Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400468.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3664.0, 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: 4045
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.28
Warning! 952 characters in sequence are not A, C, G, or T
Found at i:444 original size:171 final size:171
Alignment explanation
Indices: 1--1104 Score: 1152
Period size: 171 Copynumber: 6.5 Consensus size: 171
* * * ** *
1 TTTGAAGGAATGAGTGACTATAAATGGACTTTTCTT-CTCAACGAATGGCTTTTTATGGACGTTT
1 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGC-CAATGAATGGCTTTTTCTTTATGTTT
* * * * ** * *
65 CCTGGGGTAGGCATTCAATTATAGTCTGTTTTAATGGAAAATATAAAAAAATTTAACTTAAAATC
65 CATGAGGCAAGCATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATC
* * * *
130 AATTATGTGATTATCAAACAATTTAAAGC----AATAAGGCT
130 AATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCT
* * **
168 TTTGAAAGAATGGGTGACTAT-AATGGACTTTTTTTGCCAATGAATCTCTTTTTCTTTATGTTTC
1 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTTATGTTTC
* * * *
232 -TAAAGG-TAGACATTCAATTATAGTCTGTTTT-AGCTAAAAATGTAAAAATATTCAACTTAAAA
66 AT-GAGGCAAG-CATTCAATTATAGTCTGTTTTAATC-AAAAATGTAAAAAAATTCAACTTAAAA
* *
294 TCAGTTATGAGATTATAAAACCATTTAAAGCGATTAATAAGCCT
128 TCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCT
* * * * * *
338 TTTGAAGGAATGGGAGACTCTAAATGGACTTTTCTTGCGAATGAATGGGTTTTTCTATAAGTTTC
1 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTTATGTTTC
* * *
403 ATGAGGCAAGCATTCAATTATAGTCTATTTTAATGAAAAATGTATAAAAATTCAACTTAAAATCA
66 ATGAGGCAAGCATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCA
* * *
468 GTTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCT
131 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCT
* **
509 TTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGGCTTTTTCTACATGTTTC
1 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTTATGTTTC
*** * *
574 CCAAGGCAAGCATTCAATTATAG-CTTGTTTTAATCAAAAATGTAAAAAAAATTCAGCTCAAAAT
66 ATGAGGCAAGCATTCAATTATAGTC-TGTTTTAATCAAAAATGT-AAAAAAATTCAACTTAAAAT
* * * *
638 CAATTTTGAGATTATAAAATCGTTTAAAGTGAGTAATAAGCCT
129 CAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCT
* *
681 TTTGAAGGAATGAGTGAC-ATTAAATGGACTTTTCTTACCAATGAAT-GCTTTTTTCTTTATGTT
1 TTTGAAGGAATGGGTGACTA-TAAATGGACTTTTCTTGCCAATGAATGGC-TTTTTCTTTATG-T
* * * * *
744 TGTCA--AGGTACAA--ATTCAATTGTTGTCTGTTTTAA-CAAAAAATATAAAAAATTTTAACTT
63 T-TCATGAGG--CAAGCATTCAATTATAGTCTGTTTTAATC-AAAAATGTAAAAAAATTCAACTT
* * * *
804 GAAATCAGTTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGCCA
124 AAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCT
* ** *
852 TTTGAAGGAATGGGTGACTATAAGTGGGTTTTTCTTACCAATGAAT-GCTTTTTTCTTTATGTTT
1 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGGC-TTTTTCTTTATGTTT
* * * * * *
916 CTTGAGGTACA-TATTAAATTATTGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAAT
65 CATGAGGCA-AGCATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAAT
* *
980 CAATTATGAGATTATAAAACCATTTAAAGCGAGTAATATGGCT
129 CAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCT
* * * * * **
1023 TTTAAAGCAATAGGTGGCTATAAATGGACTTTTCTT-CTCAATGAATGGATTTTTCTGCATGTTT
1 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGC-CAATGAATGGCTTTTTCTTTATGTTT
* *
1087 C-TCAAGGTAAGCATTCAA
65 CAT-GAGGCAAGCATTCAA
1105 NNNNNNNNNN
Statistics
Matches: 789, Mismatches: 116, Indels: 60
0.82 0.12 0.06
Matches are distributed among these distances:
165 3 0.00
166 106 0.13
167 20 0.03
169 3 0.00
170 33 0.04
171 477 0.60
172 139 0.18
173 3 0.00
174 5 0.01
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (171 bp):
TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTTATGTTTC
ATGAGGCAAGCATTCAATTATAGTCTGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCA
ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCT
Found at i:726 original size:343 final size:339
Alignment explanation
Indices: 1--1078 Score: 1232
Period size: 343 Copynumber: 3.2 Consensus size: 339
* * * ** *
1 TTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAACGAATGGCTTTTTATGGACGTTTC
1 TTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATGAATGGATTTTTCTATAAGTTTC
* * * * *
66 CTGGGGTAGGCATTCAATTATAGTCTGTTTTAATGGAAAATATAAAAAAATTTAACTTAAAATCA
66 ATGAGGCAAGCATTCAATTATAGTCTGTTTTAATGAAAAATAT-AAAAAATTTAACTTAAAATCA
* * * * *
131 ATTATGTGATTATCAAACAATTTAAAGC----AATAAGGCTTTTGAAAGAATGGGTGACTAT-AA
130 GTTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAA
* * *
191 TGGACTTTTTTTGCCAATGAATCTCTTTTTCTTTATGTTTCTAAAGGTAGACATTCAATTATAGT
195 TGGACTTTTCTTGCCAATGAAT-GCTTTTTCTTTATGTTTCTAAAGGAAG-CATTCAATTATAGT
* * * *
256 CTGTTTTAGCTAAAAATGTAAAAATATTCAACTTAAAATCAGTTATGAGATTATAAAACCATTTA
258 CTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
*
321 AAGCGATTAATAAGCCT
323 AAGCGAGTAATAAGCCT
* * * * *
338 TTTGAAGGAATGGGAGACTCTAAATGGACTTTTCTTGC-GAATGAATGGGTTTTTCTATAAGTTT
1 TTTGAAGGAATGAGTGACTATAAATGGACTTTTCTT-CTCAATGAATGGATTTTTCTATAAGTTT
* * *
402 CATGAGGCAAGCATTCAATTATAGTCTATTTTAATGAAAAATGTATAAAAATTCAACTTAAAATC
65 CATGAGGCAAGCATTCAATTATAGTCTGTTTTAATGAAAAATATA-AAAAATTTAACTTAAAATC
*
467 AGTTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAA
129 AGTTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAA
* ** **
532 ATAGACTTTTCTTGCCAATGAATGGCTTTTTCTACATGTTTCCCAAGGCAAGCATTCAATTATAG
194 ATGGACTTTTCTTGCCAATGAAT-GCTTTTTCTTTATGTTTCTAAAGG-AAGCATTCAATTATAG
* * * * * *
597 -CTTGTTTTAATCAAAAATGTAAAAAAAATTCAGCTCAAAATCAATTTTGAGATTATAAAATCGT
257 TC-TGTTTTAACCAAAAATGT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
*
661 TTAAAGTGAGTAATAAGCCT
320 TTAAAGCGAGTAATAAGCCT
** * *
681 TTTGAAGGAATGAGTGAC-ATTAAATGGACTTTTCTTAC-CAATGAATGCTTTTTTCTTTATGTT
1 TTTGAAGGAATGAGTGACTA-TAAATGGACTTTTCTT-CTCAATGAATGGATTTTTCTATAAG-T
* * ** *
744 TGTCA--AGGTACAA--ATTCAATTGTTGTCTGTTTTAACAAAAAATATAAAAAATTTTAACTTG
63 T-TCATGAGG--CAAGCATTCAATTATAGTCTGTTTTAATGAAAAATATAAAAAA-TTTAACTTA
* * *
805 AAATCAGTTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGCCATTTGAAGGAATGGGTGAC
124 AAATCAGTTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGAC
* ** * ** * *
870 TATAAGTGGGTTTTTCTTACCAATGAATGCTTTTTTCTTTATGTTTCTTGAGGTACA-TATTAAA
189 TATAAATGGACTTTTCTTGCCAATGAATGC-TTTTTCTTTATGTTTCTAAAGG-A-AGCATTCAA
*
934 TTATTGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
251 TTATAGTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
* *
999 CCATTTAAAGCGAGTAATATGGCT
316 CCATTTAAAGCGAGTAATAAGCCT
* * *
1023 TTTAAAGCAAT-AGGTGGCTATAAATGGACTTTTCTTCTCAATGAATGGATTTTTCT
1 TTTGAAGGAATGA-GTGACTATAAATGGACTTTTCTTCTCAATGAATGGATTTTTCT
1079 GCATGTTTCT
Statistics
Matches: 625, Mismatches: 94, Indels: 39
0.82 0.12 0.05
Matches are distributed among these distances:
336 1 0.00
337 131 0.21
338 1 0.00
341 32 0.05
342 176 0.28
343 274 0.44
344 4 0.01
345 6 0.01
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (339 bp):
TTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATGAATGGATTTTTCTATAAGTTTC
ATGAGGCAAGCATTCAATTATAGTCTGTTTTAATGAAAAATATAAAAAATTTAACTTAAAATCAG
TTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAAT
GGACTTTTCTTGCCAATGAATGCTTTTTCTTTATGTTTCTAAAGGAAGCATTCAATTATAGTCTG
TTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG
CGAGTAATAAGCCT
Found at i:968 original size:514 final size:508
Alignment explanation
Indices: 1--1104 Score: 1403
Period size: 514 Copynumber: 2.2 Consensus size: 508
* * * * *
1 TTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAACGAATGGCTTTTTATGGACGTTTC
1 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTGCATGTTTC
*** * ** * *
66 CTGGGGTAGGCATTCAATTATAGTCTGTTTTAATGGAAAATATAAAAAAATTTAACTTAAAATCA
66 CCAAGGTAAGCATTCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACTCAAAATCA
* * * *
131 ATTATGTGATTATCAAACAATTTAAAGCAATAAGGCTTTTGAAAGAATGGGTGACTATAATGGAC
131 ATTATGAGATTATAAAACAATTTAAAGCAATAAGCCTTTTGAAAGAATGAGTGACTATAATGGAC
* * * *
196 TTTTTTTGCCAATGAATCTCTTTTTCTTTATGTTTCTAAAGGTAGACATTCAATTATAGTCTGTT
196 TTTTCTTACCAATGAATCTCTTTTTCTTTATGTTTCTAAAGGTACAAATTCAATTATAGTCTGTT
* * *
261 TTAGCTAAAAATGTAAAAATATTCAACTTAAAATCAGTTATGAGATTATAAAACCATTTAAAGCG
261 TTAACAAAAAATATAAAAATATTCAACTTAAAATCAGTTATGAGATTATAAAACCATTTAAAGCG
* * * * * *
326 ATTAATAAGCCTTTTGAAGGAATGGGAGACTCTAAATGGACTTTTCTTGCGAATGAATGGGTTTT
326 AGTAATAAGCCATTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTACCAATGAATGCGTTTT
* ** *
391 TCTATAAGTTTCATGAGGCAAGCATTCAATTATAGTCTATTTTAATGAAAAATGTATAAAAATTC
391 TCTATAAGTTTCATGAGGCAAGCATTAAATTATAGTCTATTTTAACCAAAAATGTAAAAAAATTC
*
456 AACTTAAAATCAGTTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCT
456 AACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCT
* *
509 TTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGC-CAATGAATGGCTTTTTCTACATGTTT
1 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTT-CTCAATGAATGGCTTTTTCTGCATGTTT
* * *
573 CCCAAGGCAAGCATTCAATTATAG-CTTGTTTTAATCAAAAATGTAAAAAAAATTCAGCTCAAAA
65 CCCAAGGTAAGCATTCAATTATAGTC-TGTTTTAATCAAAAATAT-AAAAAAATTCAACTCAAAA
* * * *
637 TCAATTTTGAGATTATAAAATC-GTTTAAAGTGAGTAATAAGCCTTTTGAAGGAATGAGTGAC-A
128 TCAATTATGAGATTATAAAA-CAATTT-AA---AGCAATAAGCCTTTTGAAAGAATGAGTGACTA
* *
700 TTAAATGGACTTTTCTTACCAATGAATGCT-TTTTTCTTTATGTTTGTCAAGGTACAAATTCAAT
188 -T-AATGGACTTTTCTTACCAATGAAT-CTCTTTTTCTTTATGTTTCTAAAGGTACAAATTCAAT
* * * *
764 TGTTGTCTGTTTTAACAAAAAATATAAAAA-ATTTTAACTTGAAATCAGTTATGAGATTATAAAA
250 TATAGTCTGTTTTAACAAAAAATATAAAAATA-TTCAACTTAAAATCAGTTATGAGATTATAAAA
* * * **
828 TCATTTAAAGCGAGTAATAAGCCATTTGAAGGAATGGGTGACTATAAGTGGGTTTTTCTTACCAA
314 CCATTTAAAGCGAGTAATAAGCCATTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTACCAA
* * * * * * * *
893 TGAATGCTTTTTTCTTTATGTTTCTTGAGGTACA-TATTAAATTATTGTCTGTTTTAACCAAAAA
379 TGAATGCGTTTTTCTATAAGTTTCATGAGGCA-AGCATTAAATTATAGTCTATTTTAACCAAAAA
* *
957 TGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATATGGC
443 TGTAAAAAAATTCAACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGC
1022 T
508 T
* * * * *
1023 TTTAAAGCAATAGGTGGCTATAAATGGACTTTTCTTCTCAATGAATGGATTTTTCTGCATGTTTC
1 TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTGCATGTTTC
*
1088 TCAAGGTAAGCATTCAA
66 CCAAGGTAAGCATTCAA
1105 NNNNNNNNNN
Statistics
Matches: 508, Mismatches: 74, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
507 1 0.00
508 89 0.18
509 37 0.07
510 3 0.01
512 1 0.00
513 29 0.06
514 345 0.68
515 3 0.01
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (508 bp):
TTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTGCATGTTTC
CCAAGGTAAGCATTCAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACTCAAAATCA
ATTATGAGATTATAAAACAATTTAAAGCAATAAGCCTTTTGAAAGAATGAGTGACTATAATGGAC
TTTTCTTACCAATGAATCTCTTTTTCTTTATGTTTCTAAAGGTACAAATTCAATTATAGTCTGTT
TTAACAAAAAATATAAAAATATTCAACTTAAAATCAGTTATGAGATTATAAAACCATTTAAAGCG
AGTAATAAGCCATTTGAAGGAATGGGAGACTATAAATGGACTTTTCTTACCAATGAATGCGTTTT
TCTATAAGTTTCATGAGGCAAGCATTAAATTATAGTCTATTTTAACCAAAAATGTAAAAAAATTC
AACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCT
Found at i:2464 original size:170 final size:170
Alignment explanation
Indices: 2144--2493 Score: 383
Period size: 170 Copynumber: 2.1 Consensus size: 170
2134 NNNNNNNNNN
* *
2144 GCAAGAAAAGCCCATTTATAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTCTAAATGATTT
1 GCAAGAAAAGCCCATTTATAGTCACCCATTCCTTCAAAAAGCTTATTACTCGCTCTAAAAGATTT
* * *
2209 TATAATCTTATAATAGATTTCAAGTTAAATTGTTTTATATTTTTTGTTAAAACAGACAACTATTA
66 TATAATCTCAAAATAGATTTCAAGCTAAATTGTTTTATATTTTTTGTTAAAACAGACAACTATTA
*
2274 AATTTGTACTTTGAGAAACATAAAGAAAAAAG-CATTCATT-
131 AATTTG-ACCTTGAGAAACATAAAG-AAAAAGCCATTCATTG
* * *
2314 GCAAGAAAAGTCCATTTA-ATGTCACTCATTCCTTCAAAAAGCTTATTACTCGCTTTAAACAG-T
1 GCAAGAAAAGCCCATTTATA-GTCACCCATTCCTTCAAAAAGCTTATTACTCGCTCTAAA-AGAT
* ** * * * *
2377 TTTATAATCTCAAAATTGATTTTGAGCTGAATCT-TTTTATA-TTTTTGATTACAACAGGCTA-T
64 TTTATAATCTCAAAATAGATTTCAAGCTAAAT-TGTTTTATATTTTTTG-TTAAAACAGACAACT
* * **
2439 CATTGAATGCTTG-CCTTGGGAAACATGTAGAAAAAGCCATTCATTG
127 -ATTAAAT--TTGACCTTGAGAAACATAAAGAAAAAGCCATTCATTG
2485 GCAAGAAAA
1 GCAAGAAAA
2494 NNNNNNNNNN
Statistics
Matches: 151, Mismatches: 20, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
169 14 0.09
170 123 0.81
171 11 0.07
172 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (170 bp):
GCAAGAAAAGCCCATTTATAGTCACCCATTCCTTCAAAAAGCTTATTACTCGCTCTAAAAGATTT
TATAATCTCAAAATAGATTTCAAGCTAAATTGTTTTATATTTTTTGTTAAAACAGACAACTATTA
AATTTGACCTTGAGAAACATAAAGAAAAAGCCATTCATTG
Done.