Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000182.1 Hibiscus syriacus cultivar Beakdansim tig00000318_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: 82768
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3840 original size:20 final size:19
Alignment explanation
Indices: 3802--3842 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3792 AATGAATCAA
*
3802 AATTGATAATTTAAGTATT
1 AATTGATAATTTAAATATT
*
3821 AATTGTATAGTTTAAATATT
1 AATTG-ATAATTTAAATATT
3841 AA
1 AA
3843 AATGAACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (19 bp):
AATTGATAATTTAAATATT
Found at i:3878 original size:50 final size:51
Alignment explanation
Indices: 3785--3884 Score: 125
Period size: 50 Copynumber: 2.0 Consensus size: 51
3775 GTGTAGTTAG
* *
3785 ATATTAAAATGAATCAAAATTGATAATTTAAGTATTAATTGTATAGTTTAA
1 ATATTAAAATGAATCAAAATTGATAATTTAAGTATGAATTGTATAATTTAA
* *
3836 ATATTAAAATGAA-CTAAATTGATAATTT-TGATACTGAA-TGTATAATTTA
1 ATATTAAAATGAATCAAAATTGATAATTTAAG-TA-TGAATTGTATAATTTA
3885 CCCTAGATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
49 1 0.02
50 26 0.60
51 16 0.37
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (51 bp):
ATATTAAAATGAATCAAAATTGATAATTTAAGTATGAATTGTATAATTTAA
Found at i:5786 original size:18 final size:17
Alignment explanation
Indices: 5756--5789 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5746 ATAGTTAGAC
*
5756 AATTATTTTATACGAAT
1 AATTATTTAATACGAAT
5773 AATTCATTTAATACGAA
1 AATT-ATTTAATACGAA
5790 AAAGCTACCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (17 bp):
AATTATTTAATACGAAT
Found at i:11047 original size:14 final size:14
Alignment explanation
Indices: 11036--11073 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
11026 AATTCATTTG
11036 TTTATGTTCATTCA
1 TTTATGTTCATTCA
*
11050 TTTATGTTCGTTCA
1 TTTATGTTCATTCA
*
11064 TTTATATTCA
1 TTTATGTTCA
11074 GCCCAATCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (14 bp):
TTTATGTTCATTCA
Found at i:11286 original size:23 final size:22
Alignment explanation
Indices: 11259--11314 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
11249 TTGTTGTTGT
11259 TTATGTTTGTTTACGTTCATTTA
1 TTATGTTTGTTT-CGTTCATTTA
* * *
11282 TTATGTTCGATTTTGTTCATTTG
1 TTATGTTTG-TTTCGTTCATTTA
11305 TTATGTTTGT
1 TTATGTTTGT
11315 GCAAATTCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.04
23 24 0.86
24 3 0.11
ACGTcount: A:0.14, C:0.07, G:0.16, T:0.62
Consensus pattern (22 bp):
TTATGTTTGTTTCGTTCATTTA
Found at i:11349 original size:23 final size:24
Alignment explanation
Indices: 11320--11375 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
11310 TTTGTGCAAA
*
11320 TTCGTTTATGTTCATT-TATTGTT
1 TTCGTTTATGTTCATTCTATTGTG
** *
11343 TTCGTTTCCGTTCATTCTTTTGTG
1 TTCGTTTATGTTCATTCTATTGTG
11367 TTCGTTTAT
1 TTCGTTTAT
11376 CATTTAAATG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.62
Consensus pattern (24 bp):
TTCGTTTATGTTCATTCTATTGTG
Found at i:12737 original size:3 final size:3
Alignment explanation
Indices: 12729--12759 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
12719 CAGTACAAGC
12729 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
12760 GTTGAGGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:14828 original size:31 final size:31
Alignment explanation
Indices: 14770--14828 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
14760 TACCCTTTCA
* *
14770 ATCATTTCATAATTTTCAAAAAGAAAATAGT
1 ATCATTTCATAACTATCAAAAAGAAAATAGT
*
14801 ATCATTTGATAACTATCAAGAAA-AAAAT
1 ATCATTTCATAACTATCAA-AAAGAAAAT
14829 GATAAAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.88
32 3 0.12
ACGTcount: A:0.51, C:0.10, G:0.07, T:0.32
Consensus pattern (31 bp):
ATCATTTCATAACTATCAAAAAGAAAATAGT
Found at i:15972 original size:60 final size:60
Alignment explanation
Indices: 15908--16020 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
15898 TATGGAATAG
* *
15908 TATTTAATTAAGTCTCTC-ACCTATTAAAAATTACAAAATAGTTCCTCAACTATTTAGAGT
1 TATTTAATTAAGTCCCTCGA-CTATTAAAAATTACAAAATAGTCCCTCAACTATTTAGAGT
* * * *
15968 TATTTTATTGAGTCCCTCGACTATTAAAAGTTACAAAATGGTCCCTCAACTAT
1 TATTTAATTAAGTCCCTCGACTATTAAAAATTACAAAATAGTCCCTCAACTAT
16021 AGGGAGTTAC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 45 0.98
61 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (60 bp):
TATTTAATTAAGTCCCTCGACTATTAAAAATTACAAAATAGTCCCTCAACTATTTAGAGT
Found at i:16019 original size:29 final size:29
Alignment explanation
Indices: 15923--16020 Score: 79
Period size: 29 Copynumber: 3.3 Consensus size: 29
15913 AATTAAGTCT
* * * *
15923 CTCACCTATTAAAAATTACAAAATAGTTC
1 CTCAACTATTAAAAGTTACAAAATGGTCC
* * *** *
15952 CTCAACTATTTAGAGTTATTTTATTGAGTCC
1 CTCAACTATTAAAAGTTA-CAAAATG-GTCC
*
15983 CTCGACTATTAAAAGTTACAAAATGGTCC
1 CTCAACTATTAAAAGTTACAAAATGGTCC
16012 CTCAACTAT
1 CTCAACTAT
16021 AGGGAGTTAC
Statistics
Matches: 49, Mismatches: 18, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
29 26 0.53
30 5 0.10
31 18 0.37
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (29 bp):
CTCAACTATTAAAAGTTACAAAATGGTCC
Found at i:16066 original size:58 final size:59
Alignment explanation
Indices: 15928--16078 Score: 187
Period size: 60 Copynumber: 2.6 Consensus size: 59
15918 AGTCTCTCAC
* * * ** *
15928 CTATTAAAAATTACAAAATAGTTCCTCAACTATTTAGAGTTATTTTATTGAGTCCCTCGA
1 CTATTAAAAGTTACAAAATGGTCCCTCAACTATAGAGAGTTACTTTATTGAGT-CCTCGA
* *
15988 CTATTAAAAGTTACAAAATGGTCCCTCAACTATAGGGAGTTACTTTGTTGAGT-CTCGA
1 CTATTAAAAGTTACAAAATGGTCCCTCAACTATAGAGAGTTACTTTATTGAGTCCTCGA
* * *
16046 CTTTTAAAAGTTACAAAATGGTCACTCGACTAT
1 CTATTAAAAGTTACAAAATGGTCCCTCAACTAT
16079 TCATTATGCT
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
58 35 0.44
60 45 0.56
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (59 bp):
CTATTAAAAGTTACAAAATGGTCCCTCAACTATAGAGAGTTACTTTATTGAGTCCTCGA
Found at i:17382 original size:31 final size:29
Alignment explanation
Indices: 17330--17387 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 29
17320 CCCGACAAAA
*
17330 AAATATATAATTTATCTTATA-TATTTAG
1 AAATATATAATATATCTTATATTATTTAG
17358 AAATAATATAATAATATCTCTATATTATTT
1 AAAT-ATATAAT-ATATCT-TATATTATTT
17388 TTTTAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 4 0.16
29 7 0.28
30 5 0.20
31 4 0.16
32 5 0.20
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (29 bp):
AAATATATAATATATCTTATATTATTTAG
Found at i:31850 original size:34 final size:35
Alignment explanation
Indices: 31812--31886 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 35
31802 ATTTTATTAA
31812 TTTATATATA-TATATATATATA-TATTTACTATTT
1 TTTATATATATTATATATATATATTATTTACT-TTT
* * *
31846 TTTATTTTTTATTATATATATATATTTTTTACTTTT
1 TTTA-TATATATTATATATATATATTATTTACTTTT
31882 TTTAT
1 TTTAT
31887 TATTTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 4 0.11
35 5 0.14
36 19 0.54
37 7 0.20
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (35 bp):
TTTATATATATTATATATATATATTATTTACTTTT
Found at i:31861 original size:28 final size:28
Alignment explanation
Indices: 31830--31889 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
31820 TATATATATA
*
31830 TATATATTTACTATTTTTTA-TTTTTTAT
1 TATATATATA-TATTTTTTACTTTTTTAT
31858 TATATATATATATTTTTTACTTTTTTTAT
1 TATATATATATATTTTTTAC-TTTTTTAT
31887 TAT
1 TAT
31890 TTTTTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 9 0.31
28 9 0.31
29 11 0.38
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (28 bp):
TATATATATATATTTTTTACTTTTTTAT
Found at i:31869 original size:36 final size:37
Alignment explanation
Indices: 31747--31892 Score: 131
Period size: 44 Copynumber: 3.8 Consensus size: 37
31737 TTTACTTTAG
* *
31747 TATATATT-TTTA-TTTTTTTA-GATTATATATATATA
1 TATATATTATTTACTTTTTTTATTATTTTAT-TATATA
31782 TATATATTATTTTA-TTATCAATTTTATTAATTTATATATATATA
1 TATATATTA-TTTACTT-T---TTTTATT-ATTT-TAT-TATATA
31826 TATATATATATTTACTATTTTTTATT-TTTTATTATATA
1 TATATAT-TATTTACT-TTTTTTATTATTTTATTATATA
*
31864 TATATATTTTTTACTTTTTTTATTATTTT
1 TATATATTATTTACTTTTTTTATTATTTT
31893 TTTTATTTGT
Statistics
Matches: 95, Mismatches: 3, Indels: 24
0.78 0.02 0.20
Matches are distributed among these distances:
35 8 0.08
36 9 0.09
37 17 0.18
38 14 0.15
39 3 0.03
40 3 0.03
41 5 0.05
42 7 0.07
43 3 0.03
44 21 0.22
45 4 0.04
46 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (37 bp):
TATATATTATTTACTTTTTTTATTATTTTATTATATA
Found at i:31895 original size:40 final size:40
Alignment explanation
Indices: 31747--31894 Score: 130
Period size: 39 Copynumber: 3.8 Consensus size: 40
31737 TTTACTTTAG
* * *
31747 TATATA-TTTTTA-TTTTTTTA-GATTATATATATATATA
1 TATATATTTTTTACTTTTTTTATTATTTTTTATATATATA
** * *
31784 TATATTATTTTATTA-TCAATTTTATTAATTTATATATATATA
1 TATA-TATTTT-TTACT-TTTTTTATTATTTTTTATATATATA
* *
31826 TATATATATATTTAC-TATTTT-TTATTTTTTAT-TATATA
1 TATATAT-TTTTTACTTTTTTTATTATTTTTTATATATATA
31864 TATATATTTTTTACTTTTTTTATTATTTTTT
1 TATATATTTTTTACTTTTTTTATTATTTTTT
31895 TTATTTGTTT
Statistics
Matches: 91, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
37 10 0.11
38 20 0.22
39 21 0.23
40 9 0.10
41 11 0.12
42 20 0.22
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.66
Consensus pattern (40 bp):
TATATATTTTTTACTTTTTTTATTATTTTTTATATATATA
Found at i:31915 original size:45 final size:49
Alignment explanation
Indices: 31843--31939 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 49
31833 ATATTTACTA
*
31843 TTTTTTATTTTTTATTATATATATATATTTTTTACTT-TTTTT-ATTATT
1 TTTTTTATTTGTTATTATATATATATATTTTTT-CTTCTTTTTCATTATT
*
31891 TTTTTTATTTGTT-TTAT-T-TATATATTTTTTCTTCTTTTTCTTTATT
1 TTTTTTATTTGTTATTATATATATATATTTTTTCTTCTTTTTCATTATT
31937 TTT
1 TTT
31940 ATATTTATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
44 3 0.07
45 17 0.38
46 9 0.20
47 4 0.09
48 12 0.27
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (49 bp):
TTTTTTATTTGTTATTATATATATATATTTTTTCTTCTTTTTCATTATT
Found at i:31915 original size:47 final size:47
Alignment explanation
Indices: 31843--31939 Score: 126
Period size: 47 Copynumber: 2.1 Consensus size: 47
31833 ATATTTACTA
* *
31843 TTTTTTATTTTTTATTATATATATATATTTTT-TACTTTTTTTATTATT
1 TTTTTTATTTGTTATTATATATATAT-TTTTTCTACTTTTTCT-TTATT
* *
31891 TTTTTTATTTGTT-TTATTTATATATTTTTTCTTCTTTTTCTTTATT
1 TTTTTTATTTGTTATTATATATATATTTTTTCTACTTTTTCTTTATT
31937 TTT
1 TTT
31940 ATATTTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
46 13 0.30
47 19 0.43
48 12 0.27
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (47 bp):
TTTTTTATTTGTTATTATATATATATTTTTTCTACTTTTTCTTTATT
Found at i:31919 original size:36 final size:36
Alignment explanation
Indices: 31879--31968 Score: 96
Period size: 36 Copynumber: 2.5 Consensus size: 36
31869 ATTTTTTACT
*
31879 TTTTTTATTATTTTT-TTTATTTGTTTTATTTATATA
1 TTTTTTATTATTTTTCTTTATTT-TTATATTTATATA
* *
31915 TTTTTTCTTCTTTTTCTTTATTTTTATATTTAT-T-
1 TTTTTTATTATTTTTCTTTATTTTTATATTTATATA
* *
31949 TTTCTTACTATTTTATCTTT
1 TTTTTTATTATTTT-TCTTT
31969 GCTTTCTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
34 10 0.22
35 6 0.13
36 22 0.49
37 7 0.16
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.77
Consensus pattern (36 bp):
TTTTTTATTATTTTTCTTTATTTTTATATTTATATA
Found at i:31920 original size:28 final size:26
Alignment explanation
Indices: 31843--31951 Score: 73
Period size: 25 Copynumber: 4.2 Consensus size: 26
31833 ATATTTACTA
* *
31843 TTTTTTATTT-TTTA-TTATATATAT
1 TTTTTTTTTTCTTTATTTATATATTT
* * * *
31867 ATATTTTTTACTTTTTTTATTAT-TTT
1 TTTTTTTTTTCTTTATTTA-TATATTT
* *
31893 TTTTATTTGT-TTTATTTATATATTT
1 TTTTTTTTTTCTTTATTTATATATTT
*
31918 TTTCTTCTTTTTCTTTATTTTTATATTT
1 TTT-TT-TTTTTCTTTATTTATATATTT
*
31946 ATTTTT
1 TTTTTT
31952 CTTACTATTT
Statistics
Matches: 62, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
24 9 0.15
25 16 0.26
26 12 0.19
27 9 0.15
28 16 0.26
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (26 bp):
TTTTTTTTTTCTTTATTTATATATTT
Found at i:31947 original size:49 final size:47
Alignment explanation
Indices: 31753--31949 Score: 128
Period size: 45 Copynumber: 4.3 Consensus size: 47
31743 TTAGTATATA
* * * *
31753 TTTTTATTTTTTTAGATTATATATATATA-TATATA-TTATTTTATTAT
1 TTTTTATTTATTT--ATTATATATATATATTTTTTACTTTTTTTATTAT
* * * * * *
31800 CAATTTTATTAATTTA-TATATATATATA---TATA-TATATTTACTAT
1 --TTTTTATTTATTTATTATATATATATATTTTTTACTTTTTTTATTAT
31844 TTTTTATTT-TTTATTATATATATATATTTTTTACTTTTTTTATTA-
1 TTTTTATTTATTTATTATATATATATATTTTTTACTTTTTTTATTAT
* * * *
31889 TTTTT-TTTATTTGTTTTATTTATATATTTTTT-CTTCTTTTTCTTTAT
1 TTTTTATTTATTTATTATATATATATATTTTTTACTT-TTTTT-ATTAT
31936 TTTTATATTTATTT
1 TTTT-TATTTATTT
31950 TTCTTACTAT
Statistics
Matches: 120, Mismatches: 17, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
41 4 0.03
42 19 0.16
44 18 0.15
45 33 0.28
46 23 0.19
47 5 0.04
48 1 0.01
49 17 0.14
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (47 bp):
TTTTTATTTATTTATTATATATATATATTTTTTACTTTTTTTATTAT
Found at i:31953 original size:28 final size:26
Alignment explanation
Indices: 31880--31954 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 26
31870 TTTTTTACTT
*
31880 TTTTTATTATTTTTTTTATTTGTTTTA
1 TTTTTA-TATTTTTTTTCTTTGTTTTA
* *
31907 TTTATATATTTTTTCTTCTTTTTCTTTA
1 TTTTTATATTTTTT-TTCTTTGT-TTTA
31935 TTTTTATATTTATTTTTCTT
1 TTTTTATATTT-TTTTTCTT
31955 ACTATTTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 8 0.20
27 11 0.27
28 19 0.46
29 3 0.07
ACGTcount: A:0.15, C:0.05, G:0.01, T:0.79
Consensus pattern (26 bp):
TTTTTATATTTTTTTTCTTTGTTTTA
Found at i:35122 original size:14 final size:13
Alignment explanation
Indices: 35103--35152 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
35093 AAAAAGAGAA
35103 AAAGAGAAAAAAGC
1 AAAGAGAAAAAA-C
35117 AAAGAGAAAATAA-
1 AAAGAGAAAA-AAC
35130 AAAGAGAAAAAAAC
1 AAAGAG-AAAAAAC
35144 AAAG-GAAAA
1 AAAGAGAAAA
35153 TTGAAGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 4 0.12
13 9 0.27
14 18 0.55
15 2 0.06
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (13 bp):
AAAGAGAAAAAAC
Found at i:35131 original size:27 final size:26
Alignment explanation
Indices: 35101--35153 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
35091 GCAAAAAGAG
*
35101 AAAAAGAGAAAAAAGCAAAGAGAAAAT
1 AAAAAGAGAAAAAAACAAAG-GAAAAT
35128 AAAAAGAGAAAAAAACAAAGGAAAAT
1 AAAAAGAGAAAAAAACAAAGGAAAAT
35154 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (26 bp):
AAAAAGAGAAAAAAACAAAGGAAAAT
Found at i:35133 original size:13 final size:14
Alignment explanation
Indices: 35103--35153 Score: 63
Period size: 13 Copynumber: 3.8 Consensus size: 14
35093 AAAAAGAGAA
35103 AAAGAGAAAA-AAGC
1 AAAGAGAAAATAA-C
35117 AAAGAGAAAATAA-
1 AAAGAGAAAATAAC
*
35130 AAAGAGAAAAAAAC
1 AAAGAGAAAATAAC
35144 AAAG-GAAAAT
1 AAAGAGAAAAT
35154 TGAAGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 17 0.52
14 14 0.42
15 2 0.06
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAGAAAATAAC
Found at i:35344 original size:69 final size:69
Alignment explanation
Indices: 35225--35362 Score: 197
Period size: 69 Copynumber: 2.0 Consensus size: 69
35215 GATTCAAACT
**
35225 ATGAGATTGATAAAGCAAAATCATTTCCGAATCACTGAACCACTTTACTCGAAGATCATAGGA-C
1 ATGAGATTGATAAAGCAAAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCAT-GGAGC
35289 ATCAA
65 ATCAA
* * * * *
35294 ATGAGATTGATCAAGCACAATCATTTCTGAATTACTGAATCACTCCACTCGAAGATCATGGAGCA
1 ATGAGATTGATAAAGCAAAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATGGAGCA
35359 TCAA
66 TCAA
35363 GAGAGAGACA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 3 0.05
69 58 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.25
Consensus pattern (69 bp):
ATGAGATTGATAAAGCAAAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATGGAGCA
TCAA
Found at i:36061 original size:32 final size:31
Alignment explanation
Indices: 36024--36111 Score: 86
Period size: 32 Copynumber: 2.7 Consensus size: 31
36014 GGAACAATGA
* *
36024 GGGCATCTTTGAAGATTCAACGTCAAATGTTG
1 GGGCATCTTTG-AGATTCAACATCAAATATTG
* * *
36056 GGGCATTTTTTGAGATTCAATATCGAATATTG
1 GGGCA-TCTTTGAGATTCAACATCAAATATTG
* *
36088 AGGCATCTTTGGGAATTCAACATC
1 GGGCATCTTTGAG-ATTCAACATC
36112 CTGATGCAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
31 6 0.13
32 34 0.76
33 5 0.11
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (31 bp):
GGGCATCTTTGAGATTCAACATCAAATATTG
Found at i:36814 original size:106 final size:105
Alignment explanation
Indices: 36689--37011 Score: 403
Period size: 106 Copynumber: 3.0 Consensus size: 105
36679 ATATCGTGCC
* *
36689 ACTCGAGACAACACAAGTTCAACTCCACAACGAAGGGACGGCTGGTTGTTAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-CC
* *
36754 AATTTCAGAGCCAATTTCAACTTCATAGCGATGAATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGG
* * * *
36795 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGATGACTGGTTGTCAACAAATAATTTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCC
* *
36860 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGG
* * * * * * * **
36901 ACTTGAGACAACACAAGCTCAACTTCACAGCGAAGGAACGGCTGGCTGGCAACAGACAATTTCTT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCA
* * * * *
36966 AGTTCTAGAGCCAATTTTAACTTCACGGCGGAGGATATTGG
66 ATTTC-AGAGCCAATTTCAACTTCACAGCGAAGAATATTGG
37007 ACTCG
1 ACTCG
37012 GAACAATACA
Statistics
Matches: 186, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
105 8 0.04
106 175 0.94
107 3 0.02
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (105 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGG
Found at i:37358 original size:86 final size:87
Alignment explanation
Indices: 37268--37445 Score: 297
Period size: 86 Copynumber: 2.1 Consensus size: 87
37258 GACAATTTCT
*
37268 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
37333 CTTGAAACGAAA-TTTT-TCTCC
66 CTTGAAAC-AAATTTTTGTCTCC
* * *
37354 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
37419 CTTGAAACAAATTTTTGTCTCC
66 CTTGAAACAAATTTTTGTCTCC
37441 CTTGA
1 CTTGA
37446 GACAGTTTCT
Statistics
Matches: 86, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
85 3 0.03
86 73 0.85
87 10 0.12
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (87 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGATTGAGATAGTTTCC
CTTGAAACAAATTTTTGTCTCC
Found at i:37467 original size:102 final size:102
Alignment explanation
Indices: 37354--37547 Score: 316
Period size: 102 Copynumber: 1.9 Consensus size: 102
37344 ATTTTTCTCC
* *
37354 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCC
* *
37419 CTTGAAACAAATTTTTGTCTCCCTTGAGACAGTTTCT
66 CTTAAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
* * * *
37456 CTTGAAACATAAACATTGAAAACATTTCCTTTGAAATTAATTTTGTCTCTCTTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCC
37521 CTTAAAACAAAATTTTGTCTCCCTTGA
66 CTTAAAACAAAATTTTGTCTCCCTTGA
37548 AACATAAACC
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 84 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (102 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCC
CTTAAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
Found at i:37691 original size:36 final size:36
Alignment explanation
Indices: 37616--37849 Score: 189
Period size: 36 Copynumber: 6.6 Consensus size: 36
37606 AAAACGAGTT
* *
37616 TTGAGACAGTTTCACTTGAAACAAAATCTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTC
37653 TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTC
** *
37689 TTGAGGTAGTTTCCCTTGAAACAAA------ATCT-
1 TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTC
* * * * * *
37718 TTGA-ATATCTTTTCCTTAAAACAAATTTCGTCTCCC
1 TTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCTC
* * *
37754 TTGAGACAGTTT-CTTTTATAACTAAGTTTTGTCTCTC
1 TTGAGACAGTTTCCCTTGA-AAC-AAATTTTGTCTCTC
** * *
37791 TTGAGACAGTTTCTTTTGAAACAAATTGTGTCCCTC
1 TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTC
* *
37827 TTGAGACATTTTCTCTTGAAACA
1 TTGAGACAGTTTCCCTTGAAACA
37850 CAAAAAAACC
Statistics
Matches: 160, Mismatches: 25, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.01
29 18 0.11
30 3 0.02
35 6 0.04
36 78 0.49
37 49 0.31
38 4 0.03
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (36 bp):
TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTC
Found at i:37896 original size:40 final size:39
Alignment explanation
Indices: 37847--37923 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
37837 TTCTCTTGAA
37847 ACACA-AAAAAACC-CTCAAAATTATTTCTCTTGAAACAC
1 ACACACAAAAAACCTCTCAAAA-TATTTCTCTTGAAACAC
* * *
37885 ACACACAAAAAACCTTTGAAAATGTTTCTCTTGAAACAC
1 ACACACAAAAAACCTCTCAAAATATTTCTCTTGAAACAC
37924 CAAACCCTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 5 0.15
39 24 0.71
40 5 0.15
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (39 bp):
ACACACAAAAAACCTCTCAAAATATTTCTCTTGAAACAC
Found at i:39166 original size:36 final size:36
Alignment explanation
Indices: 39055--39192 Score: 133
Period size: 36 Copynumber: 3.7 Consensus size: 36
39045 TTTACTTTAG
39055 TATA-TATTTTTATTTTTTTAGATTATATATATATATATA
1 TATATTATTTTTATTTTTTT--A-T-TATATATATATATA
39094 TATATTATTTTTTATTATCAGTTTTATTA-AT-T-TATATA
1 TATATTA-TTTTTATT-T---TTTTATTATATATATATATA
*
39132 TATA-TATTTACTATTTTTTTATTATATATATATATA
1 TATATTATTT-TTATTTTTTTATTATATATATATATA
*
39168 TATATTATTTTTACTTTTTTATTAT
1 TATATTATTTTTATTTTTTTATTAT
39193 TATTTTATTT
Statistics
Matches: 85, Mismatches: 3, Indels: 25
0.75 0.03 0.22
Matches are distributed among these distances:
33 8 0.09
34 2 0.02
35 1 0.01
36 27 0.32
37 11 0.13
38 10 0.12
39 5 0.06
40 4 0.05
41 10 0.12
42 2 0.02
43 1 0.01
45 4 0.05
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (36 bp):
TATATTATTTTTATTTTTTTATTATATATATATATA
Found at i:54240 original size:2 final size:2
Alignment explanation
Indices: 54233--54290 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
54223 ATCGTAACTC
54233 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
54275 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
54291 GTAAAGCATT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56587 original size:8 final size:8
Alignment explanation
Indices: 56574--56612 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
56564 ATGTGATAGA
56574 GATGGAGG
1 GATGGAGG
56582 GATGGAGG
1 GATGGAGG
56590 AGATGGAGG
1 -GATGGAGG
*
56599 GAGGGAGG
1 GATGGAGG
56607 GA-GGAG
1 GATGGAG
56613 ACAAGAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
7 4 0.14
8 17 0.59
9 8 0.28
ACGTcount: A:0.28, C:0.00, G:0.64, T:0.08
Consensus pattern (8 bp):
GATGGAGG
Found at i:56594 original size:17 final size:17
Alignment explanation
Indices: 56572--56606 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
56562 ACATGTGATA
*
56572 GAGATGGAGGGATGGAG
1 GAGATGGAGGGAGGGAG
56589 GAGATGGAGGGAGGGAG
1 GAGATGGAGGGAGGGAG
56606 G
1 G
56607 GAGGAGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.63, T:0.09
Consensus pattern (17 bp):
GAGATGGAGGGAGGGAG
Found at i:60915 original size:26 final size:25
Alignment explanation
Indices: 60884--60936 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 25
60874 TTAATCAAAG
*
60884 TAAAAAGGGAAAAAAGCAAAGAGAAAA
1 TAAAAA-GGAAAAAAACAAAG-GAAAA
60911 TAAAAAGGAAAAAAACAAAGGAAAA
1 TAAAAAGGAAAAAAACAAAGGAAAA
60936 T
1 T
60937 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 6 0.24
26 13 0.52
27 6 0.24
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.06
Consensus pattern (25 bp):
TAAAAAGGAAAAAAACAAAGGAAAA
Found at i:60921 original size:12 final size:13
Alignment explanation
Indices: 60891--60936 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
60881 AAGTAAAAAG
60891 GGAAAA-AAGCAAA
1 GGAAAATAA-CAAA
60904 GAGAAAATAA-AAA
1 G-GAAAATAACAAA
*
60917 GGAAAAAAACAAA
1 GGAAAATAACAAA
60930 GGAAAAT
1 GGAAAAT
60937 TGAAGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 7 0.25
13 14 0.50
14 5 0.18
15 2 0.07
ACGTcount: A:0.72, C:0.04, G:0.20, T:0.04
Consensus pattern (13 bp):
GGAAAATAACAAA
Found at i:62058 original size:33 final size:33
Alignment explanation
Indices: 61991--62086 Score: 115
Period size: 33 Copynumber: 2.9 Consensus size: 33
61981 TGAGGGCATC
* **
61991 TTTGAAGATACAACATCAAATGCTGGGGCA-TTT
1 TTTG-AGATTCAACATCAAATATTGGGGCATTTT
*
62024 TTTGAGATTTAACATCAAA-ATTTGGGGCATTTT
1 TTTGAGATTCAACATCAAATA-TTGGGGCATTTT
*
62057 TTTGAGATTCAACATCGAATATTGGGGCAT
1 TTTGAGATTCAACATCAAATATTGGGGCAT
62087 CTTTGGGAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
32 20 0.37
33 33 0.61
34 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.35
Consensus pattern (33 bp):
TTTGAGATTCAACATCAAATATTGGGGCATTTT
Found at i:63354 original size:37 final size:37
Alignment explanation
Indices: 63301--63376 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
63291 TTTCCAAGTT
*
63301 TTGTTTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
63338 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
63375 TT
1 TT
63377 TGAATATCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.38
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
Found at i:63474 original size:32 final size:34
Alignment explanation
Indices: 63411--63502 Score: 91
Period size: 36 Copynumber: 2.7 Consensus size: 34
63401 TTTCGTCTCC
* *
63411 CTTGAGATAGTTTCTTTT-AGAACTAA-GTTTT-T
1 CTTGAGACAGTTTCTTTTGA-AACAAATGTTTTCT
* *
63443 CTTGAGACATTTTCTTTTGAAACAAATTTTTTCCCT
1 CTTGAGACAGTTTCTTTTGAAACAAATGTTTT--CT
*
63479 CTTGAGACAGTTTCTCTTGAAACA
1 CTTGAGACAGTTTCTTTTGAAACA
63503 CAAAAAAACC
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
32 21 0.43
33 5 0.10
36 23 0.47
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (34 bp):
CTTGAGACAGTTTCTTTTGAAACAAATGTTTTCT
Found at i:65073 original size:71 final size:72
Alignment explanation
Indices: 64997--65143 Score: 208
Period size: 72 Copynumber: 2.1 Consensus size: 72
64987 TTCCCTCCGA
* *
64997 AGAGGACCCCATGTAGAATCAGGAC-GAGATATAA-TCTCATACAGAATCAGGATAGAGATTATG
1 AGAGGACCCCATCTAGAATCAGGACGGAGATATAATTC-CATACAGAATCAGAATAGAGATTATG
65060 CCCTTCAT
65 CCCTTCAT
* * * *
65068 AGAGGATCCCATCTAGAATCAGGACGGAGATATAATTCCATGCATAATCAGAATAGTGATTATGC
1 AGAGGACCCCATCTAGAATCAGGACGGAGATATAATTCCATACAGAATCAGAATAGAGATTATGC
*
65133 CTTTCAT
66 CCTTCAT
65140 AGAG
1 AGAG
65144 TGCAATGCCC
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
71 23 0.34
72 42 0.63
73 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24
Consensus pattern (72 bp):
AGAGGACCCCATCTAGAATCAGGACGGAGATATAATTCCATACAGAATCAGAATAGAGATTATGC
CCTTCAT
Found at i:66470 original size:19 final size:20
Alignment explanation
Indices: 66442--66525 Score: 75
Period size: 19 Copynumber: 4.2 Consensus size: 20
66432 CTTTAAATAT
66442 AAAA-TCGACTC-AACTCAA
1 AAAATTCGACTCGAACTCAA
* *
66460 AAAATTCGACTCGACCTTAAA
1 AAAATTCGACTCGAAC-TCAA
*
66481 TATAAAATCGACTCG-ACTCAA
1 -A-AAATTCGACTCGAACTCAA
* *
66502 AAAATTCAACTCGACCTCAA
1 AAAATTCGACTCGAACTCAA
66522 AAAA
1 AAAA
66526 AATTCGAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
18 4 0.08
19 17 0.33
20 12 0.23
21 6 0.12
22 2 0.04
23 11 0.21
ACGTcount: A:0.48, C:0.25, G:0.07, T:0.20
Consensus pattern (20 bp):
AAAATTCGACTCGAACTCAA
Found at i:66484 original size:42 final size:42
Alignment explanation
Indices: 66434--66518 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
66424 CTCAAAAACT
*
66434 TTAAATATAAAATCGACTCAACTCAAAAAATTCGACTCGACC
1 TTAAATATAAAATCGACTCAACTCAAAAAATTCAACTCGACC
*
66476 TTAAATATAAAATCGACTCGACTCAAAAAATTCAACTCGACC
1 TTAAATATAAAATCGACTCAACTCAAAAAATTCAACTCGACC
66518 T
1 T
66519 CAAAAAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.45, C:0.24, G:0.07, T:0.25
Consensus pattern (42 bp):
TTAAATATAAAATCGACTCAACTCAAAAAATTCAACTCGACC
Found at i:66495 original size:23 final size:23
Alignment explanation
Indices: 66434--66497 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
66424 CTCAAAAACT
*
66434 TTAAATATAAAATCGACTC-AAC
1 TTAAATATAAAATCGACTCGACC
* *
66456 -TCAA-A-AAATTCGACTCGACC
1 TTAAATATAAAATCGACTCGACC
66476 TTAAATATAAAATCGACTCGAC
1 TTAAATATAAAATCGACTCGAC
66498 TCAAAAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
19 10 0.30
20 3 0.09
21 6 0.18
22 1 0.03
23 13 0.39
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.25
Consensus pattern (23 bp):
TTAAATATAAAATCGACTCGACC
Found at i:68211 original size:7 final size:7
Alignment explanation
Indices: 68154--68256 Score: 86
Period size: 7 Copynumber: 14.9 Consensus size: 7
68144 AATCAAATTA
68154 AGGGTTT
1 AGGGTTT
*
68161 AGTGTTT
1 AGGGTTT
68168 A-GGTTT
1 AGGGTTT
*
68174 ATGGTTT
1 AGGGTTT
*
68181 ATGGTTT
1 AGGGTTT
68188 AGGGTTT
1 AGGGTTT
**
68195 ATAGTTT
1 AGGGTTT
68202 AGGGTTT
1 AGGGTTT
*
68209 AGGGGTT
1 AGGGTTT
68216 -GAGGTTT
1 AG-GGTTT
*
68223 AGAGTTT
1 AGGGTTT
68230 -GTGGTTT
1 AG-GGTTT
*
68237 AGAGTTT
1 AGGGTTT
*
68244 AAGGTTT
1 AGGGTTT
68251 AGGGTT
1 AGGGTT
68257 CATTGCAAAG
Statistics
Matches: 76, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
6 7 0.09
7 67 0.88
8 2 0.03
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.47
Consensus pattern (7 bp):
AGGGTTT
Found at i:68392 original size:11 final size:11
Alignment explanation
Indices: 68376--68438 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
68366 GTATTATAGA
68376 ATTTTTAATAT
1 ATTTTTAATAT
68387 ATTTTTAA-A-
1 ATTTTTAATAT
68396 ATTTTATAAT-T
1 ATTTT-TAATAT
*** * *
68407 ATCAATAGTGT
1 ATTTTTAATAT
68418 ATTTTTAATAT
1 ATTTTTAATAT
68429 ATTTTTAATA
1 ATTTTTAATA
68439 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Done.