Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397979.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1284.0, 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: 2401
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.27
Warning! 586 characters in sequence are not A, C, G, or T
Found at i:703 original size:343 final size:342
Alignment explanation
Indices: 144--982 Score: 836
Period size: 343 Copynumber: 2.4 Consensus size: 342
134 NNNNNNNNNN
* * *
144 AAAATCAATTATGAGATTAT-AAAGCTATTTAAAGCGAGTACTGAA-GTTTTTGAAGGAATGGGT
1 AAAATCAATTATGAGATTGTAAAAGCTATTTAAA-CGAGTAAT-AAGGTTTTTGAAAGAAT-GGT
* * * *
207 GACTATAAATAGACTTTTT-TTGCCAATGAAAGTCTTGTTCTTCACGTTTCTCGAGGTGGGTATT
63 GACTATAAATAGA-TTTTTCTTGCCAATGAAAGCCTT-TTCTTCACATTTCTCGAGGTAGGCATT
* * * * * * *****
271 CAATTATAATCTATTTTAACCAAACATTTACAAAGAATTCAAATTTAAATCAATTTTGAGNNNNN
126 CAATTATAATCTGTTTCAACCAAAAATGTACAAAGAATTCAAATATAAATAAATTTTGAGATTAT
*****
336 NNNNNCATTTAAAGTGACTAATAAGGCTTTTAAAGGAATAGTTGACTATAAATGGGCTTTTCGTA
191 GAAACCATTTAAAGTGACTAATAAGGCTTTTAAAGGAATAGTTGACTATAAATGGGCTTTTCGTA
* * * * **
401 CCAACGA-ATGTCTTTTTCTTCATATTTCTCGAGCTAGACATTCAATTATAATATGTTTTAACCC
256 CCAAC-ATATGCCTTTTTCTTCACATTTCTCAAGCTAGACATTCAATTATAACATGTTTTAACAA
* *
465 AAAATGTAAA-ATAA-TTCAATTT
320 AAAATATAAATA-AATTTCAAGTT
* *
487 AAAATAAAGTATGAGATTGTAAAAGCT-TTTACAACGAGTAATAAGGTTTTTGAAAGAATAGGTG
1 AAAATCAATTATGAGATTGTAAAAGCTATTTA-AACGAGTAATAAGGTTTTTGAAAGAAT-GGTG
* * *
551 ACTATAAATGGATTTTTCTTGCCAATGAAAGACCTTTTCGTGACATTTCTCGAGGTAGGCATTCA
64 ACTATAAATAGATTTTTCTTGCCAATGAAAG-CCTTTTCTTCACATTTCTCGAGGTAGGCATTCA
* *
616 ATTATAATCTGTTTCAGCCAAAAATGTACAAAGAATTCAAATATAGATAAATTTTGAGATTATGA
128 ATTATAATCTGTTTCAACCAAAAATGTACAAAGAATTCAAATATAAATAAATTTTGAGATTATGA
* * ********** **
681 AACCCTTTAAAGTGAGTAATAAGGCTTTTANNNNNNNNNNTGACTATAAATGGGCTTTTTTTACC
193 AACCATTTAAAGTGACTAATAAGGCTTTTAAAGGAATAGTTGACTATAAATGGGCTTTTCGTACC
* * * *
746 AACATATGCCTTTTTCTTTACGTTTCTCAAGCTAGACATTCAATTATAACATTTTTTAATAAAAA
258 AACATATGCCTTTTTCTTCACATTTCTCAAGCTAGACATTCAATTATAACATGTTTTAACAAAAA
*
811 ATATAAATAAATTTGAAGTT
323 ATATAAATAAATTTCAAGTT
* * * * *
831 AAAATCAATTTTGAGACTGTAAAA-CTATTTAAAATGAGTAATAAGGCTTTCG-AAGCAATGGAT
1 AAAATCAATTATGAGATTGTAAAAGCTATTT-AAACGAGTAATAAGGTTTTTGAAAG-AATGG-T
* * * * * ** *
894 GACTATAAATAGACTTTTCCTGCCAATG-AATCCTTTTTCTTTACATTTCTTGAGGTACACAATC
63 GACTATAAATAGATTTTTCTTGCCAATGAAAGCC-TTTTCTTCACATTTCTCGAGGTAGGCATTC
958 AATTATAATCTG-TTCTAACCAAAAA
127 AATTATAATCTGTTTC-AACCAAAAA
983 GGTCAAAAAA
Statistics
Matches: 406, Mismatches: 76, Indels: 28
0.80 0.15 0.05
Matches are distributed among these distances:
342 13 0.03
343 305 0.75
344 87 0.21
345 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.35
Consensus pattern (342 bp):
AAAATCAATTATGAGATTGTAAAAGCTATTTAAACGAGTAATAAGGTTTTTGAAAGAATGGTGAC
TATAAATAGATTTTTCTTGCCAATGAAAGCCTTTTCTTCACATTTCTCGAGGTAGGCATTCAATT
ATAATCTGTTTCAACCAAAAATGTACAAAGAATTCAAATATAAATAAATTTTGAGATTATGAAAC
CATTTAAAGTGACTAATAAGGCTTTTAAAGGAATAGTTGACTATAAATGGGCTTTTCGTACCAAC
ATATGCCTTTTTCTTCACATTTCTCAAGCTAGACATTCAATTATAACATGTTTTAACAAAAAATA
TAAATAAATTTCAAGTT
Found at i:1472 original size:172 final size:167
Alignment explanation
Indices: 144--1472 Score: 707
Period size: 172 Copynumber: 7.8 Consensus size: 167
134 NNNNNNNNNN
* * ** * ** *
144 AAAATCAATTATGAGATTATAAAGCTATTTAAAGCGAGTACTGAAGTTTTTGAAGGAATGGGTGA
1 AAAATCAATTTTGAGATTATAAAACTATTTAAAATGAGTAAT-AAGGCTTTGAAGCAATGGGTGA
* * * * * * * **
209 CTATAAATAGACTTTTTTTGCCAATGAAAGTCTTGTTCTTCACGTTTCTCGAGGTGGGTATTCAA
65 CTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCACATTTCTCGAGGTAGACATTCAA
* * * *
274 TTATAATCTATTTTAACCAAACATTTACAAAGAATTCAAATT
130 TTATAATC--TTTTAAACAAAAATATA-AAA-AATTCAACTT
* ********* * * * * * *
316 TAAATCAATTTTGAGNNNNNNNNNNC-ATTTAAAGTGACTAATAAGGCTTTTAAAGGAATAGTTG
1 AAAATCAATTTTGAG-ATTATAAAACTATTTAAAATGAGTAATAAGGC-TTTGAAGCAATGGGTG
* * * * * * *
380 ACTATAAATGGGCTTTTCGTACCAACGAATGTCTTTTTCTTCATATTTCTCGAGCTAGACATTCA
64 ACTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCACATTTCTCGAGGTAGACATTCA
* * * * *
445 ATTATAATATGTTTTAACCCAAAATGTAAAATAATTCAATTT
129 ATTAT-A-ATCTTTTAAACAAAAATATAAAA-AATTCAACTT
* * * * * * * *
487 AAAATAAAGTATGAGATTGTAAAAGCT-TTTACAACGAGTAATAAGGTTTTTGAAAG-AATAGGT
1 AAAATCAATTTTGAGATTATAAAA-CTATTTAAAATGAGTAATAAGG-CTTTG-AAGCAATGGGT
* * * * * * *
550 GACTATAAATGGATTTTTCTTGCCAATGAAAGACC-TTTTCGTGACATTTCTCGAGGTAGGCATT
63 GACTATAAATAGACTTTTCTTACCAATGAATG-CCTTTTTCTTCACATTTCTCGAGGTAGACATT
** * *
614 CAATTATAATCTGTTTCAGCCAAAAATGTACAAAGAATTCAA-AT
127 CAATTATAATCT-TTT-AAACAAAAATATA-AAA-AATTCAACTT
* * * ** * * *********
658 ATAGATAAATTTTGAGATTATGAAACCCTTTAAAGTGAGTAATAAGGCTTTTANNNNNNNNNNTG
1 A-AAATCAATTTTGAGATTATAAAACTATTTAAAATGAGTAATAAGGCTTTGA-AGCAATGGGTG
* * * * * * * *
723 ACTATAAATGGGCTTTTTTTACCAA-CATATGCCTTTTTCTTTACGTTTCTCAAGCTAGACATTC
64 ACTATAAATAGACTTTTCTTACCAATGA-ATGCCTTTTTCTTCACATTTCTCGAGGTAGACATTC
* * *
787 AATTATAACATTTTTTAATA-AAAAATATAAATAAATTTGAAGTT
128 AATTAT-A-ATCTTTTAA-ACAAAAATATAAA-AAA-TTCAACTT
* * *
831 AAAATCAATTTTGAGACTGTAAAACTATTTAAAATGAGTAATAAGGCTTTCGAAGCAATGGATGA
1 AAAATCAATTTTGAGATTATAAAACTATTTAAAATGAGTAATAAGGCTTT-GAAGCAATGGGTGA
* * * * * *
896 CTATAAATAGACTTTTCCTGCCAATGAAT-CCTTTTTCTTTACATTTCTTGAGGTACACAATCAA
65 CTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCACATTTCTCGAGGTAGACATTCAA
* ** * *
960 TTATAATCTGTTCTAACCAAAAAGGTCAAAAAAATCAACCT
130 TTATAATCT-TT-TAAACAAAAATAT-AAAAAATTCAACTT
* * * * ********* * *
1001 AAAATCAATTATAAGGTTATAAAACCATTTAAAATGAGNNNNNNNNNNTTTGAAGGAATGGGTTA
1 AAAATCAATTTTGAGATTATAAAACTATTTAAAATGAG-TAATAAGGCTTTGAAGCAATGGGTGA
* * * * **
1066 CTATAAATGGACTTTTCTTGCCAATGAAAGACC-TTTTCTTGATGTTTCTCGAGGTAGACATTCA
65 CTATAAATAGACTTTTCTTACCAATGAATG-CCTTTTTCTTCACATTTCTCGAGGTAGACATTCA
* * * *
1130 GTTATAATCTCTTTGAACCAAAAATTTACAAAGAATTCAAATT
129 ATTATAATCT-TTT-AAACAAAAATATA-AAA-AATTCAACTT
* ********** * * * **
1173 TAAATCAATTTTNNNNNNNNNNAACTATTTAAAGTGAGTAATAAAGCTTTTGAAGGAATAAGTGA
1 AAAATCAATTTTGAGATTATAAAACTATTTAAAATGAGTAATAAGGC-TTTGAAGCAATGGGTGA
* * * * *
1238 CTATAAATAGGCTTTTCTTACCAACGCATGCCTTTTTCTTCA-ACTTTCTCGAGCTTGACATTCA
65 CTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCACA-TTTCTCGAGGTAGACATTCA
* * *
1302 ATTATAATTTATATTAAATAAAAATATAAATAAATTTGAACTT
129 ATTATAATCT-T-TTAAACAAAAATATAAA-AAA-TTCAACTT
* * * *
1345 AAAATCATTTTTGAGATTATAAAACTATTTAAAGTGAGCAATAAGGCTTATGAAGCAATGGGTAA
1 AAAATCAATTTTGAGATTATAAAACTATTTAAAATGAGTAATAAGGCTT-TGAAGCAATGGGTGA
* * * *
1410 CAACAAATAGACTTTTCTTACCATTGAATGCCTTTTTCTTCACATTTCTCAAGGTAGACATTC
65 CTATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCACATTTCTCGAGGTAGACATTC
1473 NNNNNNNNNN
Statistics
Matches: 857, Mismatches: 256, Indels: 88
0.71 0.21 0.07
Matches are distributed among these distances:
169 6 0.01
170 83 0.10
171 237 0.28
172 513 0.60
173 13 0.02
174 5 0.01
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.35
Consensus pattern (167 bp):
AAAATCAATTTTGAGATTATAAAACTATTTAAAATGAGTAATAAGGCTTTGAAGCAATGGGTGAC
TATAAATAGACTTTTCTTACCAATGAATGCCTTTTTCTTCACATTTCTCGAGGTAGACATTCAAT
TATAATCTTTTAAACAAAAATATAAAAAATTCAACTT
Done.