Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398119.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1422.0, 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: 4025
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.28
Warning! 977 characters in sequence are not A, C, G, or T
Found at i:1093 original size:170 final size:168
Alignment explanation
Indices: 693--1282 Score: 582
Period size: 170 Copynumber: 3.5 Consensus size: 168
683 NNNNNNNNNN
** * * * * *
693 ATTATAAAATTATTTGAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATGAATGGACTTT
1 ATTATAAAACAATTTAAAGCGAGTAAAAAGGCTTTTGAAGGAATAAGAGACTATAAATGGACTTT
* * *
758 TCTTCTCAATGAATGGTT-TTTGCTGCATGTTTCCCAAG-ACAAGGC-TTCAATTATAGTCTATT
66 TCTTGTCAATGAATGCTTGTTT-CTTCATGTTT-CCAAGTA-AA--CATTCAATTATAGTCTATT
** * * * * * *
820 TTAACCGCAAATGCGAAAAAGGTTAGCTTAAAATCAATAATGAT
126 TTAACCAAAAAAGAGAAAAA-TTTAACTTAAAATCAATTATGAG
* * *
864 ATTATAAAACAATTTAAAGCGAATAATAAGGCTTTTCAAGGAATAAGAGACTATAAATGGACTTT
1 ATTATAAAACAATTTAAAGCGAGTAAAAAGGCTTTTGAAGGAATAAGAGACTATAAATGGACTTT
* *
929 TCTTGTCAATGAATGCTTGTTTCTTCATGTTTGCCAATGTAAATATTCAATTATAGTCTTTTTTA
66 TCTTGTCAATGAATGCTTGTTTCTTCATGTTT-CCAA-GTAAACATTCAATTATAGTCTATTTTA
* *
994 ACCAAAAAAGTGAAAAATTTAACTCAAAATCAATTATGAG
129 ACCAAAAAAGAGAAAAATTTAACTTAAAATCAATTATGAG
* * *
1034 ATTATAAAACAATTTAAAGCGAGTAAAAAGGCTTTTGAAGGAATATGAGATTGTAAATGGACTTT
1 ATTATAAAACAATTTAAAGCGAGTAAAAAGGCTTTTGAAGGAATAAGAGACTATAAATGGACTTT
* * * * * *
1099 TCTTGCCAACGAATGCCTGTTTCTTCACGTTTCTTAAGGTAAACATTCAATTATAGTCTATTTGA
66 TCTTGTCAATGAATGCTTGTTTCTTCATGTTTC-CAA-GTAAACATTCAATTATAGTCTATTTTA
** * *
1164 AGGAAAAATA-AAAAAAATTCAACTTAAAA-CTAATTATGAG
129 ACCAAAAA-AGAGAAAAATTTAACTTAAAATC-AATTATGAG
* ** * ** ** *
1204 ATTATAAAACCATTTAAATAGAGTAATAAA-GCTTTTAAAGGAATGGGTCACTATAAATAGACTT
1 ATTATAAAACAATTTAAAGCGAGTAA-AAAGGCTTTTGAAGGAATAAGAGACTATAAATGGACTT
1268 TTCTT-TCGAATGAAT
65 TTCTTGTC-AATGAAT
1283 NNNNNNNNNN
Statistics
Matches: 353, Mismatches: 57, Indels: 19
0.82 0.13 0.04
Matches are distributed among these distances:
169 3 0.01
170 221 0.63
171 122 0.35
172 6 0.02
173 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (168 bp):
ATTATAAAACAATTTAAAGCGAGTAAAAAGGCTTTTGAAGGAATAAGAGACTATAAATGGACTTT
TCTTGTCAATGAATGCTTGTTTCTTCATGTTTCCAAGTAAACATTCAATTATAGTCTATTTTAAC
CAAAAAAGAGAAAAATTTAACTTAAAATCAATTATGAG
Found at i:2852 original size:171 final size:169
Alignment explanation
Indices: 2558--4025 Score: 1375
Period size: 171 Copynumber: 8.6 Consensus size: 169
2548 NNNNNNNNNN
* * *
2558 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTT-TTTAAATAGACTATAAT
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGTTAAAACAGACTATAAT
* * ** *
2622 TGAATGTCTACTTCGAGAAACAGGAAGAAACAAATATTCATTG-GCAAGATAAGTCCATTTATAG
66 TGAATGTCTAC-TCAAGAAACATGAAGAAA-AAGCATTCATTGTGCAAGAAAAGTCCATTTATAG
* *
2686 TCTCCTATTCCTTTAATAGCCTTATTACTCGCTTTAAATAG
129 TCTCCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAG
* * * * * *
2727 TTTTATAATCTCAAAATTGATTTTAGGTTCAATTTGTTTTACATTATTTGCTGAAACAGATTATA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTT-TTTTACATT-TTTGTTAAAACAGACTATA
* *
2792 ATTG-ATGTCTAGCTCAAGTAACAT-AACGAAAAAGCTATTCATAGTGC-AGAAAAGTCCATTTA
64 ATTGAATGTCTA-CTCAAGAAACATGAA-GAAAAAGC-ATTCATTGTGCAAGAAAAGTCCATTTA
* * * * *
2854 TTA-TCACCCATTTCTTCAAAAGTCTTATTACTCACTTTAAATAG
126 -TAGTCTCCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAG
*
2898 TTTTATAATCTCATAATTGATTTTAAGTTGAATATTTTTACATTTTTAGTTAAAACAGACTATAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTT-GTTAAAACAGACTATAA
* * *
2963 TTGAATGCCTACCTCAAGAAACATGAAGAAAAAAGCATACATTG-ACAAGAAAAGTCCA-TTATA
65 TTGAATGTCTA-CTCAAGAAACATGAAG-AAAAAGCATTCATTGTGCAAGAAAAGTCCATTTATA
* * * *
3026 GTCTCATATTCCTTCAAAAGCCTTATTACTCACTTCAAATAA
128 GTCTCCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAG
3068 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAACAGACTATAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACA-TTTTTGTTAAAACAGACTATAA
* * ** *
3133 TTGAATATTTACATTGAGAAACGTGAAGAAACAAGCATTCATTG-GCAAGAAAAGTCCATTTATA
65 TTGAATGTCTAC-TCAAGAAACATGAAGAAA-AAGCATTCATTGTGCAAGAAAAGTCCATTTATA
** * * **
3197 GTCTTTTATTCCTTCAAAAGCCTTATTACTTGTTTTAAATTT
128 GTCTCCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAG
* * * * *
3239 TTTTATAATATCATAATTGATTTTAAGCT-AACCTTTTTCACATTTTTAGTTAAAATAGACTATA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTTACATTTTT-GTTAAAACAGACTATA
* * * * * * * * *
3303 ATTGAA-GGCTTGC-CTTAGAAAACGTGCAAAAAAAAACCATTCGTTGAG-AAGAAAAGTCTATT
64 ATTGAATGTC-TACTC-AAG-AAACATG--AAGAAAAAGCATTCATTGTGCAAGAAAAGTCCATT
* * * * *
3365 TATAGTC-ACTCATTCGTTCAAAAGCCTTATTACTCGCTTCAAGTAA
124 TATAGTCTCCT-ATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAG
* *
3411 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTAGTTAAAACAGACTATAT
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTT-GTTAAAACAGACTATAA
*
3476 TTGAATGTCTAC-CAAGAGAA-ATGTAAAGAAACAAGCATTCGTTGAT--AAGAAATA-TCCATT
65 TTGAATGTCTACTCAAGA-AACATG--AAGAAA-AAGCATTCATTG-TGCAAGAAA-AGTCCATT
** **
3536 TATAG-CGTCCTATTATTTTGAAAGCCTTATTACTCGCTTTAAATTA-
124 TATAGTC-TCCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAA-TAG
* * *
3582 TTTTATAATATCATAATTAATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAACAGATTATAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACA-TTTTTGTTAAAACAGACTATAA
* * ** * *
3647 TTGAATGTCTAGCTCGAGTAATGTGAAGAAAAATACATTCATTG-ACAAGAAAAGTCCATTTATA
65 TTGAATGTCTA-CTCAAGAAACATGAAGAAAAA-GCATTCATTGTGCAAGAAAAGTCCATTTATA
** * * * *
3711 GTGACCCATTCCTTCAAAAGCCATATTACTCGATTTAATTAG
128 GTCTCCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAG
* * * *
3753 TTTTATAATCTCAAAATTGATTTTAAGTTGAATTTTTGTACATTTTTTATTAAAACAGACTACAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACA-TTTTTGTTAAAACAGACTATAA
* ** * * * * * *
3818 TTGAAGGTCTACCTTGAGAAACATGAAGAAAAAGACATTCACT-AG-AAAAAAAATTCATTTAAA
65 TTGAATGTCTA-CTCAAGAAACATGAAGAAAAAG-CATTCATTGTGCAAGAAAAGTCCATTTATA
* * * * * *
3881 GTCACCCATTCCTTTAAAAGCGTTATTACTCGTTTTAAA-CG
128 GTCTCCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAG
* * ** * * *
3922 ATTTTATAATATCATAATTCATTTTAAGTTGAATGCTTTTAGATTTTTGGTTGATACAGACTATA
1 -TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTT-GTTAAAACAGACTATA
* * * *
3987 ATTAAATGTTTACCTTAAGAAACATAAAGAAAAAAGCAT
64 ATTGAATGTCTA-CTCAAGAAACATGAAG-AAAAAGCAT
Statistics
Matches: 1079, Mismatches: 169, Indels: 101
0.80 0.13 0.07
Matches are distributed among these distances:
169 47 0.04
170 323 0.30
171 531 0.49
172 163 0.15
173 15 0.01
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (169 bp):
TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGTTAAAACAGACTATAAT
TGAATGTCTACTCAAGAAACATGAAGAAAAAGCATTCATTGTGCAAGAAAAGTCCATTTATAGTC
TCCTATTCCTTCAAAAGCCTTATTACTCGCTTTAAATAG
Done.