Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398959.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2241.0, 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: 1894
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.33
Warning! 153 characters in sequence are not A, C, G, or T
Found at i:1204 original size:172 final size:169
Alignment explanation
Indices: 648--1894 Score: 1031
Period size: 172 Copynumber: 7.3 Consensus size: 169
638 NNNNNNTTTA
* * * * * * * *
648 AAGGAATGGGTTACTAGAAATGGACTTTTCTTACCAATGAATACCTTTTT-TTTATGTTGCTCGA
1 AAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAA
* * * * * * *
712 GGTAAACATTGAATTATAGTCTGTTTTAACCTAAAACGTGAAAAAAGTT--AATCGTAAAATCAA
66 GGTAGACATTCAATTATAGTCTGTTTT-ATCAAAAATGT-AAAAAAATTCAAAT--TTAAATCAA
* * * * **
775 TTATGGCATTACAAAAACATTTCAAGCAAGTAATAAGGCTTTTG
127 TTTTGG-ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
** * * * * * *
819 AAGTTACGGGTGACTATAAATGGACTTTTCTTGCCAATGAATTCCTTTTTCTTCACATTTCTCAG
1 AAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAA
* * * * *
884 GGTAGACATTTAATTATAGTCTGTTGTAACAAAAAAATGTAAAAACAATTCAACTTAAAATCAAT
66 GGTAGACATTCAATTATAGTCTGTTTTATC--AAAAATGTAAAAA-AATTCAAATTTAAATCAAT
** * * *
949 TAGGGCATCATAAAACCATTTAAAGCGAGTAATGAGGCTTTTG
128 TTTGG-ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
* * *
992 AAGGTATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTTATGTTTCTAAA
1 AAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAA
* * * *
1057 GGTAGACATTCAATTCTAGTCTGTTTTATGCGAAAATG-ACTGAAGAATTCAAATTTAAATCAAT
66 GGTAGACATTCAATTATAGTCTGTTTTAT-CAAAAATGTA--AAAAAATTCAAATTTAAATCAAT
** *
1121 TTTGAGATTGCAAAACCATTTAAAGTGAGTAATAAGGCTTTTA
128 TTTG-GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
* * * * *
1164 AATGAATGGGTGACTATAAATGGACTTTGT-TTGTCAATGAATGCCTTTTT-TTTCATGTTTGTC
1 AAGGAATGGGTGACTATAAATAGACTTT-TCTTGCCAATGAATGCCTTTTTCTTT-ACGTTTCTC
* * * * * * * * ** *
1227 GAGCTAGATACTCAGTTATAATATGTTTTAAT-ATAAAATGTAAAACAATTTGAACTTATAATCA
64 AAGGTAGACATTCAATTATAGTCTGTTTT-ATCA-AAAATGTAAAAAAATTCAAATTTA-AATCA
* * *
1291 ATCTTCGGATTATAAAAGCATTTAAAGTGAGTAATAAGACTTTTG
126 AT-TTTGGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
** * * * * * **
1336 AAACAATGGGTGACTGTAAATAGAGTTTTCTTTCCAATGAATGCCCTTTTCTTTACATTTCTTGA
1 AAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAA
* * * * * ** *
1401 GATAGACATACAATTATAATTTGTTTTAACCAAAAATGTAAAAAAATTTGAAGTTAGAATCAATT
66 GGTAGACATTCAATTATAGTCTGTTTT-ATCAAAAATGTAAAAAAATTCAAATTTA-AATCAATT
** * * *
1466 TTGAGATTATAAAACCATAAAAAGTGAGCAATAACGCTTCTG
129 TTG-GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
* * * *
1508 AAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGTCTCTTCCTTTATGTTTCTCAA
1 AAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAA
* * * * * * * *
1573 GGTAGACTTTTAATTATAGTCTATTTCAGCCAAAAATGTAAAAAAATTCAACTTAAAATCAATTA
66 GGTAGACATTCAATTATAGTCTGTTTTA-TCAAAAATGTAAAAAAATTCAAATTTAAATCAATTT
**
1638 TGGCATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTTTG
130 TGG-ATTATAAAACCATTTAAAGTGAGTAATAAGGC-TTTTG
* ** * * * ** * *
1680 AAGGTATGAATGACTATGAGTGGACTTTTCTAACCAATGAAT--ATTTCTCTCTTCACGTTTCTC
1 AAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTT-T-TCTTTACGTTTCTC
* * * *
1743 AAGGTAGACATTCAATTCTAGTCTATTTTTATC-AAAATGATAGAAAAATTCAAATTTCAATCAA
64 AAGGTAGACATTCAATTATAGTCT-GTTTTATCAAAAATG-TAAAAAAATTCAAATTTAAATCAA
* * * *
1807 TTTTGATATTACAAAACTATTTAAAGTGAGTAATAAGGCTTTTA
127 TTTTG-GATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
*
1851 AAGGAATGGGTGA-TGATAAATTGACTTTTCTTGCCAATGAATGC
1 AAGGAATGGGTGACT-ATAAATAGACTTTTCTTGCCAATGAATGC
Statistics
Matches: 862, Mismatches: 182, Indels: 62
0.78 0.16 0.06
Matches are distributed among these distances:
170 4 0.00
171 144 0.17
172 557 0.65
173 154 0.18
174 1 0.00
175 2 0.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (169 bp):
AAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCAA
GGTAGACATTCAATTATAGTCTGTTTTATCAAAAATGTAAAAAAATTCAAATTTAAATCAATTTT
GGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG
Found at i:1358 original size:344 final size:338
Alignment explanation
Indices: 648--1894 Score: 1179
Period size: 344 Copynumber: 3.6 Consensus size: 338
638 NNNNNNTTTA
* * * * * * *
648 AAGGAATGGGTTACTAGAAATGGACTTTTCTTACCAATGAATACCTTTTT-TTTATGTTGCTCGA
1 AAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTTACGTTTCTCAA
* * * *
712 GGTAAACATTGAATTATAGTCTGTTTTAACCTAAAACGT-GAAAAAAGTT--AATCGTAAAATCA
66 GGTAGACATTCAATTATAGTCTGTTTTAACC-AAAATGTAG-AAAAA-TTCAAAT--TTAAATCA
* * * ** * ** *
774 ATTATG-GCATTACAAAAACATTTCAAGCAAGTAATAAGGCTTTTGAAGTTACGGGTGACTATAA
126 ATTTTGAG-ATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAA
* * ** *
838 ATGGACTTTTCTTGCCAATGAATTCCTTTTTCTTCACATTTCTCAGGGTAGACATTTAATTATAG
190 ATGGACTTTTCTTGCCAATGAATGCCTTTTTTTTCATGTTTCTCA-GGTAGATATTTAATTATAG
* * *
903 TCTGTTGTAACAAAAAAATGTAAAAACAATTCAACTTAAAATCAATTAGGGCATCATAAAACCAT
254 TCTGTT-TTA-AAAAAAATGT-AAAACAATTCAACTTAAAATCAATT-TGGCATTATAAAACCAT
*
968 TTAAAGCGAGTAATGAGGCTTTTG
315 TTAAAGCGAGTAATAAGGCTTTTG
* * * *
992 AAGGTATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTTATGTTTCTAAA
1 AAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTTACGTTTCTCAA
* * * *
1057 GGTAGACATTCAATTCTAGTCTGTTTTATGCGAAAATG-ACTGAAGAATTCAAATTTAAATCAAT
66 GGTAGACATTCAATTATAGTCTGTTTTA-ACCAAAATGTA--GAAAAATTCAAATTTAAATCAAT
* *
1121 TTTGAGATTGCAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAATGAATGGGTGACTATAAATG
128 TTTGAGATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATG
* * * * * * * *
1186 GACTTTGT-TTGTCAATGAATGCCTTTTTTTTCATGTTTGTCGAGCTAGATACTCAGTTATAATA
193 GACTTT-TCTTGCCAATGAATGCCTTTTTTTTCATGTTTCTC-AGGTAGATATTTAATTATAGTC
* * * *
1250 TGTTTTAATATAAAATGTAAAACAATTTGAACTTATAATCAATCTTCGG-ATTATAAAAGCATTT
256 TGTTTTAA-AAAAAATGTAAAACAA-TTCAACTTAAAATCAAT-TT-GGCATTATAAAACCATTT
* *
1314 AAAGTGAGTAATAAGACTTTTG
317 AAAGCGAGTAATAAGGCTTTTG
** * * * * * **
1336 AAACAATGGGTGACTGTAAATAGAGTTTTCTTTCCAATGAATGCCCTTTTCTTTACATTTCTTGA
1 AAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTTACGTTTCTCAA
* * * * * ** *
1401 GATAGACATACAATTATAATTTGTTTTAACCAAAAATGTAAAAAAATTTGAAGTTAGAATCAATT
66 GGTAGACATTCAATTATAGTCTGTTTTAACC-AAAATGTAGAAAAATTCAAATTTA-AATCAATT
* ** * * * * *
1466 TTGAGATTATAAAACCATAAAAAGTGAGCAATAACGCTTCTGAAGGAATGGGTGACTATAAATAG
129 TTGAGATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGG
* **
1531 ACTTTTCTTGCCAATGAATGTCTCTTCCTTT-ATGTTTCTCAAGGTAGACT-TTTAATTATAGTC
194 ACTTTTCTTGCCAATGAATGCCT-TTTTTTTCATGTTTCTC-AGGTAGA-TATTTAATTATAGTC
* * ** *
1594 TATTTCAGCCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGGCATTATAAAACCATTTAA
256 TGTTTTA-AAAAAAATGTAAAACAATTCAACTTAAAATCAATT-TGGCATTATAAAACCATTTAA
*
1659 AGCAAGTAATAAGGCTTTTTG
319 AGCGAGTAATAAGGC-TTTTG
* ** * * * * * *
1680 AAGGTATGAATGACTATGAGTGGACTTTTCTAACCAATGAAT--ATTTCTCTCTTCACGTTTCTC
1 AAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTT-T-TCTTTACGTTTCTC
* * * * *
1743 AAGGTAGACATTCAATTCTAGTCTATTTTTATCAAAATGATAGAAAAATTCAAATTTCAATCAAT
64 AAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAATG-TAGAAAAATTCAAATTTAAATCAAT
* *
1808 TTTGATATTACAAAACTATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTGA-TGATAAAT
128 TTTGAGATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTGACT-ATAAAT
*
1872 TGACTTTTCTTGCCAATGAATGC
192 GGACTTTTCTTGCCAATGAATGC
Statistics
Matches: 725, Mismatches: 150, Indels: 57
0.78 0.16 0.06
Matches are distributed among these distances:
342 6 0.01
343 153 0.21
344 389 0.54
345 165 0.23
346 8 0.01
347 4 0.01
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (338 bp):
AAGGAATGGGTGACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTTACGTTTCTCAA
GGTAGACATTCAATTATAGTCTGTTTTAACCAAAATGTAGAAAAATTCAAATTTAAATCAATTTT
GAGATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGAC
TTTTCTTGCCAATGAATGCCTTTTTTTTCATGTTTCTCAGGTAGATATTTAATTATAGTCTGTTT
TAAAAAAAATGTAAAACAATTCAACTTAAAATCAATTTGGCATTATAAAACCATTTAAAGCGAGT
AATAAGGCTTTTG
Done.