Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000529.1 Hibiscus syriacus cultivar Beakdansim tig00001013_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: 48709
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:4099 original size:178 final size:177
Alignment explanation
Indices: 3784--4104 Score: 437
Period size: 178 Copynumber: 1.8 Consensus size: 177
3774 CACTATACCA
* * * *
3784 TTTATATAAAGGTTATAACTTAAGACCTCACCTAATCAATATACTTGTTTATCATGCATGTATAT
1 TTTATATAAAGGTTATAACTTAAGACATCACCTAATCAATATAATTGTTTATCATGCATATAAAT
* * * * ** *
3849 TTATGAACTATTTTATTTGAGACAATTTGAAAGGAAAATAGCATTAACGAGCACATGCGTGTGCA
66 TTATGAACTATTTTATTGGAGACAATTTGAAACGAAAATAGAATCAACGAGCACAACCCTGTGCA
3914 CATACAAAGACAGACACTGTTTATATAGTCTCATCTCACTGGAGCAT
131 CATACAAAGACAGACACTGTTTATATAGTCTCATCTCACTGGAGCAT
* * *
3961 TTTATCTAAAGGTTTTGAACTTAAGACATCACCTAATCAGTATAATTGTTTATCATGCATATAAA
1 TTTATATAAAGGTTAT-AACTTAAGACATCACCTAATCAATATAATTGTTTATCATGCATATAAA
* ** * *
4026 TTTATGACCTATTTTATTGGAGATGATTTGAAACGAAAATATAATCAACTA-CTACAACCCTGTG
65 TTTATGAACTATTTTATTGGAGACAATTTGAAACGAAAATAGAATCAACGAGC-ACAACCCTGTG
*
4090 CATATACAAAGACAG
129 CACATACAAAGACAG
4105 GCACCGTCCA
Statistics
Matches: 122, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
177 15 0.12
178 107 0.88
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (177 bp):
TTTATATAAAGGTTATAACTTAAGACATCACCTAATCAATATAATTGTTTATCATGCATATAAAT
TTATGAACTATTTTATTGGAGACAATTTGAAACGAAAATAGAATCAACGAGCACAACCCTGTGCA
CATACAAAGACAGACACTGTTTATATAGTCTCATCTCACTGGAGCAT
Found at i:7684 original size:10 final size:10
Alignment explanation
Indices: 7671--7695 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
7661 GAACTTTTTA
7671 TATATTTTGT
1 TATATTTTGT
7681 TATATTTTGT
1 TATATTTTGT
7691 TATAT
1 TATAT
7696 ATTATCGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (10 bp):
TATATTTTGT
Found at i:12041 original size:21 final size:21
Alignment explanation
Indices: 12012--12055 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
12002 CTTGCACTAC
12012 CACAACAATATTGTAAATTGT
1 CACAACAATATTGTAAATTGT
* *
12033 CACATCAATATTGTAGATTGT
1 CACAACAATATTGTAAATTGT
12054 CA
1 CA
12056 TGTAAGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (21 bp):
CACAACAATATTGTAAATTGT
Found at i:19016 original size:16 final size:16
Alignment explanation
Indices: 18995--19026 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
18985 TATATATATA
18995 TATATTATGGATTATT
1 TATATTATGGATTATT
19011 TATATTATGGATTATT
1 TATATTATGGATTATT
19027 AGATTTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (16 bp):
TATATTATGGATTATT
Found at i:19579 original size:29 final size:29
Alignment explanation
Indices: 19540--19617 Score: 138
Period size: 29 Copynumber: 2.7 Consensus size: 29
19530 GGTGACCGGA
*
19540 ATATTTACCGATCTAACACCGGTCAGATT
1 ATATTTTCCGATCTAACACCGGTCAGATT
*
19569 ATATTTTCCGATCTAACACCTGTCAGATT
1 ATATTTTCCGATCTAACACCGGTCAGATT
19598 ATATTTTCCGATCTAACACC
1 ATATTTTCCGATCTAACACC
19618 CGTAGCAGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (29 bp):
ATATTTTCCGATCTAACACCGGTCAGATT
Found at i:20057 original size:14 final size:15
Alignment explanation
Indices: 20040--20086 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
20030 TCGTTATAAA
20040 TTTTATTATAATT-T
1 TTTTATTATAATTAT
*
20054 TTTTATTATACTTAT
1 TTTTATTATAATTAT
*
20069 TATTTATTATGATTAT
1 T-TTTATTATAATTAT
20085 TT
1 TT
20087 AAAAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 12 0.43
15 3 0.11
16 13 0.46
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (15 bp):
TTTTATTATAATTAT
Found at i:20125 original size:37 final size:37
Alignment explanation
Indices: 20057--20128 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
20047 ATAATTTTTT
* *
20057 TATTATACTTATTATTTATTATGATTATTTAAAAAAA
1 TATTATACTAATTATTTATAATGATTATTTAAAAAAA
* *
20094 TATTATACTAATTATTT-TCAATTATTTTTTAAAAA
1 TATTATACTAATTATTTAT-AATGATTATTTAAAAA
20129 GCAGGAGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 1 0.03
37 29 0.97
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (37 bp):
TATTATACTAATTATTTATAATGATTATTTAAAAAAA
Found at i:21366 original size:35 final size:34
Alignment explanation
Indices: 21281--21367 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
21271 ATTTGGTATT
*
21281 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
21315 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
21353 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
21368 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:21978 original size:18 final size:18
Alignment explanation
Indices: 21955--21994 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
21945 TGGAAAGGCG
*
21955 GCGGCATCATATATGGTT
1 GCGGCATCATAAATGGTT
21973 GCGGCATCATAAATGGTT
1 GCGGCATCATAAATGGTT
21991 GCGG
1 GCGG
21995 TGGCTGTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.28
Consensus pattern (18 bp):
GCGGCATCATAAATGGTT
Found at i:23670 original size:17 final size:18
Alignment explanation
Indices: 23648--23688 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
23638 AAATTATATT
23648 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
23665 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
23683 ATTAAA
1 AGTAAA
23689 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:23959 original size:51 final size:51
Alignment explanation
Indices: 23873--23985 Score: 129
Period size: 51 Copynumber: 2.2 Consensus size: 51
23863 CATGGATCAG
* * ** * *
23873 GGGGGCGCGCTATACCCACGTGTAAGCTATGTCAGCGTATAGCGCGGTACA
1 GGGGGCGCGCTATACCCACGTGGAAGCCAAATCAGCATATAGCGCGGGACA
* *
23924 GGGGGCGCGCTATACCCCACGTGGCA-CCAAATCAGCATATAGCGCGGGGCA
1 GGGGGCGCGCTATA-CCCACGTGGAAGCCAAATCAGCATATAGCGCGGGACA
*
23975 GGGAGCGCGCT
1 GGGGGCGCGCT
23986 TTACTGCTAC
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 43 0.83
52 9 0.17
ACGTcount: A:0.21, C:0.28, G:0.35, T:0.15
Consensus pattern (51 bp):
GGGGGCGCGCTATACCCACGTGGAAGCCAAATCAGCATATAGCGCGGGACA
Found at i:25936 original size:2 final size:2
Alignment explanation
Indices: 25929--25963 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25919 TCTTTATTTC
25929 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25964 GGGTTAGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29301 original size:23 final size:23
Alignment explanation
Indices: 29275--29335 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
29265 CAGCTCATAT
29275 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
29298 AATTGCACC-AGAGTGCCGCGTAG
1 AATTGCACCGA-AGTGCCACGTAG
*
29321 AATTGCACCGTAGTG
1 AATTGCACCGAAGTG
29336 TCATATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:32585 original size:18 final size:18
Alignment explanation
Indices: 32562--32601 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
32552 TTGTGATTCG
32562 AATAAGGATTT-TGCAAAT
1 AATAAGG-TTTATGCAAAT
*
32580 AATAAGGTTTATGCAAGT
1 AATAAGGTTTATGCAAAT
32598 AATA
1 AATA
32602 CTAACTTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (18 bp):
AATAAGGTTTATGCAAAT
Found at i:33698 original size:17 final size:17
Alignment explanation
Indices: 33659--33692 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
33649 TAAGATGAAG
* *
33659 AGAATAGAGGGAATTAA
1 AGAAAAGAGGGAAATAA
33676 AGAAAAGAGGGAAATAA
1 AGAAAAGAGGGAAATAA
33693 GTAAAATCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (17 bp):
AGAAAAGAGGGAAATAA
Found at i:35148 original size:31 final size:31
Alignment explanation
Indices: 35108--35203 Score: 131
Period size: 31 Copynumber: 3.1 Consensus size: 31
35098 AAGAGTCGAG
* *
35108 GGTTACCTATGTCTTTCGAGACATATTGATA
1 GGTTACCTATGTCCTTCGAGACATATGGATA
* *
35139 GTTTACCTATGTCCTTCGGGACATATGGATA
1 GGTTACCTATGTCCTTCGAGACATATGGATA
*
35170 GGTTACCTATGTTCTTCG-GAACATATGGATA
1 GGTTACCTATGTCCTTCGAG-ACATATGGATA
35201 GGT
1 GGT
35204 CATTCGGGAC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
30 1 0.02
31 57 0.98
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (31 bp):
GGTTACCTATGTCCTTCGAGACATATGGATA
Found at i:35921 original size:2 final size:2
Alignment explanation
Indices: 35914--35951 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
35904 GGGTGTTACA
35914 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
35952 GATTTAGGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36119 original size:25 final size:25
Alignment explanation
Indices: 36082--36140 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
36072 GATCTTAAAT
*
36082 TTGTGTAAAACTAAAGAATTTTACA
1 TTGTGTAAGACTAAAGAATTTTACA
36107 TTGTGTAAGACTAAAGAATTTTACA
1 TTGTGTAAGACTAAAGAATTTTACA
*
36132 TTATGTAAG
1 TTGTGTAAG
36141 TCCCATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (25 bp):
TTGTGTAAGACTAAAGAATTTTACA
Found at i:36242 original size:16 final size:16
Alignment explanation
Indices: 36201--36246 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
36191 AGCATAATAT
*
36201 TATAAATAATTAT-AA
1 TATAAATAAATATAAA
36216 T-TAAATTTAAATATAAA
1 TATAAA--TAAATATAAA
36233 TATAAATAAATATA
1 TATAAATAAATATA
36247 TTTAATTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
14 4 0.15
15 1 0.04
16 14 0.54
17 3 0.12
18 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TATAAATAAATATAAA
Found at i:37302 original size:22 final size:21
Alignment explanation
Indices: 37268--37308 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
37258 ATAATTATTT
37268 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
37289 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
37309 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:41703 original size:44 final size:44
Alignment explanation
Indices: 41637--41723 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
41627 TAGCAACAAA
*
41637 ATATAAAACAAATACATTCATTAAGAAGCATAATAAAATAAACT
1 ATATAAAACAAATACATCCATTAAGAAGCATAATAAAATAAACT
*
41681 ATATAAAACAAATACATCCATTAAGAAGCATAATGAAATAAAC
1 ATATAAAACAAATACATCCATTAAGAAGCATAATAAAATAAAC
41724 CAGAATTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.59, C:0.13, G:0.06, T:0.23
Consensus pattern (44 bp):
ATATAAAACAAATACATCCATTAAGAAGCATAATAAAATAAACT
Found at i:42050 original size:25 final size:25
Alignment explanation
Indices: 42002--42054 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
41992 TGGTGCGAAT
*
42002 TCCATGAAATAGTACCCGTATGCCA
1 TCCATGAAATAGTACACGTATGCCA
* *
42027 TCCATGAAATAGTACATGTCTGCCA
1 TCCATGAAATAGTACACGTATGCCA
42052 TCC
1 TCC
42055 CTAATTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (25 bp):
TCCATGAAATAGTACACGTATGCCA
Found at i:44816 original size:21 final size:20
Alignment explanation
Indices: 44792--44830 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44782 TACAAATGTT
*
44792 TTAAAAATATATATTAAAATA
1 TTAAAAATA-ATATAAAAATA
*
44813 TTAACAATAATATAAAAA
1 TTAAAAATAATATAAAAA
44831 AATAATCCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAAAATAATATAAAAATA
Found at i:44931 original size:29 final size:29
Alignment explanation
Indices: 44889--44988 Score: 146
Period size: 29 Copynumber: 3.4 Consensus size: 29
44879 TGCTTGTATT
44889 GGTCGCCATGCAGTCCAAGCGAGCTTATA
1 GGTCGCCATGCAGTCCAAGCGAGCTTATA
44918 GGTCGCCATGCAGTCCAAGCGAGCTTATA
1 GGTCGCCATGCAGTCCAAGCGAGCTTATA
* *** * *
44947 AGTCGCCATGCAGTCGTTGCGACCTTGTA
1 GGTCGCCATGCAGTCCAAGCGAGCTTATA
44976 GGTCGCCATGCAG
1 GGTCGCCATGCAG
44989 GTAGCTCGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.21, C:0.28, G:0.29, T:0.22
Consensus pattern (29 bp):
GGTCGCCATGCAGTCCAAGCGAGCTTATA
Found at i:45254 original size:114 final size:114
Alignment explanation
Indices: 45052--45267 Score: 362
Period size: 114 Copynumber: 1.9 Consensus size: 114
45042 CTCCCTCAGA
45052 CCTGTCTCCCTCATACATGCAACAATAATTTAACGTAAATTGAAGGCGTGAAAATGATGCAATAA
1 CCTGTCTCCCTCATACATGCAACAATAATTTAACGTAAATTGAAGGCGTGAAAATGATGCAATAA
*
45117 TTCACGTAAATTACAGGCGTGATTTGCAACAATAGTTCGACCCCTCCGC
66 TTCACGTAAATTACAGGCATGATTTGCAACAATAGTTCGACCCCTCCGC
* *
45166 CCTGTCTCCCTCATGCATGCAATAATAATTTAACGTAAATTGAAGGCGTGAAAATGCA-GCAATA
1 CCTGTCTCCCTCATACATGCAACAATAATTTAACGTAAATTGAAGGCGTGAAAATG-ATGCAATA
* * *
45230 ATTCACGTAAATTGCATGCATGATTTGCAGCAATAGTT
65 ATTCACGTAAATTACAGGCATGATTTGCAACAATAGTT
45268 TGACATGGTG
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
114 94 0.99
115 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (114 bp):
CCTGTCTCCCTCATACATGCAACAATAATTTAACGTAAATTGAAGGCGTGAAAATGATGCAATAA
TTCACGTAAATTACAGGCATGATTTGCAACAATAGTTCGACCCCTCCGC
Found at i:45599 original size:15 final size:15
Alignment explanation
Indices: 45579--45641 Score: 71
Period size: 15 Copynumber: 4.5 Consensus size: 15
45569 GGTACGTTTA
45579 AGAAGAAAGAAAGGG
1 AGAAGAAAGAAAGGG
*
45594 AGAAGAAGGAAA--G
1 AGAAGAAAGAAAGGG
45607 -GAAG-AAGAAAGGG
1 AGAAGAAAGAAAGGG
* *
45620 ATAAAAAAGAAAGGG
1 AGAAGAAAGAAAGGG
45635 AGAAGAA
1 AGAAGAA
45642 TGGGAGAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
11 5 0.13
12 4 0.11
13 2 0.05
14 2 0.05
15 25 0.66
ACGTcount: A:0.62, C:0.00, G:0.37, T:0.02
Consensus pattern (15 bp):
AGAAGAAAGAAAGGG
Found at i:45617 original size:26 final size:26
Alignment explanation
Indices: 45580--45671 Score: 121
Period size: 26 Copynumber: 3.5 Consensus size: 26
45570 GTACGTTTAA
*
45580 GAAGAAAGAAAGGGAGAAGAAGGAAAG
1 GAAG-AAGAAAGGGAGAAAAAGGAAAG
* *
45607 GAAGAAGAAAGGGATAAAAAAGAAAG
1 GAAGAAGAAAGGGAGAAAAAGGAAAG
* *
45633 GGAGAAGAATGGGAGAAAAAGGAAAG
1 GAAGAAGAAAGGGAGAAAAAGGAAAG
*
45659 GAATAAGAAAGGG
1 GAAGAAGAAAGGG
45672 TGAAGAAGAG
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 51 0.93
27 4 0.07
ACGTcount: A:0.59, C:0.00, G:0.38, T:0.03
Consensus pattern (26 bp):
GAAGAAGAAAGGGAGAAAAAGGAAAG
Found at i:45658 original size:41 final size:41
Alignment explanation
Indices: 45584--45669 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
45574 GTTTAAGAAG
* *
45584 AAAGAAAGGGAGAAGAAGGAAAGGAAGAAGAAAGGGATAAA
1 AAAGAAAGGGAGAAGAAGGAAAGGAAAAAGAAAGGAATAAA
* *
45625 AAAGAAAGGGAGAAGAATGG-GA-GAAAAAGGAAAGGAATAAG
1 AAAGAAAGGGAGAAGAA-GGAAAGGAAAAA-GAAAGGAATAAA
45666 AAAG
1 AAAG
45670 GGTGAAGAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 5 0.13
41 32 0.82
42 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.36, T:0.03
Consensus pattern (41 bp):
AAAGAAAGGGAGAAGAAGGAAAGGAAAAAGAAAGGAATAAA
Found at i:45758 original size:28 final size:29
Alignment explanation
Indices: 45718--45782 Score: 107
Period size: 28 Copynumber: 2.3 Consensus size: 29
45708 AATTTAAATC
*
45718 ATTAGTTTGTTAGTTTAAGTT-ATATTAT
1 ATTAGTTTGTTAGATTAAGTTAATATTAT
45746 ATTAGTTTGTTAGATTAAGTTAATATTAT
1 ATTAGTTTGTTAGATTAAGTTAATATTAT
45775 ATTA-TTTG
1 ATTAGTTTG
45783 AAAAATTAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 24 0.69
29 11 0.31
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (29 bp):
ATTAGTTTGTTAGATTAAGTTAATATTAT
Found at i:45790 original size:28 final size:29
Alignment explanation
Indices: 45732--45796 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
45722 GTTTGTTAGT
** *
45732 TTAAGTT-ATATTATATTAGTTTGTTAGA
1 TTAAGTTAATATTATATTAGTTTGAAAAA
45760 TTAAGTTAATATTATATTA-TTTGAAAAA
1 TTAAGTTAATATTATATTAGTTTGAAAAA
45788 TT-AGTTAAT
1 TTAAGTTAAT
45797 TAGTTTGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 7 0.21
28 15 0.45
29 11 0.33
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (29 bp):
TTAAGTTAATATTATATTAGTTTGAAAAA
Done.