Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398054.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1362.0, 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: 2613
ACGTcount: A:0.25, C:0.09, G:0.10, T:0.26
Warning! 787 characters in sequence are not A, C, G, or T
Found at i:2526 original size:173 final size:172
Alignment explanation
Indices: 1875--2613 Score: 763
Period size: 172 Copynumber: 4.3 Consensus size: 172
1865 NNNNNNNAGT
* * * * * * *
1875 GAGTAATAAGGCTTCTGAAGGAATGGATGACTATAAATGGACTTCTCTTGCAAATTAATGCTTTC
1 GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTT
* * * *
1940 TTCTTTATGTTTCTTAGGGTAGACATTCAATTATAGTATGTTTTAACAAAAAA-ACCAAAACAAA
66 TTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATA-CAAAAAAAA
* * * * *
2004 TTGAACTTAAAATCAATTTCGAGATTATAATACAATTTAAAGT
130 TTCAAATTAAAATCAATTTCGAGATTACAAAACAATTTAAAGC
* * * *
2047 GATTAATAAGGCTTTTGAAGCAATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTT
1 GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTT
* * * * * * ** * *
2112 TTCTTCATGTTTCTTATGGTAGACATTCAATTCTAGACTATTTTCACCAAAAATGTACAAAACAT
66 TTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATACAAAAAAAAT
* * * * * *
2177 TCAAATTTAAATCAATTTTGAGATTATAAAACTATTGAAAGT
131 TCAAATTAAAATCAATTTCGAGATTACAAAACAATTTAAAGC
* * * * *
2219 GAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATAGACTTCTT-TTGCCAATAAATGCCTT
1 GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTT-TTCTTGCCAATGAATACTTT
* ** * * * *
2283 TTTCTTTACCTTTCTCAAGCTAGACATTCAATTATAGTCTG-TTTAACTAAAAATTTAAAAAAAA
65 TTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAAC-AAAAA-ATACAAAAAA
* *
2347 AATTCAACTTAAAATCAATTACG-GCATTACAAAATC-ATTTAAAGC
128 AATTCAAATTAAAATCAATTTCGAG-ATTACAAAA-CAATTTAAAGC
* * *
2392 GAGTAATAAGGCTTTTGAAGGTATGGGTGACTAGAAATGGACTTTTCTTGCCCAATGAATAATTT
1 GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTG-CCAATGAATACTTT
* * * ** *
2457 TTTCTTCATGTTTCTTAAGGTAAACATTCAATTCTAGTCTGTTTTAACAAAAAATGCCCAAATAA
65 TTTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATACAAAAAAAA
* *
2522 TTCAAATTTAAATCAATTTTGAGATT-CTACAAAC-ATTTAAAGC
130 TTCAAATTAAAATCAATTTCGAGATTAC-A-AAACAATTTAAAGC
* * * *
2565 TAGTAATAAGGCTTTTGAAGGTATGGGCGACTATAAATGGATTTTTCTT
1 GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTT
Statistics
Matches: 465, Mismatches: 90, Indels: 23
0.80 0.16 0.04
Matches are distributed among these distances:
171 5 0.01
172 234 0.50
173 166 0.36
174 54 0.12
175 6 0.01
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (172 bp):
GAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTT
TTCTTCATGTTTCTTAAGGTAGACATTCAATTATAGTCTGTTTTAACAAAAAATACAAAAAAAAT
TCAAATTAAAATCAATTTCGAGATTACAAAACAATTTAAAGC
Found at i:2541 original size:346 final size:343
Alignment explanation
Indices: 1872--2602 Score: 965
Period size: 346 Copynumber: 2.1 Consensus size: 343
1862 NNNNNNNNNN
* * *
1872 AGTGAGTAATAAGGCTTCTGAAGGAATGGATGACTATAAATGGACTTCTCTTGCAAATTAATGCT
1 AGTGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATAGACTTCTCTTGCAAATAAATGCT
** * * * *
1937 TTCTTCTTTATGTTTCTTAGGGTAGACATTCAATTATAGTATGTTTTAACAAAAAAACCAAAACA
66 TTCTTCTTTACCTTTCTCAAGCTAGACATTCAATTATAGTATGTTTTAACAAAAAAA-CAAAAAA
* * * * * *
2002 AATTGAACTTAAAATCAATTTCGAGATTATAATACAATTTAAAGTGATTAATAAGGCTTTTGAAG
130 AATTCAACTTAAAATCAATTACGAGATTACAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAG
* * *
2067 CAATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTTATGGT
195 CAATAGGTGACTAGAAATAGACTTTTCTTGCCAATGAATAATTTTTTCTTCATGTTTCTTAAGGT
* * * *
2132 AGACATTCAATTCTAGACTATTTTCACCAAAAATGTACAAAACATTCAAATTTAAATCAATTTTG
260 AAACATTCAATTCTAGACTATTTTAACAAAAAATGCACAAAACATTCAAATTTAAATCAATTTTG
2197 AGATTATA-AAACTATTGAA
325 AGATTATACAAAC-ATTGAA
* *
2216 AGTGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATAGACTTCTTTTGCCAATAAATGCC
1 AGTGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATAGACTTCTCTTGCAAATAAATG-C
*
2281 TTT-TTCTTTACCTTTCTCAAGCTAGACATTCAATTATAGTCTG-TTTAACTAAAAATTTAA-AA
65 TTTCTTCTTTACCTTTCTCAAGCTAGACATTCAATTATAGTATGTTTTAAC-AAAAA---AACAA
2343 AAAAAATTCAACTTAAAATCAATTACG-GCATTACAAAATC-ATTTAAAGCGAGTAATAAGGCTT
126 AAAAAATTCAACTTAAAATCAATTACGAG-ATTACAAAA-CAATTTAAAGCGAGTAATAAGGCTT
** * *
2406 TTGAAGGTATGGGTGACTAGAAATGGACTTTTCTTGCCCAATGAATAATTTTTTCTTCATGTTTC
189 TTGAAGCAATAGGTGACTAGAAATAGACTTTTCTTG-CCAATGAATAATTTTTTCTTCATGTTTC
* * *
2471 TTAAGGTAAACATTCAATTCTAGTCTGTTTTAACAAAAAATGCCCAAATA-ATTCAAATTTAAAT
253 TTAAGGTAAACATTCAATTCTAGACTATTTTAACAAAAAATGCACAAA-ACATTCAAATTTAAAT
* *
2535 CAATTTTGAGATTCTACAAACATTTAA
317 CAATTTTGAGATTATACAAACATTGAA
* **
2562 AGCT-AGTAATAAGGCTTTTGAAGGTATGGGCGACTATAAAT
1 AG-TGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAAT
2603 GGATTTTTCT
Statistics
Matches: 339, Mismatches: 37, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
343 6 0.02
344 98 0.29
345 89 0.26
346 138 0.41
347 8 0.02
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (343 bp):
AGTGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAAATAGACTTCTCTTGCAAATAAATGCT
TTCTTCTTTACCTTTCTCAAGCTAGACATTCAATTATAGTATGTTTTAACAAAAAAACAAAAAAA
ATTCAACTTAAAATCAATTACGAGATTACAAAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGC
AATAGGTGACTAGAAATAGACTTTTCTTGCCAATGAATAATTTTTTCTTCATGTTTCTTAAGGTA
AACATTCAATTCTAGACTATTTTAACAAAAAATGCACAAAACATTCAAATTTAAATCAATTTTGA
GATTATACAAACATTGAA
Done.