Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402882.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5932.0, 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, 893
Length: 1489
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Found at i:853 original size:171 final size:171
Alignment explanation
Indices: 4--1414 Score: 1333
Period size: 171 Copynumber: 8.2 Consensus size: 171
1 TTA
* * * ** *
4 AAGGAATGGGAGACTATAAATGGACTTTTCTTC-CAAATAAATGAGTTTTTT-TAGACGTTT-TT
1 AAGGAATGGGTGACTATAAATGGACTTTTCTTCAC-AATGAAT-ACTTTTTTCTTCACATTTCTT
* * * * * *
66 CAAGGTAGGCATTCAATTATGGTCTATTTTATCGAAAAATGTAAAA-AATTTAACTCAAAATCAA
64 -GAGGTAGACATTCAATTATAGTCTATTTTAACCAAAAATGTAAAACAATTTAACTTAAAATCAA
* * **
130 TTATGAGATTATAAAATCATTTAAAGTGAGTAATAATACTTTT-
128 TTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * ** *
173 ACAGGAATTGGAGACTATAAATGGACTTTTCTTCTA-AATAAATACACTTTTCTACATC-TTTCT
1 A-AGGAATGGGTGACTATAAATGGACTTTTCTTC-ACAATGAATACTTTTTTCTTCA-CATTTCT
* * * * ** *
236 GGAGGTAGGCATTCAATTGTAGTTTATTTTAATAAAAAATGTAAAA-AATTCAACTTAAAATCAA
63 TGAGGTAGACATTCAATTATAGTCTATTTTAACCAAAAATGTAAAACAATTTAACTTAAAATCAA
*
300 TTA-GAAGATTATAAAACCATTTAAAGCGAGTAATAAGGGTTTTG
128 TTATG-AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* ** * * ** *
344 AAGGAATGGGTGACTACAAATAAACTTTT-TTTATCAATGAAT-GTCTTTTTCTTCATGTTTCCT
1 AAGGAATGGGTGACTATAAATGGACTTTTCTTCA-CAATGAATACT-TTTTTCTTCACATTTCTT
* * * * * * * * *
407 AACGCAGACAGTCAATTATAATATGTTTTAACCAAAAATGTAAAAACAATTAAACTTAAAATCTA
64 GAGGTAGACATTCAATTATAGTCTATTTTAACCAAAAATGT-AAAACAATTTAACTTAAAATCAA
* * *
472 TTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGGTTTTG
128 TTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
** * * * * *
516 AAGGAATGGGTGGGTATAAATGGACTTTTCCTGACAATGAATTCCTTTTTCTTCAC-TTTTTTGA
1 AAGGAATGGGTGACTATAAATGGACTTTTCTTCACAATGAATACTTTTTTCTTCACATTTCTTGA
* * * * * *
580 GGTAGACATTTAATTATAATCCATTTTAACTAAAAATTTCAAAACAAATTGAA-TTCAAAATCAA
66 GGTAGACATTCAATTATAGTCTATTTTAACCAAAAATGT-AAAAC-AATTTAACTT-AAAATCAA
* *
644 TTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCG
128 TTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
** * * *
688 AAGGAATGGAAGACTATAAATGGGCTTTTCTTCACAATAAATACTTTTTTCTTTACATTTCTTGA
1 AAGGAATGGGTGACTATAAATGGACTTTTCTTCACAATGAATACTTTTTTCTTCACATTTCTTGA
* * * *
753 GGTAGACATTCAATTATAGTCTGTTTTCACTAAAAATGTAAAACAATTTAACTTAAAATCAGTTA
66 GGTAGACATTCAATTATAGTCTATTTTAACCAAAAATGTAAAACAATTTAACTTAAAATCAATTA
* * *
818 TGAAATTATAAAACTATTTAAAGCAAGTAATAAGGCTTTT-
131 TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * ** * * * * * *
858 AAGAGAATGGGTTACTATAAACGAACTTTTCTTCTTAGTGAATGGCTCTTTT-TACACGTTTCAT
1 AAG-GAATGGGTGACTATAAATGGACTTTTCTTCACAATGAAT-ACTTTTTTCTTCACATTTCTT
* * * * * * *
922 GAGGTAGACAATCCATTATAGTATATTTTAACGAAAAATATAAAATAATTCAACTTAAAATCAAT
64 GAGGTAGACATTCAATTATAGTCTATTTTAACCAAAAATGTAAAACAATTTAACTTAAAATCAAT
* *
987 TATGACATTATAAAACCATTTAAAGCGAGTTATAAGGCTTTTG
129 TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * ** * ** * * * *
1030 AAAGAACGTATGACTATAAATAGACTTTTCTTGTCGATGAATGCCTTTTTCTTCATATTTCTTGA
1 AAGGAATGGGTGACTATAAATGGACTTTTCTTCACAATGAATACTTTTTTCTTCACATTTCTTGA
* * * ** * *
1095 GGTAAAAATTCAATTATAATCGGTTTTAACCAAAAATGTAAAACAAATTGAACTCAAAATCAATT
66 GGTAGACATTCAATTATAGTCTATTTTAACCAAAAATGTAAAAC-AATTTAACTTAAAATCAATT
* * * * **
1160 ATGAGATTATCAAATCGTGTAAAATGAGTAATAAGGCTTTTG
130 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * ** *
1202 AAGGAATGAGAGACTATAAATAGACTTTTCTTTC-CAATGAATGTTTTTTTCTTTACATTTCTTG
1 AAGGAATGGGTGACTATAAATGGACTTTTC-TTCACAATGAATACTTTTTTCTTCACATTTCTTG
* * *
1266 AAGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATT
65 AGGTAGACATTCAATTATAGTCTATTTTAACCAAAAATGTAAAACAATTTAACTTAAAATCAATT
* *
1331 ATGTGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTC
130 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
* * * *
1373 AAGGAATGGGTCACTATAAATGGACTTCTCTTCTCAGTGAAT
1 AAGGAATGGGTGACTATAAATGGACTTTTCTTCACAATGAAT
1415 GGCTCTTTCT
Statistics
Matches: 1010, Mismatches: 204, Indels: 54
0.80 0.16 0.04
Matches are distributed among these distances:
168 1 0.00
169 9 0.01
170 217 0.21
171 385 0.38
172 353 0.35
173 45 0.04
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (171 bp):
AAGGAATGGGTGACTATAAATGGACTTTTCTTCACAATGAATACTTTTTTCTTCACATTTCTTGA
GGTAGACATTCAATTATAGTCTATTTTAACCAAAAATGTAAAACAATTTAACTTAAAATCAATTA
TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTG
Found at i:1140 original size:514 final size:511
Alignment explanation
Indices: 76--1440 Score: 1649
Period size: 514 Copynumber: 2.7 Consensus size: 511
66 CAAGGTAGGC
** * * * *
76 ATTCAATTATGGTCTATTTTATCGAAAAATGT-AAA-AAATTTAACTCAAAATCAATTATGAGAT
1 ATTCAATTATAATCCATTTTAACCAAAAATGTAAAACAAATTGAACTCAAAATCAATTATGAGAT
** *
139 TATAAAATCATTTAAAGTGAGTAATAATACTTTTACAGGAATTGG-AGACTATAAATGGACTTTT
66 TATAAAATCATTTAAAGTGAGTAATAAGGCTTTGA-AGGAA-TGGAAGACTATAAATGGACTTTT
** * * * * *
203 CTTCTA-AATAAATACACTTTTC--TACATCTTTCTGGAGGTAGGCATTCAATTGTAGTTTATTT
129 CTTC-ACAATAAATACTTTTTTCTTTACA--TTTCTTGAGGTAGACATTCAATTATAGTCTGTTT
* *
265 TAATAAAAAATGTAAAAAATTCAACTTAAAATCAATTA-GAAGATTATAAAACCATTTAAAGCGA
191 TACT-AAAAATGTAAAAAATTTAACTTAAAATCAATTATGAA-ATTATAAAACCATTTAAAGCGA
* * * * * * * * *
329 GTAATAAGGGTTTTGAAGGAATGGGTGACTACAAATAAACTTTTTTTATCAATGAATGTCT-TTT
254 GTAATAAGGCTTTTCAAGGAATGGGTCACTATAAATGAACTTTTCTTCTCAGTGAATGGCTCTTT
* * * * * * * *
393 TCTTCATGTTTCCTAACGCAGACAGTCAATTATAATATGTTTTAACCAAAAATGTAAAAACAATT
319 T-TACACGTTTCATAAGGTAGACAATCAATTATAATATATTTTAACCAAAAATATAAAAACAATT
* * * * * * *
458 AAACTTAAAATCTATTTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGGTTTTGAAGGAAT
383 AAACTTAAAATCAATTATGACATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAAC
* ** * * * *
523 GGGTGGGTATAAATGGACTTTTCCTGACAATGAATTCCTTTTTCTTCACTTTTTTGAGGTAGAC
448 GGATGACTATAAATAGACTTTTCCTGACAATGAATGCCTTTTTCTTCACTTTTTTGAGGTAAAA
* * * *
587 ATTTAATTATAATCCATTTTAACTAAAAATTTCAAAACAAATTGAATTCAAAATCAATTATGAGA
1 ATTCAATTATAATCCATTTTAACCAAAAATGT-AAAACAAATTGAACTCAAAATCAATTATGAGA
* *
652 TTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAGGAATGGAAGACTATAAATGGGCTTTT
65 TTATAAAATCATTTAAAGTGAGTAATAAGGCTTT-GAAGGAATGGAAGACTATAAATGGACTTTT
717 CTTCACAATAAATACTTTTTTCTTTACATTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTCA
129 CTTCACAATAAATACTTTTTTCTTTACATTTCTTGAGGTAGACATTCAATTATAGTCTGTTTT-A
* * *
782 CTAAAAATGTAAAACAATTTAACTTAAAATCAGTTATGAAATTATAAAACTATTTAAAGCAAGTA
193 CTAAAAATGTAAAA-AATTTAACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGCGAGTA
* * *
847 ATAAGGCTTTT-AAGAGAATGGGTTACTATAAACGAACTTTTCTTCTTAGTGAATGGCTCTTTTT
257 ATAAGGCTTTTCAAG-GAATGGGTCACTATAAATGAACTTTTCTTCTCAGTGAATGGCTCTTTTT
* * * * * *
911 ACACGTTTCATGAGGTAGACAATCCATTATAGTATATTTTAACGAAAAATAT-AAAATAATTCAA
321 ACACGTTTCATAAGGTAGACAATCAATTATAATATATTTTAACCAAAAATATAAAAACAATTAAA
* *
975 CTTAAAATCAATTATGACATTATAAAACCATTTAAAGCGAGTTATAAGGCTTTTGAAAGAACGTA
386 CTTAAAATCAATTATGACATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAACGGA
* * *
1040 TGACTATAAATAGACTTTTCTTGTCGATGAATGCCTTTTTCTTCA-TATTTCTTGAGGTAAAA
451 TGACTATAAATAGACTTTTCCTGACAATGAATGCCTTTTTCTTCACT-TTT-TTGAGGTAAAA
**
1102 ATTCAATTATAATCGGTTTTAACCAAAAATGTAAAACAAATTGAACTCAAAATCAATTATGAGAT
1 ATTCAATTATAATCCATTTTAACCAAAAATGTAAAACAAATTGAACTCAAAATCAATTATGAGAT
* * * * *
1167 TATCAAATCGTGTAAAATGAGTAATAAGGCTTTTGAAGGAAT-GAGAGACTATAAATAGACTTTT
66 TATAAAATCATTTAAAGTGAGTAATAAGGC-TTTGAAGGAATGGA-AGACTATAAATGGACTTTT
* ** *
1231 CTTTC-CAATGAATGTTTTTTTCTTTACATTTCTTGAAGTAGACATTCAATTATAGTCTGTTTTA
129 C-TTCACAATAAATACTTTTTTCTTTACATTTCTTGAGGTAGACATTCAATTATAGTCTGTTTT-
* **
1295 ACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGTGATTATAAAACCATTTAAAGCGAGT
192 ACTAAAAATGT-AAAAAATTTAACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGCGAGT
* * *
1360 AATAAGGCTTTTCAAGGAATGGGTCACTATAAATGGACTTCTCTTCTCAGTGAATGGCTCTTTCT
256 AATAAGGCTTTTCAAGGAATGGGTCACTATAAATGAACTTTTCTTCTCAGTGAATGGCTCTTTTT
*
1425 ATACGTTTCATAAGGT
321 ACACGTTTCATAAGGT
1441 GATAACTCTA
Statistics
Matches: 733, Mismatches: 101, Indels: 37
0.84 0.12 0.04
Matches are distributed among these distances:
511 25 0.03
513 10 0.01
514 508 0.69
515 179 0.24
516 11 0.02
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (511 bp):
ATTCAATTATAATCCATTTTAACCAAAAATGTAAAACAAATTGAACTCAAAATCAATTATGAGAT
TATAAAATCATTTAAAGTGAGTAATAAGGCTTTGAAGGAATGGAAGACTATAAATGGACTTTTCT
TCACAATAAATACTTTTTTCTTTACATTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTACTA
AAAATGTAAAAAATTTAACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGCGAGTAATAA
GGCTTTTCAAGGAATGGGTCACTATAAATGAACTTTTCTTCTCAGTGAATGGCTCTTTTTACACG
TTTCATAAGGTAGACAATCAATTATAATATATTTTAACCAAAAATATAAAAACAATTAAACTTAA
AATCAATTATGACATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAACGGATGACT
ATAAATAGACTTTTCCTGACAATGAATGCCTTTTTCTTCACTTTTTTGAGGTAAAA
Done.