Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000557.1 Hibiscus syriacus cultivar Beakdansim tig00001088_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: 57514
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4127 original size:24 final size:24
Alignment explanation
Indices: 4095--4177 Score: 139
Period size: 24 Copynumber: 3.4 Consensus size: 24
4085 GCTGATACCA
4095 GAATGCCGCCTGATAACAGCGAAT
1 GAATGCCGCCTGATAACAGCGAAT
4119 GAATGCCGCCTGATAACAGCGAAT
1 GAATGCCGCCTGATAACAGCGAAT
* *
4143 GAATGGCGCCTGTTAACAGCGAAT
1 GAATGCCGCCTGATAACAGCGAAT
4167 GAATGGCCGCC
1 GAAT-GCCGCC
4178 GAGAAAGAAG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 50 0.91
25 5 0.09
ACGTcount: A:0.30, C:0.25, G:0.28, T:0.17
Consensus pattern (24 bp):
GAATGCCGCCTGATAACAGCGAAT
Found at i:23236 original size:2 final size:2
Alignment explanation
Indices: 23231--23263 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
23221 GTGTGTGTGT
*
23231 GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
23264 CATGCGCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:26781 original size:8 final size:8
Alignment explanation
Indices: 26768--26908 Score: 210
Period size: 8 Copynumber: 17.6 Consensus size: 8
26758 ACAAGATAAT
*
26768 ATGTATGC
1 ATGTACGC
*
26776 ATGTATGC
1 ATGTACGC
26784 ATGTACGC
1 ATGTACGC
*
26792 ATGTATGC
1 ATGTACGC
26800 ATGTACGC
1 ATGTACGC
*
26808 ATGTATGC
1 ATGTACGC
26816 ATGTACGC
1 ATGTACGC
*
26824 ATGTATGC
1 ATGTACGC
26832 ATGTACGC
1 ATGTACGC
*
26840 ATGTATGC
1 ATGTACGC
26848 ATGTACGC
1 ATGTACGC
*
26856 ATGTATGC
1 ATGTACGC
26864 ATGTACGC
1 ATGTACGC
26872 ATGTACGC
1 ATGTACGC
26880 ATGTACGC
1 ATGTACGC
*
26888 ATGTATGC
1 ATGTACGC
26896 ATGTACGC
1 ATGTACGC
26904 ATGTA
1 ATGTA
26909 TATATGCGTG
Statistics
Matches: 120, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 120 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (8 bp):
ATGTACGC
Found at i:26793 original size:16 final size:16
Alignment explanation
Indices: 26768--26909 Score: 266
Period size: 16 Copynumber: 8.9 Consensus size: 16
26758 ACAAGATAAT
*
26768 ATGTATGCATGTATGC
1 ATGTACGCATGTATGC
26784 ATGTACGCATGTATGC
1 ATGTACGCATGTATGC
26800 ATGTACGCATGTATGC
1 ATGTACGCATGTATGC
26816 ATGTACGCATGTATGC
1 ATGTACGCATGTATGC
26832 ATGTACGCATGTATGC
1 ATGTACGCATGTATGC
26848 ATGTACGCATGTATGC
1 ATGTACGCATGTATGC
*
26864 ATGTACGCATGTACGC
1 ATGTACGCATGTATGC
26880 ATGTACGCATGTATGC
1 ATGTACGCATGTATGC
26896 ATGTACGCATGTAT
1 ATGTACGCATGTAT
26910 ATATGCGTGC
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
16 123 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (16 bp):
ATGTACGCATGTATGC
Found at i:26940 original size:36 final size:36
Alignment explanation
Indices: 26889--26998 Score: 175
Period size: 36 Copynumber: 3.1 Consensus size: 36
26879 CATGTACGCA
*
26889 TGTATGCATGTACGCATGTATATATGCGTGCGTGCG
1 TGTACGCATGTACGCATGTATATATGCGTGCGTGCG
26925 TGTACGCATGTACGCATGTATATATGCGTGCGTGCG
1 TGTACGCATGTACGCATGTATATATGCGTGCGTGCG
* ***
26961 TGTACGCATGTACGCATATATGCGTGCGTGCGTGCG
1 TGTACGCATGTACGCATGTATATATGCGTGCGTGCG
26997 TG
1 TG
26999 CGTGCGTGCG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 69 1.00
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (36 bp):
TGTACGCATGTACGCATGTATATATGCGTGCGTGCG
Found at i:26990 original size:4 final size:4
Alignment explanation
Indices: 26981--28383 Score: 2792
Period size: 4 Copynumber: 351.2 Consensus size: 4
26971 TACGCATATA
26981 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27029 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27077 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27125 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27173 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27221 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27269 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27317 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27365 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27413 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27461 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27509 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27557 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27605 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27653 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27701 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27749 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27797 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG T--G TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27843 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27891 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27939 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
27987 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
28035 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
28083 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
28131 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
28179 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
28227 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
28275 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
28323 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
1 TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG TGCG
28371 TGCG TGCG TGCG T
1 TGCG TGCG TGCG T
28384 ACTGTTGGCA
Statistics
Matches: 1397, Mismatches: 0, Indels: 4
1.00 0.00 0.00
Matches are distributed among these distances:
2 2 0.00
4 1395 1.00
ACGTcount: A:0.00, C:0.25, G:0.50, T:0.25
Consensus pattern (4 bp):
TGCG
Found at i:32917 original size:21 final size:21
Alignment explanation
Indices: 32892--32961 Score: 106
Period size: 21 Copynumber: 3.3 Consensus size: 21
32882 TCATGAACAG
*
32892 TGCTACATTGTA-TCGATGCAC
1 TGCTACAGTGTACT-GATGCAC
*
32913 TGCTACAGTGTACTGATGTAC
1 TGCTACAGTGTACTGATGCAC
32934 TGCTACAGTGTACTGATGCAC
1 TGCTACAGTGTACTGATGCAC
32955 TGCTACA
1 TGCTACA
32962 ATACGGCTAC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
21 44 0.98
22 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.31
Consensus pattern (21 bp):
TGCTACAGTGTACTGATGCAC
Found at i:33514 original size:22 final size:22
Alignment explanation
Indices: 33489--33530 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
33479 TATGAAATTT
*
33489 TGTCCCGAATGACCTGTGAATA
1 TGTCCCGAATGACCTATGAATA
*
33511 TGTCTCGAATGACCTATGAA
1 TGTCCCGAATGACCTATGAA
33531 ACCCTCGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (22 bp):
TGTCCCGAATGACCTATGAATA
Found at i:34964 original size:3 final size:3
Alignment explanation
Indices: 34956--34998 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
34946 TTCACGGTGG
*
34956 AGA AGA AGA A-A GGA AGA AGA AGA AGA AGA AGA AGA AGA GAGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA A
34999 TTGTGTGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 32 0.89
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:38232 original size:204 final size:203
Alignment explanation
Indices: 37919--38288 Score: 632
Period size: 204 Copynumber: 1.8 Consensus size: 203
37909 AGGACATTAC
37919 TCAAAACTGAAAAATAAAATTTCTCTTACCTCTAAATGGGGTACACAACCATGGAGCTAAAATGG
1 TCAAAACTGAAAAATAAAATTTCTCTTACCTCTAAATGGGGTACACAACCATGGAGCTAAAATGG
37984 CTAAGTTTTCATGAAATTTATAATGAATTTCATGTTAATTTAACCTTATATTAAAGCTTAAATGA
66 CTAAGTTTTCATGAAATTTATAATGAATTTCATGTTAATTTAACCTTATATTAAAGCTTAAATGA
38049 ATTAAAAATTCATTTAATGTGAAATGTTTATTTTACTATTTCATGACATGATTCAAAATCTAAAA
131 ATTAAAAATTCATTTAATGTGAAATGTTTATTTTACTATTTCATGACATGATTCAAAATCTAAAA
38114 GAAATTGT
196 GAAATTGT
* * * * * ***
38122 TCAAAATTGGAAAATAAATTTTCTCTTATCTCTGAATGGGGTACATGGCCATGGAGCTAAAAATG
1 TCAAAACTGAAAAATAAAATTTCTCTTACCTCTAAATGGGGTACACAACCATGGAGCT-AAAATG
* * *
38187 GCTAAGTTTTCATGAAATTTCTAATGAATTTTATGTTAATTTAACCTTATATTAAAGTTTAAATG
65 GCTAAGTTTTCATGAAATTTATAATGAATTTCATGTTAATTTAACCTTATATTAAAGCTTAAATG
38252 AATTAAAAATTCATTTAATGTGAAATGTTTATTTTAC
130 AATTAAAAATTCATTTAATGTGAAATGTTTATTTTAC
38289 AATTAATGAA
Statistics
Matches: 155, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
203 50 0.32
204 105 0.68
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (203 bp):
TCAAAACTGAAAAATAAAATTTCTCTTACCTCTAAATGGGGTACACAACCATGGAGCTAAAATGG
CTAAGTTTTCATGAAATTTATAATGAATTTCATGTTAATTTAACCTTATATTAAAGCTTAAATGA
ATTAAAAATTCATTTAATGTGAAATGTTTATTTTACTATTTCATGACATGATTCAAAATCTAAAA
GAAATTGT
Found at i:46437 original size:20 final size:20
Alignment explanation
Indices: 46402--46449 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
46392 TTGATTATCC
46402 AAAAAAAATCATAAATT-TT
1 AAAAAAAATCATAAATTCTT
*
46421 AAAAAAAATGATCAAATTCCTT
1 AAAAAAAATCAT-AAATT-CTT
46443 AAAAAAA
1 AAAAAAA
46450 TTAATCATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 11 0.44
20 5 0.20
22 9 0.36
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAAAAAATCATAAATTCTT
Found at i:48278 original size:14 final size:14
Alignment explanation
Indices: 48260--48327 Score: 118
Period size: 14 Copynumber: 4.9 Consensus size: 14
48250 GCTGGGCATT
*
48260 CATCCGACCGAGGT
1 CATCCGACCGAGGC
48274 CATCCGACCGAGGC
1 CATCCGACCGAGGC
48288 CATCCGACCGAGGC
1 CATCCGACCGAGGC
48302 CATCCGACCGAGGC
1 CATCCGACCGAGGC
*
48316 CATCCGAACGAG
1 CATCCGACCGAG
48328 CTATGCGAGG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 52 1.00
ACGTcount: A:0.24, C:0.40, G:0.28, T:0.09
Consensus pattern (14 bp):
CATCCGACCGAGGC
Found at i:48402 original size:29 final size:23
Alignment explanation
Indices: 48310--48381 Score: 117
Period size: 23 Copynumber: 3.1 Consensus size: 23
48300 GCCATCCGAC
* * *
48310 CGAGGCCATCCGAACGAGCTATG
1 CGAGGGCAACCGAGCGAGCTATG
48333 CGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCAACCGAGCGAGCTATG
48356 CGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCAACCGAGCGAGCTATG
48379 CGA
1 CGA
48382 ATCCGAGGGC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.26, C:0.28, G:0.36, T:0.10
Consensus pattern (23 bp):
CGAGGGCAACCGAGCGAGCTATG
Found at i:48415 original size:29 final size:28
Alignment explanation
Indices: 48333--48402 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 28
48323 ACGAGCTATG
*
48333 CGAGGGCAACCGAGCGAGCT-----ATG
1 CGAGGGCAACCGAGCGAGCTAGGCGATC
*
48356 CGAGGGCAACCGAGCGAGCTATGCGAATC
1 CGAGGGCAACCGAGCGAGCTAGGCG-ATC
48385 CGAGGGCAACCGAGCGAG
1 CGAGGGCAACCGAGCGAG
48403 GGTAGGTCGT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
23 20 0.50
29 20 0.50
ACGTcount: A:0.27, C:0.27, G:0.39, T:0.07
Consensus pattern (28 bp):
CGAGGGCAACCGAGCGAGCTAGGCGATC
Found at i:48476 original size:33 final size:33
Alignment explanation
Indices: 48435--48528 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
48425 GCGACCTACC
* *
48435 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGTTGACCTCGGATGCCCTCGCATAG
48468 CTCGCTCGGTTGACCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGACCTCGGATGCCCTCGCATAG
* * * *
48501 CTCGGTCGGATGGCCTCGGATGGCCTCG
1 CTCGCTCGGTTGACCTCGGATGCCCTCG
48529 GATGCTTCGG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.10, C:0.36, G:0.30, T:0.24
Consensus pattern (33 bp):
CTCGCTCGGTTGACCTCGGATGCCCTCGCATAG
Found at i:48494 original size:10 final size:10
Alignment explanation
Indices: 48439--48554 Score: 72
Period size: 10 Copynumber: 11.1 Consensus size: 10
48429 CCTACCCTCG
*
48439 CTCGGTTGCC
1 CTCGGATGCC
*
48449 CTCGGATTCC
1 CTCGGATGCC
*
48459 CTCGCATAGCTC
1 CTCGGAT-GC-C
* *
48471 GCTCGGTTGAC
1 -CTCGGATGCC
48482 CTCGGATGCC
1 CTCGGATGCC
*
48492 CTCGCATAGCTC
1 CTCGGAT-GC-C
* *
48504 GGTCGGATGGC
1 -CTCGGATGCC
*
48515 CTCGGATGGC
1 CTCGGATGCC
48525 CTCGGATG-C
1 CTCGGATGCC
* *
48534 TTCGGATGGC
1 CTCGGATGCC
48544 CTCGGATGCC
1 CTCGGATGCC
48554 C
1 C
48555 AGCGTGTTGG
Statistics
Matches: 82, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
9 8 0.10
10 55 0.67
11 5 0.06
12 4 0.05
13 10 0.12
ACGTcount: A:0.10, C:0.34, G:0.31, T:0.24
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:48540 original size:19 final size:19
Alignment explanation
Indices: 48506--48553 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
48496 CATAGCTCGG
48506 TCGGATGGCCTCGGATGGCC
1 TCGGAT-GCCTCGGATGGCC
*
48526 TCGGATGCTTCGGATGGCC
1 TCGGATGCCTCGGATGGCC
48545 TCGGATGCC
1 TCGGATGCC
48554 CAGCGTGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.10, C:0.29, G:0.38, T:0.23
Consensus pattern (19 bp):
TCGGATGCCTCGGATGGCC
Found at i:48624 original size:29 final size:29
Alignment explanation
Indices: 48591--48648 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
48581 GCAATCTCTT
*
48591 GTAGGTCGCCGGGAAGACATGACGACCTA
1 GTAGGTCGCCCGGAAGACATGACGACCTA
* *
48620 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGGTCGCCCGGAAGACATGACGACCTA
48649 CGGCCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.26, G:0.36, T:0.14
Consensus pattern (29 bp):
GTAGGTCGCCCGGAAGACATGACGACCTA
Found at i:49805 original size:16 final size:16
Alignment explanation
Indices: 49773--49826 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
49763 GAGAGAGAGG
49773 GAAAAATATATAATAATA
1 GAAAAAT-TA-AATAATA
49791 GAAAAATTAAATAAT-
1 GAAAAATTAAATAATA
*
49806 G-AAGA-TAAATAATAA
1 GAAAAATTAAATAAT-A
49821 GAAAAA
1 GAAAAA
49827 GAGTAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 8 0.26
14 3 0.10
15 2 0.06
16 9 0.29
17 2 0.06
18 7 0.23
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (16 bp):
GAAAAATTAAATAATA
Found at i:49814 original size:13 final size:12
Alignment explanation
Indices: 49798--49849 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
49788 ATAGAAAAAT
49798 TAAATAATGAAGA
1 TAAATAAT-AAGA
49811 TAAATAATAAGA
1 TAAATAATAAGA
* * *
49823 AAAAGAGTAA-A
1 TAAATAATAAGA
*
49834 GAAATAATAAGA
1 TAAATAATAAGA
49846 TAAA
1 TAAA
49850 ATACAAAATG
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
11 8 0.26
12 15 0.48
13 8 0.26
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.19
Consensus pattern (12 bp):
TAAATAATAAGA
Found at i:51924 original size:105 final size:105
Alignment explanation
Indices: 51737--52640 Score: 1592
Period size: 105 Copynumber: 8.7 Consensus size: 105
51727 AGGTATGATA
* *
51737 CCCTTCG-CAGTGAAGTCGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAAGTTGAAA
1 CCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* *
51801 TTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGT
65 TTGGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGCGGT
51842 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
*
51907 TGGCTCTGAATTAGAGAAATGTTTGGTGACAACCAGCGGT
66 TGGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGCGGT
*
51947 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
* *
52012 TGGCTCTGAATTGGAGAGATGTTTGGTGACAAACAGCGGT
66 TGGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGCGGT
52052 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
52117 TGG--CTGAATTGGAGAAATGTTTGGTGACAACCAGCGGT
66 TGGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGCGGT
*
52155 -CCTTCGTCGTGAAGCTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
*
52219 TGGCTCTGAATTGGAGAGATGTTTGGTGACAACCAGCGGT
66 TGGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGCGGT
*
52259 CCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
52324 TGGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGCGGT
66 TGGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGCGGT
*
52364 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGTTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
* *
52429 TGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGT
66 TGGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGCGGT
52469 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC-A-ATCCTTCGTTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
* *
52532 TGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGT
66 TGGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGCGGT
52572 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC-A-ATCCTTCGTTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
52635 T-GCTCT
66 TGGCTCT
52641 AGCTAAAACC
Statistics
Matches: 774, Mismatches: 21, Indels: 11
0.96 0.03 0.01
Matches are distributed among these distances:
102 71 0.09
103 159 0.21
104 35 0.05
105 508 0.66
106 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (105 bp):
CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
TGGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGCGGT
Found at i:52543 original size:417 final size:417
Alignment explanation
Indices: 51737--52640 Score: 1579
Period size: 417 Copynumber: 2.2 Consensus size: 417
51727 AGGTATGATA
*
51737 CCCTTCG-CAGTGAAGTCGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAAGTTGAAA
1 CCCTTCGTC-GTGAAGT-GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* * *
51801 TTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
64 TTGGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTG
51866 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTAGAGAAATGTTT
129 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTAGAGAAATGTTT
*
51931 GGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
194 GGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTC
*
51996 ATTGTGAAGTTGAAATTGGCTCTGAATTGGAGAGATGTTTGGTGACAAACAGCGGTCCCTTCGTC
259 ATTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAACAGCGGTCCCTTCGTC
52061 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTGAAT
324 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTGAAT
52126 TGGAGAAATGTTTGGTGACAACCAGCGGT
389 TGGAGAAATGTTTGGTGACAACCAGCGGT
52155 -CCTTCGTCGTGAAGCTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAG-TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
*
52219 TGGCTCTGAATTGGAGAGATGTTTGGTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGC
65 TGGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGC
*
52284 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTG
130 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTAGAGAAATGTTTG
*
52349 GTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCG
195 GTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCA
* * *
52414 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
260 TTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAACAGCGGTCCCTTCGTCG
52479 TGAAGTTGAACTTGCGTTGTCTGGAGTCC-A-ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
325 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG--CTGAA
* *
52542 TTTGAGAAATGTTTGTTGACAACCAGCGGT
388 TTGGAGAAATGTTTGGTGACAACCAGCGGT
52572 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC-A-ATCCTTCGTTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAG-TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
52635 T-GCTCT
65 TGGCTCT
52641 AGCTAAAACC
Statistics
Matches: 466, Mismatches: 15, Indels: 13
0.94 0.03 0.03
Matches are distributed among these distances:
415 31 0.07
416 25 0.05
417 371 0.80
418 39 0.08
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (417 bp):
CCCTTCGTCGTGAAGTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
GGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCG
TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTAGAGAAATGTTTGG
TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCAT
TGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAAACAGCGGTCCCTTCGTCGT
GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTGAATTG
GAGAAATGTTTGGTGACAACCAGCGGT
Done.