Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402100.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5195.0, 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: 2013
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.29
Warning! 411 characters in sequence are not A, C, G, or T
Found at i:1205 original size:170 final size:168
Alignment explanation
Indices: 786--1680 Score: 682
Period size: 170 Copynumber: 5.3 Consensus size: 168
776 ATTAAGAACT
* * * * *
786 TGAAGAAAAAGCCATGCATTGCCAAAAAAAGTCCATCTACAGAT-ACCCATGCCTTCGAAAGCCT
1 TGAAGAAAAAGTCATTCATTG-GAAGAAAAGTCCATCTATAG-TCACCCATGCCTTCGAAAGCCT
* * * * *
850 TATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTCAGTTAAATTTTTTTATATTTT
64 TATTACTAGCTTTAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTT
** * * * * *
915 TCATTAAATATATTATAATTGAATGTTT-TCTT-CGAGAACA
129 TGGTCAAA-ACAATATAATTGAATGTTTGCCTTAGGA-AACA
* * * * ***** * *
955 TGAAGCAAAAGTCATCCATTGGCAAGAAAAGTCCATTTATATTTGTTTAAGTCCTT-AAAAGCCT
1 TGAAGAAAAAGTCATTCATTGG-AAGAAAAGTCCATCTATAGTCACCCATG-CCTTCGAAAGCCT
* * * *
1019 TATTAATAACTTTAAATGATTTTATAATCTCATAATT-AGTTTTGAGTTTAA-TTTTTTACATTT
64 TATTACTAGCTTTAAATGATTTTATAATCTCATAATTGA-TTTTAAGTTGAATTTTTTTACATTT
* *
1082 TTGGTGAAAACAGATAGTATTTGAATGTTTGCCTTAGGAAACA
128 TTGGTCAAAACA-ATA-TAATTGAATGTTTGCCTTAGGAAACA
*
1125 TGAAGAAAAAGTCATTCATTGGAAGGAAAAGTCCATCTATAGTCACCCATGCCTTCGAAAGCCTC
1 TGAAGAAAAAGTCATTCATTGGAA-GAAAAGTCCATCTATAGTCACCCATGCCTTCGAAAGCCTT
* * * * * * *
1190 ATTACTTGTTTTAAAT-AGTTTTTTAATCTCATTACTGATTTTAAGTTGAAGTTTTTTACGTTTT
65 ATTACTAGCTTTAAATGA-TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAC-ATTT
* * * * * * *
1254 TTTGTCAAATATATTATAATTAAATGTCTGTCTTGGGAAACA
128 TTGGTCAAA-ACAATATAATTGAATGTTTGCCTTAGGAAACA
* * * * * ** * ** * *
1296 TGAAGCAAAAGTCA-TCTATTAGTAAAAAAAGTCCATTTATAGCCACTTAAGTTTTTGAAAGCGT
1 TGAAGAAAAAGTCATTC-ATT-GGAAGAAAAGTCCATCTATAGTCACCCATGCCTTCGAAAGCCT
* * * * *
1360 AATTATTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTCT
64 TATTACTAGCTTTAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTT
** * * * * *
1425 TGGTTC-AAACAGATAATGTTTTATTCTTTACATTAGGAAACA
129 TGG-TCAAAACA-AT-ATAATTGAATGTTTGCCTTAGGAAACA
* * * *
1467 TGAA-AAAAAGCCATTCATTAGTG-AGAAAAATCCATCTATCGTCATCCATGCCTTCGAAAGCCT
1 TGAAGAAAAAGTCATTCATT-G-GAAGAAAAGTCCATCTATAGTCACCCATGCCTTCGAAAGCCT
* * *
1530 TATTAGTAGCTTTAAAT-AGTTTTATAATCTCATAATTGCTTTTAAGTTGAATTTTGTTACATTT
64 TATTACTAGCTTTAAATGA-TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACA-TT
* * **
1594 TTTGTTCAAAA-ATATTCTAATTGAATGTTTGCCTCGGGAAACA
127 TTTGGTCAAAACA-A-TATAATTGAATGTTTGCCTTAGGAAACA
* * * *
1637 TGAAGCAAAAGTCATCCATTGGCAAGAAAGGTCCATTTATAGTC
1 TGAAGAAAAAGTCATTCATTGG-AAGAAAAGTCCATCTATAGTC
1681 GCTTAAGTCT
Statistics
Matches: 558, Mismatches: 138, Indels: 58
0.74 0.18 0.08
Matches are distributed among these distances:
167 2 0.00
168 21 0.04
169 107 0.19
170 222 0.40
171 189 0.34
172 15 0.03
173 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (168 bp):
TGAAGAAAAAGTCATTCATTGGAAGAAAAGTCCATCTATAGTCACCCATGCCTTCGAAAGCCTTA
TTACTAGCTTTAAATGATTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTG
GTCAAAACAATATAATTGAATGTTTGCCTTAGGAAACA
Found at i:1484 original size:341 final size:338
Alignment explanation
Indices: 761--1689 Score: 1073
Period size: 341 Copynumber: 2.7 Consensus size: 338
751 AAAGTTCATT
* * * * * * *
761 TATTTGAATGTCTACATTAAG-AACTTGAAGAAAAAGCCATGCATTGCCAAAAAAAGTCCATCTA
1 TATTTGAATCTTTACATTAGGAAACATGAAGAAAAAGCCATTCATTGCGAAGAAAAGTCCATCTA
* * *
825 CAGAT-ACCCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGA
66 TAG-TCACCCATGCCTTCGAAAGCCTTATTACTAGCTTTAAATAGTTTTATAATCTCATAATTGA
* * ** * * *
889 TTTTCAGTTAAATTTTTTTA-TATTTTTCATTAAATATATTATAATTGAATGTTTTCTT-CGAGA
130 TTTTAAGTTGAA-TTTTTTACT-TTTTTTGTCAAATATATTATAATTGAATGTTGTCTTGGGA-A
* * *
952 ACATGAAGCAAAAGTCATCCATTGGCAAGAAAAGTCCATTTATATTTGTTTAAGTCCTTAAAAGC
192 ACATGAAGCAAAAGTCATCCATTGGCAAGAAAAGTCCATTTATAGTCGCTTAAGTCCTTAAAAGC
* * * *
1017 CTTATTAATAACTTTAAATGATTTTATAATCTCATAATTAGTTTTGAGTTTAATTTTTTACATTT
257 CTAATTAATAACTTTAAATGATTTTATAATCTCATAATTAGTTTTAAGTTGAATTTTTTACATTC
*
1082 TTGGTGAAAACAGATAG
322 TTGGTGAAAACAGATAA
* * * *
1099 TATTTGAATGTTTGCCTTAGGAAACATGAAGAAAAAGTCATTCATTG-GAAGGAAAAGTCCATCT
1 TATTTGAATCTTTACATTAGGAAACATGAAGAAAAAGCCATTCATTGCGAA-GAAAAGTCCATCT
* * * * * *
1163 ATAGTCACCCATGCCTTCGAAAGCCTCATTACTTGTTTTAAATAGTTTTTTAATCTCATTACTGA
65 ATAGTCACCCATGCCTTCGAAAGCCTTATTACTAGCTTTAAATAGTTTTATAATCTCATAATTGA
*
1228 TTTTAAGTTGAAGTTTTTTACGTTTTTTTGTCAAATATATTATAATTAAATGTCTGTCTTGGGAA
130 TTTTAAGTTGAA-TTTTTTAC-TTTTTTTGTCAAATATATTATAATTGAATGT-TGTCTTGGGAA
* * * * * * ** *
1293 ACATGAAGCAAAAGTCATCTATTAGTAAAAAAAGTCCATTTATAGCCACTTAAGTTTTTGAAAGC
192 ACATGAAGCAAAAGTCATCCATTGGCAAGAAAAGTCCATTTATAGTCGCTTAAGTCCTTAAAAGC
* * ** *
1358 GTAATTATTCGCTTTAAATGGTTTTATAATCTCATAATT-GATTTTAAGTTGAATTTTTTTACAT
257 CTAATTAATAACTTTAAATGATTTTATAATCTCATAATTAG-TTTTAAGTTGAA-TTTTTTACAT
**
1422 TCTTGGTTCAAACAGATAA
320 TCTTGGTGAAAACAGATAA
* * * * *
1441 TGTTTTATTCTTTACATTAGGAAACATGAA-AAAAAGCCATTCATTAGTG-AGAAAAATCCATCT
1 TATTTGAATCTTTACATTAGGAAACATGAAGAAAAAGCCATTCATT-GCGAAGAAAAGTCCATCT
* * * *
1504 ATCGTCATCCATGCCTTCGAAAGCCTTATTAGTAGCTTTAAATAGTTTTATAATCTCATAATTGC
65 ATAGTCACCCATGCCTTCGAAAGCCTTATTACTAGCTTTAAATAGTTTTATAATCTCATAATTGA
* * * * *
1569 TTTTAAGTTGAATTTTGTTACATTTTTTGTTCAAAAATATTCTAATTGAATGTTTGCCTCGGGAA
130 TTTTAAGTTGAATTTT-TTACTTTTTTTG-TCAAATATATTATAATTGAATG-TTGTCTTGGGAA
*
1634 ACATGAAGCAAAAGTCATCCATTGGCAAGAAAGGTCCATTTATAGTCGCTTAAGTC
192 ACATGAAGCAAAAGTCATCCATTGGCAAGAAAAGTCCATTTATAGTCGCTTAAGTC
1690 TTTNNNNNNN
Statistics
Matches: 495, Mismatches: 82, Indels: 25
0.82 0.14 0.04
Matches are distributed among these distances:
338 20 0.04
339 106 0.21
340 38 0.08
341 276 0.56
342 54 0.11
343 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (338 bp):
TATTTGAATCTTTACATTAGGAAACATGAAGAAAAAGCCATTCATTGCGAAGAAAAGTCCATCTA
TAGTCACCCATGCCTTCGAAAGCCTTATTACTAGCTTTAAATAGTTTTATAATCTCATAATTGAT
TTTAAGTTGAATTTTTTACTTTTTTTGTCAAATATATTATAATTGAATGTTGTCTTGGGAAACAT
GAAGCAAAAGTCATCCATTGGCAAGAAAAGTCCATTTATAGTCGCTTAAGTCCTTAAAAGCCTAA
TTAATAACTTTAAATGATTTTATAATCTCATAATTAGTTTTAAGTTGAATTTTTTACATTCTTGG
TGAAAACAGATAA
Done.