Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401517.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4643.0, 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: 3630
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.30
Warning! 870 characters in sequence are not A, C, G, or T
Found at i:1959 original size:171 final size:168
Alignment explanation
Indices: 3--1970 Score: 631
Period size: 171 Copynumber: 11.5 Consensus size: 168
1 TA
* *
3 GTTTTATAATCTAATAATTGAA-TTTAAGTTGAATTTTTTTATATTTTTTATTCAAACAGACA-A
1 GTTTTATAATCTAATAATT-AATTTTAAGTTGAA-TTTTTTACATTTTTTATTAAAACA-A-ATA
* ** * **
66 TAATTGAGTGTCT-ATTTCAAGAAATATAAAGAAAAAAGCATTCATT-GCTAAGAAAAGTCTATT
62 TAATTGAATGTCTGCCTT-GAGAAACGTAAAGAAAAAAGCATTCATTGGC-AAGAAAAGTCTATT
* * ** * *
129 TATAGCCTCTCACTCCATCAAAAGCCTTATTACTCGCTTTAAATG
125 TATAGCCT-TCATTCCTTCAAAAGCCTTATTACTTACTTTAAGTT
* * ********** * * *
174 GTTTTCTAATCTCATNNNNNNNNNNAAGTTAAATTTTTTTACATTTTTGATTAAAACAGATAATA
1 GTTTTATAATCTAATAATTAATTTTAAGTTGAA-TTTTTTACATTTTTTATTAAAACAAAT-ATA
* ** * * * * * * * * *** *
239 ATTGGATGTCTATCTCGAAAAATGTGAAGGAAAAAGTACTCACTATTAAGAAAAGTTTATTTATA
64 ATTGAATGTCTGCCTTGAGAAACGTAAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTA-TT-TA
* * ********* *
304 TAGTCATCTATTCCTTCAAAAGCCTTATTNNNNNNNNNNAA-TG
127 TAGCCTTC-ATTCCTTCAAAAGCCTTATT-ACTTACTTTAAGTT
* * * * * * *
347 GTTTTATAATGTCATAATTGATTTTATGTAGAATTTTTTTACATTTTTCATTAAAACAGATTATA
1 GTTTTATAATCTAATAATTAATTTTAAGTTGAA-TTTTTTACATTTTTTATTAAAACA-AATATA
* * * * * * ** *
412 ATTAAATGTCTACCTTAACAATCGTGAAGAAAAAAGCATTCATTGATAAAAAAAGTCCT-TTTAT
64 ATTGAATGTCTGCCTTGAGAAACGTAAAGAAAAAAGCATTCATTGGCAAGAAAAGT-CTATTTAT
* * * * * * *
476 AGCCTCTCATTCCTTTAATAGCCTTTTTACTCGA-TCTAAATA
128 AGCCT-TCATTCCTTCAAAAGCCTTATTACT-TACTTTAAGTT
* * * ********** *
518 ATTTTATAATCTCATAATTAATTTTAAGTTCAATTTTTTTNNNNNNNNNNTTAAAACAGACTATA
1 GTTTTATAATCTAATAATTAATTTTAAGTTGAA-TTTTTTACATTTTTTATTAAAACA-AATATA
** * * * *
583 ATTGAATGTCTTTCTTGAGAAAAGTGAAGAAAATAGCATTCATTGGCAAGAACAGTCTATTTATA
64 ATTGAATGTCTGCCTTGAGAAACGTAAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATA
* * ********** * * * *
648 GCATCCCATTCCTTCAANNNNNNNNNNACTCATTTTAAATG
129 GCCT-TCATTCCTTCAAAAGCCTTATTACTTACTTTAAGTT
* * ** * * *
689 GTTTTCTAATCTAAAAATTAATTTTAAGTTGAATTTTTTTTATTTTTGATTAAAATAGACA-ACA
1 GTTTTATAATCTAATAATTAATTTTAAGTTGAATTTTTTACATTTTTTATTAAAACA-A-ATATA
* ** * * * * ***
753 ATTAAATGTCTATCTTAAGAAACGTGAAGGAAAAAGTATTCATTATTAAGAAAAGTCTATTTATA
64 ATTGAATGTCTGCCTTGAGAAACGTAAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATA
********** * * *
818 GTCAC-TCNNNNNNNNNNAAGCCTTATTACTCACTTTAAATG
129 G-C-CTTCATTCCTTCAAAAGCCTTATTACTTACTTTAAGTT
* * * * * * * *
859 GCTTTGTAATGTAATAATTGATTTTAAGTTAAATTTTTTTTTATATTTTTCATTAAAACAGACTA
1 GTTTTATAATCTAATAATTAATTTTAAGTTGAA---TTTTTTACATTTTTTATTAAAACA-AATA
* ** ********************* * *
924 TAATTGAATGTCTACCTCAAGAANNNNNNNNNNNNNNNNNNNNNTTGGTAAGAAAAGTCCATTTA
62 TAATTGAATGTCTGCCTTGAGAAACGTAAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTA
* * *
989 TAGTCAC-CCATTCCTTCAAAAGTCTTATTACTTACTTTTAA-TA
127 TAG-C-CTTCATTCCTTCAAAAGCCTTATTACTTAC-TTTAAGTT
* * *
1032 G-TTTATAATCTAATTATTGATTTTAAGTTGAAATTTTTTA-ATATTTTTCATTAAAACAGACTA
1 GTTTTATAATCTAATAATTAATTTTAAGTTG-AATTTTTTACAT-TTTTT-ATTAAAACA-AATA
* * * * ***
1095 TAATTGAACGTCCGCCTTGACAAATGTAAAGAAAAAAGCATTCATTAATAAGAAAAGTCTATTTA
62 TAATTGAATGTCTGCCTTGAGAAACGTAAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTA
* ** * * *
1160 TAGCCTCTCATTCCTTTAGTAGCCTTTTTACTCA-TTCTAA-AT
127 TAGCCT-TCATTCCTTCAAAAGCCTTATTACTTACTT-TAAGTT
********** * * * * *
1202 GANNNNNNNNNNTCATAATTAATTTTAAGTTCAATTTGTTTATATTTTTTAATAAAACAGACTAT
1 G-TTTTATAATCTAATAATTAATTTTAAGTTGAATTT-TTTACATTTTTTATTAAAACA-AATAT
* * * * *
1267 AATTGAATGTTTGTCTGGAGAAAAGTGAAA-AAAAAAGCATTCATTGGCAAAAAAAGTCTATTTA
63 AATTGAATGTCTGCCTTGAGAAACGT-AAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTA
* * *
1331 TAGCCTTCCATTCCTTAAAAAGCCTTATTACTTGCTTTAAGTG
127 TAGCCTT-CATTCCTTCAAAAGCCTTATTACTTACTTTAAGTT
********** * * *
1374 GTTTTATAATCTAATAATTNNNNNNNNNNTGAATTTTTTTACATTTTTGATTAAAGCAGATAATA
1 GTTTTATAATCTAATAATTAATTTTAAGTTGAA-TTTTTTACATTTTTTATTAAAACAAAT-ATA
* * ** * * * * * *
1439 ATTGACTGTTTATCTCGA-AAACGTGAAGACAAAA-TATTCATTGGCAATAAAAGTCCATTTATA
64 ATTGAATGTCTGCCTTGAGAAACGTAAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATA
* ** **
1502 GTCAC-ACATTCCTTTGAAAGCCTTATTACTCGCTTTAAAAG-T
129 G-C-CTTCATTCCTTCAAAAGCCTTATTACTTACTTT--AAGTT
* * * *********
1544 -TTTTCTAGTCTCATAATTAATTTTAAGTTGAATTTTTTTACATTTTTTATNNNNNNNNNNTATA
1 GTTTTATAATCTAATAATTAATTTTAAGTTGAA-TTTTTTACATTTTTTAT-TAAAACAAATATA
** * * * *
1608 ATTGAATGTCTGCCTCAAGAACCATGAAGAAAAAAGCATTCATTGAG-AACAAAAGTCTATTTAT
64 ATTGAATGTCTGCCTTGAGAAACGTAAAGAAAAAAGCATTCATTG-GCAAGAAAAGTCTATTTAT
* * * * * *
1672 AGCCCTCCAGTCCTTCAACAGCCTTTTTAC-T-CGTTCTAAATG
128 AG-CCTTCATTCCTTCAAAAGCCTTATTACTTAC-TT-TAAGTT
* *
1714 GTTATATAATC-ACATAATTAATTTTAAGTTCAATTGTTTTACATTTTTTATTAAAA-AAGAGTA
1 GTTTTATAATCTA-ATAATTAATTTTAAGTTGAATT-TTTTACATTTTTTATTAAAACAA-A-TA
* *
1777 TAATGGAATGTCTGCCTTGAGAAACGTAAAGAAAAAAGCATTCATTGGCAAGAATAGTCTATTTA
62 TAATTGAATGTCTGCCTTGAGAAACGTAAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTA
* *
1842 CAGCCTGTCATTCCTTCAAAAGGCTTATTACTTACTTTAAGTT
127 TAGCCT-TCATTCCTTCAAAAGCCTTATTACTTACTTTAAGTT
* * * *
1885 GTTTTATATTCTAATAATTGATTTTACGTTGAAGTTTTTTACATTTTTTATTAAAATAAATAATA
1 GTTTTATAATCTAATAATTAATTTTAAGTTGAA-TTTTTTACATTTTTTATTAAAACAAAT-ATA
**
1950 ATTGAATGTCTATCTTGAGAA
64 ATTGAATGTCTGCCTTGAGAA
1971 NNNNNNNNNN
Statistics
Matches: 1289, Mismatches: 442, Indels: 132
0.69 0.24 0.07
Matches are distributed among these distances:
169 117 0.09
170 171 0.13
171 713 0.55
172 77 0.06
173 202 0.16
174 9 0.01
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.38
Consensus pattern (168 bp):
GTTTTATAATCTAATAATTAATTTTAAGTTGAATTTTTTACATTTTTTATTAAAACAAATATAAT
TGAATGTCTGCCTTGAGAAACGTAAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATAGC
CTTCATTCCTTCAAAAGCCTTATTACTTACTTTAAGTT
Found at i:3614 original size:171 final size:171
Alignment explanation
Indices: 3234--3626 Score: 398
Period size: 171 Copynumber: 2.3 Consensus size: 171
3224 NNNNNNNNNN
* * ** ** *
3234 ACTATAATTGAATATCTATCTCAAGAAACATGAAGAAAAGAGCATTCATTGACAGGAAAAGTCTA
1 ACTATAATTGAATATCTACCTCCAGAAATGTGAAGAAAAGAGCATTCATTGACAAAAAAAGTCCA
3299 TTTATAGTCACCCATTCTTTCAAAAACCTTATTACTCACGTCAAATGGTTTTATAATCTAATAAT
66 TTTATAGTCACCCATTCTTTCAAAAACCTTATTACTCACGTCAAATGGTTTTATAATCTAATAAT
3364 TGATTTTAAGTTGAAATTTTTTATACGTTTTATTAAAACAG
131 TGATTTTAAGTTGAAATTTTTTATACGTTTTATTAAAACAG
* **********
3405 ACTATAATTGAATATCTATCTCNNNNNNNNNNAAGAAAAGAGCATTCATTGACAAAAAAAGTCCA
1 ACTATAATTGAATATCTACCTCCAGAAATGTGAAGAAAAGAGCATTCATTGACAAAAAAAGTCCA
* ** * * * * * *
3470 TTTATAGTCACTCATT-TCTTCAAAAGTCTTATTACTCGCTTCTAATGGTTTTTTAATCTCATTA
66 TTTATAGTCACCCATTCT-TTCAAAAACCTTATTACTCACGTCAAATGGTTTTATAATCTAATAA
* * * *
3534 TTGATTTT-AGATTG-AATTTTTT-TGCATTTTTCTTTAAATCAG
130 TTGATTTTAAG-TTGAAATTTTTTATAC-GTTTT-ATTAAAACAG
* * * * *
3576 GCTATAATTGAATGTTTGCCTCCAGAAATGTGAAGAAAAAAGCATTCATTG
1 ACTATAATTGAATATCTACCTCCAGAAATGTGAAGAAAAGAGCATTCATTG
3627 GCAA
Statistics
Matches: 176, Mismatches: 42, Indels: 8
0.78 0.19 0.04
Matches are distributed among these distances:
169 2 0.01
170 15 0.09
171 159 0.90
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (171 bp):
ACTATAATTGAATATCTACCTCCAGAAATGTGAAGAAAAGAGCATTCATTGACAAAAAAAGTCCA
TTTATAGTCACCCATTCTTTCAAAAACCTTATTACTCACGTCAAATGGTTTTATAATCTAATAAT
TGATTTTAAGTTGAAATTTTTTATACGTTTTATTAAAACAG
Done.