Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397630.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4837.0, 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: 3688
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.37
Warning! 202 characters in sequence are not A, C, G, or T
Found at i:405 original size:172 final size:169
Alignment explanation
Indices: 180--1789 Score: 842
Period size: 171 Copynumber: 9.5 Consensus size: 169
170 ATTCTTTTCA
* * * * ** * *
180 TCAGGAAACCTGAAGAAAAAGCCATTCATTGGTGAGAAAACTCCATCTATAGTCATTCATGCCTT
1 TCAGGAAACATAAAGAAAAAGTCATCCATTGGCAAGAAAAGTCCATCTATAGTCACTCATGCCTT
* * *
245 CGAAAACCTTATTAGTAGCTTTAAATAGTTTTTATAATCTCATAATTGTTTTTAAGTTAAATTTT
66 CGAAAGCCTTATTACTA-CTTTAAATAG-TTTTATAATCTCATAATTGATTTTAAGTTAAATTTT
* *
310 GTTATATTTTTTATTAAAAAATATTATAATTGAATGTTTACC
129 -TTATATTTTTTATTAAAATATATTATAATTGAATGTCTACC
* * * * * * * * *
352 TCCGGAAACATAAAGCAAAAGTCATCCATTGGTAAGAAAAGTCTATTTATAGTCGCTTAAGTCTT
1 TCAGGAAACATAAAGAAAAAGTCATCCATTGGCAAGAAAAGTCCATCTATAGTCACTCATGCCTT
* * * * * * *
417 CAAAAGCCTTATGACT-CTTTTAAAATAGTTTTATAATCGCACAATTGATTTTAAGCTGATTTTT
66 CGAAAGCCTTATTACTAC-TTT-AAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTT
* ** * * * * *
481 TTTTA-CATTTATGGTTAAATCAGATAATATTTGAATGTCTACA
129 TTATATTTTTTAT--TAAAAT-ATATTATAATTGAATGTCTACC
* * * * * * * *
524 TCAGGAGACGTAAAGAAAAA-ACTATTCATTGGTAAGAAAAGTCCATCTACAATCACCCATGCCT
1 TCAGGAAACATAAAGAAAAAGTC-ATCCATTGGCAAGAAAAGTCCATCTATAGTCACTCATGCCT
* * *
588 TCGAAAGCCTTATTACTTACTTTAAAT-GCTTTTACAATCTCCTAATTGATTTTAAGTTAACTAT
65 TCGAAAGCCTTATTAC-TACTTTAAATAG-TTTTATAATCTCATAATTGATTTTAAGTTAAAT-T
* * * * * *
652 TTTTGTA-TTTTTGTT-AACTATATTATAATTAAATATCTGCC
127 TTTTATATTTTTTATTAAAATATATTATAATTGAATGTCTACC
* * * * * * * *
693 TCAGGAAACGTGAAGAAAAAGTCATCCATTAGCAAGAAAAGTCTATTTATAGTCGCTCAAGTCTT
1 TCAGGAAACATAAAGAAAAAGTCATCCATTGGCAAGAAAAGTCCATCTATAGTCACTCATGCCTT
* * * *
758 CGAAAGCCTTATTACT-CTCTTAAAATAGTTTTATAATCACATAATTAATTTTAAGCTGAA----
66 CGAAAGCCTTATTACTACT-TT-AAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTT
* * * * * *
818 -T-T-TTTTTTGTTAAAGTAGATAATATTTGAATGTCTACA
129 TTATATTTTTTATTAAAATATATTATAATTGAATGTCTACC
* * * * *
856 TCAGGAAACTTGAAA-AAAAAATCATTCATTGGCAAGAAAAGTCTATCTATAGTCACCCATGCCT
1 TCAGGAAACAT-AAAGAAAAAGTCATCCATTGGCAAGAAAAGTCCATCTATAGTCACTCATGCCT
* * * * * *
920 TCGAAAGCCTTGTTTCTCGCTTTAAATGGTTTTATAATCTCATAATTCATTTTAAGTTTAACTTT
65 TCGAAAGCCTTATTACT-ACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAG-TTAAATTT
* * **
985 TTTACCA-TTTTTATTAAAATATATTATAATAGAATGTCTGTC
128 TTTA-TATTTTTTATTAAAATATATTATAATTGAATGTCTACC
** * * * * * ** * * *
1027 TTGGGAAACATGAAGCAAAAGTCATCTATTGGCAAGAAAAGTCCATTTATAATTGCTTAAGTCTT
1 TCAGGAAACATAAAGAAAAAGTCATCCATTGGCAAGAAAAGTCCATCTATAGTCACTCATGCCTT
* * * * * ********** **
1092 TGAAAGCTTTATTATTTGCTTTAAATGGTTTTATAATCTCANNNNNNNNNNTAAGTTGAACGTTT
66 CGAAAGCCTTATTA-CTACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTT-AAATTTT
* ** * * * * *
1157 TTACATTTTAGGA-TAAAACATATGATACTTCAATGTCTACA
129 TTATATTTT-TTATTAAAATATATTATAATTGAATGTCTACC
* * * * * * * * *
1198 TC-GAGAAACCTGAAGAAAAAGCCATTCATTGGCAAGAACAGTCTATCTATTGTAACCCATGCCT
1 TCAG-GAAACATAAAGAAAAAGTCATCCATTGGCAAGAAAAGTCCATCTATAGTCACTCATGCCT
* * * *
1262 TCGAAAGACATATTACTCGCTTTAAATAGTTTTATAACCTCATAATTGATTTTAAGTTAAATTTN
65 TCGAAAGCCTTATTACT-ACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTT-
*************** * ** * *
1327 NNNNNNNNNNNNNNNNAAAA-A-ATAATGTTTGACTGTCTACA
128 -TTTATATTTTTTATTAAAATATATTATAATTGAATGTCTACC
* * * * *** * * *
1368 T-TGAGAAACGTAAAGAAAAA-CCATTCATTCATAAGAAAAGTCCATCTAAAGTCACCCATGCAT
1 TCAG-GAAACATAAAGAAAAAGTCATCCATTGGCAAGAAAAGTCCATCTATAGTCACTCATGCCT
* * * * * *
1431 TCGAAAGCATTATTACTTGCTTTATATAGTTTGATAACCTCATAATTGATTTTACGTTAAATTTT
65 TCGAAAGCCTTATTAC-TACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAA-TTT
* * * * * * *
1496 TTTACATTTGTTGTGAAAATATATTATAATTGGATGTTTTCC
128 TTTATATTTTTTATTAAAATATATTATAATTGAATGTCTACC
* * * * * * * * * * * **
1538 T-TGAGAAACATGAAGGAAAGGTCATCCATTGGCAAGAAAAGTCTATTTCTAATCGCTTAAGTAT
1 TCAG-GAAACATAAAGAAAAAGTCATCCATTGGCAAGAAAAGTCCATCTATAGTCACTCATGCCT
* * *
1602 TCGAAAGCTTTATTACTCACTTTAAATGGTTTTATAATCTCAT-ATATGATTTTAAGTTGAATTG
65 TCGAAAGCCTTATTACT-ACTTTAAATAGTTTTATAATCTCATAAT-TGATTTTAAGTTAAATT-
* * * * * *
1666 TTTTATA-TTTTTATTTAAAACAGATAATATTTGAATGTTTACA
127 TTTTATATTTTTTA-TTAAAATATATTATAATTGAATGTCTACC
* * * * * * * *
1709 TCA-AAAACGTAAAAAAAAAAGACATTCATTGGTAAGAAAAGTCCATCCATAGTCACCCATGCCT
1 TCAGGAAACAT-AAAGAAAAAGTCATCCATTGGCAAGAAAAGTCCATCTATAGTCACTCATGCCT
1773 TCGAAAGCCTTATTACT
65 TCGAAAGCCTTATTACT
1790 CGCTTTNNNN
Statistics
Matches: 1062, Mismatches: 326, Indels: 101
0.71 0.22 0.07
Matches are distributed among these distances:
162 9 0.01
163 115 0.11
164 6 0.01
165 2 0.00
167 2 0.00
168 7 0.01
169 202 0.19
170 100 0.09
171 421 0.40
172 182 0.17
173 15 0.01
174 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.37
Consensus pattern (169 bp):
TCAGGAAACATAAAGAAAAAGTCATCCATTGGCAAGAAAAGTCCATCTATAGTCACTCATGCCTT
CGAAAGCCTTATTACTACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTT
ATATTTTTTATTAAAATATATTATAATTGAATGTCTACC
Found at i:1115 original size:171 final size:167
Alignment explanation
Indices: 180--1132 Score: 594
Period size: 172 Copynumber: 5.6 Consensus size: 167
170 ATTCTTTTCA
* * ** * * * ** * *
180 TCAGGAAACCTGAAGAAAAAGCCAT-TCATTGGTGAGAAAACTCCATCTATAGTCATTCATGCCT
1 TCAGGAAACATGAAGAAAAAGTCATCT-ATTGGCAAGAAAAGTCTATTTATAGTCGCTCAAGTCT
* * * * ** *
244 TCGAAAACCTTATTAGTAGCTTTAAATAGTTTTTATAATCTCATAATTGTTTTTAAGTTAAATTT
65 TCGAAAGCCTTATTATTTGCTTTAAAT-GGTTTTATAATCTCATAATTAATTTTAAGTT-AACTT
* * * *
309 TGTTATATTTTTTATTAAAAAATATTATAATTGAATGT-TTACC
128 T-TT-TA-TTTTTGTTAAAATATATTATAATAGAATGTCTGA-C
* * * * * *
352 TCCGGAAACATAAAGCAAAAGTCATCCATTGGTAAGAAAAGTCTATTTATAGTCGCTTAAGTCTT
1 TCAGGAAACATGAAGAAAAAGTCATCTATTGGCAAGAAAAGTCTATTTATAGTCGCTCAAGTCTT
* * * * * * * * **
417 CAAAAGCCTTATGACTCTT--TTAAAATAGTTTTATAATCGCACAATTGATTTTAAGCTGATTTT
66 CGAAAGCCTTATTA-T-TTGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAG-TTA-ACT
* * * * *
480 TTTTTACATTTATGGTT-AAATCAGATAATATTTGAATGTCT-AC
127 TTTTT--ATTT-TTGTTAAAAT-ATATTATAATAGAATGTCTGAC
* * * * * * * * * * * * *
523 ATCAGGAGACGTAAAGAAAAA-ACTAT-TCATTGGTAAGAAAAGTCCATCTACAATCACCCATGC
1 -TCAGGAAACATGAAGAAAAAGTC-ATCT-ATTGGCAAGAAAAGTCTATTTATAGTCGCTCAAGT
* * * * * *
586 CTTCGAAAGCCTTATTACTTACTTTAAATGCTTTTACAATCTCCTAATTGATTTTAAGTTAACTA
63 CTTCGAAAGCCTTATTATTTGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTAAC--
* * *
651 TTTTTGTATTTTTGTT-AACTATATTATAATTA-AATATCTGCC
126 TTTTT-TATTTTTGTTAAAATATATTATAA-TAGAATGTCTGAC
* * *
693 TCAGGAAACGTGAAGAAAAAGTCATCCATTAGCAAGAAAAGTCTATTTATAGTCGCTCAAGTCTT
1 TCAGGAAACATGAAGAAAAAGTCATCTATTGGCAAGAAAAGTCTATTTATAGTCGCTCAAGTCTT
* * * * *
758 CGAAAGCCTTATTACTCT-CTTAAAATAGTTTTATAATCACATAATTAATTTTAAGCTGAA----
66 CGAAAGCCTTATTA-TTTGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAG-TTAACTTT
* * * * *
818 TTT-TTTTTGTTAAAGTAGATAATATTTGAATGTCT-AC
129 TTTATTTTTGTTAAAATATATTATAATAGAATGTCTGAC
* * * * * * * *
855 ATCAGGAAACTTGAAAAAAAAATCAT-TCATTGGCAAGAAAAGTCTATCTATAGTCACCCATGCC
1 -TCAGGAAACATGAAGAAAAAGTCATCT-ATTGGCAAGAAAAGTCTATTTATAGTCGCTCAAGTC
* * *
919 TTCGAAAGCCTTGTT-TCTCGCTTTAAATGGTTTTATAATCTCATAATTCATTTTAAGTTTAACT
64 TTCGAAAGCCTTATTAT-TTGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAG-TTAACT
* *
983 TTTTTACCATTTTTATTAAAATATATTATAATAGAATGTCTGTC
127 TTTTT---ATTTTTGTTAAAATATATTATAATAGAATGTCTGAC
** * * * * *
1027 TTGGGAAACATGAAGCAAAAGTCATCTATTGGCAAGAAAAGTCCATTTATAATTGCTTAAGTCTT
1 TCAGGAAACATGAAGAAAAAGTCATCTATTGGCAAGAAAAGTCTATTTATAGTCGCTCAAGTCTT
* *
1092 TGAAAGCTTTATTATTTGCTTTAAATGGTTTTATAATCTCA
66 CGAAAGCCTTATTATTTGCTTTAAATGGTTTTATAATCTCA
1133 NNNNNNNNNN
Statistics
Matches: 594, Mismatches: 146, Indels: 83
0.72 0.18 0.10
Matches are distributed among these distances:
161 1 0.00
162 10 0.02
163 118 0.20
164 2 0.00
167 3 0.01
169 104 0.18
170 17 0.03
171 150 0.25
172 186 0.31
173 2 0.00
174 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (167 bp):
TCAGGAAACATGAAGAAAAAGTCATCTATTGGCAAGAAAAGTCTATTTATAGTCGCTCAAGTCTT
CGAAAGCCTTATTATTTGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTAACTTTTT
TATTTTTGTTAAAATATATTATAATAGAATGTCTGAC
Done.