Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400167.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3383.0, 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: 6054
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.29
Warning! 1148 characters in sequence are not A, C, G, or T
Found at i:304 original size:170 final size:172
Alignment explanation
Indices: 1--889 Score: 492
Period size: 172 Copynumber: 5.2 Consensus size: 172
* ** *
1 AAAGACATTCA-TTGACAAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGAGTTATTACA
1 AAAGACATTCAGTGGA-AAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGCCTTATTACT
*
65 CACTTTAAATGATTTTATAATCTCAAAATTGATTTAAATTCGAATTCTTTGCACATTTTTGATTA
65 CACTTTAAATGATTTTATAATCTCAAAATTGATTTAAATTCAAATTCTTTGCACATTTTTGATTA
* **
130 AAACAGATTATAATTGAATGTCAACCTTAAGAAACATG-A-NN
130 AAACAGATTATAATTGAAGGTCAACCTTAAGAAACATGAAGAA
******** * * * ** *
171 NNNNNNNNTCATTGGTAAGAGAAGTCCATTTATAGCCACCCATTCCTCCAGAAGCCTTATTACTC
1 AAAGACATTCAGTGGAAAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGCCTTATTACTC
* * * * * * *
236 ACTTTAAATGTTTTTATAATCTCATAATTGCTTTTAAGTTCAAATAT-TTT-TACTTTTTTGGTT
66 ACTTTAAATGATTTTATAATCTCAAAATTG-ATTTAAATTCAAAT-TCTTTGCACATTTTTGATT
* * * *
299 AAAACATATTATAATTGAAGGTCTAGCTTGAGAAACATGAAGAA
129 AAAACAGATTATAATTGAAGGTCAACCTTAAGAAACATGAAGAA
343 AAAGACATTCAGTGGAAAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGCCTTATTACTC
1 AAAGACATTCAGTGGAAAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGCCTTATTACTC
* * ****************** * * *
408 ACTTCAAATGGTTTTATAATCTCAANNNNNNNNNNNNNNNNNNTTCTTTGTACTTTTTTGGTTAA
66 ACTTTAAATGATTTTATAATCTCAAAATTGATTTAAATTCAAATTCTTTGCACATTTTTGATTAA
* * * *
473 AATAGATTATAATTGAATGTCAACCTCAAGAAGCATGAAGAA
131 AACAGATTATAATTGAAGGTCAACCTTAAGAAACATGAAGAA
* * * * * ***********
515 AAAG--GTTCATTCGTAAGAGAAGTCCATTTATAGCCACCCATTCCTCNNNNNNNNNNATTACTC
1 AAAGACATTCAGTGGAAAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGCCTTATTACTC
* * * * ** * *
578 ACCTTAAATGGTTTTATAATCTCATAATTGTTTTTAGGTTCAAATTGTATT--ACATTTTTGGTT
66 ACTTTAAATGATTTTATAATCTCAAAATTG-ATTTAAATTCAAATTCT-TTGCACATTTTTGATT
* * * * * * * *
641 AAATCATATCATAATTGAATGTCTAGCTCT-AGAAACGTAAAGAA
129 AAAACAGATTATAATTGAAGGTCAACCT-TAAGAAACATGAAGAA
* ********** * * *
685 AAAGACATTCA-TTGACNNNNNNNNNNCATTTATAGCCACCCATTCCTTTAAAAGCGTTGTTACA
1 AAAGACATTCAGTGGA-AAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGCCTTATTACT
* * * *
749 CACTTTAAATTG-TTTTATAATCTCAAAATTGATTTAAATTCGAATTCTTTGTATATTTTTGCTT
65 CACTTTAAA-TGATTTTATAATCTCAAAATTGATTTAAATTCAAATTCTTTGCACATTTTTGATT
** * ** * * * *
813 AAAACAGGCTAGAATTGAATATCTACATTGATG-AACAGGAAGAA
129 AAAACAGATTATAATTGAAGGTCAACCTT-AAGAAACATGAAGAA
* * *
857 AAA-AGCATTCATTGGCAAGAAAATTCCATTTAT
1 AAAGA-CATTCAGTGGAAAGAAAAGTCCATTTAT
890 NNNNNNNNNN
Statistics
Matches: 515, Mismatches: 184, Indels: 38
0.70 0.25 0.05
Matches are distributed among these distances:
170 233 0.45
171 40 0.08
172 237 0.46
173 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.34
Consensus pattern (172 bp):
AAAGACATTCAGTGGAAAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGCCTTATTACTC
ACTTTAAATGATTTTATAATCTCAAAATTGATTTAAATTCAAATTCTTTGCACATTTTTGATTAA
AACAGATTATAATTGAAGGTCAACCTTAAGAAACATGAAGAA
Found at i:425 original size:172 final size:169
Alignment explanation
Indices: 1--432 Score: 481
Period size: 170 Copynumber: 2.5 Consensus size: 169
* ** *
1 AAAGACATTCATTGACAAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGAGTTATTACAC
1 AAAGACATTCATGGA-AAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGCCTTATTACTC
*
66 ACTTTAAATGATTTTATAATCTCAAAATTGATTTAAATTCGAATTCTTTGCACATTTTTGATTAA
65 ACTTTAAATGATTTTATAATCTCAAAATTGATTTAAATTCAAATTCTTTGCACATTTTTGATTAA
* **
131 AACAGATTATAATTGAATGTCAACCTTAAGAAACATGANN
130 AACAGATTATAATTGAAGGTCAACCTTAAGAAACATGAAA
******** * * ** *
171 NNNNNNNNTCATTGGTAAGAGAAGTCCATTTATAGCCACCCATTCCTCCAGAAGCCTTATTACTC
1 AAAGACATTCA-TGGAAAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGCCTTATTACTC
* * * * * * *
236 ACTTTAAATGTTTTTATAATCTCATAATTGCTTTTAAGTTCAAATAT-TTT-TACTTTTTTGGTT
65 ACTTTAAATGATTTTATAATCTCAAAATTG-ATTTAAATTCAAAT-TCTTTGCACATTTTTGATT
* * * *
299 AAAACATATTATAATTGAAGGTCTAGCTTGAGAAACATGAAGAA
128 AAAACAGATTATAATTGAAGGTCAACCTTAAGAAACATG-A-AA
343 AAAGACATTCAGTGGAAAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGCCTTATTACTC
1 AAAGACATTCA-TGGAAAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGCCTTATTACTC
* *
408 ACTTCAAATGGTTTTATAATCTCAA
65 ACTTTAAATGATTTTATAATCTCAA
433 NNNNNNNNNN
Statistics
Matches: 208, Mismatches: 49, Indels: 8
0.78 0.18 0.03
Matches are distributed among these distances:
170 117 0.56
171 17 0.08
172 74 0.36
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.34
Consensus pattern (169 bp):
AAAGACATTCATGGAAAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGCCTTATTACTCA
CTTTAAATGATTTTATAATCTCAAAATTGATTTAAATTCAAATTCTTTGCACATTTTTGATTAAA
ACAGATTATAATTGAAGGTCAACCTTAAGAAACATGAAA
Found at i:832 original size:342 final size:342
Alignment explanation
Indices: 1--819 Score: 867
Period size: 342 Copynumber: 2.4 Consensus size: 342
* *
1 AAAGACATTCA-TTGACAAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGAGTTATTACA
1 AAAGACATTCAGTGGA-AAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGCGTTATTACA
* *
65 CACTTTAAA-TGATTTTATAATCTCAAAATTGATTTAAATTCGAATTCTTTGCACATTTTTGATT
65 CACTTTAAATTG-TTTTATAATCTCAAAATTGATTTAAATTCGAATTCTTTGTATATTTTTGATT
* ********** *
129 AAAACAGATTATAATTGAATGTCAACCTTAAGAAACATGANNNNNNNNNNTCATTGGTAAGAGAA
129 AAAACAGATTATAATTGAATGTCAACCTCAAGAAACATGAAGAAAAAGGTTCATTCGTAAGAGAA
* *
194 GTCCATTTATAGCCACCCATTCCTCCAGAAGCCTTATTACTCACTTTAAATGTTTTTATAATCTC
194 GTCCATTTATAGCCACCCATTCCTCCAGAAGCCTTATTACTCACCTTAAATGGTTTTATAATCTC
* * *
259 ATAATTGCTTTTAAGTTCAAATATTTTTACTTTTTTGGTTAAAACATATTATAATTGAAGGTCTA
259 ATAATTGCTTTTAAGTTCAAATATTATTACATTTTTGGTTAAAACATATCATAATTGAAGGTCTA
*
324 GCTTGAGAAACATGAAGAA
324 GCTTGAGAAACATAAAGAA
* *
343 AAAGACATTCAGTGGAAAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGCCTTATTACTC
1 AAAGACATTCAGTGGAAAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGCGTTATTACAC
* * ****************** *
408 ACTTCAAATGGTTTTATAATCTCAANNNNNNNNNNNNNNNNNNTTCTTTGTACT-TTTTTGGTTA
66 ACTTTAAATTGTTTTATAATCTCAAAATTGATTTAAATTCGAATTCTTTGTA-TATTTTTGATTA
* *
472 AAATAGATTATAATTGAATGTCAACCTCAAGAAGCATGAAGAAAAAGGTTCATTCGTAAGAGAAG
130 AAACAGATTATAATTGAATGTCAACCTCAAGAAACATGAAGAAAAAGGTTCATTCGTAAGAGAAG
**********
537 TCCATTTATAGCCACCCATTCCTCNNNNNNNNNNATTACTCACCTTAAATGGTTTTATAATCTCA
195 TCCATTTATAGCCACCCATTCCTCCAGAAGCCTTATTACTCACCTTAAATGGTTTTATAATCTCA
* * * *
602 TAATTGTTTTTAGGTTCAAAT-TGTATTACATTTTTGGTTAAATCATATCATAATTGAATGTCTA
260 TAATTGCTTTTAAGTTCAAATAT-TATTACATTTTTGGTTAAAACATATCATAATTGAAGGTCTA
*
666 GCTCT-AGAAACGTAAAGAA
324 GCT-TGAGAAACATAAAGAA
* ********** *
685 AAAGACATTCA-TTGACNNNNNNNNNNCATTTATAGCCACCCATTCCTTTAAAAGCGTTGTTACA
1 AAAGACATTCAGTGGA-AAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGCGTTATTACA
*
749 CACTTTAAATTGTTTTATAATCTCAAAATTGATTTAAATTCGAATTCTTTGTATATTTTTGCTTA
65 CACTTTAAATTGTTTTATAATCTCAAAATTGATTTAAATTCGAATTCTTTGTATATTTTTGATTA
814 AAACAG
130 AAACAG
820 GCTAGAATTG
Statistics
Matches: 372, Mismatches: 98, Indels: 14
0.77 0.20 0.03
Matches are distributed among these distances:
341 5 0.01
342 362 0.97
343 5 0.01
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.35
Consensus pattern (342 bp):
AAAGACATTCAGTGGAAAGAAAAGTCCATTTATAGCCACCCATTCCTTTAAAAGCGTTATTACAC
ACTTTAAATTGTTTTATAATCTCAAAATTGATTTAAATTCGAATTCTTTGTATATTTTTGATTAA
AACAGATTATAATTGAATGTCAACCTCAAGAAACATGAAGAAAAAGGTTCATTCGTAAGAGAAGT
CCATTTATAGCCACCCATTCCTCCAGAAGCCTTATTACTCACCTTAAATGGTTTTATAATCTCAT
AATTGCTTTTAAGTTCAAATATTATTACATTTTTGGTTAAAACATATCATAATTGAAGGTCTAGC
TTGAGAAACATAAAGAA
Found at i:4703 original size:171 final size:170
Alignment explanation
Indices: 3999--4708 Score: 653
Period size: 171 Copynumber: 4.1 Consensus size: 170
3989 NNNNNNNNNN
* * * *
3999 ACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCATT-ATGTTTCTCAAGCTAGATA-TC
1 ACTATAAATGGACTTTTCTTGCCAATGAATGACTTTTTC-TTCATGTTTCTTAAGGTAGACATTC
* * ** * *
4062 AATTTTAGTCTGTTTTAACTAAAAATATAAAAACGTTCAACATAAAATCAATTATGGCATTAT-A
65 AATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATAG-ATTATAA
** * *
4126 AACCATTTAAAGTAAGTGGTAAGGCTTTTTGAAGGTATGGGTG
129 AACCATTTAAAGTAAGTAATAAGGC-TTTTGAAAGAATGGGTG
* * *
4169 ACTATAAATGGACTTATCTTACCAATGAAT-ACTTTTTTCTTCATATTT-TTCAAGGTAGACATT
1 ACTATAAATGGACTTTTCTTGCCAATGAATGAC-TTTTTCTTCATGTTTCTT-AAGGTAGACATT
* * * * * *
4232 CAATTCTAATTTGTTTGAATCAAAAATATAAAAAAAAATTCAACTTAAAATCAATTATTAGTTTA
64 CAATTATAGTCTGTTTTAA-CAAAAA-ATATAAAAAAATTCAACTTAAAATCAATTA-TAGATTA
* * * ** *
4297 TAAAACCATTTAAAGTAAGTAATAGGGCTTTCGAAGGTTTGAGTG
126 TAAAACCATTTAAAGTAAGTAATAAGGCTTTTGAAAGAATGGGTG
* * * ** ** * * * * * * *
4342 ACTATAAACGGACTTTTTTTGGCAATGGTTGGGTTTTGCTTCACGGTCCCTAAGGCAAACATTCA
1 ACTATAAATGGACTTTTCTTGCCAATGAATGACTTTTTCTTCATGTTTCTTAAGGTAGACATTCA
* * * * *
4407 ATTATAGTCCT-TTTTAACCAAAAATGTAAAACAATTCAACTTAAAATCAATTTTGAGATTCTAA
66 ATTATAGT-CTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTAT-AGATTATAA
* * *
4471 AGCCATTTAAAGTGAGTAATAAGGCTTTTGAAGAAACAT--GTG
129 AACCATTTAAAGTAAGTAATAAGGCTTTTGAA-AGA-ATGGGTG
* * * * * *
4513 GCTATCAATGGACTTTTCTTGCCAATGAATGTCTTTTTTTTTATGTTTCTTGAGGTAGACATTCA
1 ACTATAAATGGACTTTTCTTGCCAATGAATGACTTTTTCTTCATGTTTCTTAAGGTAGACATTCA
* * * *
4578 ATTATAGTCGGCTTTAACAAAAAATATAAAAAAATTTAACTGAAAATCAATTATAGCATTATAAA
66 ATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATAG-ATTATAAA
* * *
4643 ACCATTTAAAGTGAGTAATGAGGCTTTTGAAAGAATGGGTT
130 ACCATTTAAAGTAAGTAATAAGGCTTTTGAAAGAATGGGTG
* *
4684 ACTATAAATGGATTTTTCTTACCAA
1 ACTATAAATGGACTTTTCTTGCCAA
4709 NNNNNNNNNN
Statistics
Matches: 426, Mismatches: 96, Indels: 35
0.76 0.17 0.06
Matches are distributed among these distances:
169 6 0.01
170 53 0.12
171 229 0.54
172 10 0.02
173 101 0.24
174 27 0.06
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (170 bp):
ACTATAAATGGACTTTTCTTGCCAATGAATGACTTTTTCTTCATGTTTCTTAAGGTAGACATTCA
ATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATAGATTATAAAA
CCATTTAAAGTAAGTAATAAGGCTTTTGAAAGAATGGGTG
Done.