Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402412.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5491.0, 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, 625
Length: 1042
ACGTcount: A:0.10, C:0.40, G:0.38, T:0.12
Found at i:96 original size:18 final size:18
Alignment explanation
Indices: 75--110 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
65 CGCCGCGGAG
75 CCCGACGCA-TCCCACGCA
1 CCCGACGCAGT-CCACGCA
93 CCCGACGCAGTCCACGCA
1 CCCGACGCAGTCCACGCA
111 GTCCACGCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.22, C:0.53, G:0.19, T:0.06
Consensus pattern (18 bp):
CCCGACGCAGTCCACGCA
Found at i:109 original size:27 final size:27
Alignment explanation
Indices: 76--137 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
66 GCCGCGGAGC
76 CCGACGCA-TCCCACGCACCCGACGCAGT
1 CCGACGCAGT-CCACGCACCCGACGCA-T
* *
104 CC-ACGCAGTCCACGCAGCCGATGCAT
1 CCGACGCAGTCCACGCACCCGACGCAT
130 CCGACGCA
1 CCGACGCA
138 CCGCGTGCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 3 0.10
27 24 0.80
28 3 0.10
ACGTcount: A:0.23, C:0.47, G:0.23, T:0.08
Consensus pattern (27 bp):
CCGACGCAGTCCACGCACCCGACGCAT
Found at i:136 original size:18 final size:19
Alignment explanation
Indices: 76--137 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 19
66 GCCGCGGAGC
*
76 CCGACGCA-TCCCACGCA-C
1 CCGACGCAGT-CCACGCAGT
94 CCGACGCAGTCCACGCAGT
1 CCGACGCAGTCCACGCAGT
*
113 CC-ACGCAG-CCGATGCA-T
1 CCGACGCAGTCC-ACGCAGT
130 CCGACGCA
1 CCGACGCA
138 CCGCGTGCAG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 5 0.13
18 30 0.79
19 3 0.08
ACGTcount: A:0.23, C:0.47, G:0.23, T:0.08
Consensus pattern (19 bp):
CCGACGCAGTCCACGCAGT
Found at i:264 original size:36 final size:35
Alignment explanation
Indices: 204--381 Score: 128
Period size: 36 Copynumber: 4.9 Consensus size: 35
194 ACAGGGTCAG
* * * * *
204 CGCGCTGCCCAGGATCCCGGCGCTGGCCGCGGTGCC
1 CGCGCTGCCGACGA-CCCCGCGCTGCCCGCCGTGCC
240 CGCGCT-CGCGACGACCCCGACGCTGCCCGCCGT-CGC
1 CGCGCTGC-CGACGACCCCG-CGCTGCCCGCCGTGC-C
* *
276 GGCGCTGCCGACGACCGCCGCGCTGCCCGCCGTGGC
1 CGCGCTGCCGACGACC-CCGCGCTGCCCGCCGTGCC
* * * * * *
312 CGCGCTGCCGACCACGACCGTGCTTCCGGCCGTG-G
1 CGCGCTGCCGACGAC-CCCGCGCTGCCCGCCGTGCC
* *
347 CGACGCTCCCGGCGACCACCGCGCTGCCCGCCGTG
1 CG-CGCTGCCGACGACC-CCGCGCTGCCCGCCGTG
382 GCGACGCTGC
Statistics
Matches: 112, Mismatches: 21, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
35 8 0.07
36 100 0.89
37 4 0.04
ACGTcount: A:0.07, C:0.48, G:0.35, T:0.10
Consensus pattern (35 bp):
CGCGCTGCCGACGACCCCGCGCTGCCCGCCGTGCC
Found at i:281 original size:18 final size:18
Alignment explanation
Indices: 260--320 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
250 ACGACCCCGA
*
260 CGCTGCCCGCCGTCGCGG
1 CGCTGCCCGCCGTCGCCG
* *
278 CGCTG-CCGACGACCGCCG
1 CGCTGCCCGCCG-TCGCCG
*
296 CGCTGCCCGCCGTGGCCG
1 CGCTGCCCGCCGTCGCCG
314 CGCTGCC
1 CGCTGCC
321 GACCACGACC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 5 0.14
18 25 0.71
19 5 0.14
ACGTcount: A:0.03, C:0.51, G:0.36, T:0.10
Consensus pattern (18 bp):
CGCTGCCCGCCGTCGCCG
Found at i:382 original size:36 final size:36
Alignment explanation
Indices: 242--389 Score: 156
Period size: 36 Copynumber: 4.1 Consensus size: 36
232 GCGGTGCCCG
* * *
242 CGCTCGCGACGACC-CCGACGCTGCCCGCCGTCGCGG
1 CGCTCCCGACGACCACCG-CGCTGCCCGCCGTGGCGA
* *
278 CGCTGCCGACGACCGCCGCGCTGCCCGCCGTGGCCG-
1 CGCTCCCGACGACCACCGCGCTGCCCGCCGTGG-CGA
* * * * * *
314 CGCTGCCGACCACGACCGTGCTTCCGGCCGTGGCGA
1 CGCTCCCGACGACCACCGCGCTGCCCGCCGTGGCGA
*
350 CGCTCCCGGCGACCACCGCGCTGCCCGCCGTGGCGA
1 CGCTCCCGACGACCACCGCGCTGCCCGCCGTGGCGA
386 CGCT
1 CGCT
390 GCGCGCCACG
Statistics
Matches: 93, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
35 2 0.02
36 86 0.92
37 5 0.05
ACGTcount: A:0.08, C:0.48, G:0.34, T:0.10
Consensus pattern (36 bp):
CGCTCCCGACGACCACCGCGCTGCCCGCCGTGGCGA
Found at i:498 original size:9 final size:9
Alignment explanation
Indices: 484--515 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
474 CCGCGGATCA
484 GTCGTCCGT
1 GTCGTCCGT
493 GTCGTCCGT
1 GTCGTCCGT
502 GTCGTCCGT
1 GTCGTCCGT
511 GTCGT
1 GTCGT
516 TCGCGTCGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.34, T:0.34
Consensus pattern (9 bp):
GTCGTCCGT
Found at i:523 original size:18 final size:18
Alignment explanation
Indices: 484--523 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
474 CCGCGGATCA
*
484 GTCGTCCGTGTCGTCCGT
1 GTCGTCCGTGTCGTCCGC
*
502 GTCGTCCGTGTCGTTCGC
1 GTCGTCCGTGTCGTCCGC
520 GTCG
1 GTCG
524 CCCGACGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.33, G:0.35, T:0.33
Consensus pattern (18 bp):
GTCGTCCGTGTCGTCCGC
Found at i:703 original size:21 final size:21
Alignment explanation
Indices: 660--703 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
650 GGGGCGGGCT
* *
660 GCTGGGCGTAGCCGGGCGCCG
1 GCTGGGCGTAGCCGGACGACG
681 GCTGGGCGTAGCCGGACGACG
1 GCTGGGCGTAGCCGGACGACG
702 GC
1 GC
704 GCCGTCGTGC
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:0.09, C:0.32, G:0.50, T:0.09
Consensus pattern (21 bp):
GCTGGGCGTAGCCGGACGACG
Done.