Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398853.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2135.0, 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: 2803
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.26
Warning! 963 characters in sequence are not A, C, G, or T
Found at i:618 original size:171 final size:171
Alignment explanation
Indices: 337--1511 Score: 1156
Period size: 171 Copynumber: 6.9 Consensus size: 171
327 NNNNNNTTAA
* ** * *
337 GTTGAATTGTTTTACATTTTTAGTTAAAACAGATTATAATTGAATGTTTTTCTTGAAAAACGTGA
1 GTTGAATTTTTTTACATTTTTAGTTAAAACAGATTATAATTGAATGTTTACCTTGAGAAACATGA
* * * * *
402 AGCAAAAGCCATTCATTGGCAATAAAAGCTC-TTGTATACTCACCCATACCTTCGAAAGCCTTAT
66 AGAAAAAGCCATTCATTGGCAAGAAAAGCCCATT-TATAGTCACCCATACCTTCAAAAGCCTTAT
* * *
466 TACTCGATTTCAATGGTTTTATAATCTCATAATTGATTTTAA
130 TACTCGATTTAAATAGTTTTATAATCTCATAATTGATTTTAG
* * * * * *
508 GTTGAATGTTTTTACATTTTTTGTTAGAACAGATTATAATTGAATGTCTGCCTTGAAAAACATGA
1 GTTGAATTTTTTTACATTTTTAGTTAAAACAGATTATAATTGAATGTTTACCTTGAGAAACATGA
* * * * * *
573 TGAAAAAGCCATTTATTGGCAACAAAAGTCCATTTATAGTCACCCA-AGTCTTGAAAAGCCTTAT
66 AGAAAAAGCCATTCATTGGCAAGAAAAGCCCATTTATAGTCACCCATA-CCTTCAAAAGCCTTAT
* * *
637 TACTCGCTTTCAATAGTTTTATAAACTCATAATTGATTTTAG
130 TACTCGATTTAAATAGTTTTATAATCTCATAATTGATTTTAG
* * * *
679 GTTGAATTTTTTTATATTTTT-GATTAAAATATATTATAATTGAATGTTTACCTTGA-AAAAAGT
1 GTTGAATTTTTTTACATTTTTAG-TTAAAACAGATTATAATTGAATGTTTACCTTGAGAAACA-T
* * * * * ** * * *
742 AAAGAAAAAGGCATTCACTGGTAAGAAAAGTCCATTTATAGTCACTTATTCCCTCAAAAGTCTTA
64 GAAGAAAAAGCCATTCATTGGCAAGAAAAGCCCATTTATAGTCACCCATACCTTCAAAAGCCTTA
* * * * *
807 TTACT-TACTTTAAATGGTTTTATAATCTCACAATTGATTGTAA
129 TTACTCGA-TTTAAATAGTTTTATAATCTCATAATTGATTTTAG
* * * * * * *
850 GTTGAATTTTTTTTACATTTTTACTAAAAAAAAATTATAATTGATTGTCTACCTTGAGAAACGTG
1 GTTGAA-TTTTTTTACATTTTTAGTTAAAACAGATTATAATTGAATGTTTACCTTGAGAAACATG
* * ** * *
915 AA-AAAAATCCATTCGTTTACAAGAAAAGCCCATTTATAGTCACTCATACCTTCAAAAGCCTTGT
65 AAGAAAAAGCCATTCATTGGCAAGAAAAGCCCATTTATAGTCACCCATACCTTCAAAAGCCTTAT
* * * *
979 TACTCGCTTTAAATAATTTT-TAATCTCATAACTGATTTTGG
130 TACTCGATTTAAATAGTTTTATAATCTCATAATTGATTTTAG
* *
1020 GTTGAA-TTTTTTATATTTTTCA-TTAAAACAGATTATAATTGAATGTTTACCTTGAGAAACAAG
1 GTTGAATTTTTTTACATTTTT-AGTTAAAACAGATTATAATTGAATGTTTACCTTGAGAAACATG
* * * * * * **
1083 AAGTAAAA-CTTATTCATTTGCAGGACAAGCCCATTTATTGTCA-CCA-AGCCTTTGAAAGCCTT
65 AAGAAAAAGC-CATTCATTGGCAAGAAAAGCCCATTTATAGTCACCCATA-CCTTCAAAAGCCTT
* * *
1145 ATTACTCGCTTTAAATAGTTTTACAACCTCATAATTGATTTTAG
128 ATTACTCGATTTAAATAGTTTTATAATCTCATAATTGATTTTAG
** * * * * * *
1189 GAAGAATGTTTTTACATTTTTGGTTAAAACATATTATAATTGACTGTTTGCCTT-AGGAAATATG
1 GTTGAATTTTTTTACATTTTTAGTTAAAACAGATTATAATTGAATGTTTACCTTGA-GAAACATG
* * ** * *
1253 AAGAAAAAGCTATTGATTGATAAGAGAAGCCCATTTATAGTCACCCATGCCTTCAAAAGCCTTAT
65 AAGAAAAAGCCATTCATTGGCAAGAAAAGCCCATTTATAGTCACCCATACCTTCAAAAGCCTTAT
*
1318 TACTC-ATTTTAAATAGTTTTATAATCTTATAATTGATTTTAG
130 TACTCGA-TTTAAATAGTTTTATAATCTCATAATTGATTTTAG
* * * * * *
1360 GTTGAATTTTTTTTATATTTTTGGTTAAAATAGATTATAATTGACTGTTTTCCTT-AGGAAACGT
1 GTTGAA-TTTTTTTACATTTTTAGTTAAAACAGATTATAATTGAATGTTTACCTTGA-GAAACAT
* * * * ** * * *
1424 TAAGGAAAAGCCATTGATAGATAAGAAAAGCCCTTTTATAGTCACCTATGCCTTCAAAAGCCTTA
64 GAAGAAAAAGCCATTCATTGGCAAGAAAAGCCCATTTATAGTCACCCATACCTTCAAAAGCCTTA
*
1489 TTACTCGTTTTAAATAGTTTTAT
129 TTACTCGATTTAAATAGTTTTAT
1512 NNNNNNNNNN
Statistics
Matches: 830, Mismatches: 150, Indels: 47
0.81 0.15 0.05
Matches are distributed among these distances:
167 1 0.00
168 84 0.10
169 54 0.07
170 107 0.13
171 405 0.49
172 176 0.21
173 3 0.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (171 bp):
GTTGAATTTTTTTACATTTTTAGTTAAAACAGATTATAATTGAATGTTTACCTTGAGAAACATGA
AGAAAAAGCCATTCATTGGCAAGAAAAGCCCATTTATAGTCACCCATACCTTCAAAAGCCTTATT
ACTCGATTTAAATAGTTTTATAATCTCATAATTGATTTTAG
Found at i:1296 original size:510 final size:512
Alignment explanation
Indices: 334--1511 Score: 1388
Period size: 510 Copynumber: 2.3 Consensus size: 512
324 NNNNNNNNNT
* * * *
334 TAAGTTGAA-TTGTTTTACATTTTTAGTTAAAACAGATTATAATTGAATGTTTTTCTTGAAAAAC
1 TAAGTTGAATTTTTTTTACATTTTTAGTTAAAAAAGATTATAATTGAATGTTTTCCTTGAGAAAC
* * * * * * *
398 GTGAAGCAAAAGCCATTCATTGGCAATAAAAGCTCTTGTATACTCACCCATACCTTCGAAAGCCT
66 GTGAAGAAAAAGCCATTCGTTGACAAGAAAAGCCCTT-TATAGTCA-CCATACCTTCAAAAGCCT
* * *
463 TATTACTCGATTTCAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATGTTTTTACATTTT
129 TATTACTCGATTTAAATAGTTTTATAATCTCATAACTGATTTTAAGTTGAATGTTTTTACATTTT
** * * * * *
528 TTGTTAGAACAGATTATAATTGAATGTCTGCCTTGAAAAACATGATGAAAAAGCCATTTATTGGC
194 TCATTAAAACAGATTATAATTGAATGTCTACCTTGAAAAACAAGAAGAAAAAGCCATTCATTGGC
* * *
593 AACAAAAGTCCATTTATAGTCACCCAAGTCTTGAAAAGCCTTATTACTCGCTTTCAATAGTTTTA
259 AACAAAAGCCCATTTATAGTCACCCAAGCCTTGAAAAGCCTTATTACTCGCTTTAAATAGTTTTA
* ** * * *
658 TAAACTCATAATTGATTTTAGGTTGAATTTTTTTATATTTTTGATTAAAATATATTATAATTGAA
324 CAAACTCATAATTGATTTTAGGAAGAATGTTTTTACATTTTTGATTAAAACATATTATAATTGAA
* * *
723 TGTTTACCTTGAAAAAAGTAAAGAAAAAGGCATTCACTGGTAAGAAAAGTCCATTTATAGTCACT
389 TGTTTACCTTGAAAAAAGTAAAGAAAAAGGCATTCACTGATAAGAAAAGCCCATTTATAGTCACC
* * * * *
788 TATTCCCTCAAAAGTCTTATTACTTACTTTAAATGGTTTTATAATCTCACAATTGATTG
454 CATGCCCTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCACAATTGATTG
* * * * * *
847 TAAGTTGAATTTTTTTTACATTTTTACTAAAAAAAAATTATAATTGATTGTCTACCTTGAGAAAC
1 TAAGTTGAATTTTTTTTACATTTTTAGTTAAAAAAGATTATAATTGAATGTTTTCCTTGAGAAAC
* *
912 GTGAA-AAAAATCCATTCGTTTACAAGAAAAGCCCATTTATAGTCACTCATACCTTCAAAAGCCT
66 GTGAAGAAAAAGCCATTCGTTGACAAGAAAAGCCC-TTTATAGTCAC-CATACCTTCAAAAGCCT
* * * ** *
976 TGTTACTCGCTTTAAATAATTTT-TAATCTCATAACTGATTTTGGGTTGAAT-TTTTTATATTTT
129 TATTACTCGATTTAAATAGTTTTATAATCTCATAACTGATTTTAAGTTGAATGTTTTTACATTTT
* * * * *
1039 TCATTAAAACAGATTATAATTGAATGTTTACCTTGAGAAACAAGAAGTAAAA-CTTATTCATTTG
194 TCATTAAAACAGATTATAATTGAATGTCTACCTTGAAAAACAAGAAGAAAAAGC-CATTCATTGG
** * *
1103 CAGGACAAGCCCATTTATTGTCA-CCAAGCCTTTG-AAAGCCTTATTACTCGCTTTAAATAGTTT
258 CAACAAAAGCCCATTTATAGTCACCCAAGCC-TTGAAAAGCCTTATTACTCGCTTTAAATAGTTT
* *
1166 TACAACCTCATAATTGATTTTAGGAAGAATGTTTTTACATTTTTGGTTAAAACATATTATAATTG
322 TACAAACTCATAATTGATTTTAGGAAGAATGTTTTTACATTTTTGATTAAAACATATTATAATTG
* * * * * * * *
1231 ACTGTTTGCCTTAGGAAATA-TGAAGAAAAA-GCTATTGATTGATAAGAGAAGCCCATTTATAGT
387 AATGTTTACCTT-GAAAAAAGTAAAGAAAAAGGC-ATTCACTGATAAGAAAAGCCCATTTATAGT
* * * * *
1294 CACCCATGCCTTCAAAAGCCTTATTACTCATTTTAAATAGTTTTATAATCTTATAATTGATTT
450 CACCCATGCCCTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCACAATTGATTG
* * * * *
1357 TAGGTTGAATTTTTTTTATATTTTTGGTTAAAATAGATTATAATTGACTGTTTTCCTT-AGGAAA
1 TAAGTTGAATTTTTTTTACATTTTTAGTTAAAAAAGATTATAATTGAATGTTTTCCTTGA-GAAA
* * * * *
1421 CGTTAAGGAAAAGCCATT-GATAGATAAGAAAAGCCCTTTTATAGTCACCTATGCCTTCAAAAGC
65 CGTGAAGAAAAAGCCATTCG-TTGACAAGAAAAGCCC-TTTATAGTCACC-ATACCTTCAAAAGC
*
1485 CTTATTACTCGTTTTAAATAGTTTTAT
127 CTTATTACTCGATTTAAATAGTTTTAT
1512 NNNNNNNNNN
Statistics
Matches: 556, Mismatches: 97, Indels: 25
0.82 0.14 0.04
Matches are distributed among these distances:
509 3 0.01
510 247 0.44
511 155 0.28
512 27 0.05
513 72 0.13
514 52 0.09
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (512 bp):
TAAGTTGAATTTTTTTTACATTTTTAGTTAAAAAAGATTATAATTGAATGTTTTCCTTGAGAAAC
GTGAAGAAAAAGCCATTCGTTGACAAGAAAAGCCCTTTATAGTCACCATACCTTCAAAAGCCTTA
TTACTCGATTTAAATAGTTTTATAATCTCATAACTGATTTTAAGTTGAATGTTTTTACATTTTTC
ATTAAAACAGATTATAATTGAATGTCTACCTTGAAAAACAAGAAGAAAAAGCCATTCATTGGCAA
CAAAAGCCCATTTATAGTCACCCAAGCCTTGAAAAGCCTTATTACTCGCTTTAAATAGTTTTACA
AACTCATAATTGATTTTAGGAAGAATGTTTTTACATTTTTGATTAAAACATATTATAATTGAATG
TTTACCTTGAAAAAAGTAAAGAAAAAGGCATTCACTGATAAGAAAAGCCCATTTATAGTCACCCA
TGCCCTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCACAATTGATTG
Found at i:2797 original size:35 final size:35
Alignment explanation
Indices: 2686--2799 Score: 122
Period size: 35 Copynumber: 3.3 Consensus size: 35
2676 AGTCCTTAAG
*** *
2686 AAGCCCAATTAACTTAATTATTTATTTTAATCAATT
1 AAGCCCAATT-ACTTAATTAAACAATTTAATCAATT
* * * *
2722 -AGTCCAATAACTTAATTAAACAATTTAATTAGTT
1 AAGCCCAATTACTTAATTAAACAATTTAATCAATT
* *
2756 AGGCCCAATTACTTAATTAAACAATTTGATCAATT
1 AAGCCCAATTACTTAATTAAACAATTTAATCAATT
2791 AAGCCCAAT
1 AAGCCCAAT
2800 AACT
Statistics
Matches: 62, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
34 19 0.31
35 43 0.69
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (35 bp):
AAGCCCAATTACTTAATTAAACAATTTAATCAATT
Done.