Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399035.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2310.0, 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: 4660
ACGTcount: A:0.22, C:0.09, G:0.08, T:0.23
Warning! 1747 characters in sequence are not A, C, G, or T
Found at i:1053 original size:171 final size:169
Alignment explanation
Indices: 614--1419 Score: 521
Period size: 171 Copynumber: 4.7 Consensus size: 169
604 NNNNNNNNNN
* * * * * *
614 CTATAATTGAATGTCTACCTC--AAGAAACATG-AAGAAACAAG-CATTTATTGACAACAAAAGT
1 CTATAATTAAATGTCTACCTCTGAA-AAACGTGCAA-AAA-AAGCCATTCATTAAGAAGAAAAGT
* * * * * * *
675 CCATTTAGAGTCACTCATTCCTTCAAAAAGCTTATTATTCGCTTTCAATAGTTTTATAA-CGTAA
63 CCATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGGTTTTTTAATC-TAA
* * * * ** *
739 TAAGTGATTTTAACTTCAAT-TTTTTGACTTTTTTTGTTAAAATAGA
127 T---TCATTTTAAGTTGAATGTTTTT-ACATTTTTCATTAAAACAGA
* * * ** * * *
785 ATATAATTGATTGTCTACC-GAGAAAAACATGC-AGAAAAGCCATTCATTAGGAAGAAAAGTCCA
1 CTATAATTAAATGTCTACCTCTGAAAAACGTGCAAAAAAAGCCATTCATTAAGAAGAAAAGTCCA
* * *******
848 TTTATAGTCACCC-TCTCTTTCAAATGGCTTATTACTCGCTTTAAATGGTTTNNNNNNNNNNTAA
66 TTTATAGTCACCCAT-TCCTTCAAAAGGCTTATTACTCGCTTTAAATGGTTT---TTTAATCTAA
912 TTCATTTTAAGTTGAAT-TTTTGTACATTTTTCATTAAAACAGA
127 TTCATTTTAAGTTGAATGTTTT-TACATTTTTCATTAAAACAGA
*
955 CTATAATTAAATG-CTTGCCT-TGAAAAACGTGCAAAAAAAGCCATTCATTAAGAAGAAAAGTCC
1 CTATAATTAAATGTC-TACCTCTGAAAAACGTGCAAAAAAAGCCATTCATTAAGAAGAAAAGTCC
* * * ***
1018 ATTTATAGTCCCCCATTCCTTCAAAAGGTTTATTACTCGCTTTAAATAGTTTTTTAATCNNNNNN
65 ATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGGTTTTTTAATC---TAA
**** ** *
1083 NNNNTTTTAAGTTGAATGTTTTTACATTTTTTGTTAAACCAGA
127 TTCATTTTAAGTTGAATGTTTTTACATTTTTCATTAAAACAGA
* * * * *
1126 CTATAATTGATTGTCTACCTCT-AGAAACGTGTAAAAAAAGCCATTCATTGAGAAGAAAAGTCCA
1 CTATAATTAAATGTCTACCTCTGAAAAACGTGCAAAAAAAGCCATTCATTAAGAAGAAAAGTCCA
* * * * ***
1190 TTTATGGTCACTCATTCCTTCAAAAGGCTTATTACTCGGTTTAAATGGTTTTATAATCTCNNNNN
66 TTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGGTTTTTTAATCT---AAT
***** * * * * *
1255 NNNNNTTAAGTTAAATTTTTTTACATTTTTGATTAAAAAATA
128 TCATTTTAAGTTGAATGTTTTTACATTTTTCATTAAAACAGA
* * * * * * *
1297 CTATAATTGAATGTTTATCTC-GAGAAACATG-AAGAAACAAG-CATTCATTGACAAGAAAAGTC
1 CTATAATTAAATGTCTACCTCTGAAAAACGTGCAA-AAA-AAGCCATTCATTAAGAAGAAAAGTC
* * * * *
1359 CATTTGA-AGTCACTCATCCCTTCAAAAAGCTTATTACTCGCTTTAAACGGTTTTATAATCT
64 CATTT-ATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGGTTTTTTAATCT
1420 CGTAATTGAT
Statistics
Matches: 515, Mismatches: 93, Indels: 54
0.78 0.14 0.08
Matches are distributed among these distances:
169 5 0.01
170 119 0.23
171 374 0.73
172 13 0.03
173 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.35
Consensus pattern (169 bp):
CTATAATTAAATGTCTACCTCTGAAAAACGTGCAAAAAAAGCCATTCATTAAGAAGAAAAGTCCA
TTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGGTTTTTTAATCTAATTCA
TTTTAAGTTGAATGTTTTTACATTTTTCATTAAAACAGA
Done.