Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398950.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2232.0, 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: 18738
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.25
Warning! 6629 characters in sequence are not A, C, G, or T
Found at i:369 original size:171 final size:169
Alignment explanation
Indices: 192--637 Score: 493
Period size: 170 Copynumber: 2.6 Consensus size: 169
182 NNNNNNNNNN
* * *
192 AATTGAATGCCTACCTCAGAAAATGTATAAAAAAACCTATTTATTTAGAAGAAAGGTCCATTTAT
1 AATTGAATGCCTGCCTCAGAAAATGTGTAAAAAAACC-ATTTATTTAGAAGAAAAGTCCATTTAT
* ********** * *
257 AGTCTCTCATTCCTTTAAAAGCCTTATTANNNNNNNNNNATGGTTTTATAATCTCATAATTGATT
65 AGTCTCTCATTCCTTCAAAAGCCTTATTAGTCGCTTTAAATGGTTTTATAATATAATAATTGATT
*
322 TTAAG-TAGAA-TTTTTTACATTTTTTCATTAAAACATACTAT
130 TTAAGTTA-AATTTTTTTAC-TTTTTT-ATTAAAACAGACTAT
* * * ** ** *
363 AATTGAATTCCTGCATCAAAAAAAATGTAAAAAATTCATTTATTTGGAAGAAAAGTCCATTTATA
1 AATTGAATGCCTGCCTCAGAAAATGTGTAAAAAAACCATTTATTTAGAAGAAAAGTCCATTTATA
* *
428 GTTTTTCATTCCTTCAAAAGCCTTATTAGTCGCTTTAAATGGTTTTATAATATAATAATTGATTT
66 GTCTCTCATTCCTTCAAAAGCCTTATTAGTCGCTTTAAATGGTTTTATAATATAATAATTGATTT
*
493 TAAGTTAAATTTTTTTTACTTTTTTGTTAAAACAGACTAT
131 TAAGTTAAA-TTTTTTTACTTTTTTATTAAAACAGACTAT
* * * *
533 AATTGAATGCCTGCCTTAGAAAATGTGTAGAAAAACCCATTTATTTA-AAAAAAAGTCAATTTAT
1 AATTGAATGCCTGCCTCAGAAAATGTGTA-AAAAAACCATTTATTTAGAAGAAAAGTCCATTTAT
* * * *
597 AGTCTCCCATTTCTCCAAAAGCCTTATTACTCGCTTTAAAT
65 AGTCTCTCATTCCTTCAAAAGCCTTATTAGTCGCTTTAAAT
638 TGTTNNNNNN
Statistics
Matches: 226, Mismatches: 45, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
170 168 0.74
171 50 0.22
172 8 0.04
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.39
Consensus pattern (169 bp):
AATTGAATGCCTGCCTCAGAAAATGTGTAAAAAAACCATTTATTTAGAAGAAAAGTCCATTTATA
GTCTCTCATTCCTTCAAAAGCCTTATTAGTCGCTTTAAATGGTTTTATAATATAATAATTGATTT
TAAGTTAAATTTTTTTACTTTTTTATTAAAACAGACTAT
Found at i:658 original size:170 final size:168
Alignment explanation
Indices: 296--748 Score: 471
Period size: 170 Copynumber: 2.7 Consensus size: 168
286 NNNNNNNNNN
* * * *
296 ATGGTTTTATAATCTCATAATTGATTTTAAG-TAGAATTTTTTACATTTTTTCATTAAAACATAC
1 ATGGTTTTATAATATAATAATTGATTTTAAGTTA-AATTTTTTACATTTTTT-GTTAAAACAGAC
* * * * * * * * *
360 TATAATTGAATTCCTGCATCAAAAAAAATGTA-AAAAATTCATTTATTTGGAAGAAAAGTCCATT
64 TATAATTGAATGCCTGCCT-TAGAAAATTGTAGAAAAACTCATTTATTT-AAAAAAAAGTCAATT
* ** * *
424 TATAGTTTTTCATTCCTTCAAAAGCCTTATTAGTCGCTTTAA
127 TATAGTCTCCCATTCCTCCAAAAGCCTTATTACTCGCTTTAA
466 ATGGTTTTATAATATAATAATTGATTTTAAGTTAAATTTTTTTTAC-TTTTTTGTTAAAACAGAC
1 ATGGTTTTATAATATAATAATTGATTTTAAGTTAAA--TTTTTTACATTTTTTGTTAAAACAGAC
*
530 TATAATTGAATGCCTGCCTTAGAAAATGTGTAGAAAAACCCATTTATTTAAAAAAAAGTCAATTT
64 TATAATTGAATGCCTGCCTTAGAAAAT-TGTAGAAAAACTCATTTATTTAAAAAAAAGTCAATTT
*
595 ATAGTCTCCCATTTCTCCAAAAGCCTTATTACTCGCTTTAA
128 ATAGTCTCCCATTCCTCCAAAAGCCTTATTACTCGCTTTAA
* ********** * * * *
636 ATTGTTNNNNNNNNNNATAATTGATTTTAAGTTGAATGTTTTACATTTTTCGTTAAAGCAGACTA
1 ATGGTTTTATAATATAATAATTGATTTTAAGTTAAATTTTTTACATTTTTTGTTAAAACAGACTA
* * *
701 TAATTGAATGCTTGCCTTAGGAAACTTGTTGAAAAACTCATTTATTTA
66 TAATTGAATGCCTGCCTTA-GAAAATTGTAGAAAAACTCATTTATTTA
749 GTGCTTGTTT
Statistics
Matches: 237, Mismatches: 39, Indels: 15
0.81 0.13 0.05
Matches are distributed among these distances:
168 7 0.03
169 61 0.26
170 139 0.59
171 22 0.09
172 8 0.03
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.41
Consensus pattern (168 bp):
ATGGTTTTATAATATAATAATTGATTTTAAGTTAAATTTTTTACATTTTTTGTTAAAACAGACTA
TAATTGAATGCCTGCCTTAGAAAATTGTAGAAAAACTCATTTATTTAAAAAAAAGTCAATTTATA
GTCTCCCATTCCTCCAAAAGCCTTATTACTCGCTTTAA
Found at i:1721 original size:169 final size:169
Alignment explanation
Indices: 1335--1880 Score: 524
Period size: 169 Copynumber: 3.2 Consensus size: 169
1325 AAACAGGTAC
* * * *
1335 TTAGAAG-AAAGTCCATTTATAGTCTCACATTCCTTCAAAAGTCC-TATTAGTCGCTTTAAATAG
1 TTAGAAGAAAAATCCATTTATAGTCTCCCATTCCTTCAAAAG-CCTTATTACTCGCTTTAAAAAG
* ********** * * * *
1398 TTTTATAANNNNNNNNNNGATTTTAAGTTGAATATTTTACATTTTTTGTTAAAATAGACTATAAT
65 TTGTATAATCTCATAATTGATTTTAAGCTAAATTTTTTATATTTTTTGTTAAAATAGACTATAAT
*
1463 TGAATGCCTGCTTCGAGAAACGTGTAAAAAACGCATTTAT
130 TGAATGCCTGCTTCGAGAAACGTGTAAAAAACTCATTTAT
* * * ********** * * **
1503 TTAGAA-AAAAAGTTCATCTATAATCTCNNNNNNNNNNAAAAGCCTTATTACTTGCTTTATATGG
1 TTAGAAGAAAAA-TCCATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAAAAG
** * * * *
1567 TTGTATAATCTCATAATTGATTTTGTGTTAAATTTTTTATATTTTTTATTAAAGTAGACTAAAAT
65 TTGTATAATCTCATAATTGATTTTAAGCTAAATTTTTTATATTTTTTGTTAAAATAGACTATAAT
* * *
1632 TGATTGCCTGCCTCAAGAAACGTGTAAAAAACTCATTTAT
130 TGAATGCCTGCTTCGAGAAACGTGTAAAAAACTCATTTAT
* * * *
1672 TTAGAAGAAAAATCCATTTATAGTTTCCCATTCCTTCAAAAGTCTTATTAGTCGGTTTAAAAAGT
1 TTAGAAGAAAAATCCATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAAAAGT
* * *
1737 TTTATAATCTCATAATTGATTTTAAGCTGAATTTTTTATATTTTTTGTTAAAACAGAC-ATAATT
66 TGTATAATCTCATAATTGATTTTAAGCTAAATTTTTTATATTTTTTGTTAAAATAGACTATAATT
* * *
1801 AAATGTCTGCTTCGAGAAACGTATAGAAAAACTCATTTAT
131 GAATGCCTGCTTCGAGAAACGTGTA-AAAAACTCATTTAT
*
1841 TTAGAAGAAAAATCCATTTATAGTCTCTCATTCCTTCAAA
1 TTAGAAGAAAAATCCATTTATAGTCTCCCATTCCTTCAAA
1881 NNNNNNNNNN
Statistics
Matches: 294, Mismatches: 79, Indels: 9
0.77 0.21 0.02
Matches are distributed among these distances:
168 35 0.12
169 254 0.86
170 5 0.02
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.38
Consensus pattern (169 bp):
TTAGAAGAAAAATCCATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAAAAGT
TGTATAATCTCATAATTGATTTTAAGCTAAATTTTTTATATTTTTTGTTAAAATAGACTATAATT
GAATGCCTGCTTCGAGAAACGTGTAAAAAACTCATTTAT
Found at i:5320 original size:170 final size:169
Alignment explanation
Indices: 5033--5419 Score: 510
Period size: 170 Copynumber: 2.3 Consensus size: 169
5023 NNNNNNNNNN
* *
5033 ATTTTATAATCTCATAATTGATTTTCAGTTGAATTTTTTACATTTTTTGTTGAAACAGACTATAA
1 ATTTTATAATCTCATAATT-ATTTTAAGTTGAATTTTTTACATTTTTTGTTAAAACAGACTATAA
* * * * *
5098 TTGAATGCATGCCTTAGGAAACGTGTAGAAAAACCTATTTATTTGGAAGAAAAGTCTATTTATAG
65 TTGAATGCATACCTTAGAAAACATGTAGAAAAACCTATTTATTTAGAAGAAAAGTCCATTTATAG
** * *
5163 TTTCTCATTCCTTCAAAAGCCTTCTTACT--TGCTTTAAATG
130 ACTCACATTCCTTCAAAAGCCTTATTACTCATG--TTAAATG
* * * *
5203 ATTTTATAATCTCATAATTCATTCTAAGTTGAATGTTTTGCATTTTTTGTTAAAATAGACTATAA
1 ATTTTATAATCTCATAATT-ATTTTAAGTTGAATTTTTTACATTTTTTGTTAAAACAGACTATAA
* * *
5268 TTGAATGCCTA-CTTTGAAAAACATGTAGAAAAACCTATTTATTTATAAGAAAAGTCCATTTATA
65 TTGAATGCATACCTTAG-AAAACATGTAGAAAAACCTATTTATTTAGAAGAAAAGTCCATTTATA
5332 GACTCACATTCCTTCAAAAGCCTTATTACTCATGTTAAATG
129 GACTCACATTCCTTCAAAAGCCTTATTACTCATGTTAAATG
* *
5373 GTTTTATAATCTCATAATTTTTTTAAGTTGAATTTTTTTTACATTTT
1 ATTTTATAATCTCATAATTATTTTAAGTTGAA--TTTTTTACATTTT
5420 NNNNNNNNNN
Statistics
Matches: 188, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
169 15 0.08
170 160 0.85
171 11 0.06
172 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (169 bp):
ATTTTATAATCTCATAATTATTTTAAGTTGAATTTTTTACATTTTTTGTTAAAACAGACTATAAT
TGAATGCATACCTTAGAAAACATGTAGAAAAACCTATTTATTTAGAAGAAAAGTCCATTTATAGA
CTCACATTCCTTCAAAAGCCTTATTACTCATGTTAAATG
Found at i:8441 original size:168 final size:167
Alignment explanation
Indices: 8239--8775 Score: 513
Period size: 168 Copynumber: 3.2 Consensus size: 167
8229 CATTAGCAAG
* * * * *
8239 AAAAGTCTATTTATATTCACCCATTCCGTCAAAAGCCTTATTACTTACTTTAAGTGGTTTTATAA
1 AAAAGTCCATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTA-TTACTTTAAATGGTTTTATAA
*
8304 CCTCATAATTGATTTTAAGTGAATTTTTTATATTTTTTGTTAAAACAGACTATAATTAAATGCCT
65 TCTCATAATTGATTTTAAGTGAATTTTTTATATTTTTTGTTAAAACAGACTATAATTAAATGCCT
* * *
8369 ACCTTGAAAAACATGTA-AAACACCCATTTATTTGGAGA
130 ACCTTGAAAAACGTGTAGAAAAACCCATTTATTT-GAAA
* * * ** *
8407 AAAAGTCTATTTATAGTTTTCCATTCCTTCAAAAGCCTTATTAGTCGCTTTAAATGGTTTTGTAA
1 AAAAGTCCATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTA-TTACTTTAAATGGTTTTATAA
* ********* * * * *** * *
8472 TCACATANNNNNNNNNNAATTGAATTTTTT-TATTTGTTCTTAAAATTTACTATAATTGAATGCT
65 TCTCATA-ATTGATTTTAAGTGAATTTTTTATATTTTTTGTTAAAACAGACTATAATTAAATGCC
*
8536 TACCTTGAAAAATGTGTAGAAAAACCCATTTATTTGAAA
129 TACCTTGAAAAACGTGTAGAAAAACCCATTTATTTGAAA
* * * *
8575 AAAAGTCCATTTATAGTCTACCATTCCTTCAAAAGCCATATTATTCACTTTAAATAGTTTTATTA
1 AAAAGTCCATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTATT-ACTTTAAATGGTTTTATAA
********** * *
8640 TCTCATAATNNNNNNNNNNNTGAATTTTTTTACATTTTTGGTTAAAACAGACTATAATTAAATGC
65 TCTCATAAT-TGATTTTAAGTGAA-TTTTTTATATTTTTTGTTAAAACAGACTATAATTAAATGC
*
8705 CTACC-TCAGAAAACGTGTAGAAAAACCCATTTATTTGAAA
128 CTACCTTGA-AAAACGTGTAGAAAAACCCATTTATTTGAAA
8745 GAAAAGTCCATTTATAGTCTCCCATTCCTTC
1 -AAAAGTCCATTTATAGTCTCCCATTCCTTC
8776 NNNNNNNNNN
Statistics
Matches: 301, Mismatches: 60, Indels: 13
0.80 0.16 0.03
Matches are distributed among these distances:
167 1 0.00
168 177 0.59
169 35 0.12
170 59 0.20
171 29 0.10
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.38
Consensus pattern (167 bp):
AAAAGTCCATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTATTACTTTAAATGGTTTTATAAT
CTCATAATTGATTTTAAGTGAATTTTTTATATTTTTTGTTAAAACAGACTATAATTAAATGCCTA
CCTTGAAAAACGTGTAGAAAAACCCATTTATTTGAAA
Found at i:11345 original size:34 final size:34
Alignment explanation
Indices: 11306--11375 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
11296 GCTTTTACAG
11306 TGGC-TTTCACAA-GCTCAGCCACAACCTTCAACAA
1 TGGCTTTTCA-AAGGCT-AGCCACAACCTTCAACAA
*
11340 TGGCTTTTCAAAGGCTAGCCACTACCTTCAACAA
1 TGGCTTTTCAAAGGCTAGCCACAACCTTCAACAA
11374 TG
1 TG
11376 ATTTTTCCTG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
34 25 0.76
35 8 0.24
ACGTcount: A:0.30, C:0.31, G:0.14, T:0.24
Consensus pattern (34 bp):
TGGCTTTTCAAAGGCTAGCCACAACCTTCAACAA
Found at i:16695 original size:168 final size:169
Alignment explanation
Indices: 16386--16865 Score: 456
Period size: 168 Copynumber: 2.8 Consensus size: 169
16376 NNNNNNNNNN
* * *
16386 AGTTGAACTTTTTTATATTTTT-AGTTAAAACAAAATATAATTGAATGTCCA-CCT-AATG-AA-
1 AGTTGAA-TTTTTTACATTTTTCA-TTAAAACAAACTATAATTGAATGT-CAGCCTCGA-GAAAC
* ** * * * * * *
16446 ACGTGAAGAAAAAAGTATTCATTAGTAAGAAAAGTCCATTTATATTCACCCATTCTTTCAAAAGC
62 ACATG--GAAAAACCTATTTATTTGGAAGAAAAGTTCATTTATATTCTCCCATTCCTTCAAAAGC
* * * ********
16511 CTTATTACTAGCTTTAAATGGTCTTGTAGCCTCATAANNNNNNNNN
125 CTTATTACTCGCTTTAAATGGTCTTATAGACTCATAA-TTGATTTA
* * * * * *
16557 NGTTGAATTTTTTACATTTTTCGTTAAAACAGACTATGATTGAATGTCAGCCT-TAGAAA-ACGT
1 AGTTGAATTTTTTACATTTTTCATTAAAACAAACTATAATTGAATGTCAGCCTCGAGAAACACAT
* * *
16620 GTAAAAA-CTAATTTATTTGGAGGAAAAGTTCATTTATAGTT-TCCCATTCCTTCAAAAGTCTTA
66 GGAAAAACCT-ATTTATTTGGAAGAAAAGTTCATTTATA-TTCTCCCATTCCTTCAAAAGCCTTA
*
16683 TTGCTCGCTTTAAATGGTCTTATAGACTCATAATTGATTTA
129 TTACTCGCTTTAAATGGTCTTATAGACTCATAATTGATTTA
* * * *
16724 AGTTGAATTTTTTATATTTTTCATTAAAACAAACTATAATTGAATGTCTGGCTCGAGAAACATAT
1 AGTTGAATTTTTTACATTTTTCATTAAAACAAACTATAATTGAATGTCAGCCTCGAGAAACACAT
* *
16789 GGAAAAACCTGTTTATTTGGAATAAAAGTTCATTTATATTCTCCCATTCCTTCAAAAGCCTTATT
66 GGAAAAACCTATTTATTTGGAAGAAAAGTTCATTTATATTCTCCCATTCCTTCAAAAGCCTTATT
*
16854 ACTCGTTTTAAA
131 ACTCGCTTTAAA
16866 NNNNNNNNNN
Statistics
Matches: 254, Mismatches: 46, Indels: 20
0.79 0.14 0.06
Matches are distributed among these distances:
167 47 0.19
168 83 0.33
169 71 0.28
170 47 0.19
171 6 0.02
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.38
Consensus pattern (169 bp):
AGTTGAATTTTTTACATTTTTCATTAAAACAAACTATAATTGAATGTCAGCCTCGAGAAACACAT
GGAAAAACCTATTTATTTGGAAGAAAAGTTCATTTATATTCTCCCATTCCTTCAAAAGCCTTATT
ACTCGCTTTAAATGGTCTTATAGACTCATAATTGATTTA
Done.