Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400766.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3944.0, 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: 2994
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.31
Warning! 353 characters in sequence are not A, C, G, or T
Found at i:288 original size:171 final size:171
Alignment explanation
Indices: 2--1634 Score: 1416
Period size: 171 Copynumber: 9.6 Consensus size: 171
1 G
* * * * *
2 AAAAATGTAAAAAATTTCAACTTAAAATCAATTATTAGATTAT-AAACTATTTAGACCGAGTAAT
1 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * *
66 AAGACTTTTAAAGCAATGGGTGACTATAAATCGACTTTTCTT-ACAAATGAATATGTTTTTCTTC
66 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGAC-AATGAATATGTTTTTCTTC
*
130 ACGTTTCTCATGATAGACATTCAATTATTA-TCTATTTTAATC
130 ACGTTTCTCATGATAGACATTCAATTA-TAGTCTGTTTTAATC
* * * *
172 AAAAATGTAAAAAACTTCAACTTAAAATCAATTATGACAGTATAAAACCATTTAAAGTGAGTAAT
1 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * *
237 AAGGGTTTTGAAGGAATGGGTTACTATAAATGGACTTTTCTTGATAATGAATACT-TTTTCCTTC
66 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGACAATGAATA-TGTTTTTCTTC
* *
301 ACGTTTCTCATGATAGACGTTCAATTATTA-TCTATTTTAATC
130 ACGTTTCTCATGATAGACATTCAATTA-TAGTCTGTTTTAATC
* * * * *
343 AAAAATATAAAAAAATTCTACTTAAAATCAATTATTAGATTAT-AAACTATTTAAAACGAGTAAT
1 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * *
407 AAGACTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGTGTTTTTCTTCA
66 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGACAATGAATATGTTTTTCTTCA
** * ** *
472 TTTTTCTTGA-GATAGACATTCAATTATAGTCTACTTTAATG
131 CGTTTC-TCATGATAGACATTCAATTATAGTCTGTTTTAATC
* *
513 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGACATTATAAAACCATTTAAAGTGAGTAAT
1 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * * * *
578 AAAGCTTTTGAAGGAATGGGAGGCAACAAATAGG-CTTTTCTT-ACCAATGAATGCT-TTTTTCT
66 AAGGCTTTTGAAGGAATGGGTGACTATAAAT-GGACTTTTCTTGA-CAATGAAT-ATGTTTTTCT
* * ** *
640 TCACTTTTCACATGGGAGACATTCAATTATAGTCTGTTTTAATG
128 TCACGTTTCTCATGATAGACATTCAATTATAGTCTGTTTTAATC
* * * * * * * *
684 AAAAATATAAAAAAAATAAACTTGAATTTAATTATGAGAATATAAAACCATTTAGAA-CGAGCAA
1 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA-AAGCGAGTAA
* * * * * * ** *
748 AAAGACTGTTGAAGGAATAGGAGGCTATAAAT-GAAATTT-TTGTATCAATGAAT-GGTTTTTTC
65 TAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTG-A-CAATGAATATG-TTTTTC
** * *** * * * * * *
810 TTCTTGCTTCTTGGGGTAAACATGCAATTATAGCCTGTTTTATTA
127 TTCACGTTTCTCATGATAGACATTCAATTATAGTCTGTTTTAATC
* *
855 AAAAATGTAAAAAAATTCAACTTAAAATCTATTATGAGATTAGAAAACCATTTAAAGCGAGTAAT
1 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * *
920 AAGTCTTTTGAAGGAAGGGGTGACTATAAATGGACTTTTCTTGCCAATG-A-ATGCTCTTTACTT
66 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGACAATGAATATG-T-TTTTCTT
* * * * * *
983 CATGTTTCTAAAGATAAAAATTCAATTATTA-TCTATTTTAATC
129 CACGTTTCTCATGATAGACATTCAATTA-TAGTCTGTTTTAATC
* ** * * * * **
1026 AAAAATGTAAAAAACTTCAACGAAAAATCAATTATTAGATTATACAACCACTTGAAGTAAGTAAT
1 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * * * * *
1091 AAGGCTTTTGAAGGAATGAGAGGCTGTAAATAGACTTTTCTTGCCAATGAATACT-TTTTTCTTT
66 AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGACAATGAATA-TGTTTTTCTTC
** * * *
1155 ACGTTTCTCATGGCAGACATTCAATTATATTCCGTTTTAATG
130 ACGTTTCTCATGATAGACATTCAATTATAGTCTGTTTTAATC
*
1197 AAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAAACCATTTAGAA-CGAGTAA
1 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA-AAGCGAGTAA
* * * ** * * * *
1261 AAAGGCTATTGAAGGACTAAGAGGCTATAAATAGACTTTTGTT-ATCAATG-A-ATGCTTTTTCC
65 TAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGA-CAATGAATATG-TTTTT-C
* * * * *
1323 TTCATGGTTCTCGAGGCA-A-ACATTCAATTATAGCCTGTTTT-AGC
127 TTCACGTTTCTC-ATG-ATAGACATTCAATTATAGTCTGTTTTAATC
* * * * * ************
1367 AAAAAATGTAAAAGAATTCAACTTAAAATCAATTATAAGACTAGAAAACTATTNNNNNNNNNNNN
1 -AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
*
1432 TAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTG-CTAATGAATACT-TTTTTCT
65 TAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGAC-AATGAATA-TGTTTTTCT
* * *
1495 AT-ACGTTTCTCGAT-ATAGATAGTCAATTATTGTCTGTTTTAATC
128 -TCACGTTTCTC-ATGATAGACATTCAATTATAGTCTGTTTTAATC
* * * * * ***
1539 AAAAATGTAAAAAACTTCAATTTAAAATCAATTATTAGATTATCAAACCATTTTAATTAAGTAAT
1 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * *
1604 AAGGCTTTTGAAAGAATGGGAGGCTATAAAT
66 AAGGCTTTTGAAGGAATGGGTGACTATAAAT
1635 TGNNNNNNNN
Statistics
Matches: 1173, Mismatches: 245, Indels: 89
0.78 0.16 0.06
Matches are distributed among these distances:
168 1 0.00
169 8 0.01
170 201 0.17
171 926 0.79
172 30 0.03
173 5 0.00
174 2 0.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (171 bp):
AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
AAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGACAATGAATATGTTTTTCTTCA
CGTTTCTCATGATAGACATTCAATTATAGTCTGTTTTAATC
Found at i:1666 original size:513 final size:510
Alignment explanation
Indices: 2--1634 Score: 1846
Period size: 513 Copynumber: 3.2 Consensus size: 510
1 G
* * * ***
2 AAAAATGTAAAAAATTTCAACTTAAAATCAATTATTAGATTATAAACTATTTAGACCGAGTAATA
1 AAAAATGTAAAAAACTTCAACTTAAAATCAATTATTAGATTATAAACCATTTAAAGTAAGTAATA
* * * * * * *
67 AGACTTTTAAAGCAATGGGTGACTATAAATCGACTTTTCTTACAAATGAATA-TGTTTTTCTTCA
66 AGGCTTTTGAAGGAATGGGAGGCTATAAATAGACTTTTCTTACCAATGAATACT-TTTTTCTTCA
** * * * *
131 CGTTTCTCATGATAGACATTCAATTAT-TATCTATTTTAATCAAAAATGTAAAAAACTTCAACTT
130 CGTTTCTCATGGCAGACATTCAATTATAT-TCTGTTTTAATGAAAAATGTAAAAAAATTAAACTT
* * * * * * * **
195 AAAATCAATTATGACAGTATAAAACCATTTA-AAGTGAGTAATAAGGGTTTTGAAGGAATGGGTT
194 AAAATCAATTATGAGAATATAAAACCATTTAGAA-CGAGTAAAAAGGCTATTGAAGGAATAGGAG
* * * * * * * *
259 ACTATAAATGGACTTTTCTTGAT-AATGAATACTTTTTCCTTCACGTTTCTC-ATGATAGACGTT
258 GCTATAAATAGACTTTTGTT-ATCAATGAATGCTTTTTCCTTCATGCTTCTCGAGGA-A-ACATT
* * * * *
322 CAATTATTA-TCTATTTTAATC-AAAAATATAAAAAAATTCTACTTAAAATCAATTATTAGATTA
320 CAATTA-TAGCCTGTTTT-ATCAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAGATTA
*
385 -TAAACTATTTAAAACGAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTT
383 GAAAACTATTTAAAACGAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTT
* * * * * * *
449 GCCAATGAATGTGTTTTTCTTCATTTTTCTTGAGATAGACATTCAATTATAGTCTACTTTAATG
448 GCCAATGAATCT-TTTTTCTTCATGTTTCTAGAGATAGAAATTCAATTATTGTCTATTTTAATC
* * * *
513 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGACATTATAAAACCATTTAAAGTGAGTAAT
1 AAAAATGTAAAAAACTTCAACTTAAAATCAATTATTAGATTAT-AAACCATTTAAAGTAAGTAAT
* * * * *
578 AAAGCTTTTGAAGGAATGGGAGGCAACAAATAGGCTTTTCTTACCAATGAATGCTTTTTTCTTCA
65 AAGGCTTTTGAAGGAATGGGAGGCTATAAATAGACTTTTCTTACCAATGAATACTTTTTTCTTCA
* * * * * * *
643 CTTTTCACATGGGAGACATTCAATTATAGTCTGTTTTAATGAAAAATATAAAAAAAATAAACTTG
130 CGTTTCTCATGGCAGACATTCAATTATATTCTGTTTTAATGAAAAATGTAAAAAAATTAAACTTA
* * * * *
708 AATTTAATTATGAGAATATAAAACCATTTAGAACGAGCAAAAAGACTGTTGAAGGAATAGGAGGC
195 AAATCAATTATGAGAATATAAAACCATTTAGAACGAGTAAAAAGGCTATTGAAGGAATAGGAGGC
* * * * * * * *
773 TATAAATGAAATTTTTG-TATCAATGAATGGTTTTTTCTTCTTGCTTCTTGGGGTAAACATGCAA
260 TATAAAT-AGACTTTTGTTATCAATGAATGCTTTTTCCTTCATGCTTCTCGAGG-AAACATTCAA
* * *
837 TTATAGCCTGTTTTATTAAAAAATGTAAAAAAATTCAACTTAAAATCTATTATGAGATTAGAAAA
323 TTATAGCCTGTTTTATCAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAGATTAGAAAA
* * * *
902 CCATTTAAAGCGAGTAATAAGTCTTTTGAAGGAAGGGGTGACTATAAATGGACTTTTCTTGCCAA
388 CTATTTAAAACGAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAA
* * * * *
967 TGAATGCTCTTTACTTCATGTTTCTAAAGATAAAAATTCAATTATTATCTATTTTAATC
453 TGAAT-CTTTTTTCTTCATGTTTCTAGAGATAGAAATTCAATTATTGTCTATTTTAATC
** * *
1026 AAAAATGTAAAAAACTTCAACGAAAAATCAATTATTAGATTATACAACCACTTGAAGTAAGTAAT
1 AAAAATGTAAAAAACTTCAACTTAAAATCAATTATTAGATTATA-AACCATTTAAAGTAAGTAAT
* * * *
1091 AAGGCTTTTGAAGGAATGAGAGGCTGTAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTTA
65 AAGGCTTTTGAAGGAATGGGAGGCTATAAATAGACTTTTCTTACCAATGAATACTTTTTTCTTCA
* *
1156 CGTTTCTCATGGCAGACATTCAATTATATTCCGTTTTAATGAAAAATGTAAAAAAATTGAACTTA
130 CGTTTCTCATGGCAGACATTCAATTATATTCTGTTTTAATGAAAAATGTAAAAAAATTAAACTTA
* * *
1221 AAATCAATTATGAGATTATAAAACCATTTAGAACGAGTAAAAAGGCTATTGAAGGACTAAGAGGC
195 AAATCAATTATGAGAATATAAAACCATTTAGAACGAGTAAAAAGGCTATTGAAGGAATAGGAGGC
*
1286 TATAAATAGACTTTTGTTATCAATGAATGCTTTTTCCTTCATGGTTCTCGAGGCAAACATTCAAT
260 TATAAATAGACTTTTGTTATCAATGAATGCTTTTTCCTTCATGCTTCTCGAGG-AAACATTCAAT
* * *
1351 TATAGCCTGTTTTAGCAAAAAATGTAAAAGAATTCAACTTAAAATCAATTATAAGACTAGAAAAC
324 TATAGCCTGTTTTATCAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAGATTAGAAAAC
************ * * *
1416 TATTNNNNNNNNNNNNTAAGGCTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCTAAT
389 TATTTAAAACGAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAAT
* * * * * *
1481 GAATACTTTTTTCTAT-ACGTTTCTCGATATAGATAGTCAATTATTGTCTGTTTTAATC
454 GAAT-CTTTTTTCT-TCATGTTTCTAGAGATAGAAATTCAATTATTGTCTATTTTAATC
* * *
1539 AAAAATGTAAAAAACTTCAATTTAAAATCAATTATTAGATTATCAAACCATTTTAATTAAGTAAT
1 AAAAATGTAAAAAACTTCAACTTAAAATCAATTATTAGATTAT-AAACCATTTAAAGTAAGTAAT
*
1604 AAGGCTTTTGAAAGAATGGGAGGCTATAAAT
65 AAGGCTTTTGAAGGAATGGGAGGCTATAAAT
1635 TGNNNNNNNN
Statistics
Matches: 934, Mismatches: 172, Indels: 30
0.82 0.15 0.03
Matches are distributed among these distances:
511 46 0.05
512 258 0.28
513 626 0.67
514 4 0.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (510 bp):
AAAAATGTAAAAAACTTCAACTTAAAATCAATTATTAGATTATAAACCATTTAAAGTAAGTAATA
AGGCTTTTGAAGGAATGGGAGGCTATAAATAGACTTTTCTTACCAATGAATACTTTTTTCTTCAC
GTTTCTCATGGCAGACATTCAATTATATTCTGTTTTAATGAAAAATGTAAAAAAATTAAACTTAA
AATCAATTATGAGAATATAAAACCATTTAGAACGAGTAAAAAGGCTATTGAAGGAATAGGAGGCT
ATAAATAGACTTTTGTTATCAATGAATGCTTTTTCCTTCATGCTTCTCGAGGAAACATTCAATTA
TAGCCTGTTTTATCAAAAAATGTAAAAAAATTCAACTTAAAATCAATTATAAGATTAGAAAACTA
TTTAAAACGAGTAATAAGACTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGA
ATCTTTTTTCTTCATGTTTCTAGAGATAGAAATTCAATTATTGTCTATTTTAATC
Done.