Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399647.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2896.0, 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: 3275
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.26
Warning! 906 characters in sequence are not A, C, G, or T
Found at i:1585 original size:171 final size:170
Alignment explanation
Indices: 1193--2747 Score: 1522
Period size: 171 Copynumber: 9.1 Consensus size: 170
1183 NNNNGAATAC
* * ** * *
1193 AAAAAAATTCAACTTAAAATCAGTTATAAGATTATAAAACCATTTAAAAG-AAGTAATATGGCTT
1 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTT-AAAGCGAGTAATAAGGCTT
* * * * * *
1257 TTGAAGGAATGGGTGACTATAAATAGACATTTCTTGACAATAAATG--TCTT-TTT---TTTC-T
65 TTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTCTTTAGGTTTCTT
* * * * *
1315 CAAGCTAGACATTTAATCATAATCTGTTTTAACCAATAATGT
130 C-AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT
* ************ *
1357 AAAAAAAATTGAACTTAAAATCANNNNNNNNNNNNTAAAACT-ATTTAAAGTGAGTAATAAGGCT
1 -AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-TAATTTAAAGCGAGTAATAAGGCT
* * * *
1421 TTTGATGGAATAGGAGACTATAAATAGACTTGTCTTGCCAATGAATGCTTGTTTCTTTAGGTTTC
64 TTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTT-TTTCTTTAGGTTTC
* *
1486 TTCAGGTAGACATTCAATTATAGTCTCTTTAAACCAAAAATGT
128 TTCAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT
*
1529 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAACCGAGTAATAAGGCTTT
1 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTT
* * * *
1594 TGAAGGAATAGGAGACTATAAATGGTCTTTTCTTGCCAATGAATGCTTTTTCTTTACGTTTCTTG
66 TGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTCTTTAGGTTTCTTC
* *
1659 AAGTCA-ACATTCAATTATAGTCTGTTTTAACCAAAAATCT
131 AGGT-AGACATTCAATTATAGTCTGTTTTAACCAAAAATGT
* ** *
1699 AAAAAAATTCAACTTAAAATCAGTTATGAGATTATAAAACCATTTAAAGCAAG-AATAAGGCTTT
1 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTT
* * *
1763 TGAAGGAAT-GGTGACTATAAATGGACTTTTTTTGCCAGTGAATGTCTTTTT-TTTCATGTTTC-
66 TGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATG-CTTTTTCTTT-AGGTTTCT
* *
1825 TCAAGGTAGACCTTCAATTATAGTCTGCTTTAACCAAAAATGT
129 TC-AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT
* * * * *
1868 AAAAAAATTCTATTTAAAATCATTTATCAGATTATAAAACT-ATTTAAAGCGAGTAATATGGCTT
1 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-TAATTTAAAGCGAGTAATAAGGCTT
* * *
1932 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGTTTTTTTCTTTAGGTTACT
65 TTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATG-CTTTTTCTTTAGGTTTCT
* * * * *
1997 TGAGCTAGACATTCAATTATAATCTGTTTTAATCAAAACTGT
129 TCAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT
* * *
2039 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTGAAAGTGAGTAATAAGGCTTT
1 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTT
*
2104 TGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTTAAGG-TTCT
66 TGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATGC-TTTTTCTTT-AGGTTTCT
* * * *
2168 TGAGGTAAACATTCAATTATAGTCTGTTTTAACAAAAAATCT
129 TCAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT
* * * * *
2210 AAAAAAATTCAACTTAAAATCAGTTATGACATTATAAAACAATGTAAAGCGAGTAATAAGACTTT
1 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTT
* *** * *
2275 TGAAAGAATAAAAGACTATAAATGGACTTTTCTTGCAAATGAATGCTTTTTCCTTTACGTTT-TT
66 TGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTT-CTTTAGGTTTCTT
* * ** *
2339 CAAGGTAAACATTCAATTATAGTTTGTTTTAATGAAAAATCT
130 C-AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT
* **********
2381 AAAAGAATTCAACTTAAAATCAATTATGAGATTATAAAACT-ANNNNNNNNNNGTACA-AAGGCT
1 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-TAATTTAAAGCGAGTA-ATAAGGCT
* * * * * *
2444 TTTGAAGGAATGGGTGACTATAAATAGAGTTTTTTTGCCAGTCAATG-TGTGTTTC-TTAGTGTT
64 TTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCT-T-TTTCTTTAG-GTT
* * *
2507 TCTTGAGGTA-A-ATGCTTAATTATAGTCTGTTTTAACCAAATATGT
126 TCTTCAGGTAGACAT--TCAATTATAGTCTGTTTTAACCAAAAATGT
* * * * * * *
2552 AAAAAAATTTAGCTTAAAATCAATTATGAGACTATAAAATAATTTAAAGCCAATAGTAGGGCTTT
1 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTT
* * ** * *
2617 TGAAGGAAT-GAGTGACTATAAATAGACTTTTCTAT-CTAATGAATGGCTTTTTCTACACGTTTA
66 TGAAGGAATAG-GTGACTATAAATGGACTTTTCT-TGCCAATGAAT-GCTTTTTCTTTAGGTTTC
* * * * * *
2680 ATAAGATAGGCATTCAATTATAGTCTGTTTTAACTAAAAATAT
128 TTCAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT
* * *
2723 AAAAAACTTCTACCTAAAATCAATT
1 AAAAAAATTCAACTTAAAATCAATT
2748 NNNNNNNNNN
Statistics
Matches: 1149, Mismatches: 197, Indels: 82
0.80 0.14 0.06
Matches are distributed among these distances:
164 4 0.00
165 81 0.07
167 1 0.00
168 38 0.03
169 117 0.10
170 133 0.12
171 716 0.62
172 54 0.05
173 5 0.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.35
Consensus pattern (170 bp):
AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTT
TGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTCTTTAGGTTTCTTC
AGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGT
Found at i:2541 original size:513 final size:508
Alignment explanation
Indices: 1392--2744 Score: 1687
Period size: 513 Copynumber: 2.6 Consensus size: 508
1382 NNNNNNNNNN
* * * * *
1392 TAAAACTATTTAAAGTGAGTAATAAGGCTTTTGATGGAATAGGAGACTATAAATAGACTTGTCTT
1 TAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTT
* * *
1457 GCCAATGAATGCTTGTTTCTTTAGGTTTCTTCAGGTAGACATTCAATTATAGTCTCTTTAAACCA
66 GCCAATGAATG-TTGTTTCTTTAGGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACC-
*
1522 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAACCGAGTAATA
129 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATA
*
1587 AGGCTTTTGAAGGAATAGGAGACTATAAATGGTCTTTTCTTGCCAATGAATGCTTTTTCTTTACG
194 AGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTCTTTACG
* * *
1652 TTTCTTGAAGTCAACATTCAATTATAGTCTGTTTTAACCAAAAATCTAAAAAAATTCAACTTAAA
259 TTTCTTGAGGTAAACATTCAATTATAGTCTGTTTTAACAAAAAATCTAAAAAAATTCAACTTAAA
* * * * * ***
1717 ATCAGTTATGAGATTATAAAACCATTTAAAGCAAGAATAAGGCTTTTGAAGGAATGGTGACTATA
324 ATCAGTTATGACATTATAAAACAATGTAAAGCAAGAATAAGACTTTTGAAAGAATAAAGACTATA
* * * * * *
1782 AATGGACTTTTTTTGCCAGTGAATGTCTTTTTTTTCATGTTTCTCAAGGTAGACCTTCAATTATA
389 AATGGACTTTTCTTGCAAATGAATGTCTTTTTTTTCACGTTTCTCAAGGTAAACATTCAATTATA
* * * *
1847 GTCTGCTTTAACCAAAAATGTAAAAAAATTCTATTTAAAATCATTTATCAGATTA
454 GTCTGCTTTAACCAAAAATCTAAAAAAATTCAACTTAAAATCAATTATCAGATTA
* *
1902 TAAAACTATTTAAAGCGAGTAATATGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTT
1 TAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTT
* * * * *
1967 GCCAATGAATGTTTTTTTCTTTAGGTTACTTGAGCTAGACATTCAATTATAATCTGTTTTAATCA
66 GCCAATGAATG-TTGTTTCTTTAGGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCA
* * *
2032 AAACTGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTGAAAGTGAGTAATA
130 AAA-TGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATA
*
2097 AGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTCTTTAA
194 AGGCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGC-TTTTTCTTTAC
*
2162 GGTTCTTGAGGTAAACATTCAATTATAGTCTGTTTTAACAAAAAATCTAAAAAAATTCAACTTAA
258 GTTTCTTGAGGTAAACATTCAATTATAGTCTGTTTTAACAAAAAATCTAAAAAAATTCAACTTAA
*
2227 AATCAGTTATGACATTATAAAACAATGTAAAGCGAGTAATAAGACTTTTGAAAGAATAAAAGACT
323 AATCAGTTATGACATTATAAAACAATGTAAAGCAAG-AATAAGACTTTTGAAAGAAT-AAAGACT
*
2292 ATAAATGGACTTTTCTTGCAAATGAATG-CTTTTTCCTTT-ACGTTTTTCAAGGTAAACATTCAA
386 ATAAATGGACTTTTCTTGCAAATGAATGTCTTTTT--TTTCACGTTTCTCAAGGTAAACATTCAA
* * ** * *
2355 TTATAGTTTGTTTTAATGAAAAATCTAAAAGAATTCAACTTAAAATCAATTATGAGATTA
449 TTATAGTCTGCTTTAACCAAAAATCTAAAAAAATTCAACTTAAAATCAATTATCAGATTA
********** * *
2415 TAAAACTANNNNNNNNNNGTACA-AAGGCTTTTGAAGGAATGGGTGACTATAAATAGAGTTTTTT
1 TAAAACTATTTAAAGCGAGTA-ATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCT
* * *
2479 TGCCAGTCAATGTGTGTTTC-TTAGTGTTTCTTGAGGTA-A-ATGCTTAATTATAGTCTGTTTTA
65 TGCCAATGAATGT-TGTTTCTTTAG-GTTTCTTGAGGTAGACAT--TCAATTATAGTCTGTTTTA
* * * * *
2541 ACCAAATATGTAAAAAAATTTAGCTTAAAATCAATTATGAGACTATAAAATAATTTAAAGCCAAT
126 ACCAAA-ATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGT
* * * * *
2606 AGTAGGGCTTTTGAAGGAAT-GAGTGACTATAAATAGACTTTTCTAT-CTAATGAATGGCTTTTT
190 AATAAGGCTTTTGAAGGAATAG-GAGACTATAAATGGACTTTTCT-TGCCAATGAAT-GCTTTTT
** ** * * ** * * * *
2669 CTACACGTTTAATAAGATAGGCATTCAATTATAGTCTGTTTTAACTAAAAATATAAAAAACTTCT
252 CTTTACGTTTCTTGAGGTAAACATTCAATTATAGTCTGTTTTAACAAAAAATCTAAAAAAATTCA
*
2734 ACCTAAAATCA
317 ACTTAAAATCA
2745 ATTNNNNNNN
Statistics
Matches: 726, Mismatches: 102, Indels: 27
0.85 0.12 0.03
Matches are distributed among these distances:
509 4 0.01
510 222 0.31
511 105 0.14
512 31 0.04
513 356 0.49
514 8 0.01
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.36
Consensus pattern (508 bp):
TAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTT
GCCAATGAATGTTGTTTCTTTAGGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACCAA
AATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAG
GCTTTTGAAGGAATAGGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTCTTTACGTT
TCTTGAGGTAAACATTCAATTATAGTCTGTTTTAACAAAAAATCTAAAAAAATTCAACTTAAAAT
CAGTTATGACATTATAAAACAATGTAAAGCAAGAATAAGACTTTTGAAAGAATAAAGACTATAAA
TGGACTTTTCTTGCAAATGAATGTCTTTTTTTTCACGTTTCTCAAGGTAAACATTCAATTATAGT
CTGCTTTAACCAAAAATCTAAAAAAATTCAACTTAAAATCAATTATCAGATTA
Done.