Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400723.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3903.0, 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, 943
Length: 1573
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:297 original size:171 final size:168
Alignment explanation
Indices: 3--370 Score: 414
Period size: 171 Copynumber: 2.2 Consensus size: 168
1 AA
* * * *
3 GGTAGACATTTAATTATAGTCTATTTTAATGAAAAATAAAAAAATTGAGCTTAAAATCAATTATG
1 GGTAGACATTCAATTATAGTCTATTTTAATAAAAAATAAAAAAATTCAACTTAAAATCAATTATG
* * ** * *
68 AGATGATAAAACCGTTGAAGGCGAGTAATAAGGCTTTTAAAAGAATGGGTGACTATAAATGGACT
66 AGATGATAAAACCATTGAAAGCGAGTAATAAACCTTTTAAAAGAAAGGGTGACTATAAAGGGACT
* *
133 TTTTTTG-TCAATGAATACCTTTTTCTTCATATTTCTTGG
131 TTTCTTGCT-AATAAAT-CCTTTTTCTTCATATTTCTTGG
* * * * *
172 GGTAGGCATTCAATTATAGTTTGTTTTAACTAAAAATATAAAAAAATTCAACTTAAAATTAGTTA
1 GGTAGACATTCAATTATAGTCTATTTTAA-TAAAAA-ATAAAAAAATTCAACTTAAAATCAATTA
* * * * *
237 TGAGATTATAAAATCATTTAAAGCGAGTAATAAACCTTTTGAAAGAAAGGGTGGCTATAAAGGGA
64 TGAGATGATAAAACCATTGAAAGCGAGTAATAAACCTTTTAAAAGAAAGGGTGACTATAAAGGGA
* ** * *
302 CTTTTCTTGCTAATAAATGCTTTTTCTTCACGTTTGTTGA
129 CTTTTCTTGCTAATAAATCCTTTTTCTTCATATTTCTTGG
* * * *
342 GGTAAACGTTCAATTATAATCTTTTTTAA
1 GGTAGACATTCAATTATAGTCTATTTTAA
371 CTTAAAGTCA
Statistics
Matches: 163, Mismatches: 33, Indels: 5
0.81 0.16 0.02
Matches are distributed among these distances:
169 25 0.15
170 45 0.28
171 92 0.56
172 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (168 bp):
GGTAGACATTCAATTATAGTCTATTTTAATAAAAAATAAAAAAATTCAACTTAAAATCAATTATG
AGATGATAAAACCATTGAAAGCGAGTAATAAACCTTTTAAAAGAAAGGGTGACTATAAAGGGACT
TTTCTTGCTAATAAATCCTTTTTCTTCATATTTCTTGG
Found at i:1084 original size:171 final size:170
Alignment explanation
Indices: 366--1573 Score: 1195
Period size: 171 Copynumber: 7.1 Consensus size: 170
356 TATAATCTTT
* * * **
366 TTTAACTTAAAGTCAATTATTAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCCAAGGA
1 TTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTAAAGGA
* ** * * **
431 ATGTGCCACTATAAATGAACTTTTCTTGCCAATGAATCCTTTTTTCTTTGTGTTTCTCCAA-GTA
66 ATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCT-CAAGGTA
* * *
495 GAGATTTAATTATAGTCTGTTTTAACTAAAAATGTAAAAAAAA
130 GACATTCAATTATAGTCTGTTTTAACCAAAAATGT--AAAAAA
* * * * ** * * *
538 ATGAACTTAAAATCAATTATGAGATTGTTAAATAATTTAAAGCGAGTGATAAGGCTTTTGAAGGA
1 TTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTAAAGGA
** * * * * ** ** *
603 ATATGTGACTATAAATGGACTTTT-TCTGTCAATGAATACTTTTTTTTTTACATTTCTTGATGTA
66 ATGGGTGACTATAAATGGACTTTTCT-TGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTA
* *
667 GACATTCAATTATAATCTTTTTTAA-C-AAAA---AAAAAA
130 GACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAA
* * * *
703 TTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTCAAAAGA
1 TTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTAAAGGA
* * * * ** *
768 ATGGGTGACTAT-AATAGACTTTTCTTGTCAATGGATG-TATTTTTCTTCACGTTTCTTGAGATA
66 ATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCT-TTTTTCTTCATGTTTCTCAAGGTA
* **
831 GACATTCAATTATTGTCTGTTTTAAGTAAAAATGTAAAAAA
130 GACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAA
*
872 TTTAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGACTTTTAAAGGA
1 TTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTAAAGGA
* *
937 ATGCGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAG
66 ATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAG
* * * * *
1002 ATATTTATTTATAGTCTGTTTTAACCAAAAAAGTATATAAA
131 ACATTCAATTATAGTCTGTTTTAACCAAAAATGTA-AAAAA
* * * *
1043 TTCAACTTAAAATTAATTATGATATTATAAAACCATTTAAAGCGAGTAATAA-AGCTTTTAAAAG
1 TTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGA-CTTTTAAAGG
* * * * * *
1107 AATGGGTGTCTATAAATGGCCTTTCCTAGCCAATTAATGACTTTTTT-TTCATGTTTCTCGAGGT
65 AATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG-CTTTTTTCTTCATGTTTCTCAAGGT
* *
1171 AGACATTCAATTATAATCTGTTTTAATCAAAAATGTTAAAAAA
129 AGACATTCAATTATAGTCTGTTTTAACCAAAAATG-TAAAAAA
** * * * **
1214 TTTTGCTTAAAATCAATTATAAAATTATAAAACCATTTAAAGAGAGTAATAA-AGCTTTCCAAGG
1 TTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGA-CTTTTAAAGG
* * * * *
1278 AATGGGTGACTATAAATGGACTTTTCTTGCTAGTAAATGTCTTTTTT-TTCATGTCTCTCTAGGT
65 AATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG-CTTTTTTCTTCATGTTTCTCAAGGT
* * * *
1342 AGACATTCATTTGTAATCTGTTTTAACTAAAAATGTAAAAAA
129 AGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAA
* * * ********** * *
1384 CTTTAGCTTGAAATCAATTATAAGATTATAAAACCATTTAAANNNNNNNNNNAGGCTTTTAAAAG
1 -TTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTAAAGG
* * * *
1449 AATGGGTGGCTAT-AATGGACTTTTCATACCAATGAATGCGTTTTTCTTCATGTTTCT-AGAGGT
65 AATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCA-AGGT
* * *
1512 AGGCATTCAATTATAGTTTTTTTTAACCAAAAATGTAAAAACA
129 AGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAA-A
*
1555 TTCAACTTAAAATCAATTA
1 TTTAACTTAAAATCAATTA
Statistics
Matches: 863, Mismatches: 153, Indels: 42
0.82 0.14 0.04
Matches are distributed among these distances:
163 1 0.00
164 61 0.07
165 71 0.08
166 4 0.00
169 83 0.10
170 168 0.19
171 343 0.40
172 132 0.15
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (170 bp):
TTTAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGACTTTTAAAGGA
ATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAGGTAG
ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAA
Done.