Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003262.1 Hibiscus syriacus cultivar Beakdansim tig00006858_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: 94263
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:6605 original size:12 final size:12
Alignment explanation
Indices: 6585--6618 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6575 AAAATCATTT
*
6585 AAATCTATTTTA
1 AAATATATTTTA
*
6597 AAATTTATTTTA
1 AAATATATTTTA
6609 AAATATATTT
1 AAATATATTT
6619 ATTTATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
AAATATATTTTA
Found at i:6647 original size:22 final size:22
Alignment explanation
Indices: 6599--6940 Score: 474
Period size: 22 Copynumber: 15.6 Consensus size: 22
6589 CTATTTTAAA
*
6599 ATTTATTTTAAAATAT--ATTT
1 ATTTATTTTAAAATATGGATTG
6619 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
6641 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
6663 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
*
6685 AATTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
6707 ATTTATTTTAAAATATGGAAAAA
1 ATTTATTTTAAAATATGG-ATTG
*
6730 ATTTATTTTAAAATATTGATTG
1 ATTTATTTTAAAATATGGATTG
6752 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
6774 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
6796 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
*
6818 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
***
6840 ATTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATGGATTG
6861 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
6884 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
6906 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
6928 ATTTATTTTAAAA
1 ATTTATTTTAAAA
6941 AAATTATTAT
Statistics
Matches: 283, Mismatches: 34, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
20 16 0.06
21 2 0.01
22 244 0.86
23 21 0.07
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:7002 original size:31 final size:31
Alignment explanation
Indices: 6964--7022 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
6954 AGTTGTATGG
* *
6964 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGGATTACAAAACTAAA
*
6995 ATTATTTAAATTTTAGGATTACAAAACT
1 ATTATTTAAATTTCAGGATTACAAAACT
7023 GTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGGATTACAAAACTAAA
Found at i:12274 original size:45 final size:44
Alignment explanation
Indices: 12128--12301 Score: 169
Period size: 44 Copynumber: 4.0 Consensus size: 44
12118 TAGAGTCATT
* * * * *
12128 AATTATAAAG-ATAAAAGTAAGATTGAAAAAAATTAGGAATCTC
1 AATTATAAAGTAAAAAAGTGAGATTGAAAAAAAATAAGAACCTC
* * *
12171 AATTATAAAGGT-AAAAAGTGAGATTG-AAAAAAATTAGAGGCTTC
1 AATTATAAA-GTAAAAAAGTGAGATTGAAAAAAAATAAGA-ACCTC
*
12215 AATTATAAAATAAAAAAGT-AGAATTGAAAAAAAATAAGAACCTC
1 AATTATAAAGTAAAAAAGTGAG-ATTGAAAAAAAATAAGAACCTC
* * *
12259 AATTACAAATGTAAAAAAGTGAGACT-AAAAAAAATAAAAACCT
1 AATTATAAA-GTAAAAAAGTGAGATTGAAAAAAAATAAGAACCT
12302 TAAGGTCGTG
Statistics
Matches: 107, Mismatches: 16, Indels: 15
0.78 0.12 0.11
Matches are distributed among these distances:
43 21 0.20
44 62 0.58
45 22 0.21
46 2 0.02
ACGTcount: A:0.58, C:0.06, G:0.13, T:0.22
Consensus pattern (44 bp):
AATTATAAAGTAAAAAAGTGAGATTGAAAAAAAATAAGAACCTC
Found at i:12274 original size:88 final size:88
Alignment explanation
Indices: 12112--12293 Score: 228
Period size: 88 Copynumber: 2.1 Consensus size: 88
12102 GTAGGGTTGG
* * * * *
12112 AAAAATTAGAGTCATTAATTATAAAGATAAAAGTAAGATTGAAAAAAATTAGGAATCTCAATTAT
1 AAAAATTAGAGGCATTAATTATAAAGATAAAAGTAAGATTGAAAAAAAATAAGAACCTCAATTAC
* *
12177 AAAGGT-AAAAAGTGAGATTGAA
66 AAAGGTAAAAAAGTGAGACTAAA
12199 AAAAATTAGAGGC-TTCAATTATAAA-ATAAAAAAGT-AGAATTGAAAAAAAATAAGAACCTCAA
1 AAAAATTAGAGGCATT-AATTATAAAGAT--AAAAGTAAG-ATTGAAAAAAAATAAGAACCTCAA
*
12261 TTACAAATGTAAAAAAGTGAGACTAAA
62 TTACAAAGGTAAAAAAGTGAGACTAAA
12288 AAAAAT
1 AAAAAT
12294 AAAAACCTTA
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
86 4 0.05
87 23 0.28
88 35 0.43
89 20 0.24
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.24
Consensus pattern (88 bp):
AAAAATTAGAGGCATTAATTATAAAGATAAAAGTAAGATTGAAAAAAAATAAGAACCTCAATTAC
AAAGGTAAAAAAGTGAGACTAAA
Found at i:21708 original size:83 final size:85
Alignment explanation
Indices: 21549--21710 Score: 256
Period size: 83 Copynumber: 1.9 Consensus size: 85
21539 AATTTCTAGA
21549 TTTGGGTGTTCATTGAATTCCTAGGAAAATGAAGTGTATATATATATCAACAAATTTTCCTTTTT
1 TTTGGGTGTTCATTGAATTCCTAGGAAAATGAAG-G-ATATATATATCAACAAATTTTCCTTTTT
21614 AGAACTACATTCTAAATCTATG
64 AGAACTACATTCTAAATCTATG
* * * *
21636 TTTGGGTGTTCATTTACTTCCTTGGAAAATGAA-G-TATATATATCAATAAATTTTCCTTTTTAG
1 TTTGGGTGTTCATTGAATTCCTAGGAAAATGAAGGATATATATATCAACAAATTTTCCTTTTTAG
21699 AACTACATTCTA
66 AACTACATTCTA
21711 GAAGTTTGAA
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
83 40 0.56
85 1 0.01
87 30 0.42
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (85 bp):
TTTGGGTGTTCATTGAATTCCTAGGAAAATGAAGGATATATATATCAACAAATTTTCCTTTTTAG
AACTACATTCTAAATCTATG
Found at i:23681 original size:19 final size:19
Alignment explanation
Indices: 23645--23681 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
23635 AGAGTAACAC
* *
23645 ATTGCTGATTTTATTCTAA
1 ATTGCTGATTTAAATCTAA
23664 ATTGCTGATTTAAATCTA
1 ATTGCTGATTTAAATCTA
23682 CAGATTTCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (19 bp):
ATTGCTGATTTAAATCTAA
Found at i:24596 original size:22 final size:24
Alignment explanation
Indices: 24551--24598 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
24541 TTATTTTTTT
* *
24551 AAAAATCCACATAAGAACTAATAA
1 AAAAATCCACATAAAAAATAATAA
24575 AAAAAT-CACATAAAAAAT-ATAA
1 AAAAATCCACATAAAAAATAATAA
24597 AA
1 AA
24599 TATAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 10 0.45
24 6 0.27
ACGTcount: A:0.69, C:0.12, G:0.02, T:0.17
Consensus pattern (24 bp):
AAAAATCCACATAAAAAATAATAA
Found at i:26894 original size:60 final size:60
Alignment explanation
Indices: 26816--26934 Score: 220
Period size: 60 Copynumber: 2.0 Consensus size: 60
26806 ATATCGTAAC
26816 TATGAGCCCACTGCAATACACCCAAGAGCTCGGAACTCCCTCCCAATCAACTCCGAGGTA
1 TATGAGCCCACTGCAATACACCCAAGAGCTCGGAACTCCCTCCCAATCAACTCCGAGGTA
* *
26876 TATGTGCCCACTGCAATACACCCAAGAGCTCGGAACTCCCTCCCAATCGACTCCGAGGT
1 TATGAGCCCACTGCAATACACCCAAGAGCTCGGAACTCCCTCCCAATCAACTCCGAGGT
26935 GACTATATTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.28, C:0.37, G:0.18, T:0.18
Consensus pattern (60 bp):
TATGAGCCCACTGCAATACACCCAAGAGCTCGGAACTCCCTCCCAATCAACTCCGAGGTA
Found at i:28169 original size:26 final size:28
Alignment explanation
Indices: 28125--28179 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 28
28115 ATATATCAAA
28125 TACAATATAAAATTAT-AA-AATATATT
1 TACAATATAAAATTATAAAGAATATATT
* * *
28151 TACAATATTATATTTTAAAGAATATATT
1 TACAATATAAAATTATAAAGAATATATT
28179 T
1 T
28180 TGAGGGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 13 0.54
27 2 0.08
28 9 0.38
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (28 bp):
TACAATATAAAATTATAAAGAATATATT
Found at i:30011 original size:74 final size:72
Alignment explanation
Indices: 29861--30028 Score: 216
Period size: 72 Copynumber: 2.3 Consensus size: 72
29851 TGTATTTGAA
*
29861 TATAATTTACAATATTTTTATATATTTTAAATTTTTAATGAAAGAAATAATGTTTAATTTTTATT
1 TATAATTTACAATATTTTTATATATTTTAAATTTTTAATGAAAGAAATAATATTTAATTTTTATT
29926 TATTAAG
66 TATTAAG
* * * * *
29933 TATAATTTATAATATTTTTTTATATTTTTAATGTTTGTTCATGGAAGAAATAATATTTAA-TTTT
1 TATAATTTACAATATTTTTATATA-TTTTAA-ATTT-TTAATGAAAGAAATAATATTTAATTTTT
*
29997 ATTTATTAAT
63 ATTTATTAAG
*
30007 TATAATTT--AATATTTATATATA
1 TATAATTTACAATATTTTTATATA
30029 ATATTAGAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
72 34 0.40
73 6 0.07
74 24 0.29
75 20 0.24
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (72 bp):
TATAATTTACAATATTTTTATATATTTTAAATTTTTAATGAAAGAAATAATATTTAATTTTTATT
TATTAAG
Found at i:30021 original size:72 final size:72
Alignment explanation
Indices: 29861--30021 Score: 202
Period size: 74 Copynumber: 2.2 Consensus size: 72
29851 TGTATTTGAA
* *
29861 TATAATTTACA-ATATTTTTATATATTTTAAATTTTTAATGAAAGAAATAATGTTTAATTTTTAT
1 TATAATTTA-ATATTTTTTTATATATTTTAAATTTTTAATGAAAGAAATAATATTTAATTTTTAT
29925 TTATTAAG
65 TTATTAAG
* * *
29933 TATAATTTATAATATTTTTTTATAT-TTTTAATGTTTGTTCATGGAAGAAATAATATTTAA-TTT
1 TATAA-TT-TAATATTTTTTTATATATTTTAA-ATTT-TTAATGAAAGAAATAATATTTAATTTT
*
29996 TATTTATTAAT
62 TATTTATTAAG
30007 TATAATTTAATATTT
1 TATAATTTAATATTT
30022 ATATATAATA
Statistics
Matches: 78, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
72 13 0.17
73 11 0.14
74 34 0.44
75 20 0.26
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (72 bp):
TATAATTTAATATTTTTTTATATATTTTAAATTTTTAATGAAAGAAATAATATTTAATTTTTATT
TATTAAG
Found at i:30208 original size:74 final size:73
Alignment explanation
Indices: 30031--30295 Score: 272
Period size: 73 Copynumber: 3.6 Consensus size: 73
30021 TATATATAAT
* * *
30031 ATTAGAAATTATTTCTTCCATTAACAACAATTCAATAGAATATAT--GAT-TATTAAATTATAAT
1 ATTA-AAATTATTTCTTCCATTAACAAAAATT-AA-A-AATATATAAAATATTTTAAATTATAAT
30093 TAATAAAT-AAA
62 TAATAAATAAAA
*
30104 ATTAAATATTATTTCTTCCACTAACAAAAATTAAAAATATATAAAATATTTTAAATTATAATTAA
1 ATTAAA-ATTATTTCTTCCATTAACAAAAATTAAAAATATATAAAATATTTTAAATTATAATTAA
*
30169 GAAATAAAA
65 TAAATAAAA
* * * * ** * * *
30178 ATTAAGAACTAATTCTTTCATTAACAAAAATTAAAAATATGTAATTTTTTTTGTAAAATATAGTT
1 ATTAA-AATTATTTCTTCCATTAACAAAAATTAAAAATATATAA-AATATTT-TAAATTATAATT
30243 AATAAATAAAA
63 AATAAATAAAA
* *
30254 ATAAAAATTATTTCTTCCATTAA-AAAAA-TAAAATTATATAAA
1 ATTAAAATTATTTCTTCCATTAACAAAAATTAAAAATATATAAA
30296 TTATAGTTAA
Statistics
Matches: 161, Mismatches: 23, Indels: 17
0.80 0.11 0.08
Matches are distributed among these distances:
70 7 0.04
71 1 0.01
72 6 0.04
73 58 0.36
74 45 0.28
75 20 0.12
76 24 0.15
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (73 bp):
ATTAAAATTATTTCTTCCATTAACAAAAATTAAAAATATATAAAATATTTTAAATTATAATTAAT
AAATAAAA
Found at i:33819 original size:20 final size:20
Alignment explanation
Indices: 33795--33842 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
33785 ATCTTGAAAC
*
33795 ATTCTTTGAAACTATTGATA
1 ATTCTTTGAAAATATTGATA
* * *
33815 TTTCTATAAAAATATTGATA
1 ATTCTTTGAAAATATTGATA
33835 ATTCTTTG
1 ATTCTTTG
33843 TTTATTTCTT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.48
Consensus pattern (20 bp):
ATTCTTTGAAAATATTGATA
Found at i:40240 original size:33 final size:32
Alignment explanation
Indices: 40181--40262 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 32
40171 AGTACCAATT
* * *
40181 CAAAAAAAATTAAGTTTATATATTAATTTAAA
1 CAAAAAAAATTAAATTAATATATTAATTGAAA
*
40213 CAAAAAAAATTAAATTCAAT-TACTTAATTGAAT
1 CAAAAAAAATTAAATT-AATATA-TTAATTGAAA
40246 CAAAATAAAAATTAAAT
1 C-AAA-AAAAATTAAAT
40263 ACTAAATTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 17 0.40
33 11 0.26
34 3 0.07
35 11 0.26
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (32 bp):
CAAAAAAAATTAAATTAATATATTAATTGAAA
Found at i:42363 original size:18 final size:18
Alignment explanation
Indices: 42337--42371 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42327 AAAATTACCT
* *
42337 AAAATTATTATTTTTATC
1 AAAAATATTATTATTATC
42355 AAAAATATTATTATTAT
1 AAAAATATTATTATTAT
42372 TACTTTATCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAAATATTATTATTATC
Found at i:44759 original size:35 final size:34
Alignment explanation
Indices: 44705--44792 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
44695 GATTATTTTG
*
44705 ATAATTAAACTT-TCAAAAAAATAAAAAATAAAAAA
1 ATAATTAAATTTATC-AAAAAA-AAAAAATAAAAAA
* * * *
44740 ATAATTAAATTTATCAAAAAAGATATATAAAATA
1 ATAATTAAATTTATCAAAAAAAAAAAATAAAAAA
*
44774 ATCATTAAATTTTATCAAA
1 ATAATTAAA-TTTATCAAA
44793 CTGTTGTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 17 0.38
35 26 0.58
36 2 0.04
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (34 bp):
ATAATTAAATTTATCAAAAAAAAAAAATAAAAAA
Found at i:46656 original size:35 final size:36
Alignment explanation
Indices: 46617--46690 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 36
46607 CGAATTCAAT
46617 GTTTTATATCATAATGTAAACGTTTAAG-ATGTTTA
1 GTTTTATATCATAATGTAAACGTTTAAGAATGTTTA
* *
46652 GTTTTATATCATAATGTTAACTTTTAAGAAATGTTTA
1 GTTTTATATCATAATGTAAACGTTTAAG-AATGTTTA
46689 GT
1 GT
46691 ATGAAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 26 0.74
37 9 0.26
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (36 bp):
GTTTTATATCATAATGTAAACGTTTAAGAATGTTTA
Found at i:48592 original size:31 final size:31
Alignment explanation
Indices: 48556--48614 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
48546 AACTTAAAAG
* *
48556 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
48587 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
48615 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:48665 original size:22 final size:22
Alignment explanation
Indices: 48639--48681 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
48629 TAATAAATTA
48639 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
48661 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
48682 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:48690 original size:22 final size:22
Alignment explanation
Indices: 48641--48689 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
48631 ATAAATTATT
**
48641 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
48663 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
48686 TAAA
1 TAAA
48690 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:48780 original size:14 final size:14
Alignment explanation
Indices: 48763--48816 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
48753 CAATCCATAC
48763 AAATAAATTATTTA
1 AAATAAATTATTTA
*
48777 AAATAAATTAATACATA
1 AAATAAATT-AT--TTA
*
48794 CTAATAAATTATTTA
1 -AAATAAATTATTTA
48809 AAATAAAT
1 AAATAAAT
48817 CAATTCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 16 0.50
15 4 0.12
17 4 0.12
18 8 0.25
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:48780 original size:32 final size:31
Alignment explanation
Indices: 48741--49251 Score: 293
Period size: 32 Copynumber: 18.4 Consensus size: 31
48731 CAATCTATAT
*
48741 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
* *
48773 TTTAAAATAAATTAATACATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
48805 TTTAAAATAAATCAAT---T-C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
48827 TTTAAAATAAATCAA-CTCATACTAATAAATTA
1 TTTAAAATAAATCAATC-CATACTAATAAA-TA
*
48859 TTTAAAATAAATCAATCCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
* **
48889 --T--AATAAATCAATTCATA-TTTTAAA-A
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
48914 --T-AAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
**
48943 TTTAAAATAAATCAATTGATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
48975 TTTAAAATAAATC-A---AT-CT-AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
48997 TTTAAAATAAATCAATCC--A----T--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
49019 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
49051 TTTAAAATAAATCAATCCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
49081 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
49099 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
49131 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
49153 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
49185 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
49207 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
49239 TTATAAAATAAAT
1 TT-TAAAATAAAT
49252 TATTTTAAAA
Statistics
Matches: 388, Mismatches: 18, Indels: 145
0.70 0.03 0.26
Matches are distributed among these distances:
20 1 0.00
22 95 0.24
23 7 0.02
24 7 0.02
25 7 0.02
26 56 0.14
27 6 0.02
28 14 0.04
29 2 0.01
30 6 0.02
31 12 0.03
32 164 0.42
33 11 0.03
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (31 bp):
TTTAAAATAAATCAATCCATACTAATAAATA
Found at i:48817 original size:166 final size:166
Alignment explanation
Indices: 48629--49205 Score: 735
Period size: 166 Copynumber: 3.5 Consensus size: 166
48619 ACAACTACAA
*
48629 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
48694 TTAAAATCAATCAATCCATACAACTACAATAATAAATCAATCTATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCTATATTTTAAAATAAATCAATCC
*
48759 ATACAAATAAATTATTTAAAATAAATTAATACATAC
131 ATACAAATAAATTATTTAAAATAAATCAATACATAC
*
48795 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAA-CTCATACTAATAAATTA
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATC-CATACTAATAAATTA
48859 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAAT-TCATATTTTAAAATAAATAAAT
65 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCT-ATATTTT---A-AAATAAAT
**
48923 CAATCCATACAAATAAATTATTTAAAATAAATCAATTGATAC
125 CAATCCATACAAATAAATTATTTAAAATAAATCAATACATAC
*
48965 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAAT-C---C--AT--A-T-T
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
* * ** *
49020 TTAAAATAAATCAATCCATACTAA-TA-AATTATTTAAAATAAATC-A-ATCCATACAACTACAA
66 TTAAAATAAATCAATCCATAC-AACTACAA-TA-AT-AAATCAATCTATAT-TTTA-AAATA-AA
** ** *
49081 T-AATAAAT-C-AATCCA-TATTTTAAAATAAATCAATCCATAC
124 TCAATCCATACAAATAAATTA-TTTAAAATAAATCAATACATAC
49121 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
49186 TTAAAATAAATCAATCCATA
66 TTAAAATAAATCAATCCATA
49206 TTTTAAAATA
Statistics
Matches: 365, Mismatches: 21, Indels: 50
0.84 0.05 0.11
Matches are distributed among these distances:
155 2 0.01
156 71 0.19
157 2 0.01
158 10 0.03
159 5 0.01
160 29 0.08
161 6 0.02
162 10 0.03
164 3 0.01
165 2 0.01
166 131 0.36
169 2 0.01
170 92 0.25
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (166 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCTATATTTTAAAATAAATCAATCC
ATACAAATAAATTATTTAAAATAAATCAATACATAC
Found at i:48830 original size:22 final size:22
Alignment explanation
Indices: 48805--48847 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
48795 TAATAAATTA
*
48805 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAACTCATAT
48827 TTTAAAATAAATCAACTCATA
1 TTTAAAATAAATCAACTCATA
48848 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAACTCATAT
Found at i:48831 original size:54 final size:54
Alignment explanation
Indices: 48629--49251 Score: 480
Period size: 54 Copynumber: 11.4 Consensus size: 54
48619 ACAACTACAA
*
48629 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATAC
* * * *
48683 TAATAAATTATTTAAAATCAATCAATCCATA----CAACTACAAT-AATAAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATA-AATCAATACATAC
** *
48732 -AATCTA-TATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATTAATACATAC
1 TAATAAATTA-TTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATACATAC
*
48795 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAACT-CATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAA-TACATAC
* ** *
48849 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATTCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATACATAC
** * ** * * * **
48906 TTTTAAAATAAAT-AAATCAATCCATACAAATAAATTATTTAAAATAAATCAATTGATAC
1 TAATAAATTATTTAAAATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATACATAC
* *
48965 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATAC
** * ** * ** ** *
49018 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATACATAC
* *
49073 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATAC
*
49121 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATAC
49175 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT-CTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATAC-ATAC
49229 TAATAAATTATTATAAAATAAAT
1 TAATAAATTATT-TAAAATAAAT
49252 TATTTTAAAA
Statistics
Matches: 462, Mismatches: 60, Indels: 93
0.75 0.10 0.15
Matches are distributed among these distances:
47 2 0.00
48 49 0.11
49 6 0.01
50 15 0.03
51 4 0.01
52 7 0.02
53 12 0.03
54 228 0.49
55 16 0.03
56 13 0.03
57 16 0.03
58 35 0.08
59 12 0.03
60 11 0.02
61 3 0.01
62 10 0.02
63 1 0.00
64 20 0.04
65 2 0.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATACATAC
Found at i:48838 original size:26 final size:26
Alignment explanation
Indices: 48809--48931 Score: 83
Period size: 26 Copynumber: 4.7 Consensus size: 26
48799 AAATTATTTA
48809 AAATAAATCAATTCATATTTTAAAAT
1 AAATAAATCAATTCATATTTTAAAAT
* * *
48835 AAATCAACTCATACTAATAAATTATTTAAAAT
1 AAAT-AAATCA-ATTCAT--A-T-TTTAAAAT
* * * * *
48867 AAATCAATCCATACA-A--CTACAAT
1 AAATAAATCAATTCATATTTTAAAAT
48890 -AATAAATCAATTCATATTTTAAAAT
1 AAATAAATCAATTCATATTTTAAAAT
*
48915 AAATAAATCAATCCATA
1 AAATAAATCAATTCATA
48932 CAAATAAATT
Statistics
Matches: 70, Mismatches: 17, Indels: 20
0.65 0.16 0.19
Matches are distributed among these distances:
22 11 0.16
23 6 0.09
25 5 0.07
26 19 0.27
27 6 0.09
28 4 0.06
30 3 0.04
31 4 0.06
32 12 0.17
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.33
Consensus pattern (26 bp):
AAATAAATCAATTCATATTTTAAAAT
Found at i:48856 original size:22 final size:22
Alignment explanation
Indices: 48807--48855 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
48797 ATAAATTATT
* **
48807 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAACTCATATAA
48829 TAAAATAAATCAACTCATACTAA
1 TAAAATAAATCAACTCATA-TAA
48852 TAAA
1 TAAA
48856 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAACTCATATAA
Found at i:48940 original size:26 final size:26
Alignment explanation
Indices: 48863--48940 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
48853 AAATTATTTA
*
48863 AAATAAATCAATCCATACAACTACAAT
1 AAATAAATCAATCCATACAAATA-AAT
* ***
48890 -AATAAATCAATTCATA-TTTTAAAAT
1 AAATAAATCAATCCATACAAAT-AAAT
48915 AAATAAATCAATCCATACAAATAAAT
1 AAATAAATCAATCCATACAAATAAAT
48941 TATTTAAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
25 4 0.10
26 35 0.88
27 1 0.03
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.28
Consensus pattern (26 bp):
AAATAAATCAATCCATACAAATAAAT
Found at i:48950 original size:14 final size:14
Alignment explanation
Indices: 48933--48986 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
48923 CAATCCATAC
48933 AAATAAATTATTTA
1 AAATAAATTATTTA
*
48947 AAATAAATCAATTGATA
1 AAATAAAT-TATT--TA
*
48964 CTAATAAATTATTTA
1 -AAATAAATTATTTA
48979 AAATAAAT
1 AAATAAAT
48987 CAATCTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 5 0.16
17 5 0.16
18 7 0.22
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:49048 original size:22 final size:22
Alignment explanation
Indices: 48975--49039 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
48965 TAATAAATTA
*
48975 TTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCCATAT
48997 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
49019 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
49040 CTAATAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:49112 original size:80 final size:78
Alignment explanation
Indices: 48943--49173 Score: 335
Period size: 80 Copynumber: 3.0 Consensus size: 78
48933 AAATAAATTA
** * * **
48943 TTTAAAATAAATCAATTGATACTAATAAATTATTTAAAATAAATCAAT-C-TATATTTTAAAATA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAAACTACAAAATA
49006 AATCAATCCATAT
66 AATCAATCCATAT
49019 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-AACTACAA-AA
49084 TAAATCAATCCATAT
64 TAAATCAATCCATAT
* **
49099 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT--ATTTTAAAATA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAAACTACAAAATA
49162 AATCAATCCATA
66 AATCAATCCATA
49174 CTAATAAATT
Statistics
Matches: 142, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
76 62 0.44
77 5 0.04
78 2 0.01
79 4 0.03
80 69 0.49
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (78 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAAACTACAAAATA
AATCAATCCATAT
Found at i:49128 original size:22 final size:23
Alignment explanation
Indices: 49053--49127 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
49043 ATAAATTATT
49053 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
49075 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
49101 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
49124 TAAA
1 TAAA
49128 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:49157 original size:22 final size:22
Alignment explanation
Indices: 49131--49173 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
49121 TAATAAATTA
49131 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
49153 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
49174 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:49182 original size:22 final size:22
Alignment explanation
Indices: 49133--49181 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
49123 ATAAATTATT
**
49133 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
49155 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
49178 TAAA
1 TAAA
49182 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:49236 original size:22 final size:22
Alignment explanation
Indices: 49187--49235 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
49177 ATAAATTATT
**
49187 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
49209 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
49232 TAAA
1 TAAA
49236 TTATTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:49250 original size:15 final size:15
Alignment explanation
Indices: 49230--49266 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
49220 AATCTATACT
49230 AATAAATTATTATAA
1 AATAAATTATTATAA
*
49245 AATAAATTATTTTAA
1 AATAAATTATTATAA
49260 AATAAAT
1 AATAAAT
49267 AACTTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATAAATTATTATAA
Found at i:49291 original size:15 final size:15
Alignment explanation
Indices: 49230--49289 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
49220 AATCTATACT
49230 AATAAATTA-TTATAA
1 AATAAATTACTT-TAA
*
49245 AATAAATTATTTTAA
1 AATAAATTACTTTAA
*
49260 AATAAATAACTTT--
1 AATAAATTACTTTAA
*
49273 ATTAAATTA-TTTAA
1 AATAAATTACTTTAA
49287 AAT
1 AAT
49290 TATTTTAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
12 3 0.08
13 7 0.19
14 2 0.05
15 23 0.62
16 2 0.05
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAAATTACTTTAA
Found at i:49297 original size:108 final size:104
Alignment explanation
Indices: 48943--49266 Score: 348
Period size: 102 Copynumber: 3.1 Consensus size: 104
48933 AAATAAATTA
** *
48943 TTTAAAATAAATCAATTGATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
* * ** * * *
49008 TCAATCCATATTTTAAAATAAATCAATCCATACTAATAAAT-TA-
66 TCAATCCATA--CT--AATAAAT-TATTTAAAATAA-CAATCTAT
*
49051 TTTAAAATAAATCAATCCATAC-AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAA
1 TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
49109 ATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
65 ATCAATCCATACTAATAAATTATTTAAAAT-AA-CAAT-C-TAT
49153 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
*
49218 TCAATCTATACTAATAAATTATTATAAAAT-A-AAT-TAT
66 TCAATCCATACTAATAAATTATT-TAAAATAACAATCTAT
49255 TTTAAAATAAAT
1 TTTAAAATAAAT
49267 AACTTTATTA
Statistics
Matches: 189, Mismatches: 13, Indels: 34
0.80 0.06 0.14
Matches are distributed among these distances:
97 5 0.03
98 13 0.07
100 1 0.01
101 2 0.01
102 77 0.41
103 2 0.01
104 2 0.01
105 3 0.02
106 2 0.01
107 3 0.02
108 73 0.39
109 6 0.03
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (104 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TCAATCCATACTAATAAATTATTTAAAATAACAATCTAT
Found at i:51077 original size:113 final size:109
Alignment explanation
Indices: 50929--51130 Score: 287
Period size: 113 Copynumber: 1.8 Consensus size: 109
50919 TCGCGCATGC
* * * * *
50929 CCAAAAAAAAAATATATATAATGGCGTTTAACCAATAAACACCACTATATATGGATCTATTGTGA
1 CCAAAAAAAAAATATATATAATGGCGTTTAACCAATAAACACCAATATAGATGAACCTATTGCGA
50994 CGTGTTTTCAAAAAACGCCACTATTATTGAGTGCCCCAAAAAATG
66 CGTGTTTTC-AAAAACGCCACTATTATTGAGTGCCCCAAAAAATG
* **
51039 CCAAAAAAATATATATATATATAGTGGCGTTTTTCCAATAAACACCAATATAGATGAACCTATTG
1 CCAAAAAAA-A-A-ATATATATAATGGCGTTTAACCAATAAACACCAATATAGATGAACCTATTG
*
51104 CGACGTTTTTTCAAAAACGCCACTATT
63 CGACGTGTTTTCAAAAACGCCACTATT
51131 GTTACCCCGA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
110 9 0.11
111 1 0.01
112 16 0.20
113 54 0.68
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (109 bp):
CCAAAAAAAAAATATATATAATGGCGTTTAACCAATAAACACCAATATAGATGAACCTATTGCGA
CGTGTTTTCAAAAACGCCACTATTATTGAGTGCCCCAAAAAATG
Found at i:54422 original size:7 final size:7
Alignment explanation
Indices: 54410--54438 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
54400 TGTTTTGTTT
54410 TATTTCA
1 TATTTCA
54417 TATTTCA
1 TATTTCA
54424 TATTTCA
1 TATTTCA
54431 TATTTCA
1 TATTTCA
54438 T
1 T
54439 TGTCATGCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.14, G:0.00, T:0.59
Consensus pattern (7 bp):
TATTTCA
Found at i:60860 original size:75 final size:79
Alignment explanation
Indices: 60732--60875 Score: 217
Period size: 75 Copynumber: 1.9 Consensus size: 79
60722 GGTTATAAGG
60732 TGAAAGTATATATATATGTGAATTATTTACGAATTAATAATAAAAAATAA-TTTTATAAACGAAG
1 TGAAAGTATATATATATGTGAATTATTTACGAATTAATAATAAAAAATAATTTTTATAAACGAAG
60796 TTAAGAATATCAGC
66 TTAAGAATATCAGC
* * *
60810 TGAAAGTATATATA-A-G-GGATTATTTATGTATTAATAATAAAAAA-ATATTTTTATAAACGAA
1 TGAAAGTATATATATATGTGAATTATTTACGAATTAATAATAAAAAATA-ATTTTTATAAACGAA
60871 GTTAA
65 GTTAA
60876 TAAGTTGTTA
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
74 1 0.02
75 26 0.43
76 19 0.31
77 1 0.02
78 14 0.23
ACGTcount: A:0.49, C:0.03, G:0.12, T:0.36
Consensus pattern (79 bp):
TGAAAGTATATATATATGTGAATTATTTACGAATTAATAATAAAAAATAATTTTTATAAACGAAG
TTAAGAATATCAGC
Found at i:60868 original size:76 final size:78
Alignment explanation
Indices: 60732--60875 Score: 222
Period size: 76 Copynumber: 1.9 Consensus size: 78
60722 GGTTATAAGG
60732 TGAAAGTATATATATATGTGAATTATTTACGAATTAATAATAAAAAATAATTTTATAAACGAAGT
1 TGAAAGTATATATATATGTGAATTATTTACGAATTAATAATAAAAAATAATTTTATAAACGAAGT
60797 TAAGAATATCAGC
66 TAAGAATATCAGC
* * * *
60810 TGAAAGTATATATA-A-G-GGATTATTTATGTATTAATAATAAAAAAATATTTTTATAAACGAAG
1 TGAAAGTATATATATATGTGAATTATTTACGAATTAATAAT-AAAAAATAATTTTATAAACGAAG
60872 TTAA
65 TTAA
60876 TAAGTTGTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
75 19 0.31
76 27 0.44
77 1 0.02
78 14 0.23
ACGTcount: A:0.49, C:0.03, G:0.12, T:0.36
Consensus pattern (78 bp):
TGAAAGTATATATATATGTGAATTATTTACGAATTAATAATAAAAAATAATTTTATAAACGAAGT
TAAGAATATCAGC
Found at i:62242 original size:16 final size:16
Alignment explanation
Indices: 62200--62246 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
62190 TGTTAGTATT
* *
62200 TTATTTAATTATTGTA
1 TTATTTAATTTTTTTA
62216 TTATTTAATTTTTTTA
1 TTATTTAATTTTTTTA
*
62232 TTATTTTATTTTTTT
1 TTATTTAATTTTTTT
62247 GCAGTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (16 bp):
TTATTTAATTTTTTTA
Found at i:62515 original size:8 final size:8
Alignment explanation
Indices: 62513--62549 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
62503 AAAATAATTA
62513 AATAAAAT
1 AATAAAAT
62521 AATAAAAT
1 AATAAAAT
62529 AATAAAAT
1 AATAAAAT
*
62537 AATTAAAAA
1 AA-TAAAAT
62546 AATA
1 AATA
62550 CTAACAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:62518 original size:21 final size:21
Alignment explanation
Indices: 62494--62538 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
62484 TTTATAACTG
*
62494 TAAAAAAATAAAATAATTAAA
1 TAAAAAAATAAAATAATAAAA
*
62515 TAAAATAATAAAATAATAAAA
1 TAAAAAAATAAAATAATAAAA
62536 TAA
1 TAA
62539 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAAAAAATAAAATAATAAAA
Found at i:62532 original size:16 final size:17
Alignment explanation
Indices: 62494--62549 Score: 68
Period size: 13 Copynumber: 3.6 Consensus size: 17
62484 TTTATAACTG
62494 TAAAAAAATAAAATAAT
1 TAAAAAAATAAAATAAT
62511 T----AAATAAAATAA-
1 TAAAAAAATAAAATAAT
*
62523 TAAAATAATAAAATAAT
1 TAAAAAAATAAAATAAT
62540 TAAAAAAATA
1 TAAAAAAATA
62550 CTAACAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
12 1 0.03
13 11 0.34
16 10 0.31
17 10 0.31
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
TAAAAAAATAAAATAAT
Found at i:62532 original size:29 final size:28
Alignment explanation
Indices: 62494--62560 Score: 98
Period size: 29 Copynumber: 2.4 Consensus size: 28
62484 TTTATAACTG
62494 TAAAAAAATAAAATAATTAAATAAAATAA
1 TAAAAAAATAAAATAATTAAA-AAAATAA
* *
62523 TAAAATAATAAAATAATTAAAAAAATAC
1 TAAAAAAATAAAATAATTAAAAAAATAA
*
62551 TAACAAAATA
1 TAAAAAAATA
62561 TGATTAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 14 0.41
29 20 0.59
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (28 bp):
TAAAAAAATAAAATAATTAAAAAAATAA
Found at i:65982 original size:37 final size:37
Alignment explanation
Indices: 65910--65982 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
65900 ATTTTATATG
* *
65910 AATTTTATAAAAAAATTCTATAAATTTTATGAACTTA
1 AATTTTATAAAAAAATTATATAAATTTTATCAACTTA
*
65947 AATTTTTTAAAGAAAA-TATATAAATATTT-TCAACTT
1 AATTTTATAAA-AAAATTATATAAAT-TTTATCAACTT
65983 GTTAAAAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
37 24 0.77
38 7 0.23
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (37 bp):
AATTTTATAAAAAAATTATATAAATTTTATCAACTTA
Found at i:66481 original size:47 final size:47
Alignment explanation
Indices: 66410--66503 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
66400 AGAGATTGTG
* **
66410 TATACTTCAAAATTATTTTGGGGTTTATACTTTATACTATTTTATAA
1 TATACTTCAAAAATATTTAAGGGTTTATACTTTATACTATTTTATAA
*
66457 TATACTTTAAAAATATTTAAGGGTTTATACTTTATACTATTTTATAA
1 TATACTTCAAAAATATTTAAGGGTTTATACTTTATACTATTTTATAA
66504 CAATTATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (47 bp):
TATACTTCAAAAATATTTAAGGGTTTATACTTTATACTATTTTATAA
Found at i:67326 original size:17 final size:17
Alignment explanation
Indices: 67304--67349 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
67294 TATTCCTTCC
67304 TTCATTCAAAACTTTCA
1 TTCATTCAAAACTTTCA
67321 TTCATTCAAAACTTTCA
1 TTCATTCAAAACTTTCA
*
67338 ATCATTCAAAAC
1 TTCATTCAAAAC
67350 CAAAAATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (17 bp):
TTCATTCAAAACTTTCA
Found at i:69494 original size:2 final size:2
Alignment explanation
Indices: 69487--69528 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
69477 TGAGACATTC
69487 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69529 TATTAGATAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73466 original size:24 final size:24
Alignment explanation
Indices: 73426--73500 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
73416 CCATGTCTCG
* *
73426 CTCTCTATAATGCTCACGATCACA
1 CTCTCTATCATGGTCACGATCACA
*
73450 GTCTCTATCATGGTCACGATCACA
1 CTCTCTATCATGGTCACGATCACA
*
73474 CTCTCTATCATGGTCACGATCATA
1 CTCTCTATCATGGTCACGATCACA
73498 CTC
1 CTC
73501 AAAGTCACTA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.25, C:0.32, G:0.12, T:0.31
Consensus pattern (24 bp):
CTCTCTATCATGGTCACGATCACA
Found at i:81961 original size:30 final size:30
Alignment explanation
Indices: 81925--82023 Score: 189
Period size: 30 Copynumber: 3.3 Consensus size: 30
81915 GGTCATGGTC
*
81925 ATGATCACGGTTGCAGTCATGTTCTTGATA
1 ATGATCACGGTTGCGGTCATGTTCTTGATA
81955 ATGATCACGGTTGCGGTCATGTTCTTGATA
1 ATGATCACGGTTGCGGTCATGTTCTTGATA
81985 ATGATCACGGTTGCGGTCATGTTCTTGATA
1 ATGATCACGGTTGCGGTCATGTTCTTGATA
82015 ATGATCACG
1 ATGATCACG
82024 ATCAAGATCA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.35
Consensus pattern (30 bp):
ATGATCACGGTTGCGGTCATGTTCTTGATA
Found at i:82114 original size:18 final size:18
Alignment explanation
Indices: 82091--82146 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
82081 GCGCTCGTGG
82091 TCTCTATCACGATCACGC
1 TCTCTATCACGATCACGC
* * *
82109 TCTCTATCATGGTCACGA
1 TCTCTATCACGATCACGC
* * *
82127 TCACAATCACGCTCACGC
1 TCTCTATCACGATCACGC
82145 TC
1 TC
82147 AAAGTCACTA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.23, C:0.38, G:0.12, T:0.27
Consensus pattern (18 bp):
TCTCTATCACGATCACGC
Found at i:90513 original size:18 final size:18
Alignment explanation
Indices: 90490--90526 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
90480 TGTGCGTGTT
90490 AATTAGCTAATTAGCTTA
1 AATTAGCTAATTAGCTTA
* *
90508 AATTAGTTAATTATCTTA
1 AATTAGCTAATTAGCTTA
90526 A
1 A
90527 TTGACATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (18 bp):
AATTAGCTAATTAGCTTA
Found at i:90526 original size:9 final size:9
Alignment explanation
Indices: 90488--90528 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
90478 GATGTGCGTG
90488 TTAATTAGC
1 TTAATTAGC
90497 -TAATTAGC
1 TTAATTAGC
90505 TTAAATTAG-
1 TT-AATTAGC
*
90514 TTAATTATC
1 TTAATTAGC
90523 TTAATT
1 TTAATT
90529 GACATAACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
8 13 0.46
9 9 0.32
10 6 0.21
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (9 bp):
TTAATTAGC
Found at i:94092 original size:32 final size:31
Alignment explanation
Indices: 94056--94130 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
94046 GGGGCCGTGA
*
94056 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
* **
94088 GGCCTACC-CAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
94118 AGCCTACCTAAGA
1 GGCCTACCTAAGA
94131 GTCACTTAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 21 0.58
31 7 0.19
32 8 0.22
ACGTcount: A:0.28, C:0.32, G:0.25, T:0.15
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:94097 original size:62 final size:62
Alignment explanation
Indices: 94009--94130 Score: 146
Period size: 62 Copynumber: 2.0 Consensus size: 62
93999 CCCTAAGGGA
* *
94009 ACATCTTAGGGCCTGGGAGCCTACCCA-AGATAGAT-TCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGGGAGCCTACCCAGA-AT-GATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
94071 ACATCTTAGGGCC-GCAGG-GCCTACCCAGAATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG--GGAGCCTACCCAGAATGATCTCAGGGCCGCAGAGCCTACCTAAGA
94131 GTCACTTAGG
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
61 4 0.08
62 44 0.83
63 5 0.09
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.16
Consensus pattern (62 bp):
ACATCTTAGGGCCTGGGAGCCTACCCAGAATGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Done.