Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398561.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1853.0, 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: 2518
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.23
Warning! 949 characters in sequence are not A, C, G, or T
Found at i:1225 original size:172 final size:167
Alignment explanation
Indices: 785--1596 Score: 492
Period size: 172 Copynumber: 4.7 Consensus size: 167
775 NNNNNNNNNN
* * *
785 TTCAGAAACATGAAGAAAAAA-GTATTCATTGGTAAGAAAAGTCCATTTATAGTC-CCCTATACC
1 TTCAGAAACA--AAAAAAAAACGTATTCATTGGCAA-AAAAGTGCATTTATAGTCACCC-ATACC
* ** *
848 TTCAAAAGCATTATTACTCGCTTTAAATAGTTTTGTAATGC-CTTAATTGATTTTAATTTGAATT
62 TTCAAAAGC-TTATTACTCGCTTTAAATAGTTTTATAAT-CTCAAAATTGATTTAAATTTGAATT
* * * ** **
912 -TTTTTATATCATTTGTTAAACAGACTACAATTGAATGTCTAGC
125 CTTTGTACAT-TTTTGTTAAACAGACTAGGATTGAATGTCTTCC
* * * * * * *
955 -TCAACAAACATAAAGAAAAATGTATTCATTGGCAAGAGAAGTCCATTTACAGTCACCCATTCCT
1 TTC-AGAAACA-AAAAAAAAACGTATTCATTGGCAA-AAAAGTGCATTTATAGTCACCCATACCT
*************** *
1019 TCAAAAGCCTTATNNNNNNNNNNNNNNNGTTTTATAATTTCAAAATTGATTTAAATTTGAATTCT
63 TCAAAAG-CTTATTACTCGCTTTAAATAGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCT
* *
1084 TTGTACATTTTTGGTTACAATAGACAAGGATTGAATGTCTTCC
127 TTGTACATTTTT-GTTA-AACAGACTAGGATTGAATGTCTTCC
******** *
1127 TTCAGAAANNNNNNNNNNAAA-GTATTCATTGGCAAGAAAAGTGCATTTCTAGTCACCCATACCT
1 TTCAGAAA--CAAAAAAAAAACGTATTCATTGGCAA-AAAAGTGCATTTATAGTCACCCATACCT
** * *
1191 TCAAAAGCGTTATTACTCGCTTTAAATAGTTTTATAATGC-CGTAATTGATTTTAAGTT-AATTT
63 TCAAAAGC-TTATTACTCGCTTTAAATAGTTTTATAAT-CTCAAAATTGATTTAAATTTGAA---
* * ** **
1254 TTTTTTTGTATA-TTTTGTTAAACAGACTATAATTGAATGTCTGGC
123 -TTCTTTGTACATTTTTGTTAAACAGACTAGGATTGAATGTCTTCC
* * ** * * * * *
1299 TTGACAAATGTAAAGAAAAAGGCATTCATTGACAAAAGAAGTGCATTTATAGTCACCCATGCCTT
1 TTCAGAAA-CAAAAAAAAAACGTATTCATTGGCAAAA-AAGTGCATTTATAGTCACCCATACCTT
* * * * * **********
1364 TAAAAGCCTTATTACCCACTTTATATGGTTTTATAATCTCAAAATTGANNNNNNNNNNAATTCTT
64 CAAAAG-CTTATTACTCGCTTTAAATAGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTT
1429 TGTACATTTTTAGTTAAAACAGACTAGGATTGAATGTCTTCC
128 TGTACATTTTT-GTT-AAACAGACTAGGATTGAATGTCTTCC
* * * * *
1471 TTCAGAAACAAGAAGAAAACGATATTCATTGGCAATAAAAGTCCATTTATAGTCACCTATTCCTT
1 TTCAGAAACAAAAAAAAAACG-TATTCATTGGCAA-AAAAGTGCATTTATAGTCACCCATACCTT
1536 CAAAAGCTATATTACTCAG-TTTAAATAGTTTTATAATCTCAAAATTGATTTAAATTTGAAT
64 CAAAAGCT-TATTACTC-GCTTTAAATAGTTTTATAATCTCAAAATTGATTTAAATTTGAAT
1597 GTNNNNNNNN
Statistics
Matches: 469, Mismatches: 144, Indels: 56
0.70 0.22 0.08
Matches are distributed among these distances:
169 18 0.04
170 88 0.19
171 36 0.08
172 300 0.64
173 14 0.03
174 4 0.01
175 9 0.02
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.35
Consensus pattern (167 bp):
TTCAGAAACAAAAAAAAAACGTATTCATTGGCAAAAAAGTGCATTTATAGTCACCCATACCTTCA
AAAGCTTATTACTCGCTTTAAATAGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGT
ACATTTTTGTTAAACAGACTAGGATTGAATGTCTTCC
Found at i:1584 original size:344 final size:341
Alignment explanation
Indices: 785--1596 Score: 846
Period size: 344 Copynumber: 2.4 Consensus size: 341
775 NNNNNNNNNN
* * * *
785 TTCAGAAACATGAAGAAAAAAGTATTCATTGGTAAGAAAAGTCCATTTATAGTCCCCTATACCTT
1 TTCAGAAACAAGAAGAAAAGA-TATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATACCTT
* * *
850 CAAAAGC-ATTATTACTCGCTTTAAATAGTTTTGTAATGCCTTAATTGATTTTAATTTGAATTTT
65 CAAAAGCTA-TATTACTCGCTTTAAATAGTTTTATAATGCCATAATTGATTTTAAGTTGAATTTT
* *
914 TTTATATCATTTGTTAAACAGACTACAATTGAATGTCTAGCTCAACAAACATAAAGAAAAATGTA
129 TTTATATCATTTGTTAAACAGACTACAATTGAATGTCTAGCTCAACAAACATAAAGAAAAAGGCA
* * * ************
979 TTCATTGGCAAGAGAAGTCCATTTACAGTCACCCATTCCTTCAAAAGCCTTATNNNNNNNNNNNN
194 TTCATTGACAAAAGAAGTCCATTTACAGTCACCCATGCCTTCAAAAGCCTTATTACCCACTTTAT
*** * * * *
1044 NNNGTTTTATAATTTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTGGTTACAATAGAC
259 ATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTAGTTAAAACAGAC
1109 AAGGATTGAATGTCTTCC
324 AAGGATTGAATGTCTTCC
******** * * *
1127 TTCAGAAANNNNNNNNNNAAAG-TATTCATTGGCAAGAAAAGTGCATTTCTAGTCACCCATACCT
1 TTCAGAAA--CAAGAAGAAAAGATATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATACCT
*
1191 TCAAAAGCGT-TATTACTCGCTTTAAATAGTTTTATAATGCCGTAATTGATTTTAAGTT-AATTT
64 TCAAAAGC-TATATTACTCGCTTTAAATAGTTTTATAATGCCATAATTGATTTTAAGTTGAA---
* * * ** **
1254 TTTTTTTGTAT-ATTTTGTTAAACAGACTATAATTGAATGTCTGGCTTGACAAATGTAAAGAAAA
125 TTTTTTTATATCA-TTTGTTAAACAGACTACAATTGAATGTCTAGCTCAACAAACATAAAGAAAA
* * *
1318 AGGCATTCATTGACAAAAGAAGTGCATTTATAGTCACCCATGCCTTTAAAAGCCTTATTACCCAC
189 AGGCATTCATTGACAAAAGAAGTCCATTTACAGTCACCCATGCCTTCAAAAGCCTTATTACCCAC
**********
1383 TTTATATGGTTTTATAATCTCAAAATTGANNNNNNNNNNAATTCTTTGTACATTTTTAGTTAAAA
254 TTTATATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTAGTTAAAA
*
1448 CAGACTAGGATTGAATGTCTTCC
319 CAGACAAGGATTGAATGTCTTCC
* *
1471 TTCAGAAACAAGAAGAAAACGATATTCATTGGCAATAAAAGTCCATTTATAGTCACCTATTCCTT
1 TTCAGAAACAAGAAGAAAA-GATATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATACCTT
* * *
1536 CAAAAGCTATATTACTCAG-TTTAAATAGTTTTATAAT-CTCAAAATTGATTTAAATTTGAAT
65 CAAAAGCTATATTACTC-GCTTTAAATAGTTTTATAATGC-CATAATTGATTTTAAGTTGAAT
1597 GTNNNNNNNN
Statistics
Matches: 377, Mismatches: 79, Indels: 28
0.78 0.16 0.06
Matches are distributed among these distances:
341 2 0.01
342 102 0.27
343 4 0.01
344 266 0.71
345 3 0.01
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.35
Consensus pattern (341 bp):
TTCAGAAACAAGAAGAAAAGATATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATACCTTC
AAAAGCTATATTACTCGCTTTAAATAGTTTTATAATGCCATAATTGATTTTAAGTTGAATTTTTT
TATATCATTTGTTAAACAGACTACAATTGAATGTCTAGCTCAACAAACATAAAGAAAAAGGCATT
CATTGACAAAAGAAGTCCATTTACAGTCACCCATGCCTTCAAAAGCCTTATTACCCACTTTATAT
GGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACATTTTTAGTTAAAACAGACAA
GGATTGAATGTCTTCC
Done.