Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402307.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_539.0, 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, 1000
Length: 11132
ACGTcount: A:0.17, C:0.10, G:0.08, T:0.18
Warning! 5314 characters in sequence are not A, C, G, or T
Found at i:464 original size:39 final size:38
Alignment explanation
Indices: 420--506 Score: 106
Period size: 39 Copynumber: 2.2 Consensus size: 38
410 CTTCGTCGGC
*
420 TTCCCTCTCTCTC-TCTTTCATTCAG-CCGGCGTCGCTCCT
1 TTCCCTCTCTCTCTTCTTTC-TGC-GTCC-GCGTCGCTCCT
459 TTCCCTCTCTCTCTTTCTTTCTGCGTCCGCGTCGCTCCT
1 TTCCCTCTCTCTC-TTCTTTCTGCGTCCGCGTCGCTCCT
*
498 TTCGCTCTC
1 TTCCCTCTC
507 ACCGCACCGG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
39 33 0.77
40 4 0.09
41 6 0.14
ACGTcount: A:0.02, C:0.44, G:0.13, T:0.41
Consensus pattern (38 bp):
TTCCCTCTCTCTCTTCTTTCTGCGTCCGCGTCGCTCCT
Found at i:1021 original size:19 final size:19
Alignment explanation
Indices: 993--1039 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
983 TTTTTTTTGA
993 ATTATT-TTATTTTAT-TT
1 ATTATTATTATTTTATATT
1010 ATTATTTATTATTTTATATT
1 ATTA-TTATTATTTTATATT
1030 ATTATTATTA
1 ATTATTATTA
1040 AAAAAAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.15
18 2 0.07
19 15 0.56
20 6 0.22
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTATTATTATTTTATATT
Found at i:1025 original size:24 final size:23
Alignment explanation
Indices: 993--1038 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
983 TTTTTTTTGA
*
993 ATTATTTTATTTTATTTATTATTT
1 ATTATTTTATATTA-TTATTATTT
1017 ATTATTTTATATTATTATTATT
1 ATTATTTTATATTATTATTATT
1039 AAAAAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (23 bp):
ATTATTTTATATTATTATTATTT
Found at i:1258 original size:15 final size:16
Alignment explanation
Indices: 1238--1275 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1228 ACATATAAGT
1238 TAATTTTA-TTAAAAA
1 TAATTTTATTTAAAAA
*
1253 TAATTTTATTTAAAAT
1 TAATTTTATTTAAAAA
1269 TAATTTT
1 TAATTTT
1276 TGTAATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATTTTATTTAAAAA
Found at i:1334 original size:18 final size:18
Alignment explanation
Indices: 1311--1345 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1301 CGAAAGAGTT
1311 TTTTTAAAAAATATTTTA
1 TTTTTAAAAAATATTTTA
* *
1329 TTTTTAAGAGATATTTT
1 TTTTTAAAAAATATTTT
1346 TGAATTTATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTTTAAAAAATATTTTA
Found at i:3341 original size:21 final size:21
Alignment explanation
Indices: 3300--3341 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3290 AAAGTCACCC
**
3300 AGCGCTGCGACGCTACTCTCT
1 AGCGCTGCGACGCTAAGCTCT
3321 AGCGCTGCAGA-GCTAAGCTCT
1 AGCGCTGC-GACGCTAAGCTCT
3342 CTGAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.19, C:0.33, G:0.26, T:0.21
Consensus pattern (21 bp):
AGCGCTGCGACGCTAAGCTCT
Done.