Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401515.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4641.0, 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: 2347
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.30
Warning! 514 characters in sequence are not A, C, G, or T
Found at i:635 original size:172 final size:170
Alignment explanation
Indices: 1--1068 Score: 807
Period size: 171 Copynumber: 6.2 Consensus size: 170
* *
1 TTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATGTTTTTTCATTTCTCA-TTAAAA
1 TTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAAT-TTTTTACATTT-TTAGTTAAAA
* * * ** **** * * *
65 CATATTATTATTGAATGTCTGTCTTGCTAAAC-GTGTAGAAAAAGTCATTCATTCAG-AAAAAAA
64 CAGACTATAATTGAATGTCTACCTCAAGAAACAG-GAAGAAAAAGCCATTCATT-AGCAAGAAAA
** * * *** * * * ** **
128 AACTATTTACAGTCTGTCATTCATTTAAAAGTCTTATTGTTTGC
127 GTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCAC
* * *
172 TTTAAATAGTTTTATAATCTAATAACTGATTTTAAGTTGAATTTTTTCACATTTCTAGTTAAAAC
1 TTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTT-ACATTTTTAGTTAAAAC
* * * * * **
237 AGAATATAATTGAATGTCTATCTTAAAAAACATGTAA-AAAATA-CTGTTCATTTAG-AAGAAAA
65 AGACTATAATTGAATGTCTACCTCAAGAAACA-GGAAGAAAA-AGCCATTCA-TTAGCAAGAAAA
* * * * * *
299 ATCTATTTATAGTCTCCCAATCCTTCAAAAGCCTTATTATTCTC
127 GTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCAC
** * * * *
343 TTTAAA-AGGTTTTGCAATCTCATAACTGATTTTAAGTTGAAAATTTTCATATTTTTAGTTAAAA
1 TTTAAATA-GTTTTATAATCTCATAATTGATTTTAAGTTG-AATTTTTTACATTTTTAGTTAAAA
* * * *
407 CAAACTATAATTGAATGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGT
64 CAGACTATAATTGAATGTCTACCTCAAGAAACAGGAAGAAAAAGCCATTCATTAGCAAGAAAAGT
* ** *
472 CCATTTATAGTCACTCATTTTTTCACAAGCCTTATTACTCAC
129 CCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCAC
*
514 TTTAAATAGTTTTATAATCTCA-ACATTGATTTTAAGGTGAAGTTGTTTTACATTTTTAGTTAAA
1 TTTAAATAGTTTTATAATCTCATA-ATTGATTTTAAGTTGAA-TT-TTTTACATTTTTAGTTAAA
* * * * * ** * *
578 ACATATTATAATTAAATGTCTACCTCAAGAAATAGGAAGAGAAAGGTATTCATTGGCAAGAGAAG
63 ACAGACTATAATTGAATGTCTACCTCAAGAAACAGGAAGAAAAAGCCATTCATTAGCAAGAAAAG
* * *
643 TCTATTTATAGTCACCCATTCCTTCAAAAGCCTCATTACTCGC
128 TCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCAC
* * * * * * **
686 TCTAAAT-GACTGTACAATCTCATAATTGCTTTTAAGTTGAATTTTTTTACATTTATCTTTAAAA
1 TTTAAATAG-TTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTACATTTTTAGTTAAAA
*** * * * ** *
750 CAGACTATAATTGAATGTCTACCTTGGGAAA-TGTGTAGAAAAAGCCATTTATTAATAAGAAAAC
64 CAGACTATAATTGAATGTCTACCTCAAGAAACAG-GAAGAAAAAGCCATTCATTAGCAAGAAAAG
* **
814 TTCATTTATAGTCACTTATT-CTCTCAAAAGCCTTATTACTCAC
128 TCCATTTATAGTCACCCATTCCT-TCAAAAGCCTTATTACTCAC
* * * ** *
857 TTTAAATGGTTTTATAATCTCATAATTGATTTTAGGTAGAATTTTTTTAC-TTTTTTTTTTAAAC
1 TTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTACATTTTTAGTTAAAAC
* * * ** * ** * * * *
921 AGATTATTATTGAATGTTTGTCTTACTAAACA-TATAGAAAAAGTCATTCATTCGGAAGAAAAGT
65 AGACTATAATTGAATGTCTACCTCAAGAAACAGGA-AGAAAAAGCCATTCATTAGCAAGAAAAGT
* * * * *
985 CCATATATAGTCTA-ACATTCCTTTAAAAGTCTTATTACTCGC
129 CCATTTATAGTC-ACCCATTCCTTCAAAAGCCTTATTACTCAC
*
1027 TTTAAA-AGGTTTTATAATCTCATAACTGATTTTAAGTTGAAT
1 TTTAAATA-GTTTTATAATCTCATAATTGATTTTAAGTTGAAT
1069 NNNNNNNNNN
Statistics
Matches: 722, Mismatches: 150, Indels: 52
0.78 0.16 0.06
Matches are distributed among these distances:
169 1 0.00
170 141 0.20
171 423 0.59
172 155 0.21
173 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.40
Consensus pattern (170 bp):
TTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTACATTTTTAGTTAAAACA
GACTATAATTGAATGTCTACCTCAAGAAACAGGAAGAAAAAGCCATTCATTAGCAAGAAAAGTCC
ATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCAC
Found at i:725 original size:343 final size:340
Alignment explanation
Indices: 171--1067 Score: 838
Period size: 343 Copynumber: 2.6 Consensus size: 340
161 TTATTGTTTG
* * * *
171 CTTTAAATAGTTTTATAATCTAATAACTGATTTTAAGTTGAATTTTTTCACATTTCTAGTTAAAA
1 CTTTAAATAGTTTTATAATCTCA-AATTGATTTTAAGGTGAATTTTTT-ACATTTTTAGTTAAAA
* * * * *
236 CAGAATATAATTGAATGTCTATCTTAAAAAACATGTAAAAAATACTGTTCATTTAGAAGAAAAAT
64 CAGAATATAATTAAATGTCTACCTCAAAAAACATGGAAAAAATACTATTCATTTAGAAGAAAAAT
* * * * * ** * *
301 CTATTTATAGTCTCCCAATCCTTCAAAAGCCTTATTATTCTCTTTAAAAGGTTTTGCAATCTCAT
129 CTATTTATAGTCACCCAATCCTTCAAAAGCCTCATTACTCGCTCTAAAAGACTGTACAATCTCAT
* *
366 AACTGATTTTAAGTTGAAAATTTTCATATTTTTAGTTAAAACAAACTATAATTGAATGTCTACCT
194 AACTGATTTTAAGTTGAAAATTTTCACATTTATAGTTAAAACAAACTATAATTGAATGTCTACCT
* ** * * *
431 CAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACTCATTTTTTC
259 CAAGAAACATGAAGAAAAAGCCATTCATTAACAAGAAAACTCCATTTATAGTCACTCATTCTCTC
*
496 ACAAGCCTTATTACTCA
324 AAAAGCCTTATTACTCA
513 CTTTAAATAGTTTTATAATCTCAACATTGATTTTAAGGTGAAGTTGTTTTACATTTTTAGTTAAA
1 CTTTAAATAGTTTTATAATCTCAA-ATTGATTTTAAGGTGAA-TT-TTTTACATTTTTAGTTAAA
* * * * ** * *
578 ACATATTATAATTAAATGTCTACCTCAAGAAATA-GGAAGAGAAA-GGTATTCA-TTGGCAAGAG
63 ACAGAATATAATTAAATGTCTACCTCAAAAAACATGGAA-A-AAATACTATTCATTTAG-AAGAA
* * *
640 AAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTCATTACTCGCTCTAAATGACTGTACAATC
125 AAATCTATTTATAGTCACCCAATCCTTCAAAAGCCTCATTACTCGCTCTAAAAGACTGTACAATC
* * ** * ** *
705 TCATAATTGCTTTTAAGTTGAATTTTTTTACATTTATCTTTAAAACAGACTATAATTGAATGTCT
190 TCATAACTGATTTTAAGTTGAAAATTTTCACATTTATAGTTAAAACAAACTATAATTGAATGTCT
*** ** * * * * *
770 ACCTTGGGAAATGTGTAGAAAAAGCCATTTATTAATAAGAAAACTTCATTTATAGTCACTTATTC
255 ACCTCAAGAAACATGAAGAAAAAGCCATTCATTAACAAGAAAACTCCATTTATAGTCACTCATTC
835 TCTCAAAAGCCTTATTACTCA
320 TCTCAAAAGCCTTATTACTCA
* ** *
856 CTTTAAATGGTTTTATAATCTCATAATTGATTTT-AGGTAGAATTTTTTTAC-TTTTTTTTTTAA
1 CTTTAAATAGTTTTATAATCTCA-AATTGATTTTAAGGT-GAA-TTTTTTACATTTTTAGTTAAA
* * * * * * * * * * * **
919 ACAGATTATTATTGAATGTTTGTCTTACTAAACATATAGAAAAAGT-C-ATTCATTCGGAAGAAA
63 ACAGAATATAATTAAATGTCT-ACCT-CAAAAAACATGGAAAAAATACTATTCATTTAGAAGAAA
* * * * * * * * * ** * *
982 AGTCCATATATAGTCTA-ACATTCCTTTAAAAGTCTTATTACTCGCTTTAAAAGGTTTTATAATC
126 AATCTATTTATAGTC-ACCCAATCCTTCAAAAGCCTCATTACTCGCTCTAAAAGACTGTACAATC
1046 TCATAACTGATTTTAAGTTGAA
190 TCATAACTGATTTTAAGTTGAA
1068 TNNNNNNNNN
Statistics
Matches: 452, Mismatches: 89, Indels: 29
0.79 0.16 0.05
Matches are distributed among these distances:
341 107 0.24
342 61 0.13
343 273 0.60
344 11 0.02
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (340 bp):
CTTTAAATAGTTTTATAATCTCAAATTGATTTTAAGGTGAATTTTTTACATTTTTAGTTAAAACA
GAATATAATTAAATGTCTACCTCAAAAAACATGGAAAAAATACTATTCATTTAGAAGAAAAATCT
ATTTATAGTCACCCAATCCTTCAAAAGCCTCATTACTCGCTCTAAAAGACTGTACAATCTCATAA
CTGATTTTAAGTTGAAAATTTTCACATTTATAGTTAAAACAAACTATAATTGAATGTCTACCTCA
AGAAACATGAAGAAAAAGCCATTCATTAACAAGAAAACTCCATTTATAGTCACTCATTCTCTCAA
AAGCCTTATTACTCA
Found at i:1851 original size:172 final size:169
Alignment explanation
Indices: 1566--2340 Score: 566
Period size: 171 Copynumber: 4.5 Consensus size: 169
1556 NNNNNNNATT
* * * * *
1566 GATTTTAAGTTGAATTTTTTTACATTTTTCATTAAAGCAAACTATAATTGAGTGTCTACCTCAAG
1 GATTTTAAGTTAAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCTACCT-TAG
*
1631 AAACATATAGAAAAAGCCATTCATTGACAAGAAAAGTTCAGTTATAGTCACCCATTCCCTTAAAA
65 AAACATA-AGAAAAAGCCATTCATTGACAAGAAAAGTTCAATTATAGTCACCCATTCCCTTAAAA
1696 GCCTTATTACTCACGTTAAATGGTTTTATAATCTCA-ACATC
129 GCCTTATTACTCACGTTAAATGGTTTTATAATCTCATA-ATC
* *
1737 GATTTTAAGTTAAATTTTTTTTACATTTTT-AGTTAAAACAGATTATAATTTAATGTCTACCTTG
1 GATTTTAAGTTAAA-TTTTTTTACATTTTTCA-TTAAAACAGACTATAATTGAATGTCTACCTT-
** * *
1801 AGAAACATGAAGTGAAAGGCATTCATTGACAAGAGAAGTTCAATTATAGTCACCCATTCCCTTAA
63 AGAAACAT-AAGAAAAAGCCATTCATTGACAAGAAAAGTTCAATTATAGTCACCCATTCCCTTAA
********** *
1866 AAGCCTTATTANNNNNNNNNNATGGTTTTATAATCTCATAATT
127 AAGCCTTATTACTCACGTTAAATGGTTTTATAATCTCATAATC
* ** * * * * * *
1909 GATTTTCAGCGAAATTGTTTTACATTTTTCATTAAAAAAGATTATTATTGAATG-CCAGTCTTAT
1 GATTTTAAGTTAAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCTA-CCTTA-
* * ** * * * *
1973 TAAACATTTAGAAAAAGTTATTCATTCAGAAGAAAAGTCCAATTATAGTCTA--CATTCCTTTAA
64 GAAACA-TAAGAAAAAGCCATTCATTGACAAGAAAAGTTCAATTATAGTC-ACCCATTCCCTTAA
* * * * *
2036 AAGTCTTGTTACTCGCTTTAAATAGTTTTATAATCTCATAA-C
127 AAGCCTTATTACTCACGTTAAATGGTTTTATAATCTCATAATC
* * * *
2078 TGATTCTAAGTTGAATTTTTTCACATTTCT-AGTTAAAACAGACTATAATTGAATGTCTACCTTA
1 -GATTTTAAGTTAAATTTTTTTACATTTTTCA-TTAAAACAGACTATAATTGAATGTCTACCTTA
* * * * * * * * * **
2142 AAAACCATGTAGAAACTA-CCGTTCATTTG-GAAGAAAAG-TCTATTTATAGTCTCTCAAT-ATT
64 GAAA-CAT-AAGAAA-AAGCCATTCA-TTGACAAGAAAAGTTC-AATTATAGTCACCCATTCCCT
* * *********
2203 TCAAAAGCCTTATTACTCACTTTAAAAGGTTTTATANNNNNNNNNNT-
124 T-AAAAGCCTTATTACTCACGTTAAATGGTTTTATA-ATCTCATAATC
* * * * *
2250 GATTTTAAGTTGAATTTTTTCACATTTTTCATTCAAATAGACTATAATTGAATGTCTACCTCAAG
1 GATTTTAAGTTAAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCTACCT-TAG
* *
2315 AAACATGAAGAAGAAGGCATTCATTG
65 AAACAT-AAGAAAAAGCCATTCATTG
2341 GCAAAAA
Statistics
Matches: 472, Mismatches: 106, Indels: 53
0.75 0.17 0.08
Matches are distributed among these distances:
169 6 0.01
170 123 0.26
171 194 0.41
172 147 0.31
173 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (169 bp):
GATTTTAAGTTAAATTTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCTACCTTAGA
AACATAAGAAAAAGCCATTCATTGACAAGAAAAGTTCAATTATAGTCACCCATTCCCTTAAAAGC
CTTATTACTCACGTTAAATGGTTTTATAATCTCATAATC
Done.