Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398666.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1950.0, 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: 4954
ACGTcount: A:0.23, C:0.10, G:0.08, T:0.25
Warning! 1704 characters in sequence are not A, C, G, or T
Found at i:2153 original size:169 final size:162
Alignment explanation
Indices: 1872--2201 Score: 330
Period size: 169 Copynumber: 2.0 Consensus size: 162
1862 ATCTCCCATA
* ** ** *
1872 CCTTCAAAAGCCTTTTTACTTGCCTTAAATGGTTTTGTAATCTGATAATTGTATTTAAGTTGAAT
1 CCTTCAAAAGCCTTATTACTCACCTTAAATGGTTTTAAAATCTCATAATTGTATTTAAGTTGAAT
* * * *
1937 TTGTTTTATATTTTTCATTAAAACAGACTATAATTGAATGTTTGCCTCAAGAAACGTGTAGAAAG
66 TTGTTTTACATTTTTCATTAAAACAGACTATAATTGAATGGTTGCCTCAAGAAACGTGTACAAAA
2002 AG-CTATTCATTAGCAAGAAAAGTCTATTTNNNNNNNNNNATT
131 AGTC-ATTCATTAGCAAGAAAAGTCTATTT----------ATT
* *
2044 CCTTCAAAA-CCTTATTACTCACTTTAAATGGTTTTAAAATCTCATAATTG-ATTTTAGGTTG-A
1 CCTTCAAAAGCCTTATTACTCACCTTAAATGGTTTTAAAATCTCATAATTGTA-TTTAAGTTGAA
* * *
2106 TTT-TTTTACATATTTT-ATTAAAACGGACTATAATTGAGTGGTTGCCTCTAGAAACGTGTACAA
65 TTTGTTTTACAT-TTTTCATTAAAACAGACTATAATTGAATGGTTGCCTCAAGAAACGTGTACAA
** * *
2169 AAAGTCATTCATTAATATGAAAAGTCCATTTAT
129 AAAGTCATTCATTAGCAAGAAAAGTCTATTTAT
2202 AGTCACCTAT
Statistics
Matches: 136, Mismatches: 19, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
159 2 0.01
169 73 0.54
170 10 0.07
171 42 0.31
172 9 0.07
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.39
Consensus pattern (162 bp):
CCTTCAAAAGCCTTATTACTCACCTTAAATGGTTTTAAAATCTCATAATTGTATTTAAGTTGAAT
TTGTTTTACATTTTTCATTAAAACAGACTATAATTGAATGGTTGCCTCAAGAAACGTGTACAAAA
AGTCATTCATTAGCAAGAAAAGTCTATTTATT
Found at i:2216 original size:169 final size:171
Alignment explanation
Indices: 1756--2240 Score: 444
Period size: 172 Copynumber: 2.8 Consensus size: 171
1746 NNNNNNNNNN
* ***
1756 TAAGTTGAATTT-TTTTACATTTTTCATTAAAACAGA-TAATAATTGAATGCTTGCCTTGGGAAA
1 TAAGTTGAATTTGTTTTACATTTTTCATTAAAACAGACT-ATAATTGAATGGTTGCCTCAAGAAA
* * * * * *** * *
1819 CATATAGAGAAAGCTATTTATTTGGAAGAAAAGTCCATTTACAATCTCCCATACCTTCAAAAGCC
65 CGTGTACAAAAAGCTATTCATTAACAAGAAAAGTCCATTTACAATCACCCATTCCTTCAAAA-CC
* ** * ** *
1884 TTTTTACTTGCCTTAAATGGTTTTGTAATCTGATAATTGTATT
129 TTATTACTCACTTTAAATGGTTTTAAAATCTCATAATTGTATT
* *
1927 TAAGTTGAATTTGTTTTATATTTTTCATTAAAACAGACTATAATTGAATGTTTGCCTCAAGAAAC
1 TAAGTTGAATTTGTTTTACATTTTTCATTAAAACAGACTATAATTGAATGGTTGCCTCAAGAAAC
* * * * **********
1992 GTGTAGAAAGAGCTATTCATTAGCAAGAAAAGTCTATTTNNNNNNNNNNATTCCTTCAAAACCTT
66 GTGTACAAAAAGCTATTCATTAACAAGAAAAGTCCATTTACAATCACCCATTCCTTCAAAACCTT
2057 ATTACTCACTTTAAATGGTTTTAAAATCTCATAATTG-ATTT
131 ATTACTCACTTTAAATGGTTTTAAAATCTCATAATTGTA-TT
* * * *
2098 TAGGTTG-ATTT-TTTTACATATTTT-ATTAAAACGGACTATAATTGAGTGGTTGCCTCTAGAAA
1 TAAGTTGAATTTGTTTTACAT-TTTTCATTAAAACAGACTATAATTGAATGGTTGCCTCAAGAAA
* * * * * *
2160 CGTGTACAAAAAG-TCATTCATTAATATGAAAAGTCCATTTATAGTCACCTATTCCTTCGAAAGC
65 CGTGTACAAAAAGCT-ATTCATTAACAAGAAAAGTCCATTTACAATCACCCATTCCTTC-AAAAC
2224 CTTATTACTCACTTTAA
128 CTTATTACTCACTTTAA
2241 NNNNNNNNNN
Statistics
Matches: 254, Mismatches: 54, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
168 1 0.00
169 81 0.32
170 30 0.12
171 54 0.21
172 87 0.34
173 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.38
Consensus pattern (171 bp):
TAAGTTGAATTTGTTTTACATTTTTCATTAAAACAGACTATAATTGAATGGTTGCCTCAAGAAAC
GTGTACAAAAAGCTATTCATTAACAAGAAAAGTCCATTTACAATCACCCATTCCTTCAAAACCTT
ATTACTCACTTTAAATGGTTTTAAAATCTCATAATTGTATT
Found at i:4792 original size:172 final size:162
Alignment explanation
Indices: 4613--4950 Score: 342
Period size: 172 Copynumber: 2.0 Consensus size: 162
4603 CTTCCAAAAG
* * *
4613 CCTTATTACT-AGCCTTAAATGGTTTTGTAATCTGATAA-TTGTATTTAAGTTGAATATTTTTTA
1 CCTTATTACTCA-CCTTAAATGGTTTTATAATCTCATAACTTAT-TTTAAGTTGAATATTTTTTA
* * * ** * * * *
4676 TATTTTTCATTAAAATAGATTATAATTGAATG-CGTACCTTGGGGAACGTATAG-AAAAAGCTAT
64 TAGTTTTCATTAAAACAGACTATAATTGAATGTC-TACCACGAGAAACATAAAGAAAAAAGC-AT
* *
4739 TCATTGACAAGAAAAGTTCATTTATAGTCTCCCATT
127 TCATTGACAAAAAAAGTCCATTTATAGTCTCCCATT
*
4775 CNNNNNNNNNNCTTATTACTCACTTTAAATGGTTTTATAATCTCATAACTTATTTTAAGTTGAAT
1 C----------CTTATTACTCACCTTAAATGGTTTTATAATCTCATAACTTATTTTAAGTTGAAT
* **
4840 TTTTTTTATAGTTTTGGTTAAAACAGACTATAATTGAATGTCTACCACGAGAAACATAAAGAAAA
56 ATTTTTTATAGTTTTCATTAAAACAGACTATAATTGAATGTCTACCACGAGAAACATAAAGAAAA
* *
4905 AAGCATTCATTGGCAAAAAAAGTCCATTTATAGTCTCCTATT
121 AAGCATTCATTGACAAAAAAAGTCCATTTATAGTCTCCCATT
4947 CCTT
1 CCTT
4951 CAAA
Statistics
Matches: 142, Mismatches: 20, Indels: 28
0.75 0.11 0.15
Matches are distributed among these distances:
162 4 0.03
172 126 0.89
173 12 0.08
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.38
Consensus pattern (162 bp):
CCTTATTACTCACCTTAAATGGTTTTATAATCTCATAACTTATTTTAAGTTGAATATTTTTTATA
GTTTTCATTAAAACAGACTATAATTGAATGTCTACCACGAGAAACATAAAGAAAAAAGCATTCAT
TGACAAAAAAAGTCCATTTATAGTCTCCCATT
Done.