Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403178.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_845.0, 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: 3073
ACGTcount: A:0.25, C:0.10, G:0.09, T:0.26
Warning! 937 characters in sequence are not A, C, G, or T
Found at i:1457 original size:169 final size:161
Alignment explanation
Indices: 1155--1812 Score: 391
Period size: 170 Copynumber: 3.9 Consensus size: 161
1145 NNNNNNNNNN
***
1155 ATTTTTGATTAAAACAGATAATAATTGAATGTCTACCTTGCGAAAAATGAAGAAAAAAATATCCA
1 ATTTTTGATTAAAACAGATAATAATTGAATGTCTACCTCAAGAAAAATGAAGAAAAAAATATCCA
* *
1220 TTAACAAGAAAAGTCCATTTATAGTCACCCATGGCTTCAAAAGCCTTATTACTCCTATTAAATAG
66 TTAACAAGAAAAGTCCATTTATAGTCACCCATGCCCTCAAAAGCCTTATTACTCCTATTAAATAG
1285 TTTTATAATCTCATAATTNNNNNNNNNNTAATTTTTTTTAC
131 TTTTATAATCTCATAATT----------TAATTTTTTTTAC
* * * * * * *
1326 ATTTTTTATTAAAATAGATAATAATTGAATGTTTGCCTCAAGAAACATGAA-AAAAAAA-ATTCT
1 ATTTTTGATTAAAACAGATAATAATTGAATGTCTACCTCAAGAAAAATGAAGAAAAAAATATCCA
** * * **
1389 TTGGCAGGAAAAGTCCATTTATAGTCACCCATGCCCTCAAAGGCCTTATTACTTGTATTAAATAG
66 TTAACAAGAAAAGTCCATTTATAGTCACCCATGCCCTCAAAAGCCTTATTACTCCTATTAAATAG
** * *
1454 TTTTATAATCTNNNNNNNNNNTTTAAGTTGAA-TTTTTTTAT
131 TTTTATAATCT----------CATAA-TTTAATTTTTTTTAC
* * * * * * *
1495 ATTTTTGGTGAAAACTGATAATAATTGAATGTCTGCCTCAA-AAAACATAAAGAAAAAGATATCT
1 ATTTTTGATTAAAACAGATAATAATTGAATGTCTACCTCAAGAAAA-ATGAAGAAAAAAATATCC
* * ** ** ** * *
1559 ATTAGCAAGAAAAGTCTATTTAT-GATTGCCCATGCTTTTGAAAGTCTTATTACCTGCT-TTAAA
65 ATTAACAAGAAAAGTCCATTTATAG-TCACCCATGCCCTCAAAAGCCTTATTA-CTCCTATTAAA
* *
1622 TGGTTTCATAATCTCATAATTNNNNNNNNNNTGAA-TTTTTTTAC
128 TAGTTTTATAATCTCATAATT----------T-AATTTTTTTTAC
* * * * ** * * *
1666 ATTTTAG-TTAAAACAGATGAGAATTCAATGTCTGTCTC-AGAAAACATGAAGAAAAAGATTTCT
1 ATTTTTGATTAAAACAGATAATAATTGAATGTCTACCTCAAGAAAA-ATGAAGAAAAAAATATCC
** * * *
1729 ATTGGCAAGAAAAGTCCATTTATAGTCACCTATACCGTCAAAAGCCTTATTACTCGCT-TTAAAT
65 ATTAACAAGAAAAGTCCATTTATAGTCACCCATGCCCTCAAAAGCCTTATTACTC-CTATTAAAT
* * *
1793 GGTTTGATAATCACATAATT
129 AGTTTTATAATCTCATAATT
1813 GATTTTAAGT
Statistics
Matches: 381, Mismatches: 76, Indels: 61
0.74 0.15 0.12
Matches are distributed among these distances:
160 2 0.01
161 3 0.01
168 3 0.01
169 121 0.32
170 127 0.33
171 117 0.31
172 3 0.01
179 3 0.01
180 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.35
Consensus pattern (161 bp):
ATTTTTGATTAAAACAGATAATAATTGAATGTCTACCTCAAGAAAAATGAAGAAAAAAATATCCA
TTAACAAGAAAAGTCCATTTATAGTCACCCATGCCCTCAAAAGCCTTATTACTCCTATTAAATAG
TTTTATAATCTCATAATTTAATTTTTTTTAC
Found at i:1610 original size:340 final size:321
Alignment explanation
Indices: 1155--1804 Score: 557
Period size: 340 Copynumber: 1.9 Consensus size: 321
1145 NNNNNNNNNN
* * *
1155 ATTTTTGATTAAAACAGATAATAATTGAATGTCTACCTTGCGAAAAATGAAGAAAAAAATATCCA
1 ATTTTTGATGAAAACAGATAATAATTGAATGTCTACCTTGCAAAAAATAAAGAAAAAAATATCCA
1220 TTAACAAGAAAAGTCCATTTATAGTCACCCATGGCTTCAAAAGCCTTATTA-CTCCTATTAAATA
66 TTAACAAGAAAAGTCCATTTATAGTCACCCATGGCTTCAAAAGCCTTATTACCTCCT-TTAAATA
* *
1284 GTTTTATAATCTCATAATTNNNNNNNNNNT-AATTTTTTTTACATTTTTTA-TTAAAATAGATAA
130 GTTTCATAATCTCATAATT----------TGAA-TTTTTTTACA--TTTTAGTTAAAACAGATAA
* * * *
1347 TAATTGAATGTTTGCCTCA-AGAAACATGAA-AAAAAAAATTCT-TTGGCAGGAAAAGTCCATTT
182 GAATTCAATGTCTGCCTCAGA-AAACATGAAGAAAAAAAATTCTATTGGCAAGAAAAGTCCATTT
* * * *
1409 ATAGTCACCCATGCCCTCAAAGGCCTTATTACTTG-TATTAAATAGTTTTATAATCTNNNNNNNN
246 ATAGTCACCCATACCCTCAAAAGCCTTATTACTCGCT-TTAAATAGTTTGATAATCT--------
1473 NNTTTAAGTTGAATTTTTTTAT
302 --TTTAAGTTGAATTTTTTTAT
* * * *
1495 ATTTTTGGTGAAAACTGATAATAATTGAATGTCTGCC-T-CAAAAAACATAAAGAAAAAGATATC
1 ATTTTTGATGAAAACAGATAATAATTGAATGTCTACCTTGC-AAAAA-ATAAAGAAAAAAATATC
* * * ** ** * *
1558 TATTAGCAAGAAAAGTCTATTTAT-GATTGCCCAT-GCTTTTGAAAGTCTTATTACCTGCTTTAA
64 CATTAACAAGAAAAGTCCATTTATAG-TCACCCATGGC-TTCAAAAGCCTTATTACCTCCTTTAA
* *
1621 ATGGTTTCATAATCTCATAATTNNNNNNNNNNTGAATTTTTTTACATTTTAGTTAAAACAGATGA
127 ATAGTTTCATAATCTCATAATT----------TGAATTTTTTTACATTTTAGTTAAAACAGATAA
* * *
1686 GAATTCAATGTCTGTCTCAGAAAACATGAAGAAAAAGATTTCTATTGGCAAGAAAAGTCCATTTA
182 GAATTCAATGTCTGCCTCAGAAAACATGAAGAAAAAAAATTCTATTGGCAAGAAAAGTCCATTTA
* * *
1751 TAGTCACCTATACCGTCAAAAGCCTTATTACTCGCTTTAAATGGTTTGATAATC
247 TAGTCACCCATACCCTCAAAAGCCTTATTACTCGCTTTAAATAGTTTGATAATC
1805 ACATAATTGA
Statistics
Matches: 265, Mismatches: 34, Indels: 21
0.83 0.11 0.07
Matches are distributed among these distances:
338 6 0.02
339 43 0.16
340 144 0.54
341 71 0.27
342 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.35
Consensus pattern (321 bp):
ATTTTTGATGAAAACAGATAATAATTGAATGTCTACCTTGCAAAAAATAAAGAAAAAAATATCCA
TTAACAAGAAAAGTCCATTTATAGTCACCCATGGCTTCAAAAGCCTTATTACCTCCTTTAAATAG
TTTCATAATCTCATAATTTGAATTTTTTTACATTTTAGTTAAAACAGATAAGAATTCAATGTCTG
CCTCAGAAAACATGAAGAAAAAAAATTCTATTGGCAAGAAAAGTCCATTTATAGTCACCCATACC
CTCAAAAGCCTTATTACTCGCTTTAAATAGTTTGATAATCTTTTAAGTTGAATTTTTTTAT
Done.