Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004212.1 Hibiscus syriacus cultivar Beakdansim tig00009222_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: 52349
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:4804 original size:5 final size:5
Alignment explanation
Indices: 4794--4862 Score: 58
Period size: 5 Copynumber: 14.6 Consensus size: 5
4784 GCTTGAAGAA
* *
4794 AAAAG AAAAG AAAAG -AAAG AAAAG AAAA- AGAAAG AAAA- AATAG AAATG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A-AAAG AAAAG AAAAG AAAAG
* *
4842 AAAA- AAGAG AAGA- AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAA
4863 GGGGGTCAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
4 14 0.27
5 37 0.71
6 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:4824 original size:15 final size:14
Alignment explanation
Indices: 4795--4862 Score: 70
Period size: 14 Copynumber: 4.9 Consensus size: 14
4785 CTTGAAGAAA
4795 AAAGAAAAGAAAAG
1 AAAGAAAAGAAAAG
4809 AAAGAAAAGAAAAAG
1 AAAGAAAAG-AAAAG
*
4824 AAAGAAAA-AATAG
1 AAAGAAAAGAAAAG
*
4837 AAATGAAAA-AAGAG
1 AAA-GAAAAGAAAAG
4851 -AAGAAAAAGAAA
1 AAAG-AAAAGAAA
4863 GGGGGTCAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
12 1 0.02
13 13 0.28
14 20 0.43
15 13 0.28
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (14 bp):
AAAGAAAAGAAAAG
Found at i:6238 original size:50 final size:50
Alignment explanation
Indices: 5994--6245 Score: 477
Period size: 50 Copynumber: 5.0 Consensus size: 50
5984 GAAAGAGACT
*
5994 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
*
6044 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
6094 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
6144 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
*
6194 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
6244 AA
1 AA
6246 CCAATCATTG
Statistics
Matches: 200, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 200 1.00
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
Found at i:7175 original size:119 final size:119
Alignment explanation
Indices: 6961--7726 Score: 1340
Period size: 119 Copynumber: 6.5 Consensus size: 119
6951 TAGCAAAGAT
* *
6961 TTGAATCCATCACTTGATGGATCATTCTTTTCCAGA-GAA-AGTTCATAATGAGAAGAA--C-TC
1 TTGAATTCATCACTTGATGGATCAATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
7021 ATCTGAAGAAGGAA-AAGGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 ATCTGAAGAAGGAAGAA-GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
7075 TTGAATTCATCACTTGATGGATCAATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCACTTGATGGATCAATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
7140 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
7194 TTGAATTCATCACTTGATGGATCAATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCACTTGATGGATCAATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
7259 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
7313 TTGAATTCATCACTTGATGGATCAATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCACTTGATGGATCAATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
*
7378 ATCTGAAGAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
7432 TTGAATTCATCACTTGATGGATC-ATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCACTTGATGGATCAATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
7496 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
7550 TTGAATTCATCACTTGATGGATC-ATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATCACTTGATGGATCAATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
7614 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * ** *
7668 TTGAATTCATCA-TTGATGGAAC-ATCATCCCCAGCA-GAA-AGTTCGTAATGAGAAGAACTC
1 TTGAATTCATCACTTGATGGATCAATCTTTTCCAG-AGGAAGAGTTCATAATGAGAAGAACTC
7727 ATCTGGAGAA
Statistics
Matches: 636, Mismatches: 9, Indels: 12
0.97 0.01 0.02
Matches are distributed among these distances:
114 34 0.05
115 3 0.00
116 38 0.06
117 21 0.03
118 225 0.35
119 313 0.49
120 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (119 bp):
TTGAATTCATCACTTGATGGATCAATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:7889 original size:3 final size:3
Alignment explanation
Indices: 7881--7959 Score: 124
Period size: 3 Copynumber: 26.7 Consensus size: 3
7871 TTTTTATCCA
* *
7881 TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
7929 TTT TAT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
7960 AATATATTAA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:8430 original size:6 final size:6
Alignment explanation
Indices: 8419--8444 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
8409 AAGAAAAAAG
8419 GAGACA GAGACA GAGACA GAGACA GA
1 GAGACA GAGACA GAGACA GAGACA GA
8445 ACCGGAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.35, T:0.00
Consensus pattern (6 bp):
GAGACA
Found at i:16110 original size:55 final size:55
Alignment explanation
Indices: 16025--16465 Score: 471
Period size: 55 Copynumber: 8.1 Consensus size: 55
16015 AGGATAAGCG
* * * * * *
16025 AGACTTGAAAAATCTTCAA-ATAACGGGTCTGCTCCCTATTCTTTTAAAGAGTATA
1 AGACTCGAACAATCTTCAACA-AACGTGTCTGCTCCCTATTCCTTCAGAGAGTATA
*** * * *
16080 AGACTCGAACAATCTTTGGCAAATGTGTCTGCTCCCTATTCATTCAGGGAGTATA
1 AGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATA
* * *
16135 AGACTCAAACAATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATA
1 AGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATA
* *
16190 AGACTCGAATAATCTTCAACAAACGGGGT-TCGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTCGAACAATCTTCAACAAAC-GTGTCT-GCTCCCTATTCCTTCAGAGAGTATA
*
16246 AGACTCG----ATCTTCAACAAACGTGTCAGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATA
* * ** *
16297 GGACTCGAACAATCTTCAACAAACGGGT-TCGCTCCCTATTAGTTCAGGGAGTAT-
1 AGACTCGAACAATCTTCAACAAACGTGTCT-GCTCCCTATTCCTTCAGAGAGTATA
*
16351 AGAACTCGAACAATCTTCATA-AAACGTGTCTGCTCTCTATTCCTTCAGAGAGTAT-
1 AG-ACTCGAACAATCTTCA-ACAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATA
*
16406 AGAACTCG----ATCTTCAAAAAACGTGTTCT-CTCCCTATTCCTTCAGAGAGTATA
1 AG-ACTCGAACAATCTTCAACAAACGTG-TCTGCTCCCTATTCCTTCAGAGAGTATA
*
16458 GGACTCGA
1 AGACTCGA
16466 TCTTCATAAA
Statistics
Matches: 332, Mismatches: 38, Indels: 35
0.82 0.09 0.09
Matches are distributed among these distances:
50 1 0.00
51 75 0.23
52 17 0.05
54 1 0.00
55 202 0.61
56 36 0.11
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (55 bp):
AGACTCGAACAATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATA
Found at i:16527 original size:37 final size:37
Alignment explanation
Indices: 16486--16599 Score: 210
Period size: 37 Copynumber: 3.1 Consensus size: 37
16476 ATAAGTTTGC
16486 TTCACTACTCTTCCGTGAAGGCTTAAGATTGACTTGT
1 TTCACTACTCTTCCGTGAAGGCTTAAGATTGACTTGT
*
16523 TTCACTACTCTTCCGTGAAGGCTTAAGATTGACTTGC
1 TTCACTACTCTTCCGTGAAGGCTTAAGATTGACTTGT
*
16560 TTCACTACTCTTCCGTGAAGGCTTAAGTTTGACTTGT
1 TTCACTACTCTTCCGTGAAGGCTTAAGATTGACTTGT
16597 TTC
1 TTC
16600 GAAGGCCAAA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 74 1.00
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (37 bp):
TTCACTACTCTTCCGTGAAGGCTTAAGATTGACTTGT
Found at i:17938 original size:35 final size:35
Alignment explanation
Indices: 17865--17938 Score: 80
Period size: 35 Copynumber: 2.1 Consensus size: 35
17855 TGAACCCCCC
* * *
17865 TTTTATTTTTCTCCTTTTTTCATTTTTTTTATTTT
1 TTTTATCTTTCTCCTTTTTTCATTTTTCTTATTCT
*
17900 TTTTATCTTTCTTCTTTTTAT-ATTTCTTCTT-TTCT
1 TTTTATCTTTCTCCTTTTT-TCATTT-TTCTTATTCT
17935 TTTT
1 TTTT
17939 TCATTTTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
35 28 0.85
36 5 0.15
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (35 bp):
TTTTATCTTTCTCCTTTTTTCATTTTTCTTATTCT
Found at i:17966 original size:55 final size:54
Alignment explanation
Indices: 17878--18031 Score: 151
Period size: 55 Copynumber: 2.8 Consensus size: 54
17868 TATTTTTCTC
*
17878 CTTTTTTCATTTTTTTTATTTT-TTTTATCTTTCTTCTTTTTATATTTCTTC-TTTT
1 CTTTTTTCA-TTTTTTCATTTTCTTTTAT-TTTCTTCTTTTTAT-TTTCTTCTTTTT
*
17933 CTTTTTTCATTTTTTCATTTTCTTTTCATTTTC-TC-ATTTATTTTCTTCATTTTTT
1 CTTTTTTCATTTTTTCATTTTCTTTT-ATTTTCTTCTTTTTATTTTCTTC--TTTTT
*
17988 CTTTTTTTTTCA-TTTTTCATTTTC-TTTATTTT-TTCTTTTCATTT
1 C---TTTTTTCATTTTTTCATTTTCTTTTATTTTCTTCTTTTTATTT
18032 ATTCCATCAT
Statistics
Matches: 85, Mismatches: 4, Indels: 19
0.79 0.04 0.18
Matches are distributed among these distances:
52 7 0.08
53 5 0.06
54 13 0.15
55 29 0.34
56 11 0.13
57 12 0.14
58 8 0.09
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (54 bp):
CTTTTTTCATTTTTTCATTTTCTTTTATTTTCTTCTTTTTATTTTCTTCTTTTT
Found at i:17979 original size:23 final size:22
Alignment explanation
Indices: 17949--18031 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 22
17939 TCATTTTTTC
17949 ATTTTCTTTTCATTTTCTCATTT
1 ATTTTCTTTTCATTTTCTC-TTT
*
17972 ATTTTC--TTCATTTTTTCTTTT
1 ATTTTCTTTTCATTTTCTC-TTT
*
17993 TTTTTCATTTTTCATTTTCT-TTAT
1 ATTTTC--TTTTCATTTTCTCTT-T
*
18017 TTTTTCTTTTCATTT
1 ATTTTCTTTTCATTT
18032 ATTCCATCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
21 18 0.35
22 9 0.18
23 8 0.16
24 7 0.14
25 9 0.18
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (22 bp):
ATTTTCTTTTCATTTTCTCTTT
Found at i:18010 original size:34 final size:34
Alignment explanation
Indices: 17871--18026 Score: 105
Period size: 34 Copynumber: 4.6 Consensus size: 34
17861 CCCCTTTTAT
* * *
17871 TTTTC-TCCTTTTTTCATTTTTTTT-ATTTTTTTTA
1 TTTTCTTCATTTTTTCTTTTTTTTTCA--TTTTTCA
* *
17905 TCTTTCTTC-TTTTTATATTTCTTCTTTTCTTTTTTCA
1 T-TTTCTTCATTTTT-TCTTT-TT-TTTTCATTTTTCA
*
17942 TTTT-TTCA--TTTTCTTTTCATTTTCTCA-TTTA--
1 TTTTCTTCATTTTTTCTTTT--TTTT-TCATTTTTCA
17973 TTTTCTTCATTTTTTCTTTTTTTTTCATTTTTCA
1 TTTTCTTCATTTTTTCTTTTTTTTTCATTTTTCA
*
18007 TTTTCTTTATTTTTTCTTTT
1 TTTTCTTCATTTTTTCTTTT
18027 CATTTATTCC
Statistics
Matches: 97, Mismatches: 9, Indels: 32
0.70 0.07 0.23
Matches are distributed among these distances:
31 7 0.07
32 12 0.12
33 10 0.10
34 35 0.36
35 12 0.12
36 8 0.08
37 9 0.09
38 4 0.04
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (34 bp):
TTTTCTTCATTTTTTCTTTTTTTTTCATTTTTCA
Found at i:18042 original size:34 final size:34
Alignment explanation
Indices: 17939--18045 Score: 91
Period size: 34 Copynumber: 3.2 Consensus size: 34
17929 TTTTCTTTTT
17939 TCATTTT-TTCA--TTTTCTTTTCA-TT-TTCTCA
1 TCATTTTCTTCATTTTTTCTTTTCATTTATTC-CA
* ** **
17969 TTTATTTTCTTCATTTTTTCTTTTTTTTTCATT-TT
1 -TCATTTTCTTCATTTTTTCTTTTCATTT-ATTCCA
*
18004 TCATTTTCTTTATTTTTTCTTTTCATTTATTCCA
1 TCATTTTCTTCATTTTTTCTTTTCATTTATTCCA
18038 TCATTTTC
1 TCATTTTC
18046 ATTTTTCTTC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
31 6 0.10
32 4 0.07
33 3 0.05
34 41 0.71
35 2 0.03
37 2 0.03
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (34 bp):
TCATTTTCTTCATTTTTTCTTTTCATTTATTCCA
Found at i:18045 original size:57 final size:58
Alignment explanation
Indices: 17934--18056 Score: 137
Period size: 57 Copynumber: 2.1 Consensus size: 58
17924 TCTTCTTTTC
* * *
17934 TTTTTTCATTTTTTCATTTTCTTTTCATTTTCTCATTTATTTTCTTCATTTTTTCTTT
1 TTTTTTCATTTTTTCATTTTCTTTTCATTTTCTCATTTATTTTCTCCATATTTTCATT
* *
17992 TTTTTTCA-TTTTTCATTTTC-TTT-ATTTTTTCTTTTCATTTAT-TCCATCATTTTCATT
1 TTTTTTCATTTTTTCATTTTCTTTTCATTTTCTCATTT-ATTT-TCTCCAT-ATTTTCATT
*
18049 TTTCTTCA
1 TTTTTTCA
18057 AGCGAAATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
55 10 0.18
56 11 0.20
57 27 0.48
58 8 0.14
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (58 bp):
TTTTTTCATTTTTTCATTTTCTTTTCATTTTCTCATTTATTTTCTCCATATTTTCATT
Found at i:33059 original size:17 final size:16
Alignment explanation
Indices: 33028--33062 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
33018 AATTGAAAAA
33028 AATATAATATATATAT
1 AATATAATATATATAT
*
33044 AATATAAGTTTATATAT
1 AATATAA-TATATATAT
33061 AA
1 AA
33063 ACTATATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
AATATAATATATATAT
Found at i:33450 original size:2 final size:2
Alignment explanation
Indices: 33443--33584 Score: 52
Period size: 2 Copynumber: 73.0 Consensus size: 2
33433 TTTAATTTTC
* * *
33443 TA TA TA TA TA TA TA TA TA AA CTA TA TA TG TA TA AA CTA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA
* * * *
33486 AA TA TA TA GTT TA TA AA T- TA TA -A TT TA TA T- TA -A TA TA GTA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * * *
33526 TA TA AA TG TA TG TA TA -A CTA -A TA TA -A GTA -A TC TA TA GA T-
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA
33565 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
33585 ATTTATAGAA
Statistics
Matches: 101, Mismatches: 23, Indels: 32
0.65 0.15 0.21
Matches are distributed among these distances:
1 10 0.10
2 84 0.83
3 7 0.07
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:33469 original size:15 final size:15
Alignment explanation
Indices: 33449--33484 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
33439 TTTCTATATA
33449 TATATATATATAAAC
1 TATATATATATAAAC
*
33464 TATATATGTATAAAC
1 TATATATATATAAAC
33479 TATATA
1 TATATA
33485 AAATATATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:33797 original size:61 final size:58
Alignment explanation
Indices: 33732--33918 Score: 182
Period size: 61 Copynumber: 3.1 Consensus size: 58
33722 ATAATAAATA
* * *
33732 ATATATGTAACCTATAGTATATGTATATGT-A-TATGTATATGTATATGTATACATATAAACT
1 ATATATGTAACCTATAGTATATGTATATATAACTATGTATA-GTATATATAAAC-TAT--A-T
* *
33793 ATATATGTAACTTATAGTACATGTATATATAAACTATGTATAGTATATATAAACTATAT
1 ATATATGTAACCTATAGTATATGTATATAT-AACTATGTATAGTATATATAAACTATAT
* * * *
33852 ATATATATAATCTATAGTATATGTATATATACAATCTATTTATATGT-TATATAAATTATAT
1 ATATATGTAACCTATAGTATATGTATATAT--AA-CTATGTATA-GTATATATAAACTATAT
33913 ATATAT
1 ATATAT
33919 ATATATATAT
Statistics
Matches: 108, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
59 27 0.25
60 3 0.03
61 54 0.50
62 5 0.05
63 11 0.10
64 8 0.07
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (58 bp):
ATATATGTAACCTATAGTATATGTATATATAACTATGTATAGTATATATAAACTATAT
Found at i:33801 original size:33 final size:32
Alignment explanation
Indices: 33761--33879 Score: 82
Period size: 35 Copynumber: 3.5 Consensus size: 32
33751 TATGTATATG
33761 TATATGTATATGTATATGTATACATATAAACTA
1 TATATGTATATGTATATGTATA-ATATAAACTA
*
33794 TATATGTAACTTATAGTACATGTAT-ATATAAACTA
1 TATATGT-A--TAT-GTATATGTATAATATAAACTA
* * * * *
33829 TGTATAGTATATATAAACTATATATATATATAA-TC
1 TATAT-GTATATGTATA-TGTATA-ATATA-AACTA
33864 TATA-GTATATGTATAT
1 TATATGTATATGTATAT
33880 ATACAATCTA
Statistics
Matches: 68, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
32 4 0.06
33 23 0.34
34 1 0.01
35 24 0.35
36 7 0.10
37 9 0.13
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (32 bp):
TATATGTATATGTATATGTATAATATAAACTA
Found at i:33823 original size:2 final size:2
Alignment explanation
Indices: 33816--33929 Score: 74
Period size: 2 Copynumber: 57.0 Consensus size: 2
33806 ATAGTACATG
* * *
33816 TA TA TA TA AA CTA TG TA TA GTA TA TA TA AA CTA TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA
* * * * * *
33859 TA -A TC TA TA GTA TA TG TA TA TA TA CA -A TC TA TT TA TA TG T-
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
33899 TA TA TA AA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33930 ACGTATAGTT
Statistics
Matches: 86, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
1 4 0.05
2 76 0.88
3 6 0.07
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:33858 original size:6 final size:6
Alignment explanation
Indices: 33744--33929 Score: 78
Period size: 6 Copynumber: 30.7 Consensus size: 6
33734 ATATGTAACC
* * * * * * *
33744 TATAGTA TATGTA TATGTA TATGTA TATGTA TATGTA TACATA TAAACTA
1 TATA-TA TATATA TATATA TATATA TATATA TATATA TATATA TATA-TA
* * * * *
33794 TATATG TA-ACT- TATAGTA CATGTA TATATA AACTATG TATAGTA TATATA
1 TATATA TATA-TA TATA-TA TATATA TATATA TA-TATA TATA-TA TATATA
* * * * * *
33844 AACTATA TATATA TATA-A TCTATA GTATATG TATATA TACA-A TCTATT
1 TA-TATA TATATA TATATA TATATA -TATATA TATATA TATATA TATATA
* *
33892 TATATG T-TATA TAAAT- TATATA TATATA TATATA TATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATA
33930 ACGTATAGTT
Statistics
Matches: 137, Mismatches: 30, Indels: 25
0.71 0.16 0.13
Matches are distributed among these distances:
5 18 0.13
6 91 0.66
7 28 0.20
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.45
Consensus pattern (6 bp):
TATATA
Found at i:33957 original size:21 final size:20
Alignment explanation
Indices: 33933--34023 Score: 67
Period size: 21 Copynumber: 4.3 Consensus size: 20
33923 ATATATAACG
33933 TATAGTTTATAAACAATAGTT
1 TATA-TTTATAAACAATAGTT
**
33954 TATA-TTAGTGTACTATATAGTT
1 TATATTTA-TAAAC-A-ATAGTT
* * *
33976 TATACTTTATAACCTATAGTA
1 TATA-TTTATAAACAATAGTT
*
33997 TATAATTTATAAACTATAGTT
1 TAT-ATTTATAAACAATAGTT
34018 TATATT
1 TATATT
34024 AATGTACTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.05
20 6 0.11
21 30 0.55
22 11 0.20
23 2 0.04
24 3 0.05
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (20 bp):
TATATTTATAAACAATAGTT
Found at i:34047 original size:22 final size:21
Alignment explanation
Indices: 33948--34050 Score: 84
Period size: 22 Copynumber: 4.8 Consensus size: 21
33938 TTTATAAACA
*
33948 ATAGTTTATATTAGTGTACTAT
1 ATAGTTTATATTAATGTAC-AT
* * *
33970 ATAGTTTATACTTTAT-AACCT
1 ATAGTTTATA-TTAATGTACAT
* * **
33991 ATAGTATATAATTTATAAAC-T
1 ATAGTTTAT-ATTAATGTACAT
34012 ATAGTTTATATTAATGTACTAT
1 ATAGTTTATATTAATGTAC-AT
34034 ATAGTTTATATTAATGT
1 ATAGTTTATATTAATGT
34051 TAATTATCTT
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
20 7 0.10
21 23 0.34
22 34 0.51
23 3 0.04
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (21 bp):
ATAGTTTATATTAATGTACAT
Found at i:34082 original size:15 final size:15
Alignment explanation
Indices: 34032--34108 Score: 56
Period size: 15 Copynumber: 5.3 Consensus size: 15
34022 TTAATGTACT
*
34032 ATATAGTTTATATTA
1 ATATAATTTATATTA
* *
34047 ATGTTAA-TTATCTTA
1 AT-ATAATTTATATTA
34062 ACTATAATTTATATTA
1 A-TATAATTTATATTA
*
34078 ATATAGTTTATA--A
1 ATATAATTTATATTA
34091 ACTATAA--TATATTA
1 A-TATAATTTATATTA
34105 ATAT
1 ATAT
34109 TAAGAGAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
12 4 0.08
13 5 0.10
14 6 0.12
15 23 0.47
16 11 0.22
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (15 bp):
ATATAATTTATATTA
Found at i:34240 original size:20 final size:19
Alignment explanation
Indices: 34215--34268 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
34205 GCGAAATAAA
34215 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
34235 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
34255 AATCGCAACGCGAT
1 AATCGCAACGCGAT
34269 TTGCGATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:34368 original size:20 final size:20
Alignment explanation
Indices: 34324--34836 Score: 314
Period size: 20 Copynumber: 25.4 Consensus size: 20
34314 GATTCTGATT
* * *
34324 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGAATACGT-AA
* *
34345 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGAATACGTAA
34365 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGAATACGT-AA
* *
34386 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGAATACGTAA
**
34406 ATCGCAACAAGAATACGTAA
1 ATCGCAACGCGAATACGTAA
* *
34426 ATCGCAACGCGTAT-CTATAA
1 ATCGCAACGCGAATAC-GTAA
*
34446 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGAATACGTAA
* * *
34466 ATAGCAATGCGTAT-CTGTAA
1 ATCGCAACGCGAATAC-GTAA
34486 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGAATACGT-AA
* *
34507 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGAATACGTAA
*
34527 ATCGCAACGTG-AT-CGATAA
1 ATCGCAACGCGAATACG-TAA
* ** *
34546 TTCGCAACGCGGTCTCCGGT--
1 ATCGCAACGC-GAATAC-GTAA
** * * * *
34566 ATCGCAAATC-AGTTTC-CAG
1 ATCGCAACGCGA-ATACGTAA
* * *
34585 ATACGTAACGCG-ATTC-TGACT
1 AT-CGCAACGCGAATACGT-A-A
*** * * **
34606 ATCGCATTACGATTTCCCAA
1 ATCGCAACGCGAATACGTAA
*** * * *
34626 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCAACGCGA-ATACGTAA
*
34648 TTCGCAACGCGAATACGTAA
1 ATCGCAACGCGAATACGTAA
*
34668 ATCGCAACGCGATTACGTAA
1 ATCGCAACGCGAATACGTAA
34688 ATCGCAACGCGAATACGTAA
1 ATCGCAACGCGAATACGTAA
34708 ATCGCAACGCGAATACGTAA
1 ATCGCAACGCGAATACGTAA
34728 ATCGCAACGCGAATACGTAA
1 ATCGCAACGCGAATACGTAA
34748 ATCGCAACGCGAATACGTAA
1 ATCGCAACGCGAATACGTAA
** *
34768 ATCGCAATACGATTACGTAA
1 ATCGCAACGCGAATACGTAA
*
34788 ATCGCAATGCGAATACGTAA
1 ATCGCAACGCGAATACGTAA
*
34808 ATCGCAATGCGAAT-CTGTAA
1 ATCGCAACGCGAATAC-GTAA
*
34828 ATCACAACG
1 ATCGCAACG
34837 AGATTCTGAC
Statistics
Matches: 396, Mismatches: 69, Indels: 55
0.76 0.13 0.11
Matches are distributed among these distances:
18 2 0.01
19 23 0.06
20 284 0.72
21 77 0.19
22 9 0.02
23 1 0.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAATACGTAA
Found at i:34369 original size:41 final size:41
Alignment explanation
Indices: 34324--34535 Score: 320
Period size: 41 Copynumber: 5.2 Consensus size: 41
34314 GATTCTGATT
* *
34324 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
34365 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* **
34406 ATCGCAACAAGAATACGT-AAATCGCAACGCGTATCTATAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
34446 ATCGCAACGAGAATACGT-AAATAGCAATGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
34486 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
34527 ATCGCAACG
1 ATCGCAACG
34536 TGATCGATAA
Statistics
Matches: 155, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 73 0.47
41 82 0.53
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:35465 original size:20 final size:21
Alignment explanation
Indices: 35440--35527 Score: 121
Period size: 20 Copynumber: 4.4 Consensus size: 21
35430 GAACGCGAAA
35440 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAATATGACT
* *
35460 ATCGCAACAC-GAAAATGACT
1 ATCGCAACGCGGAATATGACT
*
35480 ATCGCAATGCGGAAT-TGACT
1 ATCGCAACGCGGAATATGACT
35500 ATCGCAACGCGGAA-ATGACT
1 ATCGCAACGCGGAATATGACT
35520 ATCGCAAC
1 ATCGCAAC
35528 AAGAGAATCG
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
20 57 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGGAATATGACT
Found at i:35557 original size:19 final size:19
Alignment explanation
Indices: 35533--35577 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
35523 GCAACAAGAG
35533 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35552 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35571 AATCGCA
1 AATCGCA
35578 CGCGTTGCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:35643 original size:33 final size:33
Alignment explanation
Indices: 35580--35675 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
35570 AAATCGCACG
*
35580 CGTTGCGATTTTCATTTTTGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
* *
35614 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
** *
35647 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
35676 AGTCTGTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 31 0.57
34 23 0.43
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:35794 original size:14 final size:14
Alignment explanation
Indices: 35775--35811 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
35765 CATCAATTAA
35775 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
35789 ACAAATCATCTTTT
1 ACAAATCAACATTT
35803 ACAAATCAA
1 ACAAATCAA
35812 TTAAACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:37707 original size:20 final size:20
Alignment explanation
Indices: 37684--37732 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
37674 GAAACTTAAA
37684 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
37704 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
37724 ATCGCAACG
1 ATCGCAACG
37733 AGATAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:37787 original size:19 final size:19
Alignment explanation
Indices: 37765--37808 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
37755 AAATCGCAAC
37765 GCGATTATAGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
* *
37784 GCGATTTTGGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
37803 GCGATT
1 GCGATT
37809 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.30, T:0.43
Consensus pattern (19 bp):
GCGATTATAGTTTCGCGTT
Found at i:37822 original size:33 final size:33
Alignment explanation
Indices: 37780--37871 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
37770 TATAGTTTCG
**
37780 CGTTGCGATTTTGGTTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
37813 CGTTGCGATTTTCATTTCTCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
37846 CGTTGCGA--TTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
37872 AGTCATTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 17 0.31
33 38 0.69
ACGTcount: A:0.09, C:0.23, G:0.24, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:37834 original size:19 final size:17
Alignment explanation
Indices: 37794--37871 Score: 78
Period size: 14 Copynumber: 4.8 Consensus size: 17
37784 GCGATTTTGG
*
37794 TTTCGCGTTGCGATTC-
1 TTTCTCGTTGCGATTCA
37810 --TCTCGTTGCGATTTTCA
1 TTTCTCGTTGCGA--TTCA
37827 TTTCTCGTTGCGATTC-
1 TTTCTCGTTGCGATTCA
37843 --TCTCGTTGCGATTCA
1 TTTCTCGTTGCGATTCA
*
37858 TTTCGCGTTGCGAT
1 TTTCTCGTTGCGAT
37872 AGTCATTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
14 24 0.46
16 3 0.06
17 14 0.27
19 11 0.21
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (17 bp):
TTTCTCGTTGCGATTCA
Found at i:38106 original size:94 final size:94
Alignment explanation
Indices: 37959--38327 Score: 530
Period size: 94 Copynumber: 4.1 Consensus size: 94
37949 ATGGATTGCA
* *
37959 TTAC-TTCAACCAAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAG
1 TTACTTTCAACC-AAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
*
38023 TTTAGCAGAATTGGTAGCAACCGAACAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
* *
38053 TTACTTTCAACCAAAAGAAAAAACAAAGACAAATACTAACTTCACAATGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
38118 TTAGCAGAATTGGCAGAAACCGTACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
38147 TTACTTTCAACCAAAAGACAAATCAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
38212 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
38241 TTAC-TTCAA-C------C---A-AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
38294 TTAGCAGTATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
38323 TTACT
1 TTACT
38328 AAGCAATCTA
Statistics
Matches: 257, Mismatches: 16, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
82 72 0.28
86 1 0.00
92 1 0.00
93 5 0.02
94 171 0.67
95 7 0.03
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:38308 original size:82 final size:82
Alignment explanation
Indices: 38171--38327 Score: 296
Period size: 82 Copynumber: 1.9 Consensus size: 82
38161 AAGACAAATC
*
38171 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACCGAA
38236 TAAATTTACTTCAACCA
66 TAAATTTACTTCAACCA
*
38253 AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGTATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACCGAA
38318 TAAATTTACT
66 TAAATTTACT
38328 AAGCAATCTA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (82 bp):
AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACCGAA
TAAATTTACTTCAACCA
Found at i:40027 original size:20 final size:19
Alignment explanation
Indices: 40004--40060 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
39994 TGAAATGAAA
40004 ATCGC-TACGAGAGAATGACT
1 ATCGCATACG-GA-AATGACT
40024 ATCGCAATACGGAAATGACT
1 ATCGC-ATACGGAAATGACT
40044 ATCGCA-ACGCGAAATGA
1 ATCGCATACG-GAAATGA
40061 AAATCGCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.09
19 8 0.24
20 17 0.50
21 2 0.06
22 4 0.12
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.18
Consensus pattern (19 bp):
ATCGCATACGGAAATGACT
Found at i:40059 original size:19 final size:19
Alignment explanation
Indices: 40017--40074 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
40007 GCTACGAGAG
40017 AATGACTATCGCAATACG-GA
1 AATGACTATCGC-A-ACGCGA
40037 AATGACTATCGCAACGCGA
1 AATGACTATCGCAACGCGA
** *
40056 AATGAAAATCGCAATGCGA
1 AATGACTATCGCAACGCGA
40075 TTTTGGTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.09
19 19 0.56
20 12 0.35
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:40120 original size:21 final size:20
Alignment explanation
Indices: 40097--40172 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
40087 GTTGCGATTC
*
40097 TCTTATTGCGATTTTCATTT
1 TCTTGTTGCGATTTTCATTT
* **
40117 CTCTCGTTGCGATAGTCATTT
1 -TCTTGTTGCGATTTTCATTT
*
40138 TCGTGTTGCGATTTTCATTT
1 TCTTGTTGCGATTTTCATTT
*
40158 TCATGTTGCGATTTT
1 TCTTGTTGCGATTTT
40173 AAGTTTAGAA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 30 0.65
21 16 0.35
ACGTcount: A:0.13, C:0.17, G:0.17, T:0.53
Consensus pattern (20 bp):
TCTTGTTGCGATTTTCATTT
Found at i:40728 original size:20 final size:20
Alignment explanation
Indices: 40703--40919 Score: 231
Period size: 20 Copynumber: 10.7 Consensus size: 20
40693 CTTTAAAAAT
*
40703 CGCGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
40723 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
40743 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * * *
40764 TGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
40784 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
40804 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
40824 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
40844 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
40864 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
40885 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
* *
40906 CTCGTCGCGATTTA
1 CGCGTTGCGATTTA
40920 TATGTTCGCG
Statistics
Matches: 163, Mismatches: 27, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
20 110 0.67
21 53 0.33
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:40789 original size:40 final size:41
Alignment explanation
Indices: 40705--40957 Score: 343
Period size: 41 Copynumber: 6.2 Consensus size: 41
40695 TTAAAAATCG
* *
40705 CGTTACGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
40746 CGTTGCGATTTACGGATATGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
40786 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
40826 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
40867 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* ** * * *
40908 CGTCGCGATTTATATG-TTCGCGTTGCGATTTT-CATATTCG
1 CGTTGCGATTTA-CGGATACGCGTTGCGATTTTACGTATTCT
40948 CGTTGCGATT
1 CGTTGCGATT
40958 CTGGAAAATC
Statistics
Matches: 189, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
40 88 0.47
41 100 0.53
42 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:41245 original size:24 final size:24
Alignment explanation
Indices: 41218--41315 Score: 66
Period size: 24 Copynumber: 4.2 Consensus size: 24
41208 ATTTATAAAA
41218 TATAGTTTATATTAATATTAATTT
1 TATAGTTTATATTAATATTAATTT
*
41242 TATA-TACTATATT-ATATTAA---
1 TATAGT-TTATATTAATATTAATTT
*
41262 TATAGGTTAATATTAATATTAATTAT
1 TATA-GTTTATATTAATATTAATT-T
* * *
41288 AAATAG-TT-TATTAATATAAATTA
1 -TATAGTTTATATTAATATTAATTT
41311 TATAG
1 TATAG
41316 GGATGAAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
20 4 0.07
21 5 0.09
22 12 0.21
23 8 0.14
24 23 0.40
25 1 0.02
26 1 0.02
27 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (24 bp):
TATAGTTTATATTAATATTAATTT
Found at i:41387 original size:17 final size:19
Alignment explanation
Indices: 41357--41401 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
41347 ATTAATATTA
41357 ATATTAATTATAAATA-TTT
1 ATATTAA-TATAAATAGTTT
41376 -TATTAATATAAATAGTTT
1 ATATTAATATAAATAGTTT
41394 ATATTAAT
1 ATATTAAT
41402 GTCCTCATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.33
18 9 0.38
19 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATATTAATATAAATAGTTT
Found at i:42837 original size:23 final size:24
Alignment explanation
Indices: 42807--42860 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
42797 CTATTTTTTC
*
42807 TTTACATAAATTAAGCTATA-TAA
1 TTTACATAAATTAAACTATATTAA
42830 TTTACATAAATTAAACTATATTAA
1 TTTACATAAATTAAACTATATTAA
42854 TTTACAT
1 TTTACAT
42861 TTAATCATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 19 0.66
24 10 0.34
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (24 bp):
TTTACATAAATTAAACTATATTAA
Found at i:42940 original size:22 final size:24
Alignment explanation
Indices: 42899--42953 Score: 87
Period size: 22 Copynumber: 2.4 Consensus size: 24
42889 ATTAATCATG
42899 TTTTATATAATATATATTAAATAA
1 TTTTATATAATATATATTAAATAA
*
42923 TTTTAT-TAAT-TTTATTAAATAA
1 TTTTATATAATATATATTAAATAA
42945 TTTTATATA
1 TTTTATATA
42954 TAGATCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.59
23 6 0.21
24 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTATATAATATATATTAAATAA
Found at i:47258 original size:25 final size:25
Alignment explanation
Indices: 47228--47281 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
47218 ACATAAGACA
47228 GAAAGCTTAAAGAGGAGACTCTAAG
1 GAAAGCTTAAAGAGGAGACTCTAAG
47253 GAAAGCTTAAAGAGGAGACTCTAAG
1 GAAAGCTTAAAGAGGAGACTCTAAG
47278 GAAA
1 GAAA
47282 CTAAAGGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.46, C:0.11, G:0.28, T:0.15
Consensus pattern (25 bp):
GAAAGCTTAAAGAGGAGACTCTAAG
Done.