Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007297.1 Hibiscus syriacus cultivar Beakdansim tig00019410_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: 87326
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:667 original size:11 final size:11
Alignment explanation
Indices: 651--676 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
641 AATTAGTGGC
651 ATGTAATTATT
1 ATGTAATTATT
662 ATGTAATTATT
1 ATGTAATTATT
673 ATGT
1 ATGT
677 TTATTTGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (11 bp):
ATGTAATTATT
Found at i:747 original size:11 final size:11
Alignment explanation
Indices: 731--755 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
721 TATGAACTTA
731 TATGTAATTAT
1 TATGTAATTAT
742 TATGTAATTAT
1 TATGTAATTAT
753 TAT
1 TAT
756 TTTATTTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (11 bp):
TATGTAATTAT
Found at i:869 original size:13 final size:14
Alignment explanation
Indices: 850--912 Score: 71
Period size: 13 Copynumber: 4.8 Consensus size: 14
840 TCGATTCCCC
*
850 CACTATTCACTGTA
1 CACTATTCACTGGA
864 -ACTATTCA-TGGA
1 CACTATTCACTGGA
*
876 CACTATTCACTGTA
1 CACTATTCACTGGA
*
890 -ACTGTTCAC-GGA
1 CACTATTCACTGGA
902 CACTATTCACT
1 CACTATTCACT
913 ATTCATATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
12 5 0.12
13 32 0.80
14 3 0.08
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (14 bp):
CACTATTCACTGGA
Found at i:879 original size:26 final size:26
Alignment explanation
Indices: 850--912 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
840 TCGATTCCCC
*
850 CACTATTCACTGTAACTATTCATGGA
1 CACTATTCACTGTAACTATTCACGGA
*
876 CACTATTCACTGTAACTGTTCACGGA
1 CACTATTCACTGTAACTATTCACGGA
902 CACTATTCACT
1 CACTATTCACT
913 ATTCATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (26 bp):
CACTATTCACTGTAACTATTCACGGA
Found at i:8197 original size:11 final size:11
Alignment explanation
Indices: 8181--8206 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8171 AATTAGTGGC
8181 ATGTAATTATT
1 ATGTAATTATT
8192 ATGTAATTATT
1 ATGTAATTATT
8203 ATGT
1 ATGT
8207 TTTATTTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (11 bp):
ATGTAATTATT
Found at i:10164 original size:4 final size:4
Alignment explanation
Indices: 10155--11646 Score: 2915
Period size: 4 Copynumber: 374.2 Consensus size: 4
10145 TTTATTTGCC
* *
10155 ACAT ACAT ACAA ATAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10203 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10251 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10299 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10347 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10395 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10443 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10491 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10539 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10587 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10635 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10683 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10731 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10779 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10827 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10875 --AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10921 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
10969 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
11017 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
11065 ACAT ACAT ACAT ACAT ACAT ACCAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT A-CAT ACAT ACAT ACAT ACAT ACAT ACAT
11114 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
11162 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
11210 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
11258 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
11306 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
11354 AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
11400 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
11448 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
11496 ACAT ACAT ACAT ACAT --AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
11542 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
11590 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
11638 ACAT ACAT A
1 ACAT ACAT A
11647 TACCTTGAGA
Statistics
Matches: 1477, Mismatches: 4, Indels: 14
0.99 0.00 0.01
Matches are distributed among these distances:
2 6 0.00
4 1467 0.99
5 4 0.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:16223 original size:3 final size:3
Alignment explanation
Indices: 16215--16348 Score: 177
Period size: 3 Copynumber: 44.7 Consensus size: 3
16205 ATCCCTCAAC
* *
16215 CTT CTT CTT CTT CTTT CAT CTTT CTT -TT -TT CTT CCT CTT CTCT CTT
1 CTT CTT CTT CTT C-TT CTT C-TT CTT CTT CTT CTT CTT CTT CT-T CTT
*
16261 -TT CTT TTT CTT CTCT CTT CTT -TT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
16305 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
16349 ATTTGCATAA
Statistics
Matches: 118, Mismatches: 6, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
2 8 0.07
3 99 0.84
4 11 0.09
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:17278 original size:17 final size:17
Alignment explanation
Indices: 17258--17307 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
17248 TTTAGGGAAG
17258 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
17275 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
17292 TAGTTCATTTATTAAA
1 TAGTTCATTAATTAAA
17308 TTAACTCTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:20786 original size:9 final size:9
Alignment explanation
Indices: 20768--20828 Score: 59
Period size: 9 Copynumber: 6.6 Consensus size: 9
20758 CCGGATCGAG
20768 TTAAACTAT
1 TTAAACTAT
*
20777 TTAAAATAT
1 TTAAACTAT
*
20786 TTGAATATTAT
1 TT-AA-ACTAT
*
20797 TTCAACTAT
1 TTAAACTAT
*
20806 TTAAATTAT
1 TTAAACTAT
*
20815 TTTAACTAT
1 TTAAACTAT
20824 TTAAA
1 TTAAA
20829 AATAGTTTAA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
9 32 0.78
10 3 0.07
11 6 0.15
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.49
Consensus pattern (9 bp):
TTAAACTAT
Found at i:20815 original size:18 final size:18
Alignment explanation
Indices: 20768--20828 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
20758 CCGGATCGAG
* *
20768 TTAAACTATTTAAAATAT
1 TTAAATTATTTAAACTAT
*
20786 TTGAATATTATTTCAACTAT
1 TT-AA-ATTATTTAAACTAT
*
20806 TTAAATTATTTTAACTAT
1 TTAAATTATTTAAACTAT
20824 TTAAA
1 TTAAA
20829 AATAGTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 20 0.54
19 4 0.11
20 13 0.35
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.49
Consensus pattern (18 bp):
TTAAATTATTTAAACTAT
Found at i:20839 original size:19 final size:18
Alignment explanation
Indices: 20800--20840 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
20790 ATATTATTTC
* *
20800 AACTATTTAAATTATTTT
1 AACTATTTAAAATAGTTT
20818 AACTATTTAAAAATAGTTT
1 AACTATTT-AAAATAGTTT
20837 AACT
1 AACT
20841 CGATCCGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (18 bp):
AACTATTTAAAATAGTTT
Found at i:20862 original size:64 final size:64
Alignment explanation
Indices: 20788--21070 Score: 346
Period size: 64 Copynumber: 4.4 Consensus size: 64
20778 TAAAATATTT
* *
20788 GAATATTATTTCAACTATTTAAATTATTTTAACTATTTAAAAATAGTTTAACTCGATCCGGGTC
1 GAATATTATTTCAACTATTTAAAATATTTTAACTATTTAAAAATAGTTTAACTCGATCCGAGTC
20852 GAATATTATTTCAACTATTTAAAATATTTTAACTATTTAAAAATAGTTTAACTCGATCCGAGTC
1 GAATATTATTTCAACTATTTAAAATATTTTAACTATTTAAAAATAGTTTAACTCGATCCGAGTC
* * ** **
20916 CAATATTATTTCAACTATTTAAAATATTTTAACTCGATCTGGATTGAATAAATTAA----AT---
1 GAATATTATTTCAACTATTTAAAATATTTTAACT--AT-T-TA-AAAATAGTTTAACTCGATCCG
20974 AGTC
61 AGTC
* ** *
20978 AAATATTATTTCAACTATTTAAAATATTTTAACTATTTAAAAATAGTTTAACTTTATCCGGGTC
1 GAATATTATTTCAACTATTTAAAATATTTTAACTATTTAAAAATAGTTTAACTCGATCCGAGTC
*
21042 TAATATTATTTCAACTATTTTAAAATATT
1 GAATATTATTTCAACTA-TTTAAAATATT
21071 AATTTATTTG
Statistics
Matches: 190, Mismatches: 16, Indels: 25
0.82 0.07 0.11
Matches are distributed among these distances:
57 8 0.04
58 1 0.01
59 1 0.01
60 2 0.01
61 2 0.01
62 37 0.19
64 114 0.60
65 13 0.07
66 2 0.01
67 1 0.01
68 1 0.01
69 8 0.04
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (64 bp):
GAATATTATTTCAACTATTTAAAATATTTTAACTATTTAAAAATAGTTTAACTCGATCCGAGTC
Found at i:20885 original size:18 final size:19
Alignment explanation
Indices: 20858--20904 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
20848 GGTCGAATAT
*
20858 TATTTCAACTATTT-AAAA
1 TATTTTAACTATTTAAAAA
20876 TATTTTAACTATTTAAAAA
1 TATTTTAACTATTTAAAAA
*
20895 TAGTTTAACT
1 TATTTTAACT
20905 CGATCCGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.47
Consensus pattern (19 bp):
TATTTTAACTATTTAAAAA
Found at i:21011 original size:18 final size:19
Alignment explanation
Indices: 20984--21030 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
20974 AGTCAAATAT
*
20984 TATTTCAACTATTT-AAAA
1 TATTTTAACTATTTAAAAA
21002 TATTTTAACTATTTAAAAA
1 TATTTTAACTATTTAAAAA
*
21021 TAGTTTAACT
1 TATTTTAACT
21031 TTATCCGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.47
Consensus pattern (19 bp):
TATTTTAACTATTTAAAAA
Found at i:24892 original size:14 final size:14
Alignment explanation
Indices: 24869--24908 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
24859 CTAAAAATGG
24869 AAATAAAAATAAAT
1 AAATAAAAATAAAT
* *
24883 AAATAGAAATAAAAC
1 AAATAAAAAT-AAAT
24898 AAATAAAAATA
1 AAATAAAAATA
24909 TATATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:24913 original size:2 final size:2
Alignment explanation
Indices: 24906--24943 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
24896 ACAAATAAAA
24906 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24944 TTCAAAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25090 original size:35 final size:36
Alignment explanation
Indices: 24974--25299 Score: 354
Period size: 37 Copynumber: 8.8 Consensus size: 36
24964 CCCAAACACA
* **
24974 TTTTCAAAAATA-ATATTATATATATTTTCCAAAAACA
1 TTTTCAAAACTATATATTATATATATTTT--AAAAATG
* * *
25011 TCTT-AAAAATATATATTATACATATTTTCAAAAAAAATG
1 TTTTCAAAACTATATATTATATATATTTT----AAAAATG
*
25050 TTTTCAAAACTATATATTATATAT-TTTTTAAAATG
1 TTTTCAAAACTATATATTATATATATTTTAAAAATG
* *
25085 TTTTCAAAATTATATGTTATATATATTTTCAAAAATG
1 TTTTCAAAACTATATATTATATATATTTT-AAAAATG
*
25122 TTTTCAAAATTATATATTATATATATTTTCAAAAATG
1 TTTTCAAAACTATATATTATATATATTTT-AAAAATG
* *
25159 TTTTTAAAATTATATATTATATATATTTTAAAAATG
1 TTTTCAAAACTATATATTATATATATTTTAAAAATG
* *
25195 TTTTCAAAACTACATATT-TATATATTTTCGAACAATG
1 TTTTCAAAACTATATATTATATATATTTT--AAAAATG
25232 TTTTCAAAACTATATACTATATATATATTTTTTCAAAAATG
1 TTTTCAAAACTATATA-T-TATATATA--TTTT-AAAAATG
*
25273 TTTTCAAAACCATATATTATATATATT
1 TTTTCAAAACTATATATTATATATATT
25300 ATGTATATAT
Statistics
Matches: 253, Mismatches: 23, Indels: 26
0.84 0.08 0.09
Matches are distributed among these distances:
35 38 0.15
36 33 0.13
37 111 0.44
38 1 0.00
39 21 0.08
40 24 0.09
41 21 0.08
42 4 0.02
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (36 bp):
TTTTCAAAACTATATATTATATATATTTTAAAAATG
Found at i:25253 original size:110 final size:109
Alignment explanation
Indices: 24974--25299 Score: 406
Period size: 114 Copynumber: 2.9 Consensus size: 109
24964 CCCAAACACA
** * *
24974 TTTTCAAAAATAATATTATATATATTTTCCAAAAACATCTT-AAAAATATATATTATACATATTT
1 TTTTCAAAAATAATATTATATATATTTT-CAAAAATGTTTTCAAAAATATATATTATATATATTT
*
25038 TCAAAAAAAATGTTTTCAAAACTATATATTATATAT-TTTTTAAAATG
65 TC---AAAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATG
* * *
25085 TTTTCAAAATTATATGTTATATATATTTTCAAAAATGTTTTCAAAATTATATATTATATATATTT
1 TTTTCAAAAATA-ATATTATATATATTTTCAAAAATGTTTTCAAAAATATATATTATATATATTT
* *
25150 TCAAAAATGTTTTTAAAATTATATATTATATATATTTTAAAAATG
65 TCAAAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATG
* *
25195 TTTTCAAAACTACATATT-TATATATTTTCGAACAATGTTTTCAAAACTATATACTATATATATA
1 TTTTCAAAAATA-ATATTATATATATTTTC-AAAAATGTTTTCAAAA--ATATA-TAT-TATATA
* *
25259 TTTTTTCAAAAATGTTTTCAAAACCATATATTATATATATT
60 TATTTTCAAAAATGTTTTCAAAACTATATATTATATATATT
25300 ATGTATATAT
Statistics
Matches: 188, Mismatches: 19, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
109 40 0.21
110 40 0.21
111 20 0.11
112 42 0.22
113 3 0.02
114 43 0.23
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (109 bp):
TTTTCAAAAATAATATTATATATATTTTCAAAAATGTTTTCAAAAATATATATTATATATATTTT
CAAAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATG
Found at i:26380 original size:22 final size:23
Alignment explanation
Indices: 26342--26392 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
26332 TGAATTAAGC
*
26342 CGAACCCGTTCTGAATTGGCTCT
1 CGAACCCGTACTGAATTGGCTCT
*
26365 CGAACCCG-ACTGAATTGGTTCT
1 CGAACCCGTACTGAATTGGCTCT
*
26387 CAAACC
1 CGAACC
26393 TGATTTGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (23 bp):
CGAACCCGTACTGAATTGGCTCT
Found at i:31870 original size:2 final size:2
Alignment explanation
Indices: 31863--31901 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
31853 TCAATCTACA
31863 AT AT 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 AT AT A
31902 AATTTATGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32082 original size:13 final size:13
Alignment explanation
Indices: 32059--32100 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
32049 AATGATGCGC
*
32059 AATGAGCGTCATA
1 AATGCGCGTCATA
*
32072 AATGCGGGTCATA
1 AATGCGCGTCATA
32085 AATGCGCGTCATA
1 AATGCGCGTCATA
32098 AAT
1 AAT
32101 TTATGACGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.24
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:38139 original size:6 final size:6
Alignment explanation
Indices: 38122--38181 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
38112 TATTGGACCA
* * *
38122 AAAAAT AGAAAT AAAAAT AAGAAT AAAAAT AAATAAAT AGAAAT -AAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT -AA-AAAT AAAAAT AAAAAT
38171 --AAAT AAAAAT A
1 AAAAAT AAAAAT A
38182 TATATATATA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
4 4 0.09
5 4 0.09
6 29 0.66
7 3 0.07
8 4 0.09
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:38158 original size:10 final size:10
Alignment explanation
Indices: 38130--38181 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
38120 CAAAAAATAG
38130 AAATAAAAAT
1 AAATAAAAAT
38140 AAGAATAAAAAT
1 -A-AATAAAAAT
* *
38152 AAATAAATAG
1 AAATAAAAAT
38162 AAAT-AAAAT
1 AAATAAAAAT
38171 AAATAAAAAT
1 AAATAAAAAT
38181 A
1 A
38182 TATATATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 7 0.20
10 17 0.49
11 2 0.06
12 9 0.26
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:38186 original size:2 final size:2
Alignment explanation
Indices: 38179--38204 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38169 ATAAATAAAA
38179 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
38205 TTCGAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38330 original size:75 final size:75
Alignment explanation
Indices: 38246--38594 Score: 326
Period size: 73 Copynumber: 4.7 Consensus size: 75
38236 GTTTTCTAAA
* *
38246 ATATATTATATATTTTTTCCAAAAACGTCTT-AAAACTATATATTATACATATTTTCGAAAAATG
1 ATATATTATATATTTTTT-CAAAAACGTTTTCAAAACTATATATTATATATATTTTCGAAAAATG
*
38310 ATTTCAAAACTAT
65 TTTTCAAAAC--T
* ** *
38323 ATATTATATATATATTTTTTCAAAAACCTTTTTTTAAACCATATA-T-TATAT-TTTT--AAAAA
1 ATA-TAT-TATATATTTTTTCAAAAA-CGTTTTCAAAACTATATATTATATATATTTTCGAAAAA
*
38383 CGTTTTCAAAACT
63 TGTTTTCAAAACT
* * * * *
38396 ATATATTAAATATTTTTT--AAAATGTTTTCAAAATTATATATTATATATATTTTCAAAAAAAG-
1 ATATATTATATATTTTTTCAAAAACGTTTTCAAAACTATATATTATATATATTTTCGAAAAATGT
38458 TTTCAAAA-T
66 TTTCAAAACT
* * * * * * *
38467 GATATATTATATATATTTT-AAAAATGTTTTCAAGACTACATATTGTATATATTTTTGAACAATG
1 -ATATATTATATATTTTTTCAAAAACGTTTTCAAAACTATATATTATATATATTTTCGAAAAATG
* *
38531 TTTTTAAAATT
65 TTTTCAAAACT
* *
38542 ATATACTATATATATTTTCAAAAACGTTTTCAAAA-TCATATATTATATATATT
1 ATATATTATATATTTTTTCAAAAACGTTTTCAAAACT-ATATATTATATATATT
38595 ATGTATATAT
Statistics
Matches: 226, Mismatches: 31, Indels: 32
0.78 0.11 0.11
Matches are distributed among these distances:
68 12 0.05
69 5 0.02
70 5 0.02
71 16 0.07
72 27 0.12
73 46 0.20
74 25 0.11
75 44 0.19
77 7 0.03
78 13 0.06
79 17 0.08
80 9 0.04
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (75 bp):
ATATATTATATATTTTTTCAAAAACGTTTTCAAAACTATATATTATATATATTTTCGAAAAATGT
TTTCAAAACT
Found at i:38556 original size:111 final size:108
Alignment explanation
Indices: 38246--38594 Score: 350
Period size: 111 Copynumber: 3.1 Consensus size: 108
38236 GTTTTCTAAA
* * * *
38246 ATATATTATATATTTTTTCCAAAAACGTCTT-AAAACTATATATTATACATATTTTCGAAAAATG
1 ATATATTATATATATTTT--AAAAACGTTTTCAAAACTACATATTA-A-ATATTTTTG-AAAATG
* ** ** *
38310 ATTTCAAAACTATATATTA-TATATATATTTTTTCAAAAACCTTTTTTTAAACC
61 TTTTCAAAA-T-TATA-TACTATATATA--TTTTCAAAAA-AGTTTTCAAAATC
* *
38363 ATATA-T-TATAT-TTTTAAAAACGTTTTCAAAACTATATATTAAATATTTTTTAAAATGTTTTC
1 ATATATTATATATATTTTAAAAACGTTTTCAAAACTACATATTAAATATTTTTGAAAATGTTTTC
* *
38425 AAAATTATATATTATATATATTTTCAAAAAAAG-TTTCAAAATG
66 AAAATTATATACTATATATATTTTC-AAAAAAGTTTTCAAAATC
* * *
38468 ATATATTATATATATTTTAAAAATGTTTTCAAGACTACATATTGTATATATTTTTGAACAATGTT
1 ATATATTATATATATTTTAAAAACGTTTTCAAAACTACATA-T-TAAATATTTTTGAA-AATGTT
* *
38533 TTTAAAATTATATACTATATATATTTTCAAAAACGTTTTCAAAATC
63 TTCAAAATTATATACTATATATATTTTCAAAAAAGTTTTCAAAATC
38579 ATATATTATATATATT
1 ATATATTATATATATT
38595 ATGTATATAT
Statistics
Matches: 203, Mismatches: 19, Indels: 26
0.82 0.08 0.10
Matches are distributed among these distances:
105 11 0.05
106 6 0.03
107 12 0.06
108 36 0.18
109 2 0.01
110 32 0.16
111 64 0.32
112 11 0.05
113 14 0.07
114 4 0.02
115 5 0.02
116 1 0.00
117 5 0.02
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (108 bp):
ATATATTATATATATTTTAAAAACGTTTTCAAAACTACATATTAAATATTTTTGAAAATGTTTTC
AAAATTATATACTATATATATTTTCAAAAAAGTTTTCAAAATC
Found at i:38575 original size:183 final size:183
Alignment explanation
Indices: 38246--38591 Score: 420
Period size: 183 Copynumber: 1.9 Consensus size: 183
38236 GTTTTCTAAA
* * *
38246 ATATATTATATATTTTTTCCAAAAACGTCTTAAAACTATATATTATACATATTTTCGAAAAATGA
1 ATATATTATATATATTTTCAAAAAAAGTCTTAAAACTATATATTATACATATTTTC-AAAAATGA
* *
38311 TTTCAAAACTATATATTATATATATATTTTTTCAAAAACCTTTTTTTAAACCATATATTATATTT
65 TTTCAAAACTACATATTATATATATATTTTTTCAAAAA-CTTTTTTAAAACCATATATTATATTT
38376 TTAAAAACGTTTTCAAAA-CTATATATTAAATATTTTTTAAAATGTTTTCAAAATT
129 TTAAAAACGTTTTCAAAATC-ATATATTAAATATTTTTTAAAATGTTTTCAAAATT
*
38431 ATATATTATATATATTTTCAAAAAAAGT-TTCAAAA-TGATATATTATATATATTTT-AAAAATG
1 ATATATTATATATATTTTCAAAAAAAGTCTT-AAAACT-ATATATTATACATATTTTCAAAAATG
* * * * * **
38493 TTTTCAAGACTACATA-T-TGTATATA-TTTTTGAACAA-TGTTTTTAAAATTATATACTATATA
64 ATTTCAAAACTACATATTATATATATATTTTTTCAAAAACT-TTTTTAAAACCATATA-T-TATA
*
38554 TATTTTCAAAAACGTTTTCAAAATCATATATTATATAT
126 T-TTTT-AAAAACGTTTTCAAAATCATATATTAAATAT
38592 ATTATGTATA
Statistics
Matches: 139, Mismatches: 14, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
178 1 0.01
179 13 0.09
180 10 0.07
181 12 0.09
182 5 0.04
183 48 0.35
184 4 0.03
185 46 0.33
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (183 bp):
ATATATTATATATATTTTCAAAAAAAGTCTTAAAACTATATATTATACATATTTTCAAAAATGAT
TTCAAAACTACATATTATATATATATTTTTTCAAAAACTTTTTTAAAACCATATATTATATTTTT
AAAAACGTTTTCAAAATCATATATTAAATATTTTTTAAAATGTTTTCAAAATT
Found at i:38592 original size:37 final size:37
Alignment explanation
Indices: 38229--38594 Score: 269
Period size: 37 Copynumber: 9.9 Consensus size: 37
38219 TTTCAAAACC
* * *
38229 CAAACACGTTTTCTAAA--ATATATTATATATTTTTT
1 CAAAAACGTTTTCAAAATCATATATTATATATATTTT
* *
38264 CCAAAAACGTCTT-AAAA-CTATATATTATACATATTTT
1 -CAAAAACGTTTTCAAAATC-ATATATTATATATATTTT
* *
38301 CGAAAAATGATTTCAAAA-CTATATATTATATATATATTTTTT
1 C-AAAAACGTTTTCAAAATC-ATATA-T-TATATATA--TTTT
* ** *
38343 CAAAAACCTTTTTTTAAACCATATA-T-TATAT-TTTT
1 CAAAAA-CGTTTTCAAAATCATATATTATATATATTTT
38378 -AAAAACGTTTTCAAAA-CTATATATTA-A-ATATTTT
1 CAAAAACGTTTTCAAAATC-ATATATTATATATATTTT
** * *
38412 TTAAAATGTTTTCAAAATTATATATTATATATATTTT
1 CAAAAACGTTTTCAAAATCATATATTATATATATTTT
* *
38449 CAAAAAAAG-TTTCAAAATGATATATTATATATATTTT
1 C-AAAAACGTTTTCAAAATCATATATTATATATATTTT
* *
38486 -AAAAATGTTTTCAAGACTACATAT-TGTATATAT-TTTT
1 CAAAAACGTTTTCAA-AAT-CATATAT-TATATATATTTT
* * * * * *
38523 GAACAATGTTTTTAAAATTATATACTATATATATTTT
1 CAAAAACGTTTTCAAAATCATATATTATATATATTTT
38560 CAAAAACGTTTTCAAAATCATATATTATATATATT
1 CAAAAACGTTTTCAAAATCATATATTATATATATT
38595 ATGTATATAT
Statistics
Matches: 266, Mismatches: 38, Indels: 51
0.75 0.11 0.14
Matches are distributed among these distances:
32 1 0.00
33 15 0.06
34 11 0.04
35 35 0.13
36 29 0.11
37 100 0.38
38 44 0.17
39 2 0.01
40 7 0.03
41 5 0.02
42 16 0.06
43 1 0.00
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (37 bp):
CAAAAACGTTTTCAAAATCATATATTATATATATTTT
Found at i:44893 original size:31 final size:31
Alignment explanation
Indices: 44839--44914 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 31
44829 TCAAAAAGCA
* * *
44839 TAAGTATTGGTAACTTACATTATTGTTTTGT
1 TAAGTTTTGGTCACTTACATTATTGTTTTAT
** *
44870 TAAGTTTTGGTCACTTATGTTATTTTTTTAT
1 TAAGTTTTGGTCACTTACATTATTGTTTTAT
* *
44901 TAATTTTTTGTCAC
1 TAAGTTTTGGTCAC
44915 CTGGACGTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.22, C:0.08, G:0.13, T:0.57
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACATTATTGTTTTAT
Found at i:45265 original size:31 final size:31
Alignment explanation
Indices: 45227--45290 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
45217 AAATGCAACA
*
45227 AACCACATCATTAGAGGCGAAGCTATAAGTT
1 AACCACATCATTAGAGGCGAAGATATAAGTT
*
45258 AACCACATCATTAGAGGCGAAGATGTAAGTT
1 AACCACATCATTAGAGGCGAAGATATAAGTT
45289 AA
1 AA
45291 GGAAAGATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (31 bp):
AACCACATCATTAGAGGCGAAGATATAAGTT
Found at i:48563 original size:14 final size:14
Alignment explanation
Indices: 48546--48573 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
48536 TTTGTGTTTC
48546 CAAGTTTGTTGTTG
1 CAAGTTTGTTGTTG
48560 CAAGTTTGTTGTTG
1 CAAGTTTGTTGTTG
48574 ATTGGAACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.29, T:0.50
Consensus pattern (14 bp):
CAAGTTTGTTGTTG
Found at i:49976 original size:76 final size:77
Alignment explanation
Indices: 49817--50026 Score: 291
Period size: 76 Copynumber: 2.8 Consensus size: 77
49807 CAAAGCCAAA
* * * **
49817 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
49881 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
*
49894 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
49959 TTT-GCTCCGAG
66 TTTGGCCCCGAG
* * * *
49970 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
50027 TGTACAACGG
Statistics
Matches: 120, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
75 19 0.16
76 62 0.52
77 39 0.32
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:55813 original size:20 final size:19
Alignment explanation
Indices: 55788--55848 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 19
55778 TTTTGGTGCA
*
55788 GAGGGAATCGATCTCCCCCT
1 GAGGGAACCGAT-TCCCCCT
55808 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC--T
55829 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
55849 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
19 6 0.17
20 11 0.31
21 2 0.06
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.18
Consensus pattern (19 bp):
GAGGGAACCGATTCCCCCT
Found at i:55857 original size:21 final size:21
Alignment explanation
Indices: 55831--55870 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55821 CCCCCTTTGA
*
55831 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
55852 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
55871 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:57793 original size:17 final size:17
Alignment explanation
Indices: 57771--57818 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
57761 TTTCAACATT
57771 TTTGATATTTTGGATTG
1 TTTGATATTTTGGATTG
57788 TTTGAT-TTTGTGGATTG
1 TTTGATATTT-TGGATTG
*
57805 -TTG-GATTTTGGATT
1 TTTGATATTTTGGATT
57819 TATGAATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 13 0.46
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (17 bp):
TTTGATATTTTGGATTG
Found at i:58108 original size:24 final size:20
Alignment explanation
Indices: 58067--58105 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
58057 GTTAAATGTT
58067 TTACATAATAAATTGAAGGTG
1 TTACATAATAAATTGAA-GTG
58088 TTACATAATAAATTGAAG
1 TTACATAATAAATTGAAG
58106 AAGTGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.33
Consensus pattern (20 bp):
TTACATAATAAATTGAAGTG
Found at i:58584 original size:76 final size:77
Alignment explanation
Indices: 58424--58631 Score: 255
Period size: 76 Copynumber: 2.7 Consensus size: 77
58414 CAAAGCCAAA
* * * * **
58424 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCCATAGGAGGAATCGATT-CCCCCTAAATG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCCATAGGAGGAACCGATTCCCCCCTAAACA
*
58488 GTTTTGGCCTTGAG
64 GTTTTGGCCTCGAG
*
58502 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
58567 TTT-G-CTCCGAG
66 TTTGGCCT-CGAG
* * *
58578 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGG-GGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
58632 TTGTACAACG
Statistics
Matches: 116, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
74 14 0.12
75 5 0.04
76 58 0.50
77 14 0.12
78 25 0.22
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.21
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCTCGAG
Found at i:60026 original size:20 final size:20
Alignment explanation
Indices: 60001--60043 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
59991 AACCAAACAC
60001 ACCCTAGGTGTAGTATCAAT
1 ACCCTAGGTGTAGTATCAAT
*
60021 ACCCTAGGTGTAGTATCGAT
1 ACCCTAGGTGTAGTATCAAT
60041 ACC
1 ACC
60044 TCTATGAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (20 bp):
ACCCTAGGTGTAGTATCAAT
Found at i:66631 original size:19 final size:19
Alignment explanation
Indices: 66571--66631 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
66561 TTTGTGTAGA
* *
66571 GGGAATCGATACCCTCATG
1 GGGAATCGATACCCCCCTG
* *
66590 AGGGAACCGAT-TCCCCCTAG
1 -GGGAATCGATACCCCCCT-G
66610 GGGAATCGATACCCCCCTG
1 GGGAATCGATACCCCCCTG
66629 GGG
1 GGG
66632 TTCTGGATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.23, C:0.31, G:0.30, T:0.16
Consensus pattern (19 bp):
GGGAATCGATACCCCCCTG
Found at i:75359 original size:19 final size:21
Alignment explanation
Indices: 75335--75375 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
75325 AGCTTTTATA
75335 TTCTCTCA-TTT-CATTTTCT
1 TTCTCTCATTTTCCATTTTCT
75354 TTCTCTCATTTTCCATTTTCT
1 TTCTCTCATTTTCCATTTTCT
75375 T
1 T
75376 CTTCCTCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.10, C:0.27, G:0.00, T:0.63
Consensus pattern (21 bp):
TTCTCTCATTTTCCATTTTCT
Found at i:76964 original size:53 final size:53
Alignment explanation
Indices: 76853--76978 Score: 128
Period size: 53 Copynumber: 2.4 Consensus size: 53
76843 TAAGCTGACA
* * *
76853 GGGTGTACGTTTCCGATGCAACTCCGGATCTCACCCCATATATATGAGGGGTC
1 GGGTGTACGTTTCCGATGCAACTCCAGATCTCACCCCATAAATATGAGAGGTC
* ** * * **
76906 AGGTGTACGTTTTTGATGTAGCTCCAGATCTCACCTTATAAAT-TCGAGAGGTC
1 GGGTGTACGTTTCCGATGCAACTCCAGATCTCACCCCATAAATAT-GAGAGGTC
* *
76959 GGGTGTACATTTCCTATGCA
1 GGGTGTACGTTTCCGATGCA
76979 GATTTGGATC
Statistics
Matches: 56, Mismatches: 16, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
52 1 0.02
53 55 0.98
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (53 bp):
GGGTGTACGTTTCCGATGCAACTCCAGATCTCACCCCATAAATATGAGAGGTC
Found at i:77240 original size:32 final size:32
Alignment explanation
Indices: 77199--77294 Score: 129
Period size: 32 Copynumber: 3.0 Consensus size: 32
77189 GTGGATGAGT
*
77199 CACAACAGAGTTAGCATTACATTTAGATAATG
1 CACAACAGAGTCAGCATTACATTTAGATAATG
* *
77231 CACAACAGAGTCAGCATTGCATTAAGATAATG
1 CACAACAGAGTCAGCATTACATTTAGATAATG
** * *
77263 CACAGTAGAGTCAGTATCACATTTAGATAATG
1 CACAACAGAGTCAGCATTACATTTAGATAATG
77295 TGTAACGGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.26
Consensus pattern (32 bp):
CACAACAGAGTCAGCATTACATTTAGATAATG
Found at i:78930 original size:32 final size:32
Alignment explanation
Indices: 78894--78962 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
78884 GTTTATTTTG
78894 ACTTTACCT-CCTCATTTTCTATGATTAATTAT
1 ACTTT-CCTCCCTCATTTTCTATGATTAATTAT
* *
78926 ACTTTGCTCCCTCATTTTTTATGATTAATTAT
1 ACTTTCCTCCCTCATTTTCTATGATTAATTAT
78958 ACTTT
1 ACTTT
78963 GCTCTCCTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 2 0.06
32 32 0.94
ACGTcount: A:0.23, C:0.20, G:0.04, T:0.52
Consensus pattern (32 bp):
ACTTTCCTCCCTCATTTTCTATGATTAATTAT
Found at i:78963 original size:32 final size:32
Alignment explanation
Indices: 78903--78966 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
78893 GACTTTACCT
78903 CCTCATTTTCTATGATTAATTATACTTTGCTC
1 CCTCATTTTCTATGATTAATTATACTTTGCTC
*
78935 CCTCATTTTTTATGATTAATTATACTTTGCTC
1 CCTCATTTTCTATGATTAATTATACTTTGCTC
78967 TCCTTGAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.52
Consensus pattern (32 bp):
CCTCATTTTCTATGATTAATTATACTTTGCTC
Found at i:78999 original size:28 final size:28
Alignment explanation
Indices: 78959--79047 Score: 160
Period size: 28 Copynumber: 3.2 Consensus size: 28
78949 ATTAATTATA
78959 CTTTGCTCTCCTTGAATTGGAATCCTAG
1 CTTTGCTCTCCTTGAATTGGAATCCTAG
*
78987 CTTTGCTCTCCTTGATTTGGAATCCTAG
1 CTTTGCTCTCCTTGAATTGGAATCCTAG
*
79015 CTTTGCTCTCTTTGAATTGGAATCCTAG
1 CTTTGCTCTCCTTGAATTGGAATCCTAG
79043 CTTTG
1 CTTTG
79048 TCCCTGAGTA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.43
Consensus pattern (28 bp):
CTTTGCTCTCCTTGAATTGGAATCCTAG
Done.