
457395 CAGGCCCCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 14 0.35
32 26 0.65
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (32 bp):
CTTGGGTAGGCTCTGAGAACCCGATAAACTTT
Found at i:457667 original size:31 final size:30
Alignment explanation
Indices: 457629--457701 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
457619 TAAGGTGACC
*
457629 CTTGGGTAGGCTC-TGA-GGCCCCGAGATCTTT
1 CTTGGGTAGGC-CAT-ACGGCCCCAAGATC-TT
*
457660 CTTGGGTAGGCCATACGGCCCTAAGATCTT
1 CTTGGGTAGGCCATACGGCCCCAAGATCTT
457690 CTTGGGTAGGCC
1 CTTGGGTAGGCC
457702 CCGAGTAACC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
30 16 0.42
31 22 0.58
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.27
Consensus pattern (30 bp):
CTTGGGTAGGCCATACGGCCCCAAGATCTT
Found at i:462691 original size:30 final size:30
Alignment explanation
Indices: 462626--462691 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 30
462616 CTCGAGTAGG
* * *
462626 CCATGG-C-GAGATCTTTCTTGGGTAGGCC
1 CCATGGCCTGAGATCTCTCTTAGATAGGCC
*
462654 CTATGGCCTGAGATCTCTCTTAGATAGGCC
1 CCATGGCCTGAGATCTCTCTTAGATAGGCC
*
462684 CCGTGGCC
1 CCATGGCC
462692 CCAAGTAACC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 5 0.17
29 1 0.03
30 24 0.80
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.27
Consensus pattern (30 bp):
CCATGGCCTGAGATCTCTCTTAGATAGGCC
Found at i:464719 original size:35 final size:35
Alignment explanation
Indices: 464621--464747 Score: 118
Period size: 35 Copynumber: 3.6 Consensus size: 35
464611 AGGTCAGTTT
* *
464621 GGTCAAGCTGGTAATTCCTTATATAGGTTCAACATC
1 GGTCAAACTGGTAATTCCTTATATAGGTTCAGC-TC
* * * *
464657 GATC--AGTTGTAATTCCTTAT-TGCAGGTTCAGCTT
1 GGTCAAACTGGTAATTCCTTATAT--AGGTTCAGCTC
464691 GGTCAAACTGGTAATTCCTTATATAGGTTCAGAC-C
1 GGTCAAACTGGTAATTCCTTATATAGGTTCAG-CTC
* *
464726 GGTCGAGCTGGTAATTCCTTAT
1 GGTCAAACTGGTAATTCCTTAT
464748 GGACCTAAGA
Statistics
Matches: 73, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
33 1 0.01
34 17 0.23
35 36 0.49
36 18 0.25
37 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (35 bp):
GGTCAAACTGGTAATTCCTTATATAGGTTCAGCTC
Found at i:468693 original size:21 final size:21
Alignment explanation
Indices: 468667--468712 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
468657 CAAATCAGTA
*
468667 CTAAGGAACTTTAGTTAAGTG
1 CTAAGGAACTTTAGTGAAGTG
** *
468688 CTAAGGCTCTTTAGTGCAGTG
1 CTAAGGAACTTTAGTGAAGTG
468709 CTAA
1 CTAA
468713 ATCTCTTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (21 bp):
CTAAGGAACTTTAGTGAAGTG
Found at i:468718 original size:21 final size:21
Alignment explanation
Indices: 468675--468722 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
468665 TACTAAGGAA
* *
468675 CTTTAGTTAAGTGCTAAGGCT
1 CTTTAGTGAAGTGCTAAAGCT
* *
468696 CTTTAGTGCAGTGCTAAATCT
1 CTTTAGTGAAGTGCTAAAGCT
468717 CTTTAG
1 CTTTAG
468723 ATGCTATTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (21 bp):
CTTTAGTGAAGTGCTAAAGCT
Found at i:469234 original size:30 final size:29
Alignment explanation
Indices: 469200--469256 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
469190 TATTTAATAG
469200 AAGA-TAATACAATGGTATTTGGTAATTTTC
1 AAGATTAAT-CAATGGTATTT-GTAATTTTC
* *
469230 AAGATTCATTAATGGTATTTGTAATTT
1 AAGATTAATCAATGGTATTTGTAATTT
469257 CTCATTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.29
30 14 0.58
31 3 0.12
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (29 bp):
AAGATTAATCAATGGTATTTGTAATTTTC
Found at i:472225 original size:2 final size:2
Alignment explanation
Indices: 472218--472255 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
472208 TTTATGTTTA
*
472218 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
472256 CCCATATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:472627 original size:2 final size:2
Alignment explanation
Indices: 472620--472654 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
472610 TTTAAAATTA
*
472620 AT AT AT AT AT AT AT AT AT AT GT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
472655 TTTTCCCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:477886 original size:21 final size:22
Alignment explanation
Indices: 477860--477900 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
477850 TCAGGATAGG
477860 GAGTATCGGTAC-TCCTTTAAT
1 GAGTATCGGTACTTCCTTTAAT
*
477881 GAGTATTGGTACTTCCTTTA
1 GAGTATCGGTACTTCCTTTA
477901 TAATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (22 bp):
GAGTATCGGTACTTCCTTTAAT
Found at i:492507 original size:22 final size:21
Alignment explanation
Indices: 492482--492554 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 21
492472 CTATATGAAA
492482 TGATATATGAATATGCAATACG
1 TGATATATGAATATG-AATACG
**
492504 TGATACATATG-ATATGATATGAAA
1 TGAT--ATATGAATATGA-AT-ACG
*
492528 TGACATATGAATATGTAATACG
1 TGATATATGAATATG-AATACG
492550 TGATA
1 TGATA
492555 CATGTGATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
22 15 0.38
23 14 0.36
24 10 0.26
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (21 bp):
TGATATATGAATATGAATACG
Found at i:492541 original size:46 final size:46
Alignment explanation
Indices: 492474--492578 Score: 176
Period size: 46 Copynumber: 2.3 Consensus size: 46
492464 CTATGTGACT
*
492474 ATATGAAATGATATATGAATATGCAATACGTGATACATATGATATG
1 ATATGAAATGACATATGAATATGCAATACGTGATACATATGATATG
* *
492520 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGCAATACGTGATACATATGATATG
492566 ATATGAAAT-ACAT
1 ATATGAAATGACAT
492579 GGTTACACAT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 4 0.07
46 52 0.93
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (46 bp):
ATATGAAATGACATATGAATATGCAATACGTGATACATATGATATG
Found at i:492778 original size:17 final size:17
Alignment explanation
Indices: 492756--492820 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
492746 ACAGATTACA
492756 TCCTTCGGGATGACAGG
1 TCCTTCGGGATGACAGG
*
492773 TCCTTCGGGA-CACAGATG
1 TCCTTCGGGATGACAG--G
*
492791 ACATCCTTCGGGATGATAGG
1 ---TCCTTCGGGATGACAGG
492811 TCCTTCGGGA
1 TCCTTCGGGA
492821 CATTTGTACG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
16 4 0.10
17 20 0.51
18 1 0.03
20 1 0.03
21 10 0.26
22 3 0.08
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.25
Consensus pattern (17 bp):
TCCTTCGGGATGACAGG
Found at i:492783 original size:38 final size:38
Alignment explanation
Indices: 492727--492822 Score: 165
Period size: 38 Copynumber: 2.5 Consensus size: 38
492717 TATAAGACAT
* *
492727 ATGATAGGTCCTACGGGACACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
492765 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
492803 ATGATAGGTCCTTCGGGACA
1 ATGATAGGTCCTTCGGGACA
492823 TTTGTACGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:492799 original size:21 final size:21
Alignment explanation
Indices: 492735--492803 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
492725 ATATGATAGG
* *
492735 TCCTACGGGACACAGATTACA
1 TCCTTCGGGACACAGATGACA
*
492756 TCCTTCGGGATGACAG--G---
1 TCCTTCGGGA-CACAGATGACA
492773 TCCTTCGGGACACAGATGACA
1 TCCTTCGGGACACAGATGACA
492794 TCCTTCGGGA
1 TCCTTCGGGA
492804 TGATAGGTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 4 0.11
17 10 0.26
18 1 0.03
21 19 0.50
22 4 0.11
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.22
Consensus pattern (21 bp):
TCCTTCGGGACACAGATGACA
Found at i:506114 original size:25 final size:24
Alignment explanation
Indices: 506094--506149 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
506084 TAAAATATTC
*
506094 AAATATTTTAAAAAATTAAATATAA
1 AAATACTTT-AAAAATTAAATATAA
*
506119 AAATACTTTATAAATTAAATTATTAA
1 AAATACTTTAAAAATTAAA-TA-TAA
506145 AAATA
1 AAATA
506150 AAATAATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 9 0.33
25 10 0.37
26 8 0.30
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATACTTTAAAAATTAAATATAA
Found at i:506137 original size:32 final size:32
Alignment explanation
Indices: 506101--506166 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
506091 TTCAAATATT
* *
506101 TTAAAAAATTAAATATAAAAATACT-TTATAAA
1 TTAAAAAATTAAAAAT-AAAATAATCTTATAAA
**
506133 TTAAATTATTAAAAATAAAATAATCTTATAAA
1 TTAAAAAATTAAAAATAAAATAATCTTATAAA
506165 TT
1 TT
506167 TTATTAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (32 bp):
TTAAAAAATTAAAAATAAAATAATCTTATAAA
Found at i:513051 original size:40 final size:41
Alignment explanation
Indices: 513001--513080 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
512991 TTTGATAAAA
*
513001 TAAGGATCTAAATAAAA-ATATATAAAGATGTACATTATAG
1 TAAGGATCTAAATAAAATATATATAAAGATATACATTATAG
*
513041 TAAGGATCTAAATAAAATATATATAAAGATATATATTATA
1 TAAGGATCTAAATAAAATATATATAAAGATATACATTATA
513081 ACAATTATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
40 17 0.46
41 20 0.54
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.33
Consensus pattern (41 bp):
TAAGGATCTAAATAAAATATATATAAAGATATACATTATAG
Found at i:523294 original size:21 final size:21
Alignment explanation
Indices: 523270--523311 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
523260 CTGTATCCAA
523270 TATATTTAATTAAATAATTAT
1 TATATTTAATTAAATAATTAT
523291 TATATTTAATTAAATAATTAT
1 TATATTTAATTAAATAATTAT
523312 ATCTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATATTTAATTAAATAATTAT
Found at i:524261 original size:30 final size:30
Alignment explanation
Indices: 524227--524308 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
524217 AGTTTAATAC
524227 TTTTTATTTTATAAATATTTAAATAATATT
1 TTTTTATTTTATAAATATTTAAATAATATT
* **
524257 TTTTTATTTGAT-AATAATTTAAATTTTATT
1 TTTTTATTTTATAAAT-ATTTAAATAATATT
* *
524287 TTTAATATTTTTATAATTATTT
1 TTT-TTA-TTTTATAAATATTT
524309 TAAAAATTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
29 3 0.07
30 26 0.62
31 2 0.05
32 9 0.21
33 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (30 bp):
TTTTTATTTTATAAATATTTAAATAATATT
Done.