Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402715.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5777.0, 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, 748
Length: 1248
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Found at i:609 original size:171 final size:170
Alignment explanation
Indices: 309--1248 Score: 791
Period size: 171 Copynumber: 5.6 Consensus size: 170
299 TGATAAAGCG
* * * *
309 ATTCATTGGCAAAAAAAGTCCATTTATAGTCACTCATGCCTTCCAAAGCAC-TATTACTTGCTTT
1 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAAGCCTTCCAAAGC-CTTATTACTCGCTTT
* * *
373 AAA-GGCTTTGATAATCTCATAATTTATTTTTAG-TGAAATTTTTTTACACTTTTAGATAAAATA
65 AAATGG-TTTTATAATCTCATAATTGATTTTAAGTTG-AATTTTTTTACACTTTTAGATAAAATA
* * * *
436 TATTATAATTGAATATCTTCCTTGTGAAACCTAAAGAAAAAGTC
128 TATTATAATTGAATGTCTTACTTG-GAAACATGAAGAAAAAGTC
* * * * ** *
480 ATTCATTGACAAGAAAAGTCTATTTATAGTCACCCAAGCCTTCGAAAGCCTTGTTACTCATTTTG
1 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAAGCCTTCCAAAGCCTTATTACTCGCTTTA
* * * * * *
545 AATGGTTTTATAATCTCATAATTGATTTTAACTTGAATTTGTTTACATTTTTTGTTACAATATAT
66 AATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACACTTTTAGATAAAATATAT
* * ** *
610 TATAGTTGAATGTC-TACTTCAAGAAA-AGTGGCGCAAAAACT-
131 TATAATTGAATGTCTTACTT--GGAAACA-TGAAG-AAAAAGTC
* * * *
651 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTAAGCCGTT-GAAAGCTTTACTACTCGCTTT
1 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAAGCC-TTCCAAAGCCTTATTACTCGCTTT
* * * * *
715 AAATGGTTTCATAATCTCATTATTGA-TTTAAGTTGAATTTTTGTACATTTTTTA-A-AAAATAG
65 AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACA-CTTTTAGATAAAATAT
* *
777 ATTATATTTGAATGT-TTATCTTGGAAAGCATGAAGAAAAAGCC
129 ATTATAATTGAATGTCTTA-CTTGGAAA-CATGAAGAAAAAGTC
* * * * * *
820 ATTTATCGGCAAGAAAAGTCCATTTATAGTCACCCATGCTTTCCAAAGCCTTATAACTCGCTTCA
1 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAAGCCTTCCAAAGCCTTATTACTCGCTTTA
885 AAT-GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACACTTTTAGATAAAATATAT
66 AATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACACTTTTAGATAAAATATAT
* ** ** **
949 TATAATTGAATGT-TCACCGAGGGAAATGTGAA-AAAAAACC
131 TATAATTGAATGTCTTA-C-TTGGAAACATGAAGAAAAAGTC
* * * ** * * *
989 ATTCATTGGTAAAAAAAAGTCCATTTATAGTCACCTATCCCTTCCAAAACCTTATTACTCACTTA
1 ATTCATTGG-CAAGAAAAGTCCATTTATAGTCACCCAAGCCTTCCAAAGCCTTATTACTCGCTTT
* * * * * * *
1054 AAATGG---T-T--T-T-ATAATTGACTTAAAGTTGAA-TTTTTCACATTTTTTGTTAAAACATA
65 AAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACACTTTTAGATAAAATATA
* * * * *
1110 TTATAATTGAATGTC-TGCTTCATGAAACGTGATGTGAAAA--C
130 TTATAATTGAATGTCTTACTT--GGAAACATGAAG-AAAAAGTC
* * * * **
1151 AATCCATTAGCAAGAAAAGTCCCTTTATAGCCA-CCAAGCCTTTGAAAGCCTTATTACTCGCTTT
1 -ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAAGCCTTCCAAAGCCTTATTACTCGCTTT
* *
1215 AAATGGTTTTATAATCTTAGAATTGATTTTAAGT
65 AAATGGTTTTATAATCTCATAATTGATTTTAAGT
Statistics
Matches: 615, Mismatches: 119, Indels: 72
0.76 0.15 0.09
Matches are distributed among these distances:
161 30 0.05
162 63 0.10
163 25 0.04
164 6 0.01
165 2 0.00
167 2 0.00
168 37 0.06
169 127 0.21
170 104 0.17
171 207 0.34
172 12 0.02
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (170 bp):
ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAAGCCTTCCAAAGCCTTATTACTCGCTTTA
AATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACACTTTTAGATAAAATATAT
TATAATTGAATGTCTTACTTGGAAACATGAAGAAAAAGTC
Found at i:1009 original size:339 final size:341
Alignment explanation
Indices: 309--1036 Score: 816
Period size: 339 Copynumber: 2.1 Consensus size: 341
299 TGATAAAGCG
* * *
309 ATTCATTGGCAAAAAAAGTCCATTTATAGTCA-CTCATGCCTTCCAAAGCACTATTACTTGCTTT
1 ATTCATTGGCAAAAAAAGTCCATTTATAGTCACCT-AAGCCTTCCAAAGCACTACTACTCGCTTT
* * * * *
373 AAAGGCTTTGATAATCTCATAATTTATTTTTAGTGAAATTTTTTTACACTTTTAGATAAAATATA
65 AAAGGCTTTCATAATCTCATAATTGATTTTAAGTGAAATTTTTGTACACTTTTAGATAAAATAGA
* * * *
438 TTATAATTGAATATCTTCCTTGTGAAACCTAAAGAAAAAGTCATTCATTGACAAGAAAAGTCTAT
130 TTATAATTGAATATCTTCCTTGTGAAACATAAAGAAAAAGCCATTCATCGACAAGAAAAGTCCAT
* * * * **
503 TTATAGTCACCCAAGCCTTCGAAAGCCTTGTTACTCATTTTGAATGGTTTTATAATCTCATAATT
195 TTATAGTCACCCAAGCCTTCCAAAGCCTTATAACTCACTTCAAATGGTTTTATAATCTCATAATT
* * * * *
568 GATTTTAACTTGAATTTGTTTACATTTTTTGTTACAATATATTATAGTTGAATGTCTACTTCAAG
260 GATTTTAACTTGAATTTGTTTACACTTTTAGATAAAATATATTATAATTGAATGTCTAC-TCAAG
*** *
633 AAAAGTGGCGCAAAAACT
324 AAAAGTGGAAAAAAAACC
* * **
651 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTAAGCCGTT-GAAAGCTTTACTACTCGCTTT
1 ATTCATTGGCAAAAAAAGTCCATTTATAGTCACCTAAGCC-TTCCAAAGCACTACTACTCGCTTT
* *
715 AAATGG-TTTCATAATCTCATTATTGA-TTTAAGTTG-AATTTTTGTACATTTTTTA-A-AAAAT
65 AAA-GGCTTTCATAATCTCATAATTGATTTTAAG-TGAAATTTTTGTACA-CTTTTAGATAAAAT
* * * * * *
775 AGATTATATTTGAATGT-TTATCTTG-GAAAGCATGAAGAAAAAGCCATTTATCGGCAAGAAAAG
127 AGATTATAATTGAATATCTT-CCTTGTGAAA-CATAAAGAAAAAGCCATTCATCGACAAGAAAAG
* * *
838 TCCATTTATAGTCACCCATGCTTTCCAAAGCCTTATAACTCGCTTCAAAT-GTTTTATAATCTCA
190 TCCATTTATAGTCACCCAAGCCTTCCAAAGCCTTATAACTCACTTCAAATGGTTTTATAATCTCA
* *
902 TAATTGATTTTAAGTTGAATTTTTTTACACTTTTAGATAAAATATATTATAATTGAATGT-TCAC
255 TAATTGATTTTAACTTGAATTTGTTTACACTTTTAGATAAAATATATTATAATTGAATGTCT-AC
* *
966 -CGAGGGAAA-TGTGAAAAAAAACC
319 TC-AAGAAAAGTG-GAAAAAAAACC
* **
989 ATTCATTGGTAAAAAAAAGTCCATTTATAGTCACCTATCCCTTCCAAA
1 ATTCATTGG-CAAAAAAAGTCCATTTATAGTCACCTAAGCCTTCCAAA
1037 ACCTTATTAC
Statistics
Matches: 323, Mismatches: 51, Indels: 27
0.81 0.13 0.07
Matches are distributed among these distances:
337 3 0.01
338 24 0.07
339 105 0.33
340 90 0.28
341 17 0.05
342 78 0.24
343 6 0.02
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (341 bp):
ATTCATTGGCAAAAAAAGTCCATTTATAGTCACCTAAGCCTTCCAAAGCACTACTACTCGCTTTA
AAGGCTTTCATAATCTCATAATTGATTTTAAGTGAAATTTTTGTACACTTTTAGATAAAATAGAT
TATAATTGAATATCTTCCTTGTGAAACATAAAGAAAAAGCCATTCATCGACAAGAAAAGTCCATT
TATAGTCACCCAAGCCTTCCAAAGCCTTATAACTCACTTCAAATGGTTTTATAATCTCATAATTG
ATTTTAACTTGAATTTGTTTACACTTTTAGATAAAATATATTATAATTGAATGTCTACTCAAGAA
AAGTGGAAAAAAAACC
Done.