Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401936.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5036.0, 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: 2936
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.32
Warning! 466 characters in sequence are not A, C, G, or T
Found at i:1731 original size:170 final size:171
Alignment explanation
Indices: 1349--1819 Score: 413
Period size: 170 Copynumber: 2.8 Consensus size: 171
1339 NTTTAAATGC
* * * * *
1349 TTTTTTAATCTAATAATTAGTTTTAAGTTG-AACTTTTTTAT-GTTTGTTATTAAAAAAGATTAT
1 TTTTATAATCCAATAATTACTTTTAAGTTGTAA-TTTTTTATAGGTT-TTATTAAAACAGATTAT
* * * *** * *****
1412 AATTGAATGTTTACCTTGAGAAACGTAAAGAAAAAGATATCCATTGGTAAGAAAAGTTCANNNNN
64 AATTGAATGTTTACCTTGACAAACTTGAAGAAAAAGATATCCATTAAAAAGAAAAGTCCATTTAT
****** * * *
1477 NNNNNCCAATGCCTTC-GAAAGCCTTATTACTCGCTTTAAATAG
129 AGTCATCGATGACTTCAG-AAGCCTTATTACTCGCTCTAAATAG
* * * *
1520 TTTTTTAATCCCATAATTACTTTTAAGTTGTACTTTTTTATA-TTTATTATTAAAACAGATTATA
1 TTTTATAATCCAATAATTACTTTTAAGTTGTAATTTTTTATAGGTT-TTATTAAAACAGATTATA
*
1584 ATT-ACATGTTTACCTTGACAAA-TGTGAAG-AAAAGATATCCATTAAAAAGAAAAGTCTATTTA
65 ATTGA-ATGTTTACCTTGACAAACT-TGAAGAAAAAGATATCCATTAAAAAGAAAAGTCCATTTA
1646 TAGTCATCGATGACTTCAGAAGCCTTATTACTCGCTCTAAAT-G
128 TAGTCATCGATGACTTCAGAAGCCTTATTACTCGCTCTAAATAG
* * * * *
1689 ATTTTATAA-CCTAATAATTAGTTTTAATTTG-AATTATTTTATAGGTTTTGTTTAACCAGATTA
1 -TTTTATAATCC-AATAATTACTTTTAAGTTGTAATT-TTTTATAGGTTTTATTAAAACAGATTA
* * * ***
1752 TAATTGATTGTTTTCCTTGAGAAACTTGAAGAAAAAGATATCCATTGGTAAGAAAAGTCCATTTA
63 TAATTGAATGTTTACCTTGACAAACTTGAAGAAAAAGATATCCATTAAAAAGAAAAGTCCATTTA
1817 TAG
128 TAG
1820 NNNNNNNNNN
Statistics
Matches: 244, Mismatches: 44, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
169 6 0.02
170 122 0.50
171 115 0.47
172 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.39
Consensus pattern (171 bp):
TTTTATAATCCAATAATTACTTTTAAGTTGTAATTTTTTATAGGTTTTATTAAAACAGATTATAA
TTGAATGTTTACCTTGACAAACTTGAAGAAAAAGATATCCATTAAAAAGAAAAGTCCATTTATAG
TCATCGATGACTTCAGAAGCCTTATTACTCGCTCTAAATAG
Found at i:2421 original size:171 final size:169
Alignment explanation
Indices: 1984--2457 Score: 427
Period size: 171 Copynumber: 2.8 Consensus size: 169
1974 NNNNNNAATG
**
1984 ATTTTATAACCTCATAATTGATTTTAATTTGAAT-TTTTTA-ATTTTTTATTCAAACAGATTATA
1 ATTTTATAACCTCATAATTGATTTTAATTTGAATCTTTTTATATTTTTT-TGAAAACAGATTATA
* ** * * * * * * *
2047 ATTGAATGTCTGCCTCCAAAAACATAAAAGAAATAATATCCACTGGCAAGAGAAGTCCATGTATT
65 ATTGAATGTCTACCTTGAGAAACAT-AAAGAAAAAATATTCACTAGCAAGAAAAGTCCATTTATA
* * ** * *
2112 GTCACCCATGCCTTTGAAAGCCTTCTTACTTGCTTTAAATA
129 GTCACACATACCTTAAAAAGCCTTATTACTCGCTTTAAATA
* * ** * * *********
2153 GTTTTGTAATTTAATAATT-ATTTTTAAGTTGAA-CTTTTTTATATTTNNNNNNNNNNCAGATTA
1 ATTTTATAACCTCATAATTGA-TTTTAATTTGAATC-TTTTTATATTT-TTTTGAAAACAGATTA
* * * ** * * *
2216 TAATTGAATATTTATCTTGAGAAATGTGAAGAAAAAGATATTCACTAGTAACAAAAGTCCATTTA
63 TAATTGAATGTCTACCTTGAGAAACATAAAGAAAAA-ATATTCACTAGCAAGAAAAGTCCATTTA
* *
2281 CAGTCACAGATACCTTCAAAAAGCCTTATTACTCGCTTTAAATA
127 TAGTCACACATACCTT-AAAAAGCCTTATTACTCGCTTTAAATA
*
2325 ATTTTATAACCTCATAATTGATTTTATTTTGAATCTTTTTATATTTTTTTGAAAACAGATTATAA
1 ATTTTATAACCTCATAATTGATTTTAATTTGAATCTTTTTATATTTTTTTGAAAACAGATTATAA
*
2390 TTGAATGTCTACCTTGAGAAACATAAAGAAAACAATATTCA-TTGACAAGAAAAGTCCATTTATA
66 TTGAATGTCTACCTTGAGAAACATAAAGAAAA-AATATTCACTAG-CAAGAAAAGTCCATTTATA
2454 GTCA
129 GTCA
2458 TCCATGCCTT
Statistics
Matches: 227, Mismatches: 67, Indels: 20
0.72 0.21 0.06
Matches are distributed among these distances:
168 1 0.00
169 25 0.11
170 15 0.07
171 125 0.55
172 59 0.26
173 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.38
Consensus pattern (169 bp):
ATTTTATAACCTCATAATTGATTTTAATTTGAATCTTTTTATATTTTTTTGAAAACAGATTATAA
TTGAATGTCTACCTTGAGAAACATAAAGAAAAAATATTCACTAGCAAGAAAAGTCCATTTATAGT
CACACATACCTTAAAAAGCCTTATTACTCGCTTTAAATA
Done.