Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402821.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5876.0, 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, 621
Length: 1036
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Found at i:371 original size:171 final size:169
Alignment explanation
Indices: 1--1036 Score: 703
Period size: 171 Copynumber: 5.9 Consensus size: 169
* * ** * *
1 AATCTCAAAATTGATTTTAAGTTCAATTGTTTCTACATTATTGGTTAAAATAGAATATAATTGAA
1 AATCTCATAATTGATTTTAAGTTGAATT-TTT-TACATT-TTTATTAAAACAGACTATAATTGAA
* * **** * * * * * **
66 TGTTTAGCTCCTCAAACGTGAAGAAAAAGAG-ATTCATTGGTAGGAAAAGTTGATTTATAGTCAC
63 TGTCTACCTTAGGAAACATGAAGAAAAAG-GCATTCACTAGCAAGAAAAGTCCATTTATAGTCAC
* *
130 CCATTCCTTCAAAAGCCATATTTCTCGCTTTAAAT-GCTTTTAT
127 CCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAG-TTTTAT
* *
173 AATCTCGTAATTGATTTTACA-TTGAATTTTTTAGCATTTTTGATTAAAACAGACTATACTTGAA
1 AATCTCATAATTGATTTTA-AGTTGAATTTTTTA-CATTTTT-ATTAAAACAGACTATAATTGAA
* *
237 CGTCTACCTTAGGAAACATGAAGAATAAGGCATTCACTAGCAAGAAAAGTCCATTTATAGTCACC
63 TGTCTACCTTAGGAAACATGAAGAAAAAGGCATTCACTAGCAAGAAAAGTCCATTTATAGTCACC
* * *
302 CGTTCCTTGAAAAGCCTTTTTACTCGCTTTAAATAGTTTTAT
128 CATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTAT
* * * *
344 AATCTCATAATTGATTTTAAGTTGAATTGTTTACATTTTTGGTTAAAAAAGACTATAATTAAATG
1 AATCTCATAATTGATTTTAAGTTGAATTTTTTACATTTTT-ATTAAAACAGACTATAATTGAATG
* * * * * * * * *
409 TCTACC-TCGAGAAACATGAAGAAAAAAGCATTTATTGGCAAGACAGGTCAATTTATCA-TCTCC
65 TCTACCTTAG-GAAACATGAAGAAAAAGGCATTCACTAGCAAGAAAAGTCCATTTAT-AGTCACC
* *
472 TATTCCTTCAAAAGCCTTATTACTCGTTTTAAATTA-TTTTAT
128 CATTCCTTCAAAAGCCTTATTACTCGCTTTAAA-TAGTTTTAT
* * * *
514 AACCTAATAATTGATTTTAAGTTAGATTTTTTGTACATTTTTTATTAAAACAAACTATAATTGAA
1 AATCTCATAATTGATTTTAAGTT-GAATTTTT-TACA-TTTTTATTAAAACAGACTATAATTGAA
* * * * * *
579 TGTCTA-CTTCAAGAAACATGAAGAAACAA-GCGTTCA-TTGACAAGAAAAGTCTATTCATTGGT
63 TGTCTACCTT-AGGAAACATGAAGAAA-AAGGCATTCACTAG-CAAGAAAAGTCCATTTA-TAGT
*** * * * * *** * * * * *
641 -AGGAAAAGTCCATTTATAATCACCCATTCCTTCAAAAGGTATATTACTCGCTTTA-
124 CA--CCCATTCC-TTCA-AA--AGCC-TT-ATT-ACTCGCT-T-TAAATAGTTTTAT
* * ** * *
696 AATGCTTTTATAATCTCATAATTGATTTTAAGTTTAATTTTTTAGTATTTTTAGTTAAAACAGAC
1 AAT-C--TCATAA--T--TGATT--TTAA--GTTGAATTTTTTA-CATTTTTA-TTAAAACAGAC
* * * * *
761 TATAATTGAATGTCTATCTTGGGAAACAAGAAGAATAAGGCATTCACTAGCAAAAAAAGTCCATT
53 TATAATTGAATGTCTACCTTAGGAAACATGAAGAAAAAGGCATTCACTAGCAAGAAAAGTCCATT
*
826 TATAGTCACCCA-TCTCTTTAAAAGCCTTATTACTCGCTTTAAATAGTTTTAT
118 TATAGTCACCCATTC-CTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTAT
* * *
878 AATCTCAAAATTGATTTTAAGTGGAATTCTTTTATATTTTTAGTTAAAACAGACTATAATTGAAT
1 AATCTCATAATTGATTTTAAGTTGAATT-TTTTACATTTTTA-TTAAAACAGACTATAATTGAAT
* * * * * * * * * * * *
943 GTTTACCAT-GAGAAAGATAAAGAAAAAGGTAATGATTGGCAAGAAAAGTCTATTTATAGTAACA
64 GTCTACCTTAG-GAAACATGAAGAAAAAGGCATTCACTAGCAAGAAAAGTCCATTTATAGTCACC
1007 CATTCCTTCAAAAGCCTTATTACTCGCTTT
128 CATTCCTTCAAAAGCCTTATTACTCGCTTT
Statistics
Matches: 672, Mismatches: 140, Indels: 105
0.73 0.15 0.11
Matches are distributed among these distances:
169 2 0.00
170 137 0.20
171 258 0.38
172 92 0.14
173 12 0.02
174 4 0.01
175 7 0.01
176 2 0.00
177 1 0.00
178 3 0.00
179 6 0.01
180 2 0.00
181 12 0.02
182 8 0.01
183 10 0.01
184 2 0.00
185 7 0.01
186 3 0.00
187 1 0.00
188 2 0.00
189 10 0.01
190 2 0.00
191 15 0.02
192 66 0.10
193 8 0.01
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (169 bp):
AATCTCATAATTGATTTTAAGTTGAATTTTTTACATTTTTATTAAAACAGACTATAATTGAATGT
CTACCTTAGGAAACATGAAGAAAAAGGCATTCACTAGCAAGAAAAGTCCATTTATAGTCACCCAT
TCCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTAT
Found at i:988 original size:363 final size:362
Alignment explanation
Indices: 280--996 Score: 882
Period size: 363 Copynumber: 2.0 Consensus size: 362
270 TCACTAGCAA
* * * *
280 GAAAAGTCCATTTATAGTCACCCGTTCCTTGAAAAGCCTTTTTACTCGCTTTAAATAGTTTTATA
1 GAAAAGTCCATTTATAATCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATA
*
345 ATCTCATAATTGATTTTAAGTTGAATTGTTTACATTTTTGGTTAAAAAAGACTATAATTAAATGT
66 ATCTCATAATTGATTTTAAGTTGAATTGTTTACATTTTTAGTTAAAAAAGACTATAATTAAATGT
* * * * * * * * *
410 CTACCTCGAGAAACATGAAGAAAAAAGCATTTATTGGCAAGACAGGTCAATTTATCATCTCCTAT
131 CTACCTCGAGAAACAAGAAGAAAAAAGCATTCACTAGCAAAAAAAGTCAATTTATCATCACCCAT
* *
475 TCCTTCAAAAGCCTTATTACTCGTTTTAAATTATTTTATAACCTAATAATTGATTTTAAGTTAGA
196 TCCTTCAAAAGCCTTATTACTCGCTTTAAATTATTTTATAACCTAATAATTGATTTTAAGTGAGA
* *
540 TTTTTTGTACATTTTTTATTAAAACAAACTATAATTGAATGTCTACTTCAAGAAACATGAAGAAA
261 TTCTTTGTACATTTTTTATTAAAACAAACTATAATTGAATGTCTAC-TCAAGAAACATAAAGAAA
605 CAAGCGTTCATTGACAAGAAAAGTCTATTCATTGGTAG
325 CAAGCGTTCATTGACAAGAAAAGTCTATTCATTGGTAG
*
643 GAAAAGTCCATTTATAATCACCCATTCCTTCAAAAG-GTATATTACTCGCTTTAAAT-GCTTTTA
1 GAAAAGTCCATTTATAATCACCCATTCCTTCAAAAGCCT-TATTACTCGCTTTAAATAG-TTTTA
* * * * *
706 TAATCTCATAATTGATTTTAAGTTTAATTTTTTAGTATTTTTAGTTAAAACAGACTATAATTGAA
64 TAATCTCATAATTGATTTTAAGTTGAATTGTTTA-CATTTTTAGTTAAAAAAGACTATAATTAAA
* * * * * *
771 TGTCTATCTTGGGAAACAAGAAGAATAAGGCATTCACTAGCAAAAAAAGTCCATTTAT-AGTCAC
128 TGTCTACCTCGAGAAACAAGAAGAAAAAAGCATTCACTAGCAAAAAAAGTCAATTTATCA-TCAC
* *
835 CCA-TCTCTTTAAAAGCCTTATTACTCGCTTTAAA-TAGTTTTATAATCTCAA-AATTGATTTTA
192 CCATTC-CTTCAAAAGCCTTATTACTCGCTTTAAATTA-TTTTATAACCT-AATAATTGATTTTA
* * *
897 AGTG-GAATTCTTT-TATA-TTTTTAGTTAAAACAGACTATAATTGAATGTTTAC-CATGAGAAA
254 AGTGAG-ATTCTTTGTACATTTTTTA-TTAAAACAAACTATAATTGAATGTCTACTCA--AGAAA
* * *
958 GATAAAGAAA-AAG-GTAATGATTGGCAAGAAAAGTCTATT
315 CATAAAGAAACAAGCGT--TCATTGACAAGAAAAGTCTATT
997 TATAGTAACA
Statistics
Matches: 303, Mismatches: 38, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
361 4 0.01
362 11 0.04
363 154 0.51
364 132 0.44
365 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (362 bp):
GAAAAGTCCATTTATAATCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATA
ATCTCATAATTGATTTTAAGTTGAATTGTTTACATTTTTAGTTAAAAAAGACTATAATTAAATGT
CTACCTCGAGAAACAAGAAGAAAAAAGCATTCACTAGCAAAAAAAGTCAATTTATCATCACCCAT
TCCTTCAAAAGCCTTATTACTCGCTTTAAATTATTTTATAACCTAATAATTGATTTTAAGTGAGA
TTCTTTGTACATTTTTTATTAAAACAAACTATAATTGAATGTCTACTCAAGAAACATAAAGAAAC
AAGCGTTCATTGACAAGAAAAGTCTATTCATTGGTAG
Done.