Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400820.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3994.0, 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: 2764
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.30
Warning! 430 characters in sequence are not A, C, G, or T
Found at i:734 original size:171 final size:169
Alignment explanation
Indices: 142--2214 Score: 1454
Period size: 171 Copynumber: 12.2 Consensus size: 169
132 NNNNNNNNNN
* * * * ** *
142 AAATCAATTATGAGATTACAAAACCACTTAAAGCGAGTAATAAAGCTTTCGAAGGCTTGGGTGAT
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * **********
207 TATAAATAGACTTTTCTAGTCAATGAATGGCTTTTTCTTCATGTTTCNNNNNNNNNNCATTCAAT
66 TATAAAT-GACTTTTCTTGTCAATGAATGGCTTTTTCTTCACGTTTCTTAAGGCAAACATTCAAT
* * * *
272 TATAATATGTTTTGAC-AAAATATGTGAAAAAATTCAAC-CA
130 TA-AATTTGTTTTAACTAAAA-ATGTAAAAAAATTCAACTTA
* * ** *
312 GAAATCAATTATGAGATTACAAAACCATTTGAAGTTAGTACTAAGGCTTTTGAAGGAATGGGTGA
1 -AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGA
******** * * * * *
377 CNNNNNNNNNNA-TTTTCTTGCCAATGAATGTCTTTTTCTTTATGTTTC-TAGAGGCAGACATTC
65 C--TATAAATGACTTTTCTTGTCAATGAATGGCTTTTTCTTCACGTTTCTTA-AGGCAAACATTC
* * * * *
440 AATTATATTTTTTTCTAACCAAAAATGTAAAAATATTAAACTTA
127 AATTAAATTTGTTT-TAACTAAAAATGTAAAAAAATTCAACTTA
* * * **********
484 AAATCAATTGT-ACGACTATAAAACCATTTAAAGTGAGTAATAAGGCTNNNNNNNNNNTGGGTGA
1 AAATCAATTATGA-GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGA
** ** * * * *
548 CTATAAATGGACTTTTCTTACCAATGAATTTCTCTTTCTTCATGTTTCTTGAGGCAAATATTCAA
65 CTATAAAT-GACTTTTCTTGTCAATGAATGGCTTTTTCTTCACGTTTCTTAAGGCAAACATTCAA
* * *
613 TCAAAGTATGTTTTGACTAAAAATGTAAAAAAATTCAACTTA
129 TTAAA-TTTGTTTTAACTAAAAATGTAAAAAAATTCAACTTA
** * * * * * *
655 AAAAAAATTATGAGATTACAAAACCATTTAAAACGAGTAATAAGACTTTTGAAGGAAAGTGTGAT
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * * *
720 TAAAAATAGACTTTTCTTGTCAATGAATGGCTTTTTCTTCATGTTT-TTCAAGGCAGATAATCAA
66 TATAAAT-GACTTTTCTTGTCAATGAATGGCTTTTTCTTCACGTTTCTT-AAGGCAAACATTCAA
** *
784 TTATAATTTAATTTAA-TAAAAAAGTAAAAAAA-T-AACTTA
129 TTA-AATTTGTTTTAACTAAAAATGTAAAAAAATTCAACTTA
* ********** * * *
823 AAATCAATTACGAGATNNNNNNNNNNTTTAAAGCGAGTAATAAGGC-TTTGAAGGCATGGGAGAG
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * * * * ** * *
887 TATAAATAGACCTCTCTAGTCAATGAATGACTTTTTCTTTACATTTCCCATGGCACACATTCAAT
66 TATAAAT-GACTTTTCTTGTCAATGAATGGCTTTTTCTTCACGTTTCTTAAGGCAAACATTCAAT
* *********
952 TATAATATGTTTTAACTANNNNNNNNNNAAAAA-TCAACTTA
130 TA-AATTTGTTTTAACTA-AAAATGTAAAAAAATTCAACTTA
* ** * * * * * ** * *
993 AAATTAATTACAAGGTTACAAAACAATTTAAAGAGAGTAATAAGACTTTCAAAAGCATGGGTGAC
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* ** *
1058 TATAAATGGGCTTTTCTAATCAATGAATGGCTTTTTCTTCACATTTCTTAAGGCAAACATTCAAT
66 TATAAAT-GACTTTTCTTGTCAATGAATGGCTTTTTCTTCACGTTTCTTAAGGCAAACATTCAAT
* * *
1123 TATAATTTTTTTTAACAAAAAATGTAAAAAAATTTAACTTA
130 TA-AATTTGTTTTAACTAAAAATGTAAAAAAATTCAACTTA
* * * *
1164 AAATGAATTATGAGGTTATAAAACCATTTAAAGCGAGTAATAAGGCTTTAGAAGGAATGGGTCAC
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * * * * **** *
1229 TACAAATGGAGC-TTTCTCG-CTAATAAATGGCTTTTTCTTCACCTGTCTAAAGATTGACATTCT
66 TATAAAT-GA-CTTTTCTTGTC-AATGAATGGCTTTTTCTTCACGTTTCTTAAGGCAAACATTCA
* * *
1292 ATTATAGTCTGTTTTAACAAAAAAAT-T-AAAAAATTCAACTTA
128 ATTA-AATTTGTTTTAAC-TAAAAATGTAAAAAAATTCAACTTA
* * * * *
1334 AAATGAATTATGAGATTATAAAACCATTTTAAGCAAGTAATAAGGCCTTTGATGGAATGGGTGAC
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * * * * *
1399 TATAAATGACTTTTTTTG-CTAACGAATGGCTTTTCCTTTACGTTTTTTGAGGCAAAAATTCAAT
66 TATAAATGACTTTTCTTGTC-AATGAATGGCTTTTTCTTCACGTTTCTTAAGGCAAACATTCAAT
** * * *
1463 TATAGCTTGTTTCAACCAAAAAAGTAAAAAAATTCAACTTA
130 TA-AATTTGTTTTAACTAAAAATGTAAAAAAATTCAACTTA
* * * * * *
1504 AAATCAATTATAAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAAGCATAGGTAAC
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * * * * *
1569 TATAAATGAACTTTTCTAGTCAATGAATGACTTTTTCTTCATGTTT-TCTGAGGTAGACATTTAA
66 TATAAATG-ACTTTTCTTGTCAATGAATGGCTTTTTCTTCACGTTTCT-TAAGGCAAACATTCAA
* * * *
1633 TTATAATCTGTTTTAACTAAAAAGGTAAAAGAATTCAACTCA
129 TTA-AATTTGTTTTAACTAAAAATGTAAAAAAATTCAACTTA
* * * *
1675 AAATCAATTATGAGATCATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAAGCGTGAC
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * * * * ** * *
1740 TATAAATGAACTTTTATTGCCTATAAATTGCCTTTTCTTCGTGTTTTTTAAAGCAAACATTCAAT
66 TATAAATG-ACTTTTCTTGTCAATGAATGGCTTTTTCTTCACGTTTCTTAAGGCAAACATTCAAT
* * * * *
1805 TATACTTGTTTTAGCCAAAAATGTAAAAAAATTAAACTTA
130 TAAATTTGTTTTAACTAAAAATGTAAAAAAATTCAACTTA
* * *
1845 AAAACAATTATGAGATT-TCAAAACTATTTAAAGCGAGCAATAAGGCTTTTGAAGGAATGGGTTG
1 AAATCAATTATGAGATTAT-AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGG-TG
* ** * ** * * *
1909 -CTATAAATAGACTTTTTTTGTCAATGAATTACTTTTTCTTCACGTTACTCGAGTCAGACAGTCA
64 ACTATAAAT-GACTTTTCTTGTCAATGAATGGCTTTTTCTTCACGTTTCTTAAGGCAAACATTCA
* * * *
1973 ATTTTAATTTATTTTAA-TAAAAAATATAAAAAAATTTAACTTA
128 A-TTAAATTTGTTTTAACT-AAAAATGTAAAAAAATTCAACTTA
* * *
2016 AAATCAATTACGAGGTTATAAAACCTTTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* * * * ** * *
2081 TATAAATGGACATTTCTTGTTAATGAAT-GCTTTTTTCTTCATGTTT-TCAAGATAGACATTAAA
66 TATAAAT-GACTTTTCTTGTCAATGAATGGC-TTTTTCTTCACGTTTCTTAAGGCAAACATTCAA
* * * * **
2144 TTATATCTGTTTGAACCAAAAATACAAAAAAATTCAACTTA
129 TTAAATTTGTTTTAACTAAAAATGTAAAAAAATTCAACTTA
* *
2185 AAATCAATTATGAGATTACAAAATCATTTA
1 AAATCAATTATGAGATTATAAAACCATTTA
2215 NNNNNNNNNN
Statistics
Matches: 1476, Mismatches: 387, Indels: 80
0.76 0.20 0.04
Matches are distributed among these distances:
167 75 0.05
168 45 0.03
169 117 0.08
170 369 0.25
171 844 0.57
172 26 0.02
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.34
Consensus pattern (169 bp):
AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
TATAAATGACTTTTCTTGTCAATGAATGGCTTTTTCTTCACGTTTCTTAAGGCAAACATTCAATT
AAATTTGTTTTAACTAAAAATGTAAAAAAATTCAACTTA
Found at i:1396 original size:341 final size:336
Alignment explanation
Indices: 142--2214 Score: 1401
Period size: 341 Copynumber: 6.1 Consensus size: 336
132 NNNNNNNNNN
* * * * ** * *
142 AAATCAATTATGAGATTACAAAACCACTTAAAGCGAGTAATAAAGCTTTCGAAGGCTTGGGTGAT
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTAGAAGGAATGGGTAAC
* ** ******** *
207 TATAAATAGACTTTTCTAGTCAATGAATGGCTTTTTCTTCATGTTTCNNNNNNNNNNCATTCAAT
66 TATAAAT-GACTTTTCTAGTCAATGAATGACTTTTTCTTCA-CCTTC--TGAGTAGACATTCTAT
* * * * *
272 TATAATATGTTTTGAC-AAAATATGTGAAAAAATTCAAC-CAGAAATCAATTATGAGATTACAAA
127 TATAATCTGTTTTAACAAAAAAAT-T-AAAAAATTCAACTTA-AAATCAATTATGAGATTATAAA
* ** * ********* *
335 ACCATTTGAAGTTAGTACTAAGGCTTTTGAAGGAATGGGTGACNNNNNNNNNNA-TTTTCTTGCC
189 ACCATTTTAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC-TATAAATGGACTTTTCTTGTC
* * * * * * * *
399 AATGAATGTCTTTTTCTTTATG-TTTCTAGAGGCAGACATTCAATTATATTTTTTTCTAACCAAA
253 AATGAATGGCTTTTTCTTCACGTTTTTTA-AGGCAAACATTCAATTATACTTGTTT-TAACAAAA
* *
463 AATGTAAAAATATTAAACTTA
316 AATGTAAAAAAATTCAACTTA
* * * ********** *
484 AAATCAATTGT-ACGACTATAAAACCATTTAAAGTGAGTAATAAGGCTNNNNNNNNNNTGGGTGA
1 AAATCAATTATGA-GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTAGAAGGAATGGGTAA
* ** * ** * * * *
548 CTATAAATGGACTTTTCTTA-CCAATGAATTTCTCTTTCTTCATGTTTCTTGAGGCAAATATTCA
65 CTATAAAT-GACTTTTC-TAGTCAATGAATGACTTTTTCTTCA-CCTTC-TGA-GTAGACATTCT
* * * * ** *
612 ATCA-AAGTATGTTTTGAC-TAAAAATGTAAAAAAATTCAACTTAAAAAAAATTATGAGATTACA
125 ATTATAA-TCTGTTTTAACAAAAAAAT-T-AAAAAATTCAACTTAAAATCAATTATGAGATTATA
* * * * * * * *
675 AAACCATTTAAAACGAGTAATAAGACTTTTGAAGGAAAGTGTGATTAAAAATAGACTTTTCTTGT
187 AAACCATTTTAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGT
* * * * * * *
740 CAATGAATGGCTTTTTCTTCATGTTTTTCAAGGCAGATAATCAATTATAATT-TAATTTAATAAA
252 CAATGAATGGCTTTTTCTTCACGTTTTTTAAGGCAAACATTCAATTATACTTGT--TTTAACAAA
804 AAA-GTAAAAAAA-T-AACTTA
315 AAATGTAAAAAAATTCAACTTA
* ********** *
823 AAATCAATTACGAGATNNNNNNNNNNTTTAAAGCGAGTAATAAGGCTTT-GAAGGCATGGG-AGA
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTAGAAGGAATGGGTA-A
* * * * * * * *
886 GTATAAATAGACCTCTCTAGTCAATGAATGACTTTTTCTTTACATTTCCCATG-GCACACATTCA
65 CTATAAAT-GACTTTTCTAGTCAATGAATGACTTTTTCTTCAC-CTT--C-TGAGTAGACATTCT
* ********* * ** * *
950 ATTATAATATGTTTTAACTANNNNNNNNNNAAAAA-TCAACTTAAAATTAATTACAAGGTTACAA
125 ATTATAATCTGTTTTAAC-A-AAAAAATTAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
* * * * ** * * * **
1014 AACAATTTAAAGAGAGTAATAAGACTTTCAAAAGCATGGGTGACTATAAATGGGCTTTTCTAATC
188 AACCATTTTAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTC
* * * *
1079 AATGAATGGCTTTTTCTTCACATTTCTTAAGGCAAACATTCAATTATAATTTTTTTTAACAAAAA
253 AATGAATGGCTTTTTCTTCACGTTTTTTAAGGCAAACATTCAATTAT-ACTTGTTTTAACAAAAA
*
1144 ATGTAAAAAAATTTAACTTA
317 ATGTAAAAAAATTCAACTTA
* * *
1164 AAATGAATTATGAGGTTATAAAACCATTTAAAGCGAGTAATAAGGCTTTAGAAGGAATGGGTCAC
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTAGAAGGAATGGGTAAC
* * * * * *
1229 TACAAATGGAGC-TTTCTCG-CTAATAAATGGCTTTTTCTTCACCTGTCTAAAGATTGACATTCT
66 TATAAAT-GA-CTTTTCTAGTC-AATGAATGACTTTTTCTTCACCT-TCT-GAG-TAGACATTCT
* *
1292 ATTATAGTCTGTTTTAACAAAAAAATTAAAAAATTCAACTTAAAATGAATTATGAGATTATAAAA
125 ATTATAATCTGTTTTAACAAAAAAATTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
* * * *
1357 CCATTTTAAGCAAGTAATAAGGCCTTTGATGGAATGGGTGACTATAAAT-GACTTTTTTTG-CTA
190 CCATTTTAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTC-A
* * * * * *
1420 ACGAATGGCTTTTCCTTTACGTTTTTTGAGGCAAAAATTCAATTATAGCTTGTTTCAACCAAAAA
254 ATGAATGGCTTTTTCTTCACGTTTTTTAAGGCAAACATTCAATTATA-CTTGTTTTAA-CAAAAA
1485 A-GTAAAAAAATTCAACTTA
317 ATGTAAAAAAATTCAACTTA
* * * * *
1504 AAATCAATTATAAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAAAGCATAGGTAAC
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTAGAAGGAATGGGTAAC
**
1569 TATAAATGAACTTTTCTAGTCAATGAATGACTTTTTCTTCATGTTTTCTGAGGTAGACATT-TAA
66 TATAAATG-ACTTTTCTAGTCAATGAATGACTTTTTCTTCA--CCTTCTGA-GTAGACATTCT-A
* ** * *
1633 TTATAATCTGTTTTAACTAAAAAGGTAAAAGAATTCAACTCAAAATCAATTATGAGATCATAAAA
126 TTATAATCTGTTTTAACAAAAAAATTAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAA
* * * * * * * *
1698 CTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAAGCGTGACTATAAATGAACTTTTATTGCCTA
190 CCATTTTAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAA
* * * ** * * *
1763 TAAATTGCCTTTTCTTCGTGTTTTTTAAAGCAAACATTCAATTATACTTGTTTTAGCCAAAAATG
255 TGAATGGCTTTTTCTTCACGTTTTTTAAGGCAAACATTCAATTATACTTGTTTTAACAAAAAATG
*
1828 TAAAAAAATTAAACTTA
320 TAAAAAAATTCAACTTA
* * * * **
1845 AAAACAATTATGAGATT-TCAAAACTATTTAAAGCGAGCAATAAGGCTTTTGAAGGAATGGGTTG
1 AAATCAATTATGAGATTAT-AAAACCATTTAAAGCGAGTAATAAGGCTTTAGAAGGAATGGGTAA
* * * * * *
1909 CTATAAATAGACTTTTTTTGTCAATGAATTACTTTTTCTTCACGTTACTCGAGTCAGACAGTCAA
65 CTATAAAT-GACTTTTCTAGTCAATGAATGACTTTTTCTTCACCTT-CT-GAGT-AGACATTCTA
* * * * * * * *
1974 TTTTAATTTATTTTAATAAAAAATATAAAAAAATTTAACTTAAAATCAATTACGAGGTTATAAAA
126 TTATAATCTGTTTTAACAAAAAA-ATTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
* *
2039 CC-TTTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACATTTCTTGTTA
190 CCATTTT-AAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCA
* * ** * * * *
2103 ATGAAT-GCTTTTTTCTTCATG-TTTTCAAGATAGACATTAAATTATA-TCTGTTTGAACCAAAA
254 ATGAATGGC-TTTTTCTTCACGTTTTTTAAGGCAAACATTCAATTATACT-TGTTTTAACAAAAA
**
2165 ATACAAAAAAATTCAACTTA
317 ATGTAAAAAAATTCAACTTA
* *
2185 AAATCAATTATGAGATTACAAAATCATTTA
1 AAATCAATTATGAGATTATAAAACCATTTA
2215 NNNNNNNNNN
Statistics
Matches: 1351, Mismatches: 322, Indels: 118
0.75 0.18 0.07
Matches are distributed among these distances:
337 2 0.00
338 185 0.14
339 65 0.05
340 296 0.22
341 443 0.33
342 349 0.26
343 11 0.01
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.34
Consensus pattern (336 bp):
AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTAGAAGGAATGGGTAAC
TATAAATGACTTTTCTAGTCAATGAATGACTTTTTCTTCACCTTCTGAGTAGACATTCTATTATA
ATCTGTTTTAACAAAAAAATTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
TAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATGAATG
GCTTTTTCTTCACGTTTTTTAAGGCAAACATTCAATTATACTTGTTTTAACAAAAAATGTAAAAA
AATTCAACTTA
Done.