Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402027.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5122.0, 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: 2198
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.34
Warning! 132 characters in sequence are not A, C, G, or T
Found at i:1433 original size:172 final size:171
Alignment explanation
Indices: 1126--2189 Score: 736
Period size: 171 Copynumber: 6.2 Consensus size: 171
1116 TCAAGGCAAG
* * * * * *
1126 CATTCAATTACAGTCTGTTTTAA-GAAAAATGTAAAAAACTTTAACTTATAATCAATTATAAGAT
1 CATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCACTTATAAGAT
* * * * * *
1190 TAAAAAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGAAATGAGTGA-TAATAAAAGGACTTTT
66 TATAAAACCATTTAAATCGAGTAATAAGGCTTTTGAAGGAATGAGAGACT-ATAAATGGACTTTT
* * *
1254 CTTGCCAATGAATATC-TTTTTCTTCACGTTTCTCCATGTAGA
130 CTTGCCAATGAAT-GCATTTCTCTTCACGTTTCTCCACGTAGA
* * * * *
1296 CATTCAATTATAATATGTTTTAACCAAAAAAGTAAACAAAATTGAACTTAAAATCACTTTTAAGA
1 CATTCAATTATAGTCTGTTTTAACCAAAAATGTAAA-AAAATTCAACTTAAAATCACTTATAAGA
* * *
1361 TTATAAAACCATTTAAATCGGGTAACAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTCTT
65 TTATAAAACCATTTAAATCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTT
** *
1426 CTTGCCAATGAATGCATTTCTCTTCACGTTTCTTGACGTAGG
130 CTTGCCAATGAATGCATTTCTCTTCACGTTTCTCCACGTAGA
* * * * *
1468 CATTCAATTATAGTCTGTTTTAACTAAAAATGTGAAAAAACTCAACTTAAAATTAAC-TATGAGA
1 CATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAA-TCACTTATAAGA
* * *
1532 TTATAAAACCATTTAAATCGAGTAATAAGGCTTTTGAAGGAATGAAAAACTATAAATGAACTTTT
65 TTATAAAACCATTTAAATCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTT
* * ** ** *
1597 CTT-CAGAATAAAT--ATTCTTCTCAACACGTTTCTTGAGGTAGGA
130 CTTGC-CAATGAATGCA-T-TTCTCTTCACGTTTCTCCACGTA-GA
* * ** * * **********
1640 -ATTTAATTATAGTCTATTTTAATGAAAAATAT-AAAACATTCAACTTAAAATCAANNNNNNNNN
1 CATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCACTTATAAGAT
* ** * * * *
1703 NATAAAACCATTTAAGAT-GAGTAATAAGAATTTTGAAAGAATGGGTGACTACAAATGGACTTTT
66 TATAAAACCATTTAA-ATCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTT
** * * * * * *
1767 CTTGTTAATGAATGCTTTTTTCTTCACATTTCTCAAGGTAAA
130 CTTGCCAATGAATGCATTTCTCTTCACGTTTCTCCACGTAGA
* ** * * * * * *
1809 CATTCAAATATAGTCTGTTTGGACAAAAAATGCAAAACAATTCAACTTAAAATAAATTATGAGAT
1 CATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCACTTATAAGAT
* ********** * *
1874 TTTAAAACCATTTAAAGT-GAGTAATAAGGNNNNNNNNNNAAT-AGGTGACTATAAATGGATTTT
66 TATAAAACCATTTAAA-TCGAGTAATAAGGCTTTTGAAGGAATGA-GAGACTATAAATGGACTTT
* * * *
1937 TCTTACCAATGAATGC-TTTCTTCTTCAAGTTTCTCGAGGTAGA
129 TCTTGCCAATGAATGCATTTC-TCTTCACGTTTCTCCACGTAGA
** * * * *
1980 CATTCAATTATAGTCTGTTTTAA-TTAAAATGTAAAAAAAATTGATCTTAAAAT-AATTATGAGA
1 CATTCAATTATAGTCTGTTTTAACCAAAAATGT-AAAAAAATTCAACTTAAAATCACTTATAAGA
* ********** * * * *
2043 TTATAAAATCATTTANNNNNNNNNNTAAGGCTTTTGAAGGAATGGGTGCCTATAAATAGACTTTT
65 TTATAAAACCATTTAAATCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTT
* * * ** * *
2108 CTTGCCAATGAAAGCCTTTCTCTTCAAGTTTCTTAAAGTAAA
130 CTTGCCAATGAATGCATTTCTCTTCACGTTTCTCCACGTAGA
* * * *
2150 TATTCAATTATAATCTGTTTTAAACAATAATGTAAAAAAA
1 CATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAA
2190 ATTGAATCT
Statistics
Matches: 695, Mismatches: 175, Indels: 48
0.76 0.19 0.05
Matches are distributed among these distances:
169 4 0.01
170 255 0.37
171 289 0.42
172 146 0.21
173 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.34
Consensus pattern (171 bp):
CATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCACTTATAAGAT
TATAAAACCATTTAAATCGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTC
TTGCCAATGAATGCATTTCTCTTCACGTTTCTCCACGTAGA
Found at i:1573 original size:171 final size:170
Alignment explanation
Indices: 1053--2189 Score: 844
Period size: 170 Copynumber: 6.7 Consensus size: 170
1043 NNNNNNNNNN
* * * * * * * *
1053 TGAAGGAATGGGTGGCTATGAATGGACTTTTC-TCCTCAATGAATGGTTTTTTCTACACGTTTAT
1 TGAAGGAATGAGTGACTATAAATGGACTTTTCTTGC-CAATGAAT-GCTTTCTCTTCACGTTTCT
* * * * * * * *
1117 CAAGGCA-AGCATTCAATTACAGTCTGTTTTAA-GAAAAATGTAAAAAACTTTAACTTATAATCA
64 CGAGGTAGA-CATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATTA
* * *
1180 ATTATAAGATTAAAAAACCATTTAAAGCGAGTAATAAGGCTTT
128 ATTATGAGATTATAAAACCATTTAAATCGAGTAATAAGGCTTT
* * * * *
1223 TAAAGAAATGAGTGA-TAATAAAAGGACTTTTCTTGCCAATGAATATCTTTTTCTTCACGTTTCT
1 TGAAGGAATGAGTGACT-ATAAATGGACTTTTCTTGCCAATGAAT-GCTTTCTCTTCACGTTTCT
* * * * * * * *
1287 CCATGTAGACATTCAATTATAATATGTTTTAACCAAAAAAGTAAACAAAATTGAACTTAAAATCA
64 CGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAA-AAAATTCAACTTAAAATTA
* * * * *
1352 CTTTTAAGATTATAAAACCATTTAAATCGGGTAACAAGGCTTT
128 ATTATGAGATTATAAAACCATTTAAATCGAGTAATAAGGCTTT
* * *
1395 TGAAGGAATGAGAGACTATAAATGGACTCTTCTTGCCAATGAATGCATTTCTCTTCACGTTTCTT
1 TGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGC-TTTCTCTTCACGTTTCTC
* * * * *
1460 GACGTAGGCATTCAATTATAGTCTGTTTTAACTAAAAATGTGAAAAAACTCAACTTAAAATTAAC
65 GAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATTAAT
1525 TATGAGATTATAAAACCATTTAAATCGAGTAATAAGGCTTT
130 TATGAGATTATAAAACCATTTAAATCGAGTAATAAGGCTTT
*** * * * ** **
1566 TGAAGGAATGAAAAACTATAAATGAACTTTTCTT-CAGAATAAATATTCTTCTCAACACGTTTCT
1 TGAAGGAATGAGTGACTATAAATGGACTTTTCTTGC-CAATGAATGCT-TTCTCTTCACGTTTCT
* * * * * *
1630 TGAGGTAGGA-ATTTAATTATAGTCTATTTTAA-TGAAAAATAT-AAAACATTCAACTTAAAATC
64 CGAGGTA-GACATTCAATTATAGTCTGTTTTAACT-AAAAATGTAAAAAAATTCAACTTAAAATT
********** **
1692 AANNNNNNNNNNATAAAACCATTTAAGAT-GAGTAATAAGAATTT
127 AATTATGAGATTATAAAACCATTTAA-ATCGAGTAATAAGGCTTT
* * * ** * *
1736 TGAAAGAATGGGTGACTACAAATGGACTTTTCTTGTTAATGAATGCTTTTTTCTTCACATTTCTC
1 TGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGC-TTTCTCTTCACGTTTCTC
* * * ** * * * *
1801 AAGGTAAACATTCAAATATAGTCTGTTTGGACAAAAAATGCAAAACAATTCAACTTAAAATAAAT
65 GAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATTAAT
* ****
1866 TATGAGATTTTAAAACCATTTAAAGT-GAGTAATAAGGNNNN
130 TATGAGATTATAAAACCATTTAAA-TCGAGTAATAAGGCTTT
****** * * *
1907 NNNNNNAAT-AGGTGACTATAAATGGATTTTTCTTACCAATGAATGCTTTCTTCTTCAAGTTTCT
1 TGAAGGAATGA-GTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTC-TCTTCACGTTTCT
* * *
1971 CGAGGTAGACATTCAATTATAGTCTGTTTTAA-TTAAAATGTAAAAAAAATTGATCTTAAAA-TA
64 CGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGT-AAAAAAATTCAACTTAAAATTA
* **********
2034 ATTATGAGATTATAAAATCATTTANNNNNNNNNNTAAGGCTTT
128 ATTATGAGATTATAAAACCATTTAAATCGAGTAATAAGGCTTT
* * * * * *
2077 TGAAGGAATGGGTGCCTATAAATAGACTTTTCTTGCCAATGAAAGCCTTTCTCTTCAAGTTTCTT
1 TGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATG-CTTTCTCTTCACGTTTCTC
* * * * * *
2142 AAAGTAAATATTCAATTATAATCTGTTTTAAAC-AATAATGTAAAAAAA
65 GAGGTAGACATTCAATTATAGTCTGTTTT-AACTAAAAATGTAAAAAAA
2190 ATTGAATCT
Statistics
Matches: 749, Mismatches: 192, Indels: 52
0.75 0.19 0.05
Matches are distributed among these distances:
169 2 0.00
170 307 0.41
171 296 0.40
172 143 0.19
173 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.34
Consensus pattern (170 bp):
TGAAGGAATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTCTCTTCACGTTTCTCG
AGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATTAATT
ATGAGATTATAAAACCATTTAAATCGAGTAATAAGGCTTT
Done.