Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009161.1 Hibiscus syriacus cultivar Beakdansim tig00112689_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: 57013
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Found at i:10308 original size:21 final size:21
Alignment explanation
Indices: 10284--10323 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
10274 TTTTCAAATG
10284 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
10305 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
10324 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:10429 original size:17 final size:19
Alignment explanation
Indices: 10401--10449 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
10391 ATTTTTTAAA
10401 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
10419 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
10438 CACCGATGCACT
1 CATCGATGCACT
10450 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:20162 original size:260 final size:260
Alignment explanation
Indices: 19641--20901 Score: 1905
Period size: 260 Copynumber: 4.8 Consensus size: 260
19631 CAAGTTATTT
* * * * * *** * *
19641 TGAAAATAAGAAATCGATTTCCAAAGTTTCTCATTTATTCCTTTTTGAAAAATAAAATTTTTGAA
1 TGAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAAT-GTTCAAG-AAAATGAAATTCTTGAA
* * *
19706 AAGTAAGAAAGCGATTTTCAAAATTTCTTACCCAGTAAATTATTTCCCAAATTTGTAAATCCTTC
64 AAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCCAAATTTGTAAATCCTTC
* * * * * *
19771 TGATCATCTGTCAGTCTTTCGAGCGTGATACTTAAATCCTTATGGTCATTTGTCAGTCTTTTGAG
129 GGGTCATCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGTCAGTCTTTTGAG
* *
19836 CAAGATGATAAGTCCTTAGGGCCATCCGTCAGACCATTGGGTAGGATTTTTACACGTGATTTTCA
194 CAAGATGATAAGTCCTTAGGGCCATCCGTCAGACCATTGGGTAGGATGTTTACACATGATTTTCA
*
19901 TA
259 CA
*
19903 TGAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTCAATAAAATGAAATTCTTGAAAA
1 TGAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATGAAATTCTTGAAAA
* * *
19968 GTAAGAAAGTGATTTCCAAAGTGTCTTACCTAGTAAATTATTTCCCAAATTTGTAAACCCTTCGG
66 GTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCCAAATTTGTAAATCCTTCGG
* **
20033 ATCATCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGTCAGTCTTTTGAATA
131 GTCATCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGTCAGTCTTTTGAGCA
* * * * *
20098 AGATGATAAGTCATTAGGGCCATCCTTCAGACAATTGGGTAGGATGTTTACACGTGATTTTCATA
196 AGATGATAAGTCCTTAGGGCCATCCGTCAGACCATTGGGTAGGATGTTTACACATGATTTTCACA
* *
20163 TGAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATGAAATTATTGAAAA
1 TGAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATGAAATTCTTGAAAA
* * *
20228 GTAAGAAAGCGATTTCCAAAGTTTCTTA-CCAGTAAATTATTTCCCAAATTTGTAAATTCTTTGG
66 GTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCCAAATTTGTAAATCCTTCGG
* *
20292 GTCATATGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGTTAGTCTTTTGAGCA
131 GTCATCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGTCAGTCTTTTGAGCA
* * *
20357 AGATAATAAGTCCTTAGGGCCATCCGTCAGACCTTTGGGTAGGATGTTTACAAATGATTTTCACA
196 AGATGATAAGTCCTTAGGGCCATCCGTCAGACCATTGGGTAGGATGTTTACACATGATTTTCACA
*
20422 TGAAAATGAGAAAGCGATTTTCAAAGTTCCTCATTTAATGTTCAAGAAAATGAAATTCTTGAAAA
1 TGAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATGAAATTCTTGAAAA
* *
20487 GTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAATTATTTCCCAAATTTGTAAATCCTTGGG
66 GTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCCAAATTTGTAAATCCTTCGG
* * *
20552 GTCATCCGTCAGTCTTTTGAGCATGGTGCTTAAATCCTTAGGGTCATCTGTCAGTCTTTTGAGCA
131 GTCATCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGTCAGTCTTTTGAGCA
** * *
20617 AGATGATAAGTCCTTAGGGCCATCTTTCAGACCTTTGGGTATGATGTTTACACATGATTTTCACA
196 AGATGATAAGTCCTTAGGGCCATCCGTCAGACCATTGGGTAGGATGTTTACACATGATTTTCACA
* *
20682 TGAAAATGAGAAAGTGATTTTCAAAGTTTATCATTTAATGTTCAAGAAAATGAAATTCTTGAAAA
1 TGAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATGAAATTCTTGAAAA
* * * *
20747 GTAAGAAA-TCAATTTCCAAAGTTTCTTACCCAGTAAATTATTTCTCAAATTTGTAAATCTTTAG
66 GTAAGAAAGT-GATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCCAAATTTGTAAATCCTTCG
* *
20811 GGTCATCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGTCAGTCTTTTAAGT
130 GGTCATCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGTCAGTCTTTTGAGC
* *
20876 AAGATGATAAGTCCTTATGGTCATCC
195 AAGATGATAAGTCCTTAGGGCCATCC
20902 ATAAGACGAG
Statistics
Matches: 914, Mismatches: 83, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
259 239 0.26
260 638 0.70
261 2 0.00
262 35 0.04
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Consensus pattern (260 bp):
TGAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATGAAATTCTTGAAAA
GTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCCAAATTTGTAAATCCTTCGG
GTCATCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGTCAGTCTTTTGAGCA
AGATGATAAGTCCTTAGGGCCATCCGTCAGACCATTGGGTAGGATGTTTACACATGATTTTCACA
Found at i:20718 original size:519 final size:520
Alignment explanation
Indices: 19689--20901 Score: 1982
Period size: 519 Copynumber: 2.3 Consensus size: 520
19679 TCCTTTTTGA
* * * *
19689 AAAATAAAATTTTTGAAAAGTAAGAAAGCGATTTTCAAAATTTCTTACCCAGTAAATTATTTCCC
1 AAAATGAAATTATTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCC
* * * * *
19754 AAATTTGTAAATCCTTCT-GATCATCTGTCAGTCTTTCGAGCGTGATACTTAAATCCTTATGGTC
66 AAATTTGTAAATTCTT-TGGGTCATCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTC
*
19818 ATTTGTCAGTCTTTTGAGCAAGATGATAAGTCCTTAGGGCCATCCGTCAGACCATTGGGTAGGAT
130 ATCTGTCAGTCTTTTGAGCAAGATGATAAGTCCTTAGGGCCATCCGTCAGACCATTGGGTAGGAT
* ** * *
19883 TTTTACACGTGATTTTCATATGAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTCAA
195 GTTTACAAATGATTTTCACATGAAAATGAGAAAGCGATTTTCAAAGTTCCTCATTTAATGTTCAA
*
19948 TAAAATGAAATTCTTGAAAAGTAAGAAAGTGATTTCCAAAGTGTCTTACCTAGTAAATTATTTCC
260 GAAAATGAAATTCTTGAAAAGTAAGAAAGTGATTTCCAAAGTGTCTTACCTAGTAAATTATTTCC
*
20013 CAAATTTGTAAACCCTTCGGATCATCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTC
325 CAAATTTGTAAACCCTTCGGATCATCCGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTC
*
20078 ATCTGTCAGTCTTTTGAATAAGATGATAAGTCATTAGGGCCATCCTTCAGACAATTGGGTAGGAT
390 ATCTGTCAGTCTTTTGAACAAGATGATAAGTCATTAGGGCCATCCTTCAGACAATTGGGTAGGAT
* * *
20143 GTTTACACGTGATTTTCATATGAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATGTTCAA
455 GTTTACACATGATTTTCACATGAAAATGAGAAAGTGATTTTCAAAGTTTATCATTTAATGTTCAA
20208 G
520 G
20209 AAAATGAAATTATTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTA-CCAGTAAATTATTTCCC
1 AAAATGAAATTATTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCC
*
20273 AAATTTGTAAATTCTTTGGGTCATATGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCA
66 AAATTTGTAAATTCTTTGGGTCATCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCA
* * *
20338 TCTGTTAGTCTTTTGAGCAAGATAATAAGTCCTTAGGGCCATCCGTCAGACCTTTGGGTAGGATG
131 TCTGTCAGTCTTTTGAGCAAGATGATAAGTCCTTAGGGCCATCCGTCAGACCATTGGGTAGGATG
20403 TTTACAAATGATTTTCACATGAAAATGAGAAAGCGATTTTCAAAGTTCCTCATTTAATGTTCAAG
196 TTTACAAATGATTTTCACATGAAAATGAGAAAGCGATTTTCAAAGTTCCTCATTTAATGTTCAAG
*
20468 AAAATGAAATTCTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAATTATTTCCC
261 AAAATGAAATTCTTGAAAAGTAAGAAAGTGATTTCCAAAGTGTCTTACCTAGTAAATTATTTCCC
* * * * *
20533 AAATTTGTAAATCCTTGGGGTCATCCGTCAGTCTTTTGAGCATGGTGCTTAAATCCTTAGGGTCA
326 AAATTTGTAAACCCTTCGGATCATCCGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCA
* * * ** *
20598 TCTGTCAGTCTTTTGAGCAAGATGATAAGTCCTTAGGGCCATCTTTCAGACCTTTGGGTATGATG
391 TCTGTCAGTCTTTTGAACAAGATGATAAGTCATTAGGGCCATCCTTCAGACAATTGGGTAGGATG
20663 TTTACACATGATTTTCACATGAAAATGAGAAAGTGATTTTCAAAGTTTATCATTTAATGTTCAAG
456 TTTACACATGATTTTCACATGAAAATGAGAAAGTGATTTTCAAAGTTTATCATTTAATGTTCAAG
* * * *
20728 AAAATGAAATTCTTGAAAAGTAAGAAATCAATTTCCAAAGTTTCTTACCCAGTAAATTATTTCTC
1 AAAATGAAATTATTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCC
20793 AAATTTGTAAA-TCTTTAGGGTCATCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTC
66 AAATTTGTAAATTCTTT-GGGTCATCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTC
* * * *
20857 ATCTGTCAGTCTTTTAAGTAAGATGATAAGTCCTTATGGTCATCC
130 ATCTGTCAGTCTTTTGAGCAAGATGATAAGTCCTTAGGGCCATCC
20902 ATAAGACGAG
Statistics
Matches: 642, Mismatches: 48, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
518 1 0.00
519 486 0.76
520 155 0.24
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (520 bp):
AAAATGAAATTATTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAATTATTTCCC
AAATTTGTAAATTCTTTGGGTCATCTGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCA
TCTGTCAGTCTTTTGAGCAAGATGATAAGTCCTTAGGGCCATCCGTCAGACCATTGGGTAGGATG
TTTACAAATGATTTTCACATGAAAATGAGAAAGCGATTTTCAAAGTTCCTCATTTAATGTTCAAG
AAAATGAAATTCTTGAAAAGTAAGAAAGTGATTTCCAAAGTGTCTTACCTAGTAAATTATTTCCC
AAATTTGTAAACCCTTCGGATCATCCGTCAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCA
TCTGTCAGTCTTTTGAACAAGATGATAAGTCATTAGGGCCATCCTTCAGACAATTGGGTAGGATG
TTTACACATGATTTTCACATGAAAATGAGAAAGTGATTTTCAAAGTTTATCATTTAATGTTCAAG
Found at i:21099 original size:3 final size:3
Alignment explanation
Indices: 21091--21152 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
21081 CGAGTTTACG
21091 TAT TAT TAT TAT TAT TAT TAT 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
21139 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
21153 CAAAACCCAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:25129 original size:40 final size:39
Alignment explanation
Indices: 25084--25171 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 39
25074 AGTTAAAAGA
*
25084 AATAATTTAGATTGTTACAATGAAATAATTTAAAAAAATT
1 AATAATTTAGAATGTTACAATGAAATAATTT-AAAAAATT
* * ** *
25124 AATAATTTAGAATGTTATAGTGAAATGGTTTAAGAAATT
1 AATAATTTAGAATGTTACAATGAAATAATTTAAAAAATT
*
25163 AAGAATTTA
1 AATAATTTA
25172 AAATATTAGG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 15 0.37
40 26 0.63
ACGTcount: A:0.49, C:0.01, G:0.12, T:0.38
Consensus pattern (39 bp):
AATAATTTAGAATGTTACAATGAAATAATTTAAAAAATT
Found at i:34241 original size:36 final size:36
Alignment explanation
Indices: 34199--34274 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
34189 TTATAGCTAA
*
34199 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
34235 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
34271 AAAA
1 AAAA
34275 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:38770 original size:15 final size:15
Alignment explanation
Indices: 38752--38781 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38742 CCACGGTGCT
38752 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
38767 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
38782 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:39244 original size:35 final size:35
Alignment explanation
Indices: 39203--39278 Score: 143
Period size: 35 Copynumber: 2.2 Consensus size: 35
39193 TATAGCTAAA
*
39203 AAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
39238 AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
39273 AAAATC
1 AAAATC
39279 CCGAAAATCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.33
Consensus pattern (35 bp):
AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:43770 original size:15 final size:15
Alignment explanation
Indices: 43752--43781 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
43742 CCACGGTGCT
43752 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
43767 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
43782 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:44244 original size:36 final size:36
Alignment explanation
Indices: 44202--44277 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
44192 TATAGCTAAA
*
44202 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
44238 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
44274 AAAA
1 AAAA
44278 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:48764 original size:15 final size:15
Alignment explanation
Indices: 48746--48775 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
48736 CCACGGTGCT
48746 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
48761 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
48776 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:49237 original size:36 final size:36
Alignment explanation
Indices: 49195--49270 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
49185 TTATAGCTAA
*
49195 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
49231 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
49267 AAAA
1 AAAA
49271 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:53426 original size:2 final size:2
Alignment explanation
Indices: 53421--53456 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
53411 ATTATTTAGA
53421 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
53457 TAAAGAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53948 original size:13 final size:13
Alignment explanation
Indices: 53930--53975 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
53920 AATCTCAACC
53930 ATCTATTTCACTA
1 ATCTATTTCACTA
*
53943 ATCTATTTCACTC
1 ATCTATTTCACTA
53956 ATCTATTGTC-CTA
1 ATCTATT-TCACTA
53969 ACTCTAT
1 A-TCTAT
53976 GAAAACTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 22 0.76
14 7 0.24
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.46
Consensus pattern (13 bp):
ATCTATTTCACTA
Done.