Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399343.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2610.0, 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, 997
Length: 1663
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.36
Warning! 124 characters in sequence are not A, C, G, or T
Found at i:676 original size:172 final size:171
Alignment explanation
Indices: 376--1500 Score: 991
Period size: 172 Copynumber: 6.6 Consensus size: 171
366 NNGATTTTAA
* * * ** *
376 GTTGAATTTTTTTGTA-TTTTTAATAAAACAGATTATAATTGAATGT-TAAACTCACGAAACATT
1 GTTGAATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCT-ACCTCGGGAAACATA
* * * *
439 AAGAAAAAGATATTCATTGGCAAGAAAAGTTCA-TTAGTAGACACTCATGCCTTCGAAACCCTTA
65 AAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTA-TAGTCACTCATGCCTTCGAAAGCCTTA
*
503 TTACTCGCTTTGAATGATTTTATAATCTCATAATTGATTTTGT
129 TTACTCGCTTTAAATGATTTTATAATCTCATAATTGATTTTGT
* * * * * *
546 GCTGAATTTTTTTTTATTTTTTTATTAAAACAGATTACAATTGAATGTCTTCCTCGGGAAACGTC
1 GTTGAATTTTTTTATA-TTTTTTATTAAAACAGATTATAATTGAATGTCTACCTCGGGAAACATA
* *
611 AAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACTCATTCCTGCGAAAGCCTTAT
65 AAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTAT
* **
676 TACTCGGC-TTAAAT-AGTTTTATAATCTCATAAGTGATTTTAA
130 TACTC-GCTTTAAATGA-TTTTATAATCTCATAATTGATTTTGT
* * * * * * * *
718 GTTAAATTTTTTTATATTTTTTACTAAAACATATTATAGTTAAATGTCTACTTTGAGAAACATGA
1 GTTGAATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACCTCGGGAAACAT-A
* * **********
783 AA-AAATATATATCCATTGGCAAGAAAAGTCCATTTATANNNNNNNNNNCCTTCGAAAGCCTTAT
65 AAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTAT
* * * * **
847 TACTCGCTTTGAATGGTTTTACAATCTCATAATCGATTTTAA
130 TACTCGCTTTAAATGATTTTATAATCTCATAATTGATTTTGT
* * * * * *
889 CTTGAATTTTTTTA-ATTTTTTATTAAAACTGATTATAATTAAATGTCTGCCAT-AGGAAACGTG
1 GTTGAATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACC-TCGGGAAACAT-
* * ** * * *
952 AAAAAAAAATGATATCCATTGACAAGAAAAGTTGATTTATAATCACCCATG-TTGTCGAAAGCCT
64 AAAGAAAAA-GATATCCATTGGCAAGAAAAGTCCATTTATAGTCACTCATGCCT-TCGAAAGCCT
* * * * * *
1016 TGTTACAC-ATATTAAATGGTTTTACAATCTCATAACTGATTTT-T
127 TATTACTCGCT-TTAAATGATTTTATAATCTCATAATTGATTTTGT
* * * * ***
1060 AGTTTAATTTCTTTACATTTTTTTATTAAAACAGATTATAATTGGATGTTTCTA--TCTAAAAAT
1 -GTTGAATTTTTTTATA-TTTTTTATTAAAACAGATTATAATTGAATG--TCTACCTCGGGAAA-
* * * *
1123 TATAAAGAACAAGATATCCATTGGCAAGAAAAATCCGTTTATAGTCAC-CAATGCCTTCGAAAGC
61 CATAAAGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACTC-ATGCCTTCGAAAGC
* * *
1187 CTGT-TTAGTCGCTTTAAATGTTTTTAT-ATCTCATAATTGATTCTGT
125 CT-TATTACTCGCTTTAAATGATTTTATAATCTCATAATTGATTTTGT
* * * * **
1233 GTTGATTTTTTTTATATTTTTTATTAAAACAAATTATAATTGAATATCTACCTTGGGAAATGTAA
1 GTTGAATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACCTCGGGAAACATAA
* *
1298 AGAAAAAGATATTCATTGGCAAGAAAAGT-TATTTATAGTTTC-CT-ATGCCTTCGAAAGCCTTA
66 AGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAG--TCACTCATGCCTTCGAAAGCCTTA
* *
1360 TTACTCGCTTTAAATGTTTTTATAATATCATAATTGATTTTAG-
129 TTACTCGCTTTAAATGATTTTATAATCTCATAATTGATTTT-GT
* * * * * *
1403 ATTG-ACTTTTTTATATTTTTTATTAAAACAAATTATAATTGAATGTCAACCTC-GGTAACTATG
1 GTTGAATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACCTCGGGAAAC-ATA
* *
1466 AAGAAAAATATATCCACTGGCAAGAGAAA-TCCATT
65 AAGAAAAAGATATCCATTGGCAAGA-AAAGTCCATT
1501 NNNNNNNNNN
Statistics
Matches: 770, Mismatches: 148, Indels: 74
0.78 0.15 0.07
Matches are distributed among these distances:
168 5 0.01
169 117 0.15
170 112 0.15
171 173 0.22
172 251 0.33
173 68 0.09
174 40 0.05
175 1 0.00
176 3 0.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.39
Consensus pattern (171 bp):
GTTGAATTTTTTTATATTTTTTATTAAAACAGATTATAATTGAATGTCTACCTCGGGAAACATAA
AGAAAAAGATATCCATTGGCAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATT
ACTCGCTTTAAATGATTTTATAATCTCATAATTGATTTTGT
Found at i:853 original size:343 final size:334
Alignment explanation
Indices: 368--1500 Score: 1013
Period size: 343 Copynumber: 3.3 Consensus size: 334
358 NNNNNNNNNN
* * * *** *
368 GATTTTAAGTTGAATTTTTTTGTA-TTTTTAATAAAACAGATTATAATTGAATGT-TAAACTCAC
1 GATTTT-AGTT-AATTTTTTTATATTTTTTATTAAAACAAATTATAATTGAATGTCTACTTTGA-
* * * * *
431 GAAACATTAAGAAAAAGATATTCATTGGCAAGAAAAGTTCA-TTAGTAGACACTC-ATGCCTTCG
63 GAAACATGAA-AAAAATATATCCATTGGCAAGAAAA-TCCATTTA-TAGTCAC-CAATGCCTTCG
*
494 AAACCCTTATTACTCGCTTTGAATGATTTTATAATCTCATAATTGATTTTGTGCTGAATTTTTTT
124 AAAGCCTTATTACTCGCTTTGAATGATTTTATAATCTCATAATTGATTTTGTGCTGAA-TTTTTT
* * *
559 TTATTTTTTTATTAAAACAGATTACAATTGAATGTCTTCCTCGGGAAACGTCAAGAAAAAGATAT
188 TTATTTTTTTATTAAAACAGATTATAATTGAATGTCTACCT-GGGAAACGTAAAGAAAAAGATAT
624 CCATTGGCAAGAAAAGTCCATTTATAGTCACTCATTCCTGCGAAAGCCTTATTACTCGGCTTAAA
252 CCATTGGCAAGAAAAGT-CATTTATAGTCACTCATTCCTGCGAAAGCCTTATTACTC-GCTTAAA
*
689 TAGTTTTATAATCTCATAAGT
315 T-GTTTTATAATCTCATAACT
* * * *
710 GATTTTAAGTTAAATTTTTTTATATTTTTTACTAAAACATATTATAGTTAAATGTCTACTTTGAG
1 GATTTT-AGTT-AATTTTTTTATATTTTTTATTAAAACAAATTATAATTGAATGTCTACTTTGAG
**********
775 AAACATGAAAAAATATATATCCATTGGCAAGAAAAGTCCATTTATANNNNNNNNNNCCTTCGAAA
64 AAACATGAAAAAA-ATATATCCATTGGCAAGAAAA-TCCATTTATAGTCACCAATGCCTTCGAAA
* * * **
840 GCCTTATTACTCGCTTTGAATGGTTTTACAATCTCATAATCGATTTT-AACTTGAA-TTTTTTTA
127 GCCTTATTACTCGCTTTGAATGATTTTATAATCTCATAATTGATTTTGTGC-TGAATTTTTTTTA
* * * * * *
903 ATTTTTTATTAAAACTGATTATAATTAAATGTCTGCCATAGGAAACGTGAAAAAAAAATGATATC
191 TTTTTTTATTAAAACAGATTATAATTGAATGTCTACC-TGGGAAACGT-AAAGAAAAA-GATATC
* * * * * * **
968 CATTGACAAGAAAAGTTGATTTATAATCACCCATGT--TGTCGAAAGCCTTGTTACACATATTAA
253 CATTGGCAAGAAAAG-TCATTTATAGTCACTCAT-TCCTG-CGAAAGCCTTATTACTC-GCTTAA
*
1031 ATGGTTTTACAATCTCATAACT
314 AT-GTTTTATAATCTCATAACT
* * * * *
1053 GATTTTTAGTTTAATTTCTTTACATTTTTTTATTAAAACAGATTATAATTGGATGTTTCTA-TCT
1 GA-TTTTAG-TTAATTTTTTTATA-TTTTTTATTAAAACAAATTATAATTGAATG--TCTACTTT
* * * *
1117 -AAAAATTAT-AAAGAACAAGATATCCATTGGCAAGAAAAATCCGTTTATAGTCACCAATGCCTT
61 GAGAAA-CATGAAA-AA-AATATATCCATTGGCAAG-AAAATCCATTTATAGTCACCAATGCCTT
* * * * *
1180 CGAAAGCCTGT-TTAGTCGCTTTAAATGTTTTTAT-ATCTCATAATTGATTCTGTGTTG-ATTTT
122 CGAAAGCCT-TATTACTCGCTTTGAATGATTTTATAATCTCATAATTGATTTTGTGCTGAATTTT
* * *
1242 TTTTATATTTTTTATTAAAACAAATTATAATTGAATATCTACCTTGGGAAATGTAAAGAAAAAGA
186 TTTTAT-TTTTTTATTAAAACAGATTATAATTGAATGTCTACC-TGGGAAACGTAAAGAAAAAGA
* * * *
1307 TATTCATTGGCAAGAAAAGTTATTTATAGTTTC-CT-ATGCCTTCGAAAGCCTTATTACTCGCTT
249 TATCCATTGGCAAGAAAAGTCATTTATAG--TCACTCATTCCTGCGAAAGCCTTATTACTCGC-T
* *
1370 TAAATGTTTTTATAATATCATAATT
311 TAAATG-TTTTATAATCTCATAACT
* * * * * *
1395 GATTTTAGATTGACTTTTTTATATTTTTTATTAAAACAAATTATAATTGAATGTCAACCTCG-GT
1 GATTTTAG-TTAATTTTTTTATATTTTTTATTAAAACAAATTATAATTGAATGTCTACTTTGAGA
*
1459 AACTATGAAGAAAAATATATCCACTGGCAAGAGAAATCCATT
65 AAC-ATGAA-AAAAATATATCCATTGGCAAGA-AAATCCATT
1501 NNNNNNNNNN
Statistics
Matches: 633, Mismatches: 121, Indels: 77
0.76 0.15 0.09
Matches are distributed among these distances:
338 4 0.01
339 28 0.04
340 32 0.05
341 66 0.10
342 85 0.13
343 224 0.35
344 82 0.13
345 102 0.16
346 10 0.02
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.39
Consensus pattern (334 bp):
GATTTTAGTTAATTTTTTTATATTTTTTATTAAAACAAATTATAATTGAATGTCTACTTTGAGAA
ACATGAAAAAAATATATCCATTGGCAAGAAAATCCATTTATAGTCACCAATGCCTTCGAAAGCCT
TATTACTCGCTTTGAATGATTTTATAATCTCATAATTGATTTTGTGCTGAATTTTTTTTATTTTT
TTATTAAAACAGATTATAATTGAATGTCTACCTGGGAAACGTAAAGAAAAAGATATCCATTGGCA
AGAAAAGTCATTTATAGTCACTCATTCCTGCGAAAGCCTTATTACTCGCTTAAATGTTTTATAAT
CTCATAACT
Done.