Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401029.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4190.0, 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: 2782
ACGTcount: A:0.24, C:0.08, G:0.09, T:0.24
Warning! 963 characters in sequence are not A, C, G, or T
Found at i:1129 original size:21 final size:21
Alignment explanation
Indices: 1105--1153 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1095 ATAAATGGAG
*
1105 TTTTGTTACCAATGAATACTT
1 TTTTCTTACCAATGAATACTT
*
1126 TTTTCTTCCCAATGAATACTT
1 TTTTCTTACCAATGAATACTT
1147 TTTTCTT
1 TTTTCTT
1154 CATGTTTCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.18, G:0.06, T:0.53
Consensus pattern (21 bp):
TTTTCTTACCAATGAATACTT
Found at i:1154 original size:21 final size:21
Alignment explanation
Indices: 1113--1154 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1103 AGTTTTGTTA
1113 CCAATGAATACTTTTTTCTTC
1 CCAATGAATACTTTTTTCTTC
1134 CCAATGAATACTTTTTTCTTC
1 CCAATGAATACTTTTTTCTTC
1155 ATGTTTCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.48
Consensus pattern (21 bp):
CCAATGAATACTTTTTTCTTC
Found at i:1727 original size:172 final size:171
Alignment explanation
Indices: 1321--2363 Score: 804
Period size: 172 Copynumber: 6.1 Consensus size: 171
1311 NNNNTGAATA
* * * * * *
1321 AATTTTTAGATTATAAAACTATTTCAAGTGAGTAACAAGGCTTTTGAAAGAATGGCTGACTATAA
1 AATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAA
* * ** * * *
1386 TTAGACTTCTCTTGCCAATGAATGTTTTTTTAGTTC-CGTTTCTTG-AGGTAGACATTCAATTAT
66 ATGGACTTCTCTTGCCAATGAATACTTTTTT-CTTCATGTTTC-TGAAGGTAGACATTCAATCAT
* *
1449 TGTCTGTTTAACTAAAAATAT-CAAAGAAATTCAATTTAAAATC
129 AGTCTGTTTAACTAAAAATATACAAAG-AATTCAACTTAAAATC
* * * * * *
1492 AATTATG-GCATTACAAAACCGTTGAAA-TCGAGTAATAAGGCTTTTGAAGGTATGGACGACTAT
1 AATTTTGAG-ATTATAAAACCATTTAAAGT-GAGTAATAAGGCTTTTGAAGGAATGGATGACTAT
* *
1555 AAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAATCCT
64 AAATGGACTTCTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAATCAT
* * *
1620 AGTCTGTTTTAACCAAAAATGTGCAAAGAATTCAAACTT-AAATC
129 AGTCTG-TTTAACTAAAAATATACAAAGAATTC-AACTTAAAATC
* *
1664 AATTTTGAGATTATAAAATCATTTAAAGTGAGTAATAAGGATTTTGAAGGAATGGATGACTATAA
1 AATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAA
* * * * *
1729 ATGGACTTCTCTTGCCAAAGAATGACTTTTTTTTTTATGTTTCTCG-AGATAGACATTCAATTAT
66 ATGGACTTCTCTTGCCAATGAAT-ACTTTTTTCTTCATGTTTCT-GAAGGTAGACATTCAATCAT
** * *
1793 TTTCTGTTTAACTAAAAATATAAAAACAATTCAACTTAAAATC
129 AGTCTGTTTAACTAAAAATATACAAAGAATTCAACTTAAAATC
* ** ** ***
1836 AATTATG-GTATTCCAAAACCATTTAAAACGAGTAATAAGGCTTTTGAATCTATAGG-TGACTAT
1 AATTTTGAG-ATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-GGATGACTAT
******************** * *
1899 AAATNNNNNNNNNNNNNNNNNNNNTACTTTTTTCTTCATGTTTCTAAAGGTAGACATTCAATCCT
64 AAATGGACTTCTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAATCAT
* * * *
1964 AGTTTGTTTTAACTAAAAATATACAAAGAATTCAAATTTAAATT
129 AGTCTG-TTTAACTAAAAATATACAAAGAATTCAACTTAAAATC
* * * * * * *
2008 AATTTTAAGATTATCAAACTATTTAAAGTGAGTAATAGGGATTCTT-AAGGAATTGTTGACTATA
1 AATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTT-TTGAAGGAATGGATGACTATA
* ** * * *
2072 ATTGGACTTCTCTTGCCAATGAAGGGCTTTTTAT-TT-GTGTTTCTCAAGGTAGACATTCAATTA
65 AATGGACTTCTCTTGCCAATGAA-TACTTTTT-TCTTCATGTTTCTGAAGGTAGACATTCAATCA
* *
2135 TTGTCTATTTAACTAAAAATATA-AAA-ATATTCAACTTAAAATC
128 TAGTCTGTTTAACTAAAAATATACAAAGA-ATTCAACTTAAAATC
* * * * * * *
2178 AATTATG-GTTTTACAAAACCATTGAAA-TCGATTAATAAGGCTTTTGAAGGTATGGGTGACTAT
1 AATTTTGAG-ATTATAAAACCATTTAAAGT-GAGTAATAAGGCTTTTGAAGGAATGGATGACTAT
********** * * *
2241 AAANNNNNNNNNNTTGCCAATGAATACATTTTTCTTTATGTTTCTGAAGGTAGACATTCAATCCT
64 AAATGGACTTCTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAATCAT
* * * * *
2306 AGTTTGATTTAACCAAAAATGTACAAAGAATTCAAATTTAAATC
129 AGTCTG-TTTAACTAAAAATATACAAAGAATTCAACTTAAAATC
2350 AATTTTGAGATTAT
1 AATTTTGAGATTAT
2364 NNNNNNNNNN
Statistics
Matches: 662, Mismatches: 179, Indels: 61
0.73 0.20 0.07
Matches are distributed among these distances:
168 1 0.00
169 12 0.02
170 105 0.16
171 174 0.26
172 305 0.46
173 63 0.10
174 2 0.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.36
Consensus pattern (171 bp):
AATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGATGACTATAA
ATGGACTTCTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAATCATAG
TCTGTTTAACTAAAAATATACAAAGAATTCAACTTAAAATC
Found at i:1954 original size:344 final size:341
Alignment explanation
Indices: 1321--2363 Score: 1221
Period size: 344 Copynumber: 3.0 Consensus size: 341
1311 NNNNTGAATA
* * * * * *
1321 AATTTTTAGATTATAAAACTATTTCAAGTGAGTAACAAGGCTTTTGAAAGAATGGCTGACTATAA
1 AATTTTAAGATTATAAAACTATTTAAAGTGAGTAATAAGGATTTTGAAGGAATGGATGACTATAA
* * ** *
1386 TTAGACTTCTCTTGCCAATGAATG-TTTTTTTAGTTCCGTTTCTTGAGGTAGACATTCAATTATT
66 TTGGACTTCTCTTGCCAATGAATGCTTTTTTT-TTTATGTTTCTCGAGGTAGACATTCAATTATT
* * * *
1450 GTCTGTTTAACTAAAAATATCAAAGAAATTCAATTTAAAATCAATTATGGCATTACAAAACCGTT
130 GTCTGTTTAACTAAAAATAT-AAAAAAATTCAACTTAAAATCAATTATGGTATTACAAAACCATT
*
1515 GAAATCGAGTAATAAGGCTTTTGAAGGTATGGACGACTATAAATGGACTTTTCTTGCCAATGAAT
194 GAAATCGAGTAATAAGGCTTTTGAAGGTATGG-TGACTATAAATGGACTTTTCTTGCCAATGAAT
* * *
1580 ACTTTTTTCTTCATGTTTCTGAAGGTAGACATTCAATCCTAGTCTGTTTTAACCAAAAATGTGCA
258 ACTTTTTTCTTCATGTTTCTAAAGGTAGACATTCAATCCTAGTCTGTTTTAACCAAAAATATACA
1645 AAGAATTCAAACTTAAATC
323 AAGAATTCAAACTTAAATC
*
1664 AATTTTGAGATTATAAAA-TCATTTAAAGTGAGTAATAAGGATTTTGAAGGAATGGATGACTATA
1 AATTTTAAGATTATAAAACT-ATTTAAAGTGAGTAATAAGGATTTTGAAGGAATGGATGACTATA
* * *
1728 AATGGACTTCTCTTGCCAAAGAATGACTTTTTTTTTTATGTTTCTCGAGATAGACATTCAATTAT
65 ATTGGACTTCTCTTGCCAATGAATG-CTTTTTTTTTTATGTTTCTCGAGGTAGACATTCAATTAT
* *
1793 TTTCTGTTTAACTAAAAATATAAAAACAATTCAACTTAAAATCAATTATGGTATTCCAAAACCAT
129 TGTCTGTTTAACTAAAAATATAAAAA-AATTCAACTTAAAATCAATTATGGTATTACAAAACCAT
* * ** ********************
1858 TTAAAACGAGTAATAAGGCTTTTGAATCTATAGGTGACTATAAATNNNNNNNNNNNNNNNNNNNN
193 TGAAATCGAGTAATAAGGCTTTTGAAGGTAT-GGTGACTATAAATGGACTTTTCTTGCCAATGAA
* *
1923 TACTTTTTTCTTCATGTTTCTAAAGGTAGACATTCAATCCTAGTTTGTTTTAACTAAAAATATAC
257 TACTTTTTTCTTCATGTTTCTAAAGGTAGACATTCAATCCTAGTCTGTTTTAACCAAAAATATAC
* *
1988 AAAGAATTCAAATTTAAATT
322 AAAGAATTCAAACTTAAATC
* * * *
2008 AATTTTAAGATTATCAAACTATTTAAAGTGAGTAATAGGGATTCTT-AAGGAATTGTTGACTATA
1 AATTTTAAGATTATAAAACTATTTAAAGTGAGTAATAAGGATT-TTGAAGGAATGGATGACTATA
* * * *
2072 ATTGGACTTCTCTTGCCAATGAAGGGC-TTTTTATTTGTGTTTCTCAAGGTAGACATTCAATTAT
65 ATTGGACTTCTCTTGCCAATGAA-TGCTTTTTTTTTTATGTTTCTCGAGGTAGACATTCAATTAT
* * *
2136 TGTCTATTTAACTAAAAATATAAAAATATTCAACTTAAAATCAATTATGGTTTTACAAAACCATT
129 TGTCTGTTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGGTATTACAAAACCATT
* **********
2201 GAAATCGATTAATAAGGCTTTTGAAGGTATGGGTGACTATAAANNNNNNNNNNTTGCCAATGAAT
194 GAAATCGAGTAATAAGGCTTTTGAAGGTAT-GGTGACTATAAATGGACTTTTCTTGCCAATGAAT
* * * * * *
2266 ACATTTTTCTTTATGTTTCTGAAGGTAGACATTCAATCCTAGTTTGATTTAACCAAAAATGTACA
258 ACTTTTTTCTTCATGTTTCTAAAGGTAGACATTCAATCCTAGTCTGTTTTAACCAAAAATATACA
*
2331 AAGAATTCAAATTTAAATC
323 AAGAATTCAAACTTAAATC
*
2350 AATTTTGAGATTAT
1 AATTTTAAGATTAT
2364 NNNNNNNNNN
Statistics
Matches: 597, Mismatches: 95, Indels: 17
0.84 0.13 0.02
Matches are distributed among these distances:
342 174 0.29
343 139 0.23
344 271 0.45
345 13 0.02
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.36
Consensus pattern (341 bp):
AATTTTAAGATTATAAAACTATTTAAAGTGAGTAATAAGGATTTTGAAGGAATGGATGACTATAA
TTGGACTTCTCTTGCCAATGAATGCTTTTTTTTTTATGTTTCTCGAGGTAGACATTCAATTATTG
TCTGTTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGGTATTACAAAACCATTGA
AATCGAGTAATAAGGCTTTTGAAGGTATGGTGACTATAAATGGACTTTTCTTGCCAATGAATACT
TTTTTCTTCATGTTTCTAAAGGTAGACATTCAATCCTAGTCTGTTTTAACCAAAAATATACAAAG
AATTCAAACTTAAATC
Done.