Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005874.1 Hibiscus syriacus cultivar Beakdansim tig00013804_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: 93558
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:16134 original size:10 final size:10
Alignment explanation
Indices: 16119--16146 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
16109 AAGGCAGAAT
16119 AGAAAGAGAG
1 AGAAAGAGAG
16129 AGAAAGAGAG
1 AGAAAGAGAG
16139 AGAAAGAG
1 AGAAAGAG
16147 CAGTAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (10 bp):
AGAAAGAGAG
Found at i:26601 original size:16 final size:16
Alignment explanation
Indices: 26580--26610 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26570 CAAAAACTAT
*
26580 ACTATATATCTTATAA
1 ACTATATATATTATAA
26596 ACTATATATATTATA
1 ACTATATATATTATA
26611 TATTTTTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (16 bp):
ACTATATATATTATAA
Found at i:26605 original size:25 final size:24
Alignment explanation
Indices: 26577--26653 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 24
26567 TTTCAAAAAC
26577 TATACTATATATCTTATAAACTATA
1 TATA-TATATATCTTATAAACTATA
* *
26602 TATATTATATAT-TTTTGAAATTATA
1 TATA-TATATATCTTAT-AAACTATA
* *
26627 TATATATATTATCATATATACTATA
1 TATATATA-TATCTTATAAACTATA
26652 TA
1 TA
26654 ATGTAATAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
24 7 0.17
25 33 0.79
26 2 0.05
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.49
Consensus pattern (24 bp):
TATATATATATCTTATAAACTATA
Found at i:30286 original size:63 final size:63
Alignment explanation
Indices: 30208--30335 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
30198 AATTAATCTT
30208 ATTTACGAAGAATAACATCTATATGAGTACACCATCAATTGCTCCAATGCAATCCTAAAATAA
1 ATTTACGAAGAATAACATCTATATGAGTACACCATCAATTGCTCCAATGCAATCCTAAAATAA
30271 ATTTACGAAGAATAACATCTATATGAGTACACCATCAATTGCTCCAATGCAATCCTAAAATAA
1 ATTTACGAAGAATAACATCTATATGAGTACACCATCAATTGCTCCAATGCAATCCTAAAATAA
30334 AT
1 AT
30336 GAATCTATTA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.27
Consensus pattern (63 bp):
ATTTACGAAGAATAACATCTATATGAGTACACCATCAATTGCTCCAATGCAATCCTAAAATAA
Found at i:36092 original size:17 final size:17
Alignment explanation
Indices: 36056--36095 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
36046 CATCTGTTTA
*
36056 ATATTATTTTTATATTT
1 ATATTATTTTTATATAT
36073 ATATTATTTTATAATATAT
1 ATATTATTTT-T-ATATAT
36092 ATAT
1 ATAT
36096 ATATATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 1 0.05
19 9 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTATTTTTATATAT
Found at i:38831 original size:16 final size:16
Alignment explanation
Indices: 38810--38845 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
38800 CTTATTTCTA
38810 AGAACAACTGCATATG
1 AGAACAACTGCATATG
38826 AGAACAACTGCATATG
1 AGAACAACTGCATATG
38842 AGAA
1 AGAA
38846 AGATGGTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (16 bp):
AGAACAACTGCATATG
Found at i:40708 original size:114 final size:114
Alignment explanation
Indices: 40506--40737 Score: 419
Period size: 114 Copynumber: 2.0 Consensus size: 114
40496 AAATGTAAAC
*
40506 CGAGAGTCAATCTATAAAATATAACTTAAACAGCTATAAAATCATATTTTATCAAATATCATTCA
1 CGAGAATCAATCTATAAAATATAACTTAAACAGCTATAAAATCATATTTTATCAAATATCATTCA
* *
40571 ACAGACTGACATCCAACTTAGAGAACCGTCATTTTTTAACGAAAAAGAA
66 ACAAACTGACATCCAACTCAGAGAACCGTCATTTTTTAACGAAAAAGAA
*
40620 CGAGAATCAATCTATAAAATATAACTTAAACAGCTATAAAATCATATTTTATCAAATCTCATTCA
1 CGAGAATCAATCTATAAAATATAACTTAAACAGCTATAAAATCATATTTTATCAAATATCATTCA
*
40685 ACAAACTTACATCCAACTCAGAGAACCGTCATTTTTTAACGAAAAAGAA
66 ACAAACTGACATCCAACTCAGAGAACCGTCATTTTTTAACGAAAAAGAA
40734 CGAG
1 CGAG
40738 TTTAGAACCT
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 113 1.00
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.28
Consensus pattern (114 bp):
CGAGAATCAATCTATAAAATATAACTTAAACAGCTATAAAATCATATTTTATCAAATATCATTCA
ACAAACTGACATCCAACTCAGAGAACCGTCATTTTTTAACGAAAAAGAA
Found at i:41036 original size:30 final size:32
Alignment explanation
Indices: 41000--41070 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
40990 CTTTTGGTAT
*
41000 TCGGGTCGGA-TTTTT-AAAAAAAATTC-GGG
1 TCGGGTCGGATTTTTTAAAAAAAAAATCAGGG
41029 ATCGGGTCGGATTTTTTAAAAAAAAAATCAGGG
1 -TCGGGTCGGATTTTTTAAAAAAAAAATCAGGG
41062 TCGGGTCGG
1 TCGGGTCGG
41071 GTCGGTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
30 10 0.27
31 5 0.14
32 19 0.51
33 3 0.08
ACGTcount: A:0.31, C:0.11, G:0.30, T:0.28
Consensus pattern (32 bp):
TCGGGTCGGATTTTTTAAAAAAAAAATCAGGG
Found at i:41112 original size:68 final size:67
Alignment explanation
Indices: 41000--41140 Score: 187
Period size: 68 Copynumber: 2.1 Consensus size: 67
40990 CTTTTGGTAT
**
41000 TCGGGTCGGATTTTTAAAAAAAATTCGGGATCGGGTCGGATTTTTTAAAAAAAAAATCAGGG-TC
1 TCGGGTCGGATTTTTAAAAAAAATTCGGGATCGAATCGGATTTTTTAAAAAAAAAATC-GGGTTC
41064 GGG
65 GGG
* ** *
41067 TCGGGTCGGTTTTTTTTTAAAAAATTCGGGATC-AATCGAGTTTTTTTAAAAAAAAAATCGGGTT
1 TCGGGTCGG-ATTTTTAAAAAAAATTCGGGATCGAATCG-GATTTTTTAAAAAAAAAATCGGGTT
41131 CGGG
64 CGGG
41135 TCGGGT
1 TCGGGT
41141 TTTTTTTAAG
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
67 15 0.23
68 50 0.77
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.33
Consensus pattern (67 bp):
TCGGGTCGGATTTTTAAAAAAAATTCGGGATCGAATCGGATTTTTTAAAAAAAAAATCGGGTTCG
GG
Found at i:41207 original size:34 final size:33
Alignment explanation
Indices: 41124--41210 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 33
41114 AAAAAAAAAA
*
41124 TCGGGTTCGGGTCGGGTTTTTTTTAAGTTTAATAT
1 TCGGG-TCGGGTCGGG-TTTTTTTAAGTGTAATAT
* ** *
41159 TCAGGTCATGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTCGGGTTTTTTTAAGTGTAATAT
41192 TCGGGTCGGGTTCGGGTTT
1 TCGGGTCGGG-TCGGGTTT
41211 AGGGTGAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
33 23 0.53
34 16 0.37
35 4 0.09
ACGTcount: A:0.13, C:0.10, G:0.32, T:0.45
Consensus pattern (33 bp):
TCGGGTCGGGTCGGGTTTTTTTAAGTGTAATAT
Found at i:41896 original size:6 final size:6
Alignment explanation
Indices: 41880--41911 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
41870 TCTCGTCTCG
41880 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
41912 AATGGTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:42173 original size:21 final size:21
Alignment explanation
Indices: 42147--42195 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
42137 TTACATATTT
42147 GCATTGCGATAGTCCAAGTTC
1 GCATTGCGATAGTCCAAGTTC
*
42168 GCATTGTGATAGTCCAAGTTC
1 GCATTGCGATAGTCCAAGTTC
*
42189 GCGTTGC
1 GCATTGC
42196 AAATCTGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (21 bp):
GCATTGCGATAGTCCAAGTTC
Found at i:43661 original size:36 final size:38
Alignment explanation
Indices: 43612--43688 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 38
43602 ATAATATTAC
43612 AAATTGTAAAATATTTATAT-ATTTTCTTTAAAAAATT
1 AAATTGTAAAATATTTATATAATTTTCTTTAAAAAATT
* * * *
43649 AAATT-TATAATATTTATATAATTTTTTTTACAAATTT
1 AAATTGTAAAATATTTATATAATTTTCTTTAAAAAATT
43686 AAA
1 AAA
43689 AATATAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (38 bp):
AAATTGTAAAATATTTATATAATTTTCTTTAAAAAATT
Found at i:45269 original size:14 final size:14
Alignment explanation
Indices: 45223--45260 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
45213 CGTTGGGCAT
*
45223 CCGAAGCCATCCGA
1 CCGAGGCCATCCGA
*
45237 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
45251 CCGAGGCCAT
1 CCGAGGCCAT
45261 TCGAGCGAGC
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:0.24, C:0.39, G:0.29, T:0.08
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:48601 original size:29 final size:30
Alignment explanation
Indices: 48561--48641 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
48551 ATTCAGTTAA
48561 AAAAATATGATCGAAAATATTATTAGATGTT
1 AAAAA-ATGATCGAAAATATTATTAGATGTT
* *
48592 -AAAAATGATCGAAAATATTTTTAGGTGTT
1 AAAAAATGATCGAAAATATTATTAGATGTT
* *
48621 AAAAAATAATTGAAAATATTA
1 AAAAAATGATCGAAAATATTA
48642 AAAAAATAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 23 0.52
30 21 0.48
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35
Consensus pattern (30 bp):
AAAAAATGATCGAAAATATTATTAGATGTT
Found at i:48665 original size:21 final size:21
Alignment explanation
Indices: 48641--48683 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
48631 TGAAAATATT
*
48641 AAAAAAATAATGTTTTAGGTA
1 AAAAAAATAATATTTTAGGTA
* *
48662 AAAATAATAATATTTTATGTA
1 AAAAAAATAATATTTTAGGTA
48683 A
1 A
48684 TTTTTTACCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (21 bp):
AAAAAAATAATATTTTAGGTA
Found at i:50094 original size:79 final size:75
Alignment explanation
Indices: 49967--50109 Score: 232
Period size: 79 Copynumber: 1.9 Consensus size: 75
49957 TCGAAAGTTT
*
49967 TTTATTTTGATGTTAATGATTCATTGGATGCATGTCATTACATGAAACTTTATCTTGTACTATGC
1 TTTATTTTGATGTTAATGATTCATTGGATACATGTCATTACATGAAACTTTATCTTGTACTATGC
50032 TTTTCTTTTA
66 TTTTCTTTTA
*
50042 TTTATTTTGATGTTAATGATTCAAAAGTTGGATACATGTCATTGCATGAAACTTTATCTTGTACT
1 TTTATTTTGATGTTAATGATTC---A-TTGGATACATGTCATTACATGAAACTTTATCTTGTACT
50107 ATG
62 ATG
50110 TTAGTGGGAT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
75 22 0.35
78 1 0.02
79 39 0.63
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.48
Consensus pattern (75 bp):
TTTATTTTGATGTTAATGATTCATTGGATACATGTCATTACATGAAACTTTATCTTGTACTATGC
TTTTCTTTTA
Found at i:50135 original size:45 final size:45
Alignment explanation
Indices: 50071--50156 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
50061 TTCAAAAGTT
*
50071 GGATACATGTCATTGCATGAAACTTTATCTTGTACTATGTTAGTG
1 GGATACATGTCATTACATGAAACTTTATCTTGTACTATGTTAGTG
50116 GGATACATGTCATTACATGAAACTTTATCTTGTACTATGTT
1 GGATACATGTCATTACATGAAACTTTATCTTGTACTATGTT
50157 TTTCTTTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (45 bp):
GGATACATGTCATTACATGAAACTTTATCTTGTACTATGTTAGTG
Found at i:51741 original size:13 final size:13
Alignment explanation
Indices: 51720--51779 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
51710 ATTTTGTTAG
51720 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
51733 TATTGTA-TTATT
1 TATTTTATTTAAT
51745 TAATTTT-TTT-AT
1 T-ATTTTATTTAAT
51757 TATTTTATTTAAT
1 TATTTTATTTAAT
51770 TATTTTATTT
1 TATTTTATTT
51780 TTTTACAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 5 0.13
12 10 0.26
13 24 0.62
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:51745 original size:21 final size:20
Alignment explanation
Indices: 51720--51784 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
51710 ATTTTGTTAG
51720 TATTTTATTTAATTATTGTAT
1 TATTTTATTTAATTATT-TAT
*
51741 TA-TTTAATT--TT-TTTAT
1 TATTTTATTTAATTATTTAT
51757 TATTTTATTTAATTATTTTAT
1 TATTTTATTTAATTA-TTTAT
*
51778 TTTTTTA
1 TATTTTA
51785 CAGTTATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 5 0.14
17 8 0.22
18 2 0.06
19 2 0.06
20 6 0.17
21 13 0.36
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
TATTTTATTTAATTATTTAT
Found at i:51755 original size:29 final size:29
Alignment explanation
Indices: 51722--51784 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
51712 TTTGTTAGTA
51722 TTTTATT-TAATTATTGT-ATTATTTAATTT
1 TTTTATTAT-ATTATT-TAATTATTTAATTT
* *
51751 TTTTATTATTTTATTTAATTATTTTATTT
1 TTTTATTATATTATTTAATTATTTAATTT
51780 TTTTA
1 TTTTA
51785 CAGTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 28 0.93
30 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (29 bp):
TTTTATTATATTATTTAATTATTTAATTT
Found at i:51766 original size:16 final size:16
Alignment explanation
Indices: 51724--51766 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
51714 TGTTAGTATT
* *
51724 TTATTTAATTATTGTA
1 TTATTTAATTTTTTTA
51740 TTATTTAATTTTTTTA
1 TTATTTAATTTTTTTA
*
51756 TTATTTTATTT
1 TTATTTAATTT
51767 AATTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATTTAATTTTTTTA
Found at i:52054 original size:13 final size:13
Alignment explanation
Indices: 52036--52095 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
52026 AACTGTAAAA
52036 AAATAAAATAATT
1 AAATAAAATAATT
52049 AAATAAAATAA-T
1 AAATAAAATAATT
*
52061 AAA-AAAATTAAAT
1 AAATAAAA-TAATT
*
52074 -AATACAATAATT
1 AAATAAAATAATT
52086 AAATAAAATA
1 AAATAAAATA
52096 CTAACAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 4 0.10
12 13 0.32
13 23 0.57
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:52055 original size:21 final size:21
Alignment explanation
Indices: 52031--52075 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
52021 TTTATAACTG
*
52031 TAAAAAAATAAAATAATTAAA
1 TAAAAAAATAAAAAAATTAAA
*
52052 TAAAATAATAAAAAAATTAAA
1 TAAAAAAATAAAAAAATTAAA
52073 TAA
1 TAA
52076 TACAATAATT
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):
TAAAAAAATAAAAAAATTAAA
Found at i:52068 original size:16 final size:16
Alignment explanation
Indices: 52031--52091 Score: 56
Period size: 16 Copynumber: 4.0 Consensus size: 16
52021 TTTATAACTG
52031 TAAAAAAATAAAATAA
1 TAAAAAAATAAAATAA
*
52047 T---TAAATAAAATAA
1 TAAAAAAATAAAATAA
*
52060 TAAAAAAATTAAATAA
1 TAAAAAAATAAAATAA
* * *
52076 TACAATAATTAAATAA
1 TAAAAAAATAAAATAA
52092 AATACTAACA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
13 12 0.32
16 25 0.68
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAAAAATAAAATAA
Found at i:52089 original size:21 final size:21
Alignment explanation
Indices: 52031--52083 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
52021 TTTATAACTG
* *
52031 TAAAAAAATAAAATAATTAAA
1 TAAAACAATAAAAAAATTAAA
*
52052 TAAAATAATAAAAAAATTAAA
1 TAAAACAATAAAAAAATTAAA
*
52073 TAATACAATAA
1 TAAAACAATAA
52084 TTAAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAAACAATAAAAAAATTAAA
Found at i:52094 original size:21 final size:20
Alignment explanation
Indices: 52031--52095 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
52021 TTTATAACTG
*
52031 TAAAAAAATAAAATAATTAAA
1 TAAAATAAT-AAATAATTAAA
52052 TAAAATAAT-AA-AA--AAA
1 TAAAATAATAAATAATTAAA
*
52068 TTAAATAATACAATAATTAAA
1 TAAAATAATA-AATAATTAAA
52089 TAAAATA
1 TAAAATA
52096 CTAACAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 11 0.31
18 4 0.11
19 4 0.11
21 17 0.47
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAATAATAAATAATTAAA
Found at i:55049 original size:24 final size:24
Alignment explanation
Indices: 54987--55079 Score: 82
Period size: 24 Copynumber: 3.7 Consensus size: 24
54977 GAAAATACAA
54987 ATAAAATA-ATTTTAAATTAAGTTAAT
1 ATAAAATATA-TTT-AA-TAAGTTAAT
55013 AATAAAATATATTTAATAAGTTAAT
1 -ATAAAATATATTTAATAAGTTAAT
**
55038 ATAAAA-AGTATTTTTTAAGTTAAT
1 ATAAAATA-TATTTAATAAGTTAAT
* *
55062 ATATATATATATATAATA
1 ATA-AAATATATTTAATA
55080 TTATGAATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
23 1 0.02
24 23 0.41
25 17 0.30
26 3 0.05
27 11 0.20
28 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
ATAAAATATATTTAATAAGTTAAT
Found at i:57992 original size:18 final size:19
Alignment explanation
Indices: 57962--58012 Score: 77
Period size: 18 Copynumber: 2.7 Consensus size: 19
57952 AACATGTCAT
*
57962 GTCAAACTCAACGGGTTGG
1 GTCAAAGTCAACGGGTTGG
*
57981 GTC-AAGTCAACGGTTTGG
1 GTCAAAGTCAACGGGTTGG
57999 GTCAAAGTCAACGG
1 GTCAAAGTCAACGG
58013 ATCAGATTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (19 bp):
GTCAAAGTCAACGGGTTGG
Found at i:59731 original size:2 final size:2
Alignment explanation
Indices: 59724--59751 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
59714 ATCAATGTAT
59724 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59752 ACGTAATCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60758 original size:21 final size:22
Alignment explanation
Indices: 60732--60783 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 22
60722 GGCCGAAATT
60732 ACTGTAGCAGGGTATCGATA-C
1 ACTGTAGCAGGGTATCGATACC
60753 ACTGTAGCAGGGTATCGATACC
1 ACTGTAGCAGGGTATCGATACC
*
60775 CCTGTAGCA
1 ACTGTAGCA
60784 TTCTAGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (22 bp):
ACTGTAGCAGGGTATCGATACC
Found at i:60832 original size:22 final size:22
Alignment explanation
Indices: 60804--60860 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
60794 TTTTTAAAAT
* *
60804 CGGTAATGTTCGTTACTGTTCA
1 CGGTAATGTTCATTACTATTCA
60826 CGGTAATGTTCATTACTATTCA
1 CGGTAATGTTCATTACTATTCA
*
60848 CGGTACTGTTCAT
1 CGGTAATGTTCAT
60861 ACAGTATAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (22 bp):
CGGTAATGTTCATTACTATTCA
Found at i:61187 original size:7 final size:7
Alignment explanation
Indices: 61177--61217 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
61167 ACTTAACACT
61177 TAACAAA
1 TAACAAA
61184 TAACAAA
1 TAACAAA
61191 TAACAAA
1 TAACAAA
61198 TAACAAA
1 TAACAAA
61205 TAACAAA
1 TAACAAA
61212 TAACAA
1 TAACAA
61218 CAATCTCGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.71, C:0.15, G:0.00, T:0.15
Consensus pattern (7 bp):
TAACAAA
Found at i:67487 original size:21 final size:22
Alignment explanation
Indices: 67463--67505 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
67453 CCGCCGATGA
67463 ATATTA-G-TTTTCTTATTTTTT
1 ATATTATGTTTTTC-TATTTTTT
67484 ATATTATGTTTTTCTATTTTTT
1 ATATTATGTTTTTCTATTTTTT
67506 TAGTCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 9 0.45
23 5 0.25
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.72
Consensus pattern (22 bp):
ATATTATGTTTTTCTATTTTTT
Found at i:70081 original size:29 final size:29
Alignment explanation
Indices: 70044--70102 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
70034 AAAAATGTTC
*
70044 CGTCCCTTAAAATTTTATAA-TCTCAAGTT
1 CGTCACTTAAAATTTTATAAGT-TCAAGTT
70073 CGTCACTTAAAATTTTATAAGTTCAAGTT
1 CGTCACTTAAAATTTTATAAGTTCAAGTT
70102 C
1 C
70103 ATCCCCTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (29 bp):
CGTCACTTAAAATTTTATAAGTTCAAGTT
Found at i:72012 original size:51 final size:51
Alignment explanation
Indices: 71904--72012 Score: 121
Period size: 51 Copynumber: 2.1 Consensus size: 51
71894 TATCATCTTT
** * * *
71904 AATAACAACGACTTTGATAATAAAATGCAGTCCCCTAACCTCCGATATTCC
1 AATAACAACGACTCCGATAATAAAATACAATCCCCTAACCTCCGATACTCC
* * *
71955 AATAACAACGACTCCGATAATAAAAATATAATCTCCTAA-CTCTGATACTCC
1 AATAACAACGACTCCGATAAT-AAAATACAATCCCCTAACCTCCGATACTCC
*
72006 AGTAACA
1 AATAACA
72013 TCAATTCCAA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
51 35 0.73
52 13 0.27
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (51 bp):
AATAACAACGACTCCGATAATAAAATACAATCCCCTAACCTCCGATACTCC
Found at i:75911 original size:28 final size:28
Alignment explanation
Indices: 75853--75918 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
75843 AAATACACAA
* *
75853 AATTTTC-TTTATTATGAAAAAATTAGT
1 AATTTTCTTTTATTATGAAAAAAATAAT
75880 -ATTTTCTTTTATTATGAAAAAAATAAT
1 AATTTTCTTTTATTATGAAAAAAATAAT
*
75907 AATTTACTTTTA
1 AATTTTCTTTTA
75919 AACTCGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.18
27 18 0.53
28 10 0.29
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (28 bp):
AATTTTCTTTTATTATGAAAAAAATAAT
Found at i:79661 original size:20 final size:20
Alignment explanation
Indices: 79636--79676 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
79626 AATTATATAT
79636 TACTAATATAGTAATAAAAA
1 TACTAATATAGTAATAAAAA
79656 TACTAATATAGTAATAAAAA
1 TACTAATATAGTAATAAAAA
79676 T
1 T
79677 GACTCCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (20 bp):
TACTAATATAGTAATAAAAA
Found at i:84843 original size:3 final size:3
Alignment explanation
Indices: 84835--84875 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
84825 GATTAATCAA
*
84835 AAT AAT AAT AGT AAT AAT AATT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT A
84876 GAGTTATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:84861 original size:19 final size:19
Alignment explanation
Indices: 84837--84874 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
84827 TTAATCAAAA
*
84837 TAATAATAGTAATAATAAT
1 TAATAATAATAATAATAAT
84856 TAATAATAATAATAATAAT
1 TAATAATAATAATAATAAT
84875 AGAGTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (19 bp):
TAATAATAATAATAATAAT
Found at i:86557 original size:14 final size:14
Alignment explanation
Indices: 86538--86564 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
86528 GCTGGGCATC
86538 CGAGGCCATCCGAT
1 CGAGGCCATCCGAT
86552 CGAGGCCATCCGA
1 CGAGGCCATCCGA
86565 AAGCATCCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.37, G:0.30, T:0.11
Consensus pattern (14 bp):
CGAGGCCATCCGAT
Found at i:86591 original size:20 final size:22
Alignment explanation
Indices: 86532--86599 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 22
86522 CAACACGCTG
86532 GGCATCCGAGGCCATCCGATCGA
1 GGCATCCGAGGCCATCCGA-CGA
*
86555 GGCCATCCGAAAG-CATCCGA-GA
1 GG-CATCCG-AGGCCATCCGACGA
86577 -GCATCCGAGGCCATCCGAACGA
1 GGCATCCGAGGCCATCCG-ACGA
86599 G
1 G
86600 CTATGCGAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
19 2 0.05
20 12 0.32
21 2 0.05
22 4 0.11
23 2 0.05
24 13 0.35
25 2 0.05
ACGTcount: A:0.26, C:0.34, G:0.29, T:0.10
Consensus pattern (22 bp):
GGCATCCGAGGCCATCCGACGA
Found at i:86617 original size:23 final size:23
Alignment explanation
Indices: 86582--86645 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
86572 CGAGAGCATC
* * * *
86582 CGAGGCCATCCGAACGAGCTATG
1 CGAGGGCAACCGAGCGAGCTATA
86605 CGAGGGCAACCGAGCGAGCTATA
1 CGAGGGCAACCGAGCGAGCTATA
86628 CGAGGGCAACCGAGCGAG
1 CGAGGGCAACCGAGCGAG
86646 TGTAGGACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.28, C:0.28, G:0.36, T:0.08
Consensus pattern (23 bp):
CGAGGGCAACCGAGCGAGCTATA
Found at i:86762 original size:33 final size:33
Alignment explanation
Indices: 86713--86795 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
86703 GCGACCTACC
86713 CTCGCTCGG-TG-CCTCGGATTCCCTCGTATAG
1 CTCGCTCGGTTGCCCTCGGATTCCCTCGTATAG
*
86744 CTCTCTCGGTTGCCCTCGGATTCCCTCGTATAG
1 CTCGCTCGGTTGCCCTCGGATTCCCTCGTATAG
86777 CTCGCTCGGTTGCCCTCGG
1 CTCGCTCGGTTGCCCTCGG
86796 TCGGATGGCC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 8 0.17
32 2 0.04
33 38 0.79
ACGTcount: A:0.07, C:0.37, G:0.25, T:0.30
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATTCCCTCGTATAG
Found at i:87532 original size:21 final size:21
Alignment explanation
Indices: 87506--87550 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
87496 GATTTCTGGG
* *
87506 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
87527 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
87548 CAA
1 CAA
87551 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:88415 original size:30 final size:31
Alignment explanation
Indices: 88355--88447 Score: 127
Period size: 31 Copynumber: 3.0 Consensus size: 31
88345 AGGGTCGAGG
88355 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
88386 GTTTACCTATGTCCTTCGGGACA-ATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
88416 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
88447 G
1 G
88448 GTCCTTCGGG
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
30 24 0.44
31 31 0.56
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:91334 original size:21 final size:21
Alignment explanation
Indices: 91308--91352 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
91298 GATTTCTGGG
* *
91308 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
91329 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
91350 CAA
1 CAA
91353 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:92193 original size:31 final size:31
Alignment explanation
Indices: 92155--92279 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
92145 AGGGTCGAGG
92155 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
92186 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
92217 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
92248 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
92279 G
1 G
92280 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 85 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Done.