Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399990.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3216.0, 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: 2632
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.29
Warning! 581 characters in sequence are not A, C, G, or T
Found at i:1679 original size:171 final size:171
Alignment explanation
Indices: 1303--2632 Score: 1229
Period size: 171 Copynumber: 7.8 Consensus size: 171
1293 NNNNNAAAAT
* *** **
1303 GAGTAATAAGGCTTTTGAAGGAATG-GAAGGCTATAAATAGACTTTTCTCGCCAATGAATTTTTT
1 GAGTAATAAGGCTTTTGAAGGAATGAG-AGGCTATAAATGGACTTTTCTTATCAATGAATGCTTT
* * *
1367 TTTCTTGACTTTTCTCAAGGCAGACATTCAATTATA--CTATTTTAATGAAAAATATAAAAATAT
65 TTTCTTCACGTTTCTCAAGGCAGACATTCAATTATAGTCTATTTTAATGAAAAATATAAAAAAAT
* * * * *
1430 T-GAGTCTAAAATTAATTATGAGATTATAAAATCATTTAGAA-C
130 TCAACT-TAAAATCAATTATGAGATTAGAAAACCATTTA-AAGC
* * * * * * * *
1472 TAGTAAAAAGGCTATTAAAGAAATAAAAGGCTATAAATGGACTTTTCTTATAAATGAATGCTTTT
1 GAGTAATAAGGCTTTTGAAGGAATGAGAGGCTATAAATGGACTTTTCTTATCAATGAATGCTTTT
* * * * * *
1537 TTCTTCACGATTGTCAAGACAGACAATCAATTATAGTCTGTTTTAATAAAAAATATAAAAAAATT
66 TTCTTCACGTTTCTCAAGGCAGACATTCAATTATAGTCTATTTTAATGAAAAATATAAAAAAATT
* * * * *
1602 CAACTTAAAATCAATTATAACATTACAAAATCATTCAAAGC
131 CAACTTAAAATCAATTATGAGATTAGAAAACCATTTAAAGC
* * * *
1643 GTGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTGAT-AATGAATACTTT
1 GAGTAATAAGGCTTTTGAAGGAATGAGAGGCTATAAATGGACTTTTCTT-ATCAATGAATGCTTT
* * * ** * * * *
1707 TTCCTTCATGTTTCTCTAGATAAACATTCAATTATAGCCTATTTTAATGAGAAATATAAAAATAT
65 TTTCTTCACGTTTCTCAAGGCAGACATTCAATTATAGTCTATTTTAATGAAAAATATAAAAAAAT
* * * *
1772 TCAAGTTAAAATCAATTATGAGATTATAAAACCATTTGAAGT
130 TCAACTTAAAATCAATTATGAGATTAGAAAACCATTTAAAGC
* * * * * *
1814 GAGTAATATGGCTTTTGAAGGAAAGGGTGACTATAAATGGACTTTTCTTGTCAATGAATGCTTTT
1 GAGTAATAAGGCTTTTGAAGGAATGAGAGGCTATAAATGGACTTTTCTTATCAATGAATGCTTTT
* * ** * * * * **
1879 GTCTTCATGTTTCTTGAGGCAAATATTCAATTATAGTCTGTTTTAATCG-AAGAT-GGAAAAAAT
66 TTCTTCACGTTTCTCAAGGCAGACATTCAATTATAGTCTATTTTAAT-GAAAAATATAAAAAAAT
* * * * *
1942 TCAACCTAAAATCAATTATTAGACTAGAAAACTATTTTAAGC
130 TCAACTTAAAATCAATTATGAGATTAGAAAACCATTTAAAGC
* ** *
1984 GAGTAATAAGTCTTTTGAAGGAAT-AG-GTGACTATAAATGGACTTTTCTGGT-TATGAATGCTT
1 GAGTAATAAGGCTTTTGAAGGAATGAGAG-G-CTATAAATGGACTTTTCTTATCAATGAATGCTT
* ** * ** * *
2046 CTATT-TTCATATTTCTCGAGATAGACAGTCAATTATTA-TCTATTTTAA-GAAAAAATGTAAAA
64 -TTTTCTTCACGTTTCTCAAGGCAGACATTCAATTA-TAGTCTATTTTAATG-AAAAATATAAAA
* * * **
2108 CAATTC-ACTTTAAAATCAATTATTAGATTAGAAAACCTTTTAAAAT
126 AAATTCAAC-TTAAAATCAATTATGAGATTAGAAAACCATTTAAAGC
* * *
2154 GAGTAATAAGGCTTTTGAAGGAATGGGAGGCTATAAATAGACTTTTCTTCA-CAATGAATACTTT
1 GAGTAATAAGGCTTTTGAAGGAATGAGAGGCTATAAATGGACTTTTCTT-ATCAATGAATGCTTT
* *
2218 TTTCTTCACTTTTCTCAAGGCAGACATTTAATTATAGT-TAGTTTTAATGAAAAATGA-AAAAAA
65 TTTCTTCACGTTTCTCAAGGCAGACATTCAATTATAGTCTA-TTTTAATGAAAAAT-ATAAAAAA
* * * * **
2281 AATCAACTTAAAATCAATTATTAAATAAGAAAACCATTTAAAAT
128 ATTCAACTTAAAATCAATTATGAGATTAGAAAACCATTTAAAGC
* * **
2325 GAGTAATAAGGCTTTCGAAGGAATGAGAGGCTATAAATAGACTTTTCTTGCCAATGAATGCTTTT
1 GAGTAATAAGGCTTTTGAAGGAATGAGAGGCTATAAATGGACTTTTCTTATCAATGAATGCTTTT
* *
2390 TTCTTCACTTTTCTCAAGGCAAACATTCAATTATAGTCTATTTTAATGAAAAATAT-AAAAAATT
66 TTCTTCACGTTTCTCAAGGCAGACATTCAATTATAGTCTATTTTAATGAAAAATATAAAAAAATT
* * *
2454 AAACTTAAAATTAATTATGAGATTATAAAACCATTTAGAA-C
131 CAACTTAAAATCAATTATGAGATTAGAAAACCATTTA-AAGC
* * * * *
2495 GAGTAAAAAGGC-TATGAAAGGAATGGGAGGCTATAAATGGACTTTTATTATTAATGAATG----
1 GAGTAATAAGGCTTTTG-AAGGAATGAGAGGCTATAAATGGACTTTTCTTATCAATGAATGCTTT
* * * * * * * *
2555 --TCTTTATGTTTGTCATGGCAGACGTTCAATTATAGTCTATTTTAATAAAAAATGTAAAAAATT
65 TTTCTTCACGTTTCTCAAGGCAGACATTCAATTATAGTCTATTTTAATGAAAAATATAAAAAAAT
*
2618 TTAACTTAAAATCAA
130 TCAACTTAAAATCAA
Statistics
Matches: 955, Mismatches: 174, Indels: 68
0.80 0.15 0.06
Matches are distributed among these distances:
164 46 0.05
165 19 0.02
167 1 0.00
168 1 0.00
169 130 0.14
170 260 0.27
171 487 0.51
172 11 0.01
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (171 bp):
GAGTAATAAGGCTTTTGAAGGAATGAGAGGCTATAAATGGACTTTTCTTATCAATGAATGCTTTT
TTCTTCACGTTTCTCAAGGCAGACATTCAATTATAGTCTATTTTAATGAAAAATATAAAAAAATT
CAACTTAAAATCAATTATGAGATTAGAAAACCATTTAAAGC
Found at i:2265 original size:511 final size:511
Alignment explanation
Indices: 1298--2632 Score: 1380
Period size: 511 Copynumber: 2.6 Consensus size: 511
1288 NNNNNNNNNN
* * * *
1298 AAAATGAGTAATAAGGCTTTTGAAGGAATG-GAAGGCTATAAATAGACTTTTCTCGCCAATGAAT
1 AAAATGAGTAATAAGGCTTTCGAAGGAAAGAG-AGACTATAAATAGACTTTTCTTGCCAATGAAT
** * * * *
1362 TTTTTTTTCTTGACTTTTCTCAAGGCAGACATTCAATTATA--CTATTTTAATGAAAAATATAAA
65 GCTTTTGTCTTCACTTTTCTCAAGGCAAACATTCAATTATAGTCTATTTTAATGAAAAATAGAAA
* ** * * * * * *
1425 AATATTGAGTCTAAAATTAATTATGAGATTATAAAATCATTTAGAACTAGTAAAAAGGCTATTAA
130 AA-ATTAAACCTAAAATCAATTATGAGACTAGAAAACCATTTAGAACGAGTAAAAAGGCTATGAA
* ** * ** * * * * *
1490 AGAAATAAAAGGCTATAAATGGACTTTTCTTATAAATGAATGCTT-TTTTCTTCACGA-TTGTCA
194 AGGAATAGGAGACTATAAATGGACTTTTCTGGT-TATGAATGCTTCTATT-TTCA-TATTTCTCG
* * *
1553 AGACAGACAATCAATTATAGTCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATT
256 AGATAGACAATCAATTATAGTCTATTTTAAGAAAAAATATAAAAAAATTCAACTTAAAATCAATT
* * * * *
1618 ATAACATTACAAAATCATTCAAAGCGTGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGG
321 ATAACATTACAAAACCATTCAAAACGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAG
* * * *
1683 ACTTTTCTTGATAATGAATACTTTTTCCTTCATGTTTCTCTAGATAAACATTCAATTATAGCCTA
386 ACTTTTCTTCACAATGAATACTTTTTCCTTCATGTTTCTCAAGACAAACATTCAATTATAGCCTA
* * * * * * *
1748 TTTTAATGAGAAAT-ATAAAAATATTCAAGTTAAAATCAATTATGAGATTATAAAACCATTT
451 TTTTAATGAAAAATGA-AAAAAAAATCAACTTAAAATCAATTATGAAATAAGAAAACCATTT
* * * * * * * *
1809 GAAGTGAGTAATATGGCTTTTGAAGGAAAGGGTGACTATAAATGGACTTTTCTTGTCAATGAATG
1 AAAATGAGTAATAAGGCTTTCGAAGGAAAGAGAGACTATAAATAGACTTTTCTTGCCAATGAATG
** * * * *
1874 CTTTTGTCTTCA-TGTTTCTTGAGGCAAATATTCAATTATAGTCTGTTTTAATCG-AAGATGGAA
66 CTTTTGTCTTCACT-TTTCTCAAGGCAAACATTCAATTATAGTCTATTTTAAT-GAAAAATAGAA
* * * * * * *
1937 AAAATTCAACCTAAAATCAATTATTAGACTAGAAAACTATTTTA-AGCGAGTAATAAGTCTTTTG
129 AAAATTAAACCTAAAATCAATTATGAGACTAGAAAACCA-TTTAGAACGAGTAAAAAGGC-TATG
*
2001 -AAGGAATAGGTGACTATAAATGGACTTTTCTGGTTATGAATGCTTCTATTTTCATATTTCTCGA
192 AAAGGAATAGGAGACTATAAATGGACTTTTCTGGTTATGAATGCTTCTATTTTCATATTTCTCGA
* * *
2065 GATAGACAGTCAATTATTA-TCTATTTTAAGAAAAAATGTAAAACAATTC-ACTTTAAAATCAAT
257 GATAGACAATCAATTA-TAGTCTATTTTAAGAAAAAATATAAAAAAATTCAAC-TTAAAATCAAT
* * * * * * * *
2128 TATTAGATTAGAAAACCTTTTAAAATGAGTAATAAGGCTTTTGAAGGAATGGGAGGCTATAAATA
320 TATAACATTACAAAACCATTCAAAACGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATA
* * * * *
2193 GACTTTTCTTCACAATGAATACTTTTTTCTTCACT-TTTCTCAAGGCAGACATTTAATTATAG-T
385 GACTTTTCTTCACAATGAATACTTTTTCCTTCA-TGTTTCTCAAGACAAACATTCAATTATAGCC
*
2256 TAGTTTTAATGAAAAATGAAAAAAAAATCAACTTAAAATCAATTATTAAATAAGAAAACCATTT
449 TA-TTTTAATGAAAAATGAAAAAAAAATCAACTTAAAATCAATTATGAAATAAGAAAACCATTT
* *
2320 AAAATGAGTAATAAGGCTTTCGAAGGAATGAGAGGCTATAAATAGACTTTTCTTGCCAATGAATG
1 AAAATGAGTAATAAGGCTTTCGAAGGAAAGAGAGACTATAAATAGACTTTTCTTGCCAATGAATG
* *
2385 CTTTTTTCTTCACTTTTCTCAAGGCAAACATTCAATTATAGTCTATTTTAATGAAAAATATAAAA
66 CTTTTGTCTTCACTTTTCTCAAGGCAAACATTCAATTATAGTCTATTTTAATGAAAAATAGAAAA
* * * *
2450 AATTAAACTTAAAATTAATTATGAGATTATAAAACCATTTAGAACGAGTAAAAAGGCTATGAAAG
131 AATTAAACCTAAAATCAATTATGAGACTAGAAAACCATTTAGAACGAGTAAAAAGGCTATGAAAG
* * * ** * * *
2515 GAATGGGAGGCTATAAATGGACTTTTATTATTAATGAATG--TC---TTT-ATGTTTGTC-ATGG
196 GAATAGGAGACTATAAATGGACTTTTCTGGTT-ATGAATGCTTCTATTTTCATATTTCTCGA-GA
* ** * * * *
2573 CAGACGTTCAATTATAGTCTATTTTAATAAAAAATGTAAAAAATTTTAACTTAAAATCAA
259 TAGACAATCAATTATAGTCTATTTTAAGAAAAAATATAAAAAAATTCAACTTAAAATCAA
Statistics
Matches: 673, Mismatches: 129, Indels: 49
0.79 0.15 0.06
Matches are distributed among these distances:
505 3 0.00
506 55 0.08
507 5 0.01
510 16 0.02
511 488 0.73
512 81 0.12
513 24 0.04
514 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (511 bp):
AAAATGAGTAATAAGGCTTTCGAAGGAAAGAGAGACTATAAATAGACTTTTCTTGCCAATGAATG
CTTTTGTCTTCACTTTTCTCAAGGCAAACATTCAATTATAGTCTATTTTAATGAAAAATAGAAAA
AATTAAACCTAAAATCAATTATGAGACTAGAAAACCATTTAGAACGAGTAAAAAGGCTATGAAAG
GAATAGGAGACTATAAATGGACTTTTCTGGTTATGAATGCTTCTATTTTCATATTTCTCGAGATA
GACAATCAATTATAGTCTATTTTAAGAAAAAATATAAAAAAATTCAACTTAAAATCAATTATAAC
ATTACAAAACCATTCAAAACGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAATAGACTTT
TCTTCACAATGAATACTTTTTCCTTCATGTTTCTCAAGACAAACATTCAATTATAGCCTATTTTA
ATGAAAAATGAAAAAAAAATCAACTTAAAATCAATTATGAAATAAGAAAACCATTT
Done.