Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397705.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1003.0, 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: 5684
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.25
Warning! 1702 characters in sequence are not A, C, G, or T
Found at i:986 original size:171 final size:171
Alignment explanation
Indices: 672--1985 Score: 1230
Period size: 172 Copynumber: 7.7 Consensus size: 171
662 NNNNNNNNNN
* *
672 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATACCTTTTTCCTTGTA--TTT
1 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTT-CTT-TACGTTT
* *** * * * * **
735 CTAGAAAATGACATTCAATTTTTATCTGTTTT-ACCTAAAAATA-TAAAAAACTTCAACTGAAAA
64 CTTGAGGTTGACATTCAATTATAATCTGTTTTAACC-AAAAA-AGTAAAAAAATTCAAATTTAAA
* *
798 TGAATTATG-GCATTATAAAACCATTTAAAGCT-AGTAATGAGGCTT
127 TCAATTATGAG-ATTATAAAACCATTTAAAG-TGAGTAATAAGGCTT
** * * * *
843 TCAAAGGAATGGGTAACTATAAATGGATTTTTCTTGCCAATGTATGCCTTTTTCTTTACGTCTCT
1 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCT
* * *
908 TGAGGTTGACATTCAATTGTAATCTGTTTTGACCAAAAAAGTACAAACAA-TCAAATTTAAATCA
66 TGAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAAAGTA-AAAAAATTCAAATTTAAATCA
* *
972 ATTTTGAGATTATAAAACCATTTAAAGTGAGTAAAAAGGCTT
130 ATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTT
* * *
1014 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACCGATGAA--CCTTTTT-TTTCATGTTT-
1 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTT-ACGTTTC
* ** * * *
1075 TTGGAGGTTGACATTCAATTATAATCTCTTTTAAAGAAAAATGTACAAAGAATTCAAATATAAAT
65 TT-GAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAAAGTA-AAAAAATTCAAATTTAAAT
* * * **
1140 CAATTTTGAGATTATAAAACCATTTAAAGTGACTAAAAATACTT
128 CAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTT
* * **** * *
1184 TTGAAGGAATGGGTAACAATAAATGGACTTTTCTCATTAATGAATGTCTTTTTCATTACGTTTC-
1 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCT
* * * * * * * * ** *
1248 T--CGTAGCCA-TCAATTCTAGTCTGTTTTATCCAAAAATA-TGAAAAAGTTCAACGTAAAATCA
66 TGAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAA-AGTAAAAAAATTCAAATTTAAATCA
* * *
1309 ATTATG-GCATTATAAAACCATATAAAGCGAGTAATAAGTCTTT
130 ATTATGAG-ATTATAAAACCATTTAAAGTGAGTAATAAGGC-TT
* * *
1352 TTGAAGGTATGAGTGACTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTTCTTTACGTTTCT
1 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCT
* ** * * * * *
1417 TAAGGTAAACAATCAATTATAGTCCT-TTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCA
66 TGAGGTTGACATTCAATTATAAT-CTGTTTTAACCAAAAAAGTAAAAAAATTCAAATTTAAATCA
*
1481 ATTATG-GCATTATAAAACCATTTAAAGTGAGTAACAAGGCTT
130 ATTATGAG-ATTATAAAACCATTTAAAGTGAGTAATAAGGCTT
* * * * * * * *
1523 TTAAAGGAATGAGTGACTATAATTGGACTTTTCTTGCCAATGACTGCCTTTGTCTTCATGTTCCT
1 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCT
** * * * * *
1588 CAAGCTAGACATTCAATTATAATTTGTTTTAACCAAAAAAATAAAAAAATTTAAATTTAAAATCA
66 TGAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAAAGTAAAAAAATTCAAATTT-AAATCA
* * * *
1653 ATTATGAGATTATAAGACCATTGAAAGTGTGTAATAAGGTTT
130 ATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTT
** * * * *
1695 TTGAAGGAATAAGTGACTATTAATGGACTTTTCTTGCCAATGAATGCCTTTTCCTTCATGTTTCT
1 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCT
* * * * *
1760 TGATGTTGACATTCAATTATAATCTTTTTTAACCAAAAATGTACAAATAATTCAAATTTCAATCA
66 TGAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAAAGTA-AAAAAATTCAAATTTAAATCA
* * *
1825 ACTT-TGAGATTACAAAACCATTTAAATTGAGTATTAAGGCTT
130 A-TTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTT
* * * * * *
1867 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGTCAATAAATACTTTTTTCTTTGCATTTCT
1 TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCT
*** ** * * *
1932 AT-AAAATGACATTCAATTATTGTCTGTTTTAACTAAAAATGTAAAAAACTTCAA
66 -TGAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAAAGTAAAAAAATTCAA
1986 CTAAAANNNN
Statistics
Matches: 943, Mismatches: 171, Indels: 58
0.80 0.15 0.05
Matches are distributed among these distances:
166 1 0.00
167 46 0.05
168 84 0.09
169 61 0.06
170 96 0.10
171 280 0.30
172 354 0.38
173 21 0.02
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (171 bp):
TTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCT
TGAGGTTGACATTCAATTATAATCTGTTTTAACCAAAAAAGTAAAAAAATTCAAATTTAAATCAA
TTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTT
Found at i:4672 original size:173 final size:171
Alignment explanation
Indices: 4264--5221 Score: 592
Period size: 172 Copynumber: 5.6 Consensus size: 171
4254 NNNNNNNNNG
* * * * *
4264 AATGTCTACCTCAAGAAACATAAAGAAAAAGACATTCATTGGCAAGAAAAGTCAATTTATAGTCA
1 AATGTCAACCTCAAGAAACGTGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCA
*** * * * * **
4329 CTTGTTCTTTCAAAAGCCTTATTACTCACTTTAA-ATGGCTTTATAATCTTAAAATTGATTTTAA
66 CCCATTCCTTCAAAAGCCTTATTACTCACTTTAATA-GGTTTTGTAATCTCAAAATTGATTGAAA
* * *
4393 GTTGAATTGTTTTACATTTTTGGTTAAAAAAGGCTATAATTA
130 GTTGAATTCTTTTACATTTTTGGTTAAAAAAGACTAAAATTA
* * *
4435 AATGTCAACCTTAAGAAACGTGAAGAAAAAGGCATACATTGGCAACAGAAA-TCCATTTATAGTC
1 AATGTCAACCTCAAGAAACGTGAAGAAAAAGGCATTCATTGGCAAGA-AAAGTCCATTTATAGTC
* * *
4499 ACCCATACCTTCAAAAGCCTCATTACTCGCTTTAATAGGTTTTGTAATCTCAAAATTGATTGAAA
65 ACCCATTCCTTCAAAAGCCTTATTACTCACTTTAATAGGTTTTGTAATCTCAAAATTGATTGAAA
* * *
4564 TTTGAATTCTTTGTACATTTTTGGTTAAAAAAAGATTAAAATTC
130 GTTGAATTCTTT-TACATTTTTGGTT-AAAAAAGACTAAAATTA
* ** * *
4608 AATGTCAACCTCAAGAAATGTGAAGGTAAAGGCATTCATTGGCAAGAAAAGTCCAGTAATAGTCA
1 AATGTCAACCTCAAGAAACGTGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCA
* * * * * **
4673 CCCATTCCTTCAAAAAGCCTTGTTACTCACTTGAAATA-GTTTTGTAACCTCAGAATTTATTTTA
66 CCCATTCCTTC-AAAAGCCTTATTACTCACTT-TAATAGGTTTTGTAATCTCAAAATTGATTGAA
* * * * * ** ** ** *
4737 GGTTCAATT-TTTTGACCTTTTTAGTTAGAGTAGGTTGCAATTG
129 AGTTGAATTCTTTT-ACATTTTTGGTTAAAAAAGACTAAAATTA
** ** * * * * * *
4780 AATGTCTGCCTTGAGAAACATGAGGAAAAAAGAATTGATTGGCAAGAAAAGTCCATTTATAGTCG
1 AATGTCAACCTCAAGAAACGTGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCA
*** * * ** * **
4845 GTTATTTCTTCAAAACCCTTATTACTCACTTTAA-ATGACTTTATAATCTCAAAATTGATTTTAA
66 CCCATTCCTTCAAAAGCCTTATTACTCACTTTAATA-GGTTTTGTAATCTCAAAATTGATTGAAA
** * * * * * *
4909 GTACAATTTTTTTATATTTTTCGGTTTAAAAAGGCTATAATTG
130 GTTGAATTCTTTTACATTTTT-GGTTAAAAAAGACTAAAATTA
*** * * * ** * * ** * *
4952 AATGTTTGCCTTAGGGAACACGAAGCAAAAGCCAGCCATTGACACA-AAAAGTCCATTTAGAGTC
1 AATGTCAACCTCAAGAAACGTGAAGAAAAAGGCATTCATTGGCA-AGAAAAGTCCATTTATAGTC
** ** ** * * ** **
5016 ATTCAAGCCTTCAAAAGCCTTATTACTTGCTTTAA-ATGGTTTTATAAACT-AATAATAAATTTT
65 ACCCATTCCTTCAAAAGCCTTATTACTCACTTTAATA-GGTTTTGTAATCTCAA-AATTGATTGA
* * * * * *
5079 AAGTT-AACTTTTTTTATATTTTTAGTT-AAAAGGACTAGAATTG
128 AAGTTGAA-TTCTTTTACATTTTTGGTTAAAAAAGACTAAAATTA
** * * * * * *
5122 AATGTTTACAAT-GAGAAACATGCAGAGAAAA-GC-TATCGTTGGCAAGAAAAGTCCATTTATGG
1 AATGTCAAC-CTCAAGAAACGTGAAGA-AAAAGGCAT-TCATTGGCAAGAAAAGTCCATTTATAG
* *
5184 TCACCCATACCTTCAAAAAGCCTTATTACTCGCTTTAA
63 TCACCCATTCCTTC-AAAAGCCTTATTACTCACTTTAA
5222 ATTGATTTAA
Statistics
Matches: 617, Mismatches: 150, Indels: 40
0.76 0.19 0.05
Matches are distributed among these distances:
169 2 0.00
170 62 0.10
171 198 0.32
172 217 0.35
173 90 0.15
174 44 0.07
175 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (171 bp):
AATGTCAACCTCAAGAAACGTGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCA
CCCATTCCTTCAAAAGCCTTATTACTCACTTTAATAGGTTTTGTAATCTCAAAATTGATTGAAAG
TTGAATTCTTTTACATTTTTGGTTAAAAAAGACTAAAATTA
Done.