Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403139.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_806.0, 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: 2214
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.33
Warning! 133 characters in sequence are not A, C, G, or T
Found at i:268 original size:21 final size:21
Alignment explanation
Indices: 239--278 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
229 GCATGGGTGA
*
239 GTATAAATGGACTTTTCTTGT
1 GTATAAATGGAATTTTCTTGT
*
260 GTATGAATGGAATTTTCTT
1 GTATAAATGGAATTTTCTT
279 CATGTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.47
Consensus pattern (21 bp):
GTATAAATGGAATTTTCTTGT
Found at i:283 original size:170 final size:169
Alignment explanation
Indices: 1--597 Score: 607
Period size: 170 Copynumber: 3.5 Consensus size: 169
* * * *
1 CCTAAAATCAATTATGAGTTTATAAAATCATTTAAAGCGAA-TAATAAGGCCTTCGAAGGCATGT
1 CCTAAAATCAATTATGAGATTATAAAACCATTTAAAGC-AACTAATAAAGCCTTCGAAGGCATGG
* * *
65 GTGACTATACATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTCATGTTTTCCAAGGTAAATAT
65 GTGACTATAAATGGACTTTTCTTGTCAATGAATGG-ATTTTCTTCATGTTTTCCAAGGTAAATAT
130 TCAATTATAATCTGTTTTAA-TCAAAAATGTAGAAAAATTCA
129 TCAATTATAATCTGTTTTAACT-AAAAATGTAGAAAAATTCA
* * * *
171 CCTAAAATCAGTTATGTGATTATAAAACCATTTGAAGCAACTAATAAAGCTTTCGAAGGCATGGG
1 CCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAACTAATAAAGCCTTCGAAGGCATGGG
* ** * *
236 TGAGTATAAATGGACTTTTCTTGTGTATGAATGGAATTTTCTTCATGTTTT-TAGAGG-AAGACA
66 TGACTATAAATGGACTTTTCTTGTCAATGAATGG-ATTTTCTTCATGTTTTCCA-AGGTAA-ATA
* * *
299 TTCAATTATAATCTGTTTTGACTAATAAA-ATAAAAAAATTCA
128 TTCAATTATAATCTGTTTTAACTAA-AAATGTAGAAAAATTCA
* * * * * ** * * *
341 -ATAAAATCAATTGTGAGATTATAAAACCATTTCAACCAAGC-AACATGGCCTTCAAAAGCTTGG
1 CCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAA-CTAATAAAGCCTTCGAAGGCATGG
* * * * * * ** * *
404 GTGACTCTAAATAGACTTTACTTGTCAATGAGTGGCTTTTGTTCATGGGTCCCATGGTAAATATT
65 GTGACTATAAATGGACTTTTCTTGTCAATGAATGGATTTTCTTCATGTTTTCCAAGGTAAATATT
* * * *
469 CAATTATAAGCTATTTTAACTAAAAATG-CGAAATAACTCAA
130 CAATTATAATCTGTTTTAACTAAAAATGTAGAAA-AATTC-A
* ** * * *
510 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAAGCTTTCGAAGGCTTGGG
1 CCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAACTAATAAAGCCTTCGAAGGCATGGG
575 TGACTATAAATGGACTTTTCTTG
66 TGACTATAAATGGACTTTTCTTG
598 CCAGTAAATA
Statistics
Matches: 343, Mismatches: 71, Indels: 26
0.78 0.16 0.06
Matches are distributed among these distances:
167 6 0.02
168 41 0.12
169 85 0.25
170 207 0.60
171 4 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.34
Consensus pattern (169 bp):
CCTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAACTAATAAAGCCTTCGAAGGCATGGG
TGACTATAAATGGACTTTTCTTGTCAATGAATGGATTTTCTTCATGTTTTCCAAGGTAAATATTC
AATTATAATCTGTTTTAACTAAAAATGTAGAAAAATTCA
Found at i:740 original size:128 final size:128
Alignment explanation
Indices: 512--742 Score: 338
Period size: 128 Copynumber: 1.8 Consensus size: 128
502 TAACTCAACT
* *
512 TAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAAGCTTTCGAAGGCTTGGGTG
1 TAAAACCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGCTTTCGAAGGCTTGGGTG
* * * *
577 ACTATAAATGGACTTTTCTTGCCAGTAAATAGCTTTTTCTTTACTTATGAATAATAAGTATAA
66 ACTATAAATAGACTTTACTTACCAATAAATAGCTTTTTCTTTACTTATGAATAATAAGTATAA
* *
640 TAAAACCAATTGTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCCTTT-GAAGGCTTGGGT
1 TAAAACCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAG-CTTTCGAAGGCTTGGGT
* ** *
704 GACTATAAATAGTCTTTACTTATGAATGAATAGCTTTTT
65 GACTATAAATAGACTTTACTTACCAATAAATAGCTTTTT
743 GTTCACGACT
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
128 86 0.96
129 4 0.04
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (128 bp):
TAAAACCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGCTTTCGAAGGCTTGGGTG
ACTATAAATAGACTTTACTTACCAATAAATAGCTTTTTCTTTACTTATGAATAATAAGTATAA
Found at i:883 original size:298 final size:298
Alignment explanation
Indices: 340--891 Score: 800
Period size: 298 Copynumber: 1.9 Consensus size: 298
330 AAAAAAATTC
* * *
340 AATAAAATCAATTGTGAGATTATAAAACCATTTCAACCAAGCAACATGGCCTTCAAAAGCTTGGG
1 AATAAAACCAATTGTGAGATTATAAAACCATTTAAACCAAGCAACAAGGCCTTCAAAAGCTTGGG
* * * * * ** *
405 TGACTCTAAATAGACTTTACTTGTCAATGAGTGGCTTTTGTTCATGGGTCCCATGGTAAATATTC
66 TGACTATAAATAGACTTTACTTATCAATGAATAGCTTTTGTTCACGACTCCCATGGTAAACATTC
*
470 AATTATAAGCTATTTTAACTAAAAATGCGAAATAACTCAACTTAAAATCAATTATGAGATTATAA
131 AATTATAAGCTATTTTAACTAAAAATGCGAAATAACTCAACTTAAAATCAATTATGAAATTATAA
*
535 AACCATTTAAAGTGAGTAATAAAGCTTTCGAAGGCTTGGGTGACTATAAATGGACTTTTCTTGCC
196 AACCATTTAAAGTGAGTAATAAAGCTTTCGAAGGCTTGGATGACTATAAATGGACTTTTCTTGCC
600 AGTAAATAGCTTTTTCTTTACTTATGAATAATAAGTAT
261 AGTAAATAGCTTTTTCTTTACTTATGAATAATAAGTAT
* * * * ** *
638 AATAAAACCAATTGTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCCTTTGAAGGCTTGGG
1 AATAAAACCAATTGTGAGATTATAAAACCATTTAAACCAAGCAACAAGGCCTTCAAAAGCTTGGG
* * ** *
703 TGACTATAAATAGTCTTTACTTATGAATGAATAGCTTTTTGTTCACGACTCTTATGGTAGACATT
66 TGACTATAAATAGACTTTACTTATCAATGAATAGC-TTTTGTTCACGACTCCCATGGTAAACATT
* * * *
768 CAATTATAATCTCTTTTAA-TAAAAATGTGAAATAATTCAACTTAAAATCAATTATGAAATTATA
130 CAATTATAAGCTATTTTAACTAAAAATGCGAAATAACTCAACTTAAAATCAATTATGAAATTATA
* * *
832 AAACTATTTAAAGTGAGTAATAAAGCTTTTGAAGGCTTGGATGATTATAAATGGACTTTT
195 AAACCATTTAAAGTGAGTAATAAAGCTTTCGAAGGCTTGGATGACTATAAATGGACTTTT
892 TGCCAATGAA
Statistics
Matches: 221, Mismatches: 32, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
298 182 0.82
299 39 0.18
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (298 bp):
AATAAAACCAATTGTGAGATTATAAAACCATTTAAACCAAGCAACAAGGCCTTCAAAAGCTTGGG
TGACTATAAATAGACTTTACTTATCAATGAATAGCTTTTGTTCACGACTCCCATGGTAAACATTC
AATTATAAGCTATTTTAACTAAAAATGCGAAATAACTCAACTTAAAATCAATTATGAAATTATAA
AACCATTTAAAGTGAGTAATAAAGCTTTCGAAGGCTTGGATGACTATAAATGGACTTTTCTTGCC
AGTAAATAGCTTTTTCTTTACTTATGAATAATAAGTAT
Found at i:1184 original size:170 final size:167
Alignment explanation
Indices: 653--1595 Score: 730
Period size: 170 Copynumber: 5.6 Consensus size: 167
643 AACCAATTGT
* * * *
653 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCCTTTGAAGGCTTGGGTGACTATAAATAGTC
1 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCTTGGGTGATTATAAATGGAC
* ** * * ** * * * *
718 TTTACTTATGAATGAATA-GCTTTTTGTTCACG-ACTCTTATGGTAGACATTCAATTATAATCTC
66 TTTTCTT-CCAATGAA-AGGCTTTTTCTTTACGTTTTCTAAT--AAAACATTCAATTATAATCTA
* * *
781 TTTTAATAAAAATGTGAAATAATTCAACTTAAAATCAATTAT
127 TTTTAATAAAAATAT-AAAAAATTCAACTTAAAATCAATTAA
* * * * *
823 GAAATTATAAAACTATTTAAAGTGAGTAATAAAGCTTTTGAAGGCTTGGATGATTATAAATGGAC
1 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCTTGGGTGATTATAAATGGAC
* * * *
888 TTTT-TGCCAATGAATGACTTTTT-TTTCACGTTTTCTGAAGT-AAACATTCAATTATAATTTAT
66 TTTTCTTCCAATGAAAGGCTTTTTCTTT-ACGTTTTCT-AA-TAAAACATTCAATTATAATCTAT
* *
950 TTTAAT-----TA-AGAAAAATTCAACTTAAAATTAACTAA
128 TTTAATAAAAATATA-AAAAATTCAACTTAAAATCAATTAA
* * ** * * *
985 GATATTACAAAACCATTTAAAATGAGTAATAAGGCATTCGATGG-TATGGGTGATTATAAATGGA
1 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCT-TGGGTGATTATAAATGGA
* * * * ** *
1049 CTTTTCTTCACATTTAACGGCTTTTTCTTTACGTTTCCTAATACAAACATTCAATTATTTTCTGT
65 CTTTTCTTC-CAATGAAAGGCTTTTTCTTTACGTTTTCTAATA-AAACATTCAATTATAATCTAT
* *
1114 TTTAACTAAATATATAAAAAATTCAACATAAAATCAATTAA
128 TTTAA-TAAAAATATAAAAAATTCAACTTAAAATCAATTAA
* * *
1155 GAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGCTTGGGTAACTATAAATGGAC
1 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCTTGGGTGATTATAAATGGAC
* * ** * * *
1220 TTTTCTTTCCAATGAAAGGCTTTTTCTTGATGTTTTCTCACAGGAAATATTCAATTGTAATATAT
66 TTTTC-TTCCAATGAAAGGCTTTTTCTTTACGTTTTCT-A-ATAAAACATTCAATTATAATCTAT
* * * * * *
1285 TTTAACCAAAAATGTAAAAACTTCAACCTAAAATAAATTAT
128 TTTAA-TAAAAATATAAAAAATTCAACTTAAAATCAATTAA
* * * * * *
1326 GAGATTATAAAACCATTTAAAGCTAGTAATAAGGCCTTTGAAGGCTTGGATGACTATAAATAGTC
1 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCTTGGGTGATTATAAATGGAC
* * * ** * * * *
1391 TTTACTTGTCAATGAATA-GATTTTT-TTTCACG-ACTCGT-ATGGTAGAGATTCAATTATAACC
66 TTTTCTT-CCAATGAA-AGGCTTTTTCTTT-ACGTTTTC-TAAT--AAAACATTCAATTATAATC
* * * * * *
1452 TCTTTTAAAAAAAATGTGAAATAATTCAACTTAAAATTAATTAT
125 TATTTTAATAAAAATAT-AAAAAATTCAACTTAAAATCAATTAA
* * * * *
1496 GAAATTATAAAACTATTTAAAGCGAGTAATAAAGATTTTGAAGGCTTGGGTGACTATAAATGGAC
1 GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCTTGGGTGATTATAAATGGAC
* * * *
1561 TTTTCTTGCCAATGAATGACTCTTTCTTCACGTTT
66 TTTTCTT-CCAATGAAAGGCTTTTTCTTTACGTTT
1596 NNNNNNNNNN
Statistics
Matches: 615, Mismatches: 125, Indels: 65
0.76 0.16 0.08
Matches are distributed among these distances:
161 2 0.00
162 80 0.13
163 5 0.01
164 42 0.07
165 4 0.01
167 2 0.00
168 40 0.07
169 12 0.02
170 290 0.47
171 136 0.22
172 2 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.37
Consensus pattern (167 bp):
GAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGCTTGGGTGATTATAAATGGAC
TTTTCTTCCAATGAAAGGCTTTTTCTTTACGTTTTCTAATAAAACATTCAATTATAATCTATTTT
AATAAAAATATAAAAAATTCAACTTAAAATCAATTAA
Found at i:1508 original size:341 final size:334
Alignment explanation
Indices: 647--1595 Score: 1131
Period size: 341 Copynumber: 2.8 Consensus size: 334
637 TAATAAAACC
* *
647 AATTGTGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCCTTTGAAGGCTTGGGTGACTATAA
1 AATTATGAGATTATAAAACCATTTAAAGCTAGTAATAAGGCCTTTGAAGGCTTGGGTGACTATAA
* * *
712 ATAGTCTTTACTTATGAATGAATAGCTTTTTGTTCACGACTCTTATGGTAGACATTCAATTATAA
66 ATAGTCTTTACTTATCAATGAATAGCTTTTTTTTCACGACTCCTATGGTAGACATTCAATTATAA
777 TCTCTTTTAATAAAAATGTGAAATAATTCAACTTAAAATCAATTATGAAATTATAAAACTATTTA
131 TCTCTTTTAATAAAAATGTGAAATAATTCAACTTAAAATCAATTATGAAATTATAAAACTATTTA
* * * *
842 AAGTGAGTAATAAAGCTTTTGAAGGCTTGGATGATTATAAATGGAC-TTT-TTGCCAATGAATGA
196 AAGCGAGTAATAAAGCTTTTGAAGGCTTGGGTGACTATAAATGGACTTTTCTTGCCAATGAAAGA
* * * * **
905 CTTTTTTTTCACGTTTTCTGAAGTAAACATTCAATTATAATTTATTTTAATTAAGAAAAATTCAA
261 CTTTTTCTTCACGTTTTCTCAAGGAAACATTCAATTATAATATATTTTAAAAAAGAAAAATTCAA
* *
970 CTTAAAATT
326 CCTAAAATA
* * * * * * * * *
979 AACTAAGATATTACAAAACCATTTAAA-ATGAGTAATAAGGCATTCGATGG-TATGGGTGATTAT
1 AATTATGAGATTATAAAACCATTTAAAGCT-AGTAATAAGGCCTTTGAAGGCT-TGGGTGACTAT
* * * * * ** ** ** *
1042 AAATGGACTTTTCTTCA-CATTTAACGGCTTTTTCTTT-ACGTTTCCTAAT-ACAAACATTCAAT
64 AAATAGTCTTTACTT-ATCAATGAATAGCTTTTT-TTTCACGACTCCT-ATGGTAGACATTCAAT
** * * * * * * *
1104 TATTTTCTGTTTTAACTAAATATAT-AAAAAATTCAACATAAAATCAATTAAGAGATTATAAAAC
126 TATAATCTCTTTTAA-TAAAAATGTGAAATAATTCAACTTAAAATCAATTATGAAATTATAAAAC
* * *
1168 TATTTAAAGCGAGTAATAAGGCTTTTGAAGGCTTGGGTAACTATAAATGGACTTTTCTTTCCAAT
190 TATTTAAAGCGAGTAATAAAGCTTTTGAAGGCTTGGGTGACTATAAATGGACTTTTCTTGCCAAT
* * * * *
1233 GAAAGGCTTTTTCTTGATGTTTTCTCACAGGAAATATTCAATTGTAATATATTTTAACCAAAAAT
255 GAAAGACTTTTTCTTCACGTTTTCTCA-AGGAAACATTCAATTATAATATATTTT-A--AAAAA-
1298 GTAAAAACTTCAACCTAAAATA
315 G-AAAAA-TTCAACCTAAAATA
*
1320 AATTATGAGATTATAAAACCATTTAAAGCTAGTAATAAGGCCTTTGAAGGCTTGGATGACTATAA
1 AATTATGAGATTATAAAACCATTTAAAGCTAGTAATAAGGCCTTTGAAGGCTTGGGTGACTATAA
* * * *
1385 ATAGTCTTTACTTGTCAATGAATAGATTTTTTTTCACGACTCGTATGGTAGAGATTCAATTATAA
66 ATAGTCTTTACTTATCAATGAATAGCTTTTTTTTCACGACTCCTATGGTAGACATTCAATTATAA
* * *
1450 CCTCTTTTAAAAAAAATGTGAAATAATTCAACTTAAAATTAATTATGAAATTATAAAACTATTTA
131 TCTCTTTTAATAAAAATGTGAAATAATTCAACTTAAAATCAATTATGAAATTATAAAACTATTTA
* *
1515 AAGCGAGTAATAAAGATTTTGAAGGCTTGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGA
196 AAGCGAGTAATAAAGCTTTTGAAGGCTTGGGTGACTATAAATGGACTTTTCTTGCCAATGAAAGA
*
1580 CTCTTTCTTCACGTTT
261 CTTTTTCTTCACGTTT
1596 NNNNNNNNNN
Statistics
Matches: 494, Mismatches: 102, Indels: 33
0.79 0.16 0.05
Matches are distributed among these distances:
331 1 0.00
332 182 0.37
333 15 0.03
334 28 0.06
335 23 0.05
336 1 0.00
338 3 0.01
339 1 0.00
340 16 0.03
341 222 0.45
342 2 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.37
Consensus pattern (334 bp):
AATTATGAGATTATAAAACCATTTAAAGCTAGTAATAAGGCCTTTGAAGGCTTGGGTGACTATAA
ATAGTCTTTACTTATCAATGAATAGCTTTTTTTTCACGACTCCTATGGTAGACATTCAATTATAA
TCTCTTTTAATAAAAATGTGAAATAATTCAACTTAAAATCAATTATGAAATTATAAAACTATTTA
AAGCGAGTAATAAAGCTTTTGAAGGCTTGGGTGACTATAAATGGACTTTTCTTGCCAATGAAAGA
CTTTTTCTTCACGTTTTCTCAAGGAAACATTCAATTATAATATATTTTAAAAAAGAAAAATTCAA
CCTAAAATA
Done.