Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399988.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3214.0, 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: 3053
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.32
Warning! 576 characters in sequence are not A, C, G, or T
Found at i:834 original size:172 final size:170
Alignment explanation
Indices: 402--799 Score: 505
Period size: 172 Copynumber: 2.3 Consensus size: 170
392 AAAAGGTATT
* * ** * *
402 CATTGGCAAGTAAAGTCCATTTATAGTCACCCATTCCTTCGAAAACCTTATTATTCGCTTTAAAT
1 CATTGGCAAGAAAAATCCATTTATAGTCACCCAAGCCTTCGAAAGCCTTATTACTCGCTTTAAAT
* *
467 -AGTTTTATAATCTCATAATTAATTTTAAGTAAATTTTTTTACATTTTTGATTGAAATATATTAT
66 GA-TTTTATAATCTCATAATTAATTTTAAGTAAATTTTTTTACATTTTCGATTAAAATATATTAT
* *
531 AACTGAATCTTCCATTTAGGAAACGTGAAGCAAAAGCCATC
130 AACTGAATCGTCCATTTAGGAAACATGAAGCAAAAGCCATC
* * * *
572 CATTGGCAAGTAAAGTCCATTTATAGTCACCCAAGCTTTCGAAAGTCTTATTACTCGCTTTAAAT
1 CATTGGCAAGAAAAATCCATTTATAGTCACCCAAGCCTTCGAAAGCCTTATTACTCGCTTTAAAT
* * *
637 GATTTTATAATCTCCTAATTGATTTTACGTTAAATTGTTTTTACATATTTCG-TTAAAATATATT
66 GATTTTATAATCTCATAATTAATTTTAAG-TAAATT-TTTTTACAT-TTTCGATTAAAATATATT
* * * *
701 GTAATTGAAT-GTCTATCTTGGGAAACATGAAGCAAAAGCCATC
128 ATAACTGAATCGTCCAT-TTAGGAAACATGAAGCAAAAGCCATC
* * * *
744 CATTGGTAGGAAAAATCCATTTATAGTTACTCAAGCCTTCGAAAGCCTTATTACTC
1 CATTGGCAAGAAAAATCCATTTATAGTCACCCAAGCCTTCGAAAGCCTTATTACTC
800 NNNNNNNNNN
Statistics
Matches: 198, Mismatches: 25, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
170 83 0.42
171 11 0.06
172 100 0.51
173 4 0.02
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (170 bp):
CATTGGCAAGAAAAATCCATTTATAGTCACCCAAGCCTTCGAAAGCCTTATTACTCGCTTTAAAT
GATTTTATAATCTCATAATTAATTTTAAGTAAATTTTTTTACATTTTCGATTAAAATATATTATA
ACTGAATCGTCCATTTAGGAAACATGAAGCAAAAGCCATC
Found at i:1108 original size:169 final size:160
Alignment explanation
Indices: 810--1119 Score: 315
Period size: 169 Copynumber: 1.9 Consensus size: 160
800 NNNNNNNNNN
* * * *
810 GTTTTATAATCTCATAATTGATTTTTAGTTGAATTTTTTAATATTTTGGGTTAACACTAGATATA
1 GTTTTATAATCTCATAATTGATTTTAAGTAGAATTTTTTAATATTTTGAGTTAACAATAGATATA
* * * *
875 ATTGAATGTCTACCTCGACAAACGTGAAAAAAATGTCATTAATTGGTAAAAAAAGTCCATTTATA
66 ATTGAATGTCTACCTAGACAAACATGAAAAAAATGCCATTAATTGGCAAAAAAAGTCCATTTATA
*
940 GTCAGTCATTCTTCAAAAACNNNNNNNNNNACTTTAAATG
131 GTCACTCATTCTTCAAAAAC----------ACTTTAAATG
**
980 GTTTTATAATCTTGTAATTGATTTTAAGTAGAATTTTTTACAT-TTTT-AGTTAA-AATAGATTA
1 GTTTTATAATCTCATAATTGATTTTAAGTAGAATTTTTTA-ATATTTTGAGTTAACAATAGA-TA
* * * * *
1042 TAATTTAATGTCTACCTTAG-TAAACATGAAGAGAAA-GCCATTGATTGGCAAGAAAAGTCCATT
64 TAATTGAATGTCTACC-TAGACAAACATGAA-AAAAATGCCATTAATTGGCAAAAAAAGTCCATT
1105 TATAGTCACTCATTC
127 TATAGTCACTCATTC
1120 CTCTAAAAGC
Statistics
Matches: 120, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
168 5 0.04
169 67 0.56
170 46 0.38
171 2 0.02
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.38
Consensus pattern (160 bp):
GTTTTATAATCTCATAATTGATTTTAAGTAGAATTTTTTAATATTTTGAGTTAACAATAGATATA
ATTGAATGTCTACCTAGACAAACATGAAAAAAATGCCATTAATTGGCAAAAAAAGTCCATTTATA
GTCACTCATTCTTCAAAAACACTTTAAATG
Found at i:2190 original size:171 final size:171
Alignment explanation
Indices: 1478--2913 Score: 872
Period size: 171 Copynumber: 8.4 Consensus size: 171
1468 NNNNNNNNNN
* * * * * * *
1478 TAATCTCATAATTTATTTTAGGTTGAATTGTTTT-ACATTTCTAGTTAAAACAGATTATAATTGA
1 TAATCTCAGAATTGATTTTAAGTTGAATT-TTTTGACATTTTTGGTTAAAACAAATTATGATTGA
* ** * * ** * *
1542 ATGTTTGTCTTAAGAAACGTGAAGAAAAAACCATTCATTAGG-AAAAAAAGTCCATTTATAGTCA
65 ATGTCTACCTTAGGAAACATGAAGAAAAAGGCATTCATT-GGCAAGAGAAGTCCATTTATAGTCA
* ********** ***
1606 CCCATTCCTNNNNNNNNNNTATTACTCACTTTAAAT-AGTTTTA
129 CTCATTCCTTCAAAAGCCTTATTACTTGTTTTAAATGA-TTTTA
* * * * * * * *
1649 TAATCTCACAATTTATTGTAGGTTGAATTTTTTTACATTTTTTGTTAAAACAAATTATAATTAAA
1 TAATCTCAGAATTGATTTTAAGTTGAATTTTTTGACATTTTTGGTTAAAACAAATTATGATTGAA
* * * *
1714 TGTCTACCTAAGAAAACATGAAG-AAAAGGCTATAT-ATTGGCACGAAAAGTCCATTTATAGTCA
66 TGTCTACCTTAGGAAACATGAAGAAAAAGGC-AT-TCATTGGCAAGAGAAGTCCATTTATAGTCA
** * ********** *
1777 CTCAAGCCTTCGAAAGCCTTATTNNNNNNNNNNAATTATTTTA
129 CTCATTCCTTCAAAAGCCTTATTACTTGTTTTAAATGATTTTA
* * * * * * * ** *
1820 TACTCTCACAATTAATTTTAAATT-AATTTTTTTATATTTTTAGTTAAAACAGGTTATAATTGAA
1 TAATCTCAGAATTGATTTTAAGTTGAATTTTTTGACATTTTTGGTTAAAACAAATTATGATTGAA
* * ** * *
1884 TGTCTACTTTAGGAAACATGAA-AAAAAGCCATTCATTAACAAAAAAAGTCCATTTATAGTCAC-
66 TGTCTACCTTAGGAAACATGAAGAAAAAGGCATTCATTGGCAAGAGAAGTCCATTTATAGTCACT
* * ** * * *****
1947 CCTAGCCTTCGGAAGCCTTATT-CTCGCTTTAAATGANNNNN
131 CAT-TCCTTCAAAAGCCTTATTACTTGTTTTAAATGATTTTA
***** * * * * * *
1988 NNNNNTCATAATTGATTTTAAGTTGAATTTTTTCACATTTTTTGTTAGAACAAATTATAATTAAA
1 TAATCTCAGAATTGATTTTAAGTTGAATTTTTTGACATTTTTGGTTAAAACAAATTATGATTGAA
* ** *
2053 TGTTTACCTTAGGAAACATGAAGAAAAAGGCATTCATTGGTGAGTGAAGTCCATTTATAGTCACT
66 TGTCTACCTTAGGAAACATGAAGAAAAAGGCATTCATTGGCAAGAGAAGTCCATTTATAGTCACT
* *
2118 CATTCCTTCAAAAACCTTATTACTTGCTTTAAATGATTTTA
131 CATTCCTTCAAAAGCCTTATTACTTGTTTTAAATGATTTTA
*
2159 TAATCT-AGGAATTGATTTTAAGTTAAATTTTTTGACATTTTTGGTTAAAACAAATTATGATTGA
1 TAATCTCA-GAATTGATTTTAAGTTGAATTTTTTGACATTTTTGGTTAAAACAAATTATGATTGA
* * * *
2223 ATGTCTACCTTCA-AAAACATGAAGAAAAAGTCATTCTTTGGCAAAAGAAGTCCATTTATAGTCA
65 ATGTCTACCTT-AGGAAACATGAAGAAAAAGGCATTCATTGGCAAGAGAAGTCCATTTATAGTCA
* * ********** *
2287 CCCATTCTTTCAAAAGCCTTATTANNNNNNNNNNATGGTTTTA
129 CTCATTCCTTCAAAAGCCTTATTACTTGTTTTAAATGATTTTA
* * * * **
2330 TAATCTCATAATTGATTTTAAGTTGTAGTTTTTT-ACATTTTTGTTTAAAACATATTATTCTTGA
1 TAATCTCAGAATTGATTTTAAGTTG-AATTTTTTGACATTTTTGGTTAAAACAAATTATGATTGA
* * * **********
2394 ATGT-T-CGCTTAGGAAAACATGAAGCAAAAGCCATCCATTGGNNNNNNNNNNCCATTTATAGTC
65 ATGTCTAC-CTTAGG-AAACATGAAGAAAAAGGCATTCATTGGCAAGAGAAGTCCATTTATAGTC
** ** * *
2457 ACTCAAGCCTTTGAAAGTCATATTACTTGTTTTAAATGATTTTA
128 ACTCATTCCTTCAAAAGCCTTATTACTTGTTTTAAATGATTTTA
* * * *
2501 TAATCTCAGAATTGATTTTAAGTTGAATTCTTTGACATTTTTGGCTT-GAAGAGATTATGATTGA
1 TAATCTCAGAATTGATTTTAAGTTGAATTTTTTGACATTTTTGG-TTAAAACAAATTATGATTGA
* ** * * * * * *
2565 ATGTCTGCCCCATGAAACATGAAGGAAAAGTCATTTATTGGCAAGAAAAGACCATTTATAGTCAC
65 ATGTCTACCTTAGGAAACATGAAGAAAAAGGCATTCATTGGCAAGAGAAGTCCATTTATAGTCAC
********** * *
2630 TCATTCCTTCAAANNNNNNNNNNCTCGTTTTAAATGGTTTTA
130 TCATTCCTTCAAAAGCCTTATTACTTGTTTTAAATGATTTTA
* * * *
2672 TAATCTCATAATTGATTTGAAGTTGAATCTTTTGACATTTTTAGTTAAAACAAATTATGATTGAA
1 TAATCTCAGAATTGATTTTAAGTTGAATTTTTTGACATTTTTGGTTAAAACAAATTATGATTGAA
* *
2737 TGTCTACCTCAGGAAACATGAAGAAAAA-GCAATTCAATGGCAAGAGAAGTCCATTTATAGTCAC
66 TGTCTACCTTAGGAAACATGAAGAAAAAGGC-ATTCATTGGCAAGAGAAGTCCATTTATAGTCAC
* ********** * * *
2801 CCATTCCTTCAAANNNNNNNNNNCTCGCTTTAAATTATTTTA
130 TCATTCCTTCAAAAGCCTTATTACTTGTTTTAAATGATTTTA
* * * ** *
2843 TAATCTTATAATTGATTTTAAGTTAAAGTTTTTT-ACATTTTTGGTTAAAACAGTTTATAATTGA
1 TAATCTCAGAATTGATTTTAAGTTGAA-TTTTTTGACATTTTTGGTTAAAACAAATTATGATTGA
*
2907 ATATCTA
65 ATGTCTA
2914 TCTTGGGTAA
Statistics
Matches: 980, Mismatches: 259, Indels: 52
0.76 0.20 0.04
Matches are distributed among these distances:
168 22 0.02
169 99 0.10
170 132 0.13
171 704 0.72
172 22 0.02
173 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.37
Consensus pattern (171 bp):
TAATCTCAGAATTGATTTTAAGTTGAATTTTTTGACATTTTTGGTTAAAACAAATTATGATTGAA
TGTCTACCTTAGGAAACATGAAGAAAAAGGCATTCATTGGCAAGAGAAGTCCATTTATAGTCACT
CATTCCTTCAAAAGCCTTATTACTTGTTTTAAATGATTTTA
Done.