Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399170.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2443.0, 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: 3401
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.32
Warning! 249 characters in sequence are not A, C, G, or T
Found at i:1568 original size:340 final size:342
Alignment explanation
Indices: 938--3339 Score: 2295
Period size: 340 Copynumber: 7.1 Consensus size: 342
928 NNNNNNNNNN
* * *** * * *
938 ATTATGAGATTATAAAATCATTTAAAGTGAGTAATAAAACTTTCGAATGCATAGGTGATTATAGA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGTTTTCGAACGCATGGGTGACTATAGA
* * ** * ** ** * * *
1003 TGCACCTTTCTTGTCAATGAATGGCTTTGTCTTCTTATTTTTCAAGGTAAACATTCAAATATTAT
66 TGGACTTTTCTTACCAATGAATGGCTTTTTCTTCACATTTCCCTATGTAGACATTCAAATATTAT
* * ** * *
1068 TTGTTTCAGCGTAAAATGTAAAAAAAATCAACTTAAAATCAATTATGAGACTATAAAACCATTTA
131 CTGTTTTAGCCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
* * * * * * * *
1133 AAGCAAGTAATAAGGATTTTGAAGACTTAAGCAACTATAAATGGACTTTTC-TAGCTAACGGGTG
196 AAGCTAGTAATAAGGCTTTCGAAGACTTAAGCGACTATAAATGGACTTTTCTTA-CCAATGGATA
* * * *
1197 ACTTTTGCCTCATGTTTTTTGAGGCAGACATTCAATTATAATACATTTTAACAAAAAATATAAAA
260 ACTTTTGCTTCATGTTTCTTAAGGCAGACATTCAATTATAATATATTTTAACAAAAAATATAAAA
*
1262 AAATTCAACTTAAAATGA
325 AAATTCAACTTAAAATCA
* * * * *
1280 ATTGTGAGATTAAAAAATCATTTAAAGTGAGTAATAAGGTTTTCGAAGGCATGGGTGACTATAGA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGTTTTCGAACGCATGGGTGACTATAGA
* *
1345 TGGAGTTTTCATACCAATGAAT-GCTTTTTCTTCACATTTCCCTATGTAGACATTCAAATATTAT
66 TGGACTTTTCTTACCAATGAATGGCTTTTTCTTCACATTTCCCTATGTAGACATTCAAATATTAT
* * *
1409 CTGTTTTA-CCAAAAAT-TAAAAACAATTCAACTTAACATCAATTATGAAATTATAAAACTATTT
131 CTGTTTTAGCCAAAAATGTAAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTT
*
1472 AAAGCTAGTAATAAGGCTTACGAAGACTTAAGCGACTATAAATGGACTTTTCTTACCAATGGATA
195 AAAGCTAGTAATAAGGCTTTCGAAGACTTAAGCGACTATAAATGGACTTTTCTTACCAATGGATA
* * * * *
1537 ACTTTTGCTTAATGTTTCTTAAGGTAGACATTCAATTATAATATACTTTAATAAAAAATTTAAAA
260 ACTTTTGCTTCATGTTTCTTAAGGCAGACATTCAATTATAATATATTTTAACAAAAAATATAAAA
*
1602 AAATTCAACTTAAAATGA
325 AAATTCAACTTAAAATCA
* * * *
1620 ATTATAAGATTCTAAAACCATTTAAAGCGAGTAACAAGGCTTTT-GAACGCATGGGTAACTATAG
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGG-TTTTCGAACGCATGGGTGACTATAG
* * ** * * *
1684 ATGTACTTTTCTTGA-CAATGAATGGTTTTTTCTTCACATTTTTCAATATAGACATTTAAATATT
65 ATGGACTTTTCTT-ACCAATGAATGGCTTTTTCTTCACATTTCCCTATGTAGACATTCAAATATT
* * * * * *
1748 ATCTGTTTTAGCCAAAAATGTGAGAAAATTTAACTTAAACTGAATTATGAGATTATAAAATCATT
129 ATCTGTTTTAGCCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
* * * *
1813 TAAAG-TGAATAATAAGGCTTTCGAAGACTTAAGCGACTATAAATGGACTTTTTTTATCAATCGA
194 TAAAGCT-AGTAATAAGGCTTTCGAAGACTTAAGCGACTATAAATGGACTTTTCTTACCAATGGA
* ** * *
1877 TAACTTTTGCTTCATGTTACCCAAGGCAGACATTCAATTACAATATATTTTAACAAAAAATATTA
258 TAACTTTTGCTTCATGTTTCTTAAGGCAGACATTCAATTATAATATATTTTAACAAAAAATATAA
* *
1942 AACAATTCAACTTAAAATTA
323 AAAAATTCAACTTAAAATCA
* ** ** *
1962 ATTATAAGATTATAAAATTATTTAAAATGAGTAAAAAGGCTTTT-GAACGCATGGGTGACTATAG
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGG-TTTTCGAACGCATGGGTGACTATAG
* * *
2026 AT-GAATTTT-TTGCCAATGAATAGCTTTTTCTTCA-AGTTT-CCTGATGTAGACATTCAAATAT
65 ATGGACTTTTCTTACCAATGAATGGCTTTTTCTTCACA-TTTCCCT-ATGTAGACATTCAAATAT
* * * * * * * *
2087 TATCCGTTTTAACCAAAACTGTAAAAGAGTACAACTTAAAATTAATTATAAGATTATAAAACCAT
128 TATCTGTTTTAGCCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCAT
* * * * * * * * * *
2152 TAAAAGCGAGTAATAAGACTTTCAAAGACTAAAGCGGCTACAAATAGATTTTTCTTATCAATGGA
193 TTAAAGCTAGTAATAAGGCTTTCGAAGACTTAAGCGACTATAAATGGACTTTTCTTACCAATGGA
* * * * * * * *
2217 TGACTTTTGCTTTATGTTTCCTGAGGTAAACATTCAGTTATAATATATTTTAATAAAAAATAT--
258 TAACTTTTGCTTCATGTTTCTTAAGGCAGACATTCAATTATAATATATTTTAACAAAAAATATAA
*
2280 AAAAATTAAACTTAAAATC-
323 AAAAATTCAACTTAAAATCA
** * * * *
2299 ATATATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTCAAATGCATGAGTTACTATAG
1 AT-TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGTTTTCGAACGCATGGGTGACTATAG
* * ** * * *
2364 ATGGACTTTTCTTACCAATAAATGGTTTTTTCTTCATGTTTCCCCATGCAAACATTCAAATATTA
65 ATGGACTTTTCTTACCAATGAATGGCTTTTTCTTCACATTTCCCTATGTAGACATTCAAATATTA
** * * * * * *
2429 TCTGCGTT-GACCAAAAAAGTAAAACAATTCAATTTAACATCAATTATGAGATTATAAAGCCGTT
130 TCTGTTTTAG-CCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
* * * *
2493 TAAAG-TGAGTCATAAGGCTTACGAAGACTCAAGCGACTATAAATGGACTTTTCTTGCCAATGGA
194 TAAAGCT-AGTAATAAGGCTTTCGAAGACTTAAGCGACTATAAATGGACTTTTCTTACCAATGGA
* * * * * * *
2557 TAACTTTCGTTTTAAGTTT-TCAGAGGCAGACATTCAATTATAATATACTTTAA-TAAAAATATA
258 TAACTTTTGCTTCATGTTTCTTA-AGGCAGACATTCAATTATAATATATTTTAACAAAAAATATA
***
2620 AAAAAATTTTGCTTAAAATCA
322 AAAAAATTCAACTTAAAATCA
* * * * *
2641 ATTATGACATTATAAAACCATTTAAAGCAAGTGATAAAGCTTTT-GAACGCATGGGTGACTATGG
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAAT-AAGGTTTTCGAACGCATGGGTGACTATAG
*** *
2705 ATGGACTTTTCTTGGTAATGAATGGCTTTTTCTTCACATTTCCCCT-CGTAGACATTCAAATATT
65 ATGGACTTTTCTTACCAATGAATGGCTTTTTCTTCACATTT-CCCTATGTAGACATTCAAATATT
* * * * * *
2769 ATCTGTTTTATCAAAAAATGTAAGAAAATTTAACTTAAAATGAATTATGAGATTATAATACCATT
129 ATCTGTTTTAGCCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
* * * * * **
2834 TAAAACGAGTAATAAGGATTTCGAAGACTTAAGTGACTATAAATAGACTTTTCTTGTCAATGGAT
194 TAAAGCTAGTAATAAGGCTTTCGAAGACTTAAGCGACTATAAATGGACTTTTCTTACCAATGGAT
* * * *
2899 GACTTTTGCTTCACGTTTCTTGAGGCAGACATTCAATTAAAATATATTTTAACAAAAAATATAAA
259 AACTTTTGCTTCATGTTTCTTAAGGCAGACATTCAATTATAATATATTTTAACAAAAAATATAAA
* *
2964 AAAATTTAACTTAGAATCA
324 AAAATTCAACTTAAAATCA
* * * * *
2983 ATTATAAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTCAAACGCATGGGTGACTGTAGA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGTTTTCGAACGCATGGGTGACTATAGA
** * * * *
3048 TAAACTTTTCTT--C------T--C-GTTT-TT--CA-------AGGTAAAGATTCAAATATTAT
66 TGGACTTTTCTTACCAATGAATGGCTTTTTCTTCACATTTCCCTATGTAGACATTCAAATATTAT
* * * * * *
3092 CTGTTTTAACAAAAAATGAAAAAAAATTCAACTTAAAATCAATTATGAGATTGTTAAACTATTTA
131 CTGTTTTAGCCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
* * * * * * * * **
3157 AAGCGAGTAATAACGCTTTTGAATG--TATGAGTGACTATAGATAGACTTTTCCTACCAATAAAT
196 AAGCTAGTAATAAGGCTTTCGAA-GACT-TAAGCGACTATAAATGGACTTTTCTTACCAATGGAT
* * * * * * * * * * *
3220 AATTTTTTCTTCATGTTTCCCTACA--TAGACAATCAAATATTATCTGTTTTTACCAAAAATATA
259 AACTTTTGCTTCATGTTT-CTTA-AGGCAGACATTCAATTATAATATATTTTAACAAAAAATAT-
*
3283 AAAAAAATTCAACTTAAAATTA
321 AAAAAAATTCAACTTAAAATCA
* *
3305 ATTATGAGATTATAAAACTATTTAAAGCAAGTAAT
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
3340 GAAGATTTCG
Statistics
Matches: 1699, Mismatches: 324, Indels: 94
0.80 0.15 0.04
Matches are distributed among these distances:
320 1 0.00
321 163 0.10
322 55 0.03
323 1 0.00
328 2 0.00
330 2 0.00
331 3 0.00
332 1 0.00
334 1 0.00
337 5 0.00
338 64 0.04
339 22 0.01
340 614 0.36
341 361 0.21
342 400 0.24
343 4 0.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (342 bp):
ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGTTTTCGAACGCATGGGTGACTATAGA
TGGACTTTTCTTACCAATGAATGGCTTTTTCTTCACATTTCCCTATGTAGACATTCAAATATTAT
CTGTTTTAGCCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTA
AAGCTAGTAATAAGGCTTTCGAAGACTTAAGCGACTATAAATGGACTTTTCTTACCAATGGATAA
CTTTTGCTTCATGTTTCTTAAGGCAGACATTCAATTATAATATATTTTAACAAAAAATATAAAAA
AATTCAACTTAAAATCA
Found at i:3057 original size:171 final size:171
Alignment explanation
Indices: 938--3059 Score: 1469
Period size: 171 Copynumber: 12.5 Consensus size: 171
928 NNNNNNNNNN
* * ** * *
938 ATTATGAGATTATAAAATCATTTAAAGTGAGTAATAAAACTTTCGAATGCAT-AGGTGATTATAG
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAACGCATGA-GTGACTATAG
* * ** * * * * *
1002 ATGCACCTTTCTTGTCAATGAATGGC-TTTGTCTTCTTAT-TTTTC-AAGGTAAACATTCAAATA
65 ATGGACTTTTCTTACCAATGAATGACTTTTG-CTTC--ATGTTTCCTGAGGTAGACATTCAATTA
* * * * * ** * *
1064 TTATTTGTTTCAGCGTAAAATGTAAAAAAAATCAACTTAAAATCA
127 TAATATATTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCA
* * * * * * ** *
1109 ATTATGAGACTATAAAACCATTTAAAGCAAGTAATAAGGATTTTGAA-GACTTAAGCAACTATAA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAACG-CATGAGTGACTATAG
* * ** * ** *
1173 ATGGACTTTTC-TAGCTAACGGGTGACTTTTGCCTCATGTTTTTTGAGGCAGACATTCAATTATA
65 ATGGACTTTTCTTA-CCAATGAATGACTTTTGCTTCATGTTTCCTGAGGTAGACATTCAATTATA
* *
1237 ATACATTTTAACAAAAAATATAAAAAAATTCAACTTAAAATGA
129 ATATATTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCA
* * * * * * *
1280 ATTGTGAGATTAAAAAATCATTTAAAGTGAGTAATAAGGTTTTCGAAGGCATGGGTGACTATAGA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAACGCATGAGTGACTATAGA
* * * ** * * *
1345 TGGAGTTTTCATACCAATGAATG-CTTTTTCTTCACATTTCCCT-ATGTAGACATTCAAATATTA
66 TGGACTTTTCTTACCAATGAATGACTTTTGCTTCATGTTT-CCTGAGGTAGACATTCAATTATAA
* * * *
1408 TCTGTTTT-ACCAAAAAT-TAAAAACAATTCAACTTAACATCA
130 TATATTTTAACAAAAAATATAAAAA-AATTCAACTTAAAATCA
* * * * * * * *
1449 ATTATGAAATTATAAAACTATTTAAAGCTAGTAATAAGGCTTACGAA-GACTTAAGCGACTATAA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAACG-CATGAGTGACTATAG
* * * * *
1513 ATGGACTTTTCTTACCAATGGATAACTTTTGCTTAATGTTTCTTAAGGTAGACATTCAATTATAA
65 ATGGACTTTTCTTACCAATGAATGACTTTTGCTTCATGTTTCCTGAGGTAGACATTCAATTATAA
* * * *
1578 TATACTTTAATAAAAAATTTAAAAAAATTCAACTTAAAATGA
130 TATATTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCA
* * * * * *
1620 ATTATAAGATTCTAAAACCATTTAAAGCGAGTAACAAGGCTTTTGAACGCATGGGTAACTATAGA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAACGCATGAGTGACTATAGA
* ** * * * * *
1685 TGTACTTTTCTTGA-CAATGAATGGTTTTTTCTTCACATTTTTCAAT-A--TAGACATTTAAATA
66 TGGACTTTTCTT-ACCAATGAATGACTTTTGCTT--CATGTTTC-CTGAGGTAGACATTCAATTA
* * * * * * * * * * *
1746 TTATCTGTTTTAGCCAAAAATGTGAGAAAATTTAACTTAAACTGA
127 TAATATATTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCA
* * * * * * *
1791 ATTATGAGATTATAAAATCATTTAAAGTGAATAATAAGGCTTTCGAA-GACTTAAGCGACTATAA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAACG-CATGAGTGACTATAG
* * * * ** * *
1855 ATGGACTTTTTTTATCAATCG-ATAACTTTTGCTTCATGTTACCCAAGGCAGACATTCAATTACA
65 ATGGACTTTTCTTACCAAT-GAATGACTTTTGCTTCATGTTTCCTGAGGTAGACATTCAATTATA
* * *
1919 ATATATTTTAACAAAAAATATTAAACAATTCAACTTAAAATTA
129 ATATATTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCA
* ** ** * * *
1962 ATTATAAGATTATAAAATTATTTAAAATGAGTAAAAAGGCTTTTGAACGCATGGGTGACTATAGA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAACGCATGAGTGACTATAGA
* * * * * * *
2027 T-GAATTTT-TTGCCAATGAAT-AGCTTTTTCTTCAAGTTTCCTGATGTAGACATTCAAATATTA
66 TGGACTTTTCTTACCAATGAATGA-CTTTTGCTTCATGTTTCCTGAGGTAGACATTCAATTATAA
*** * * * * * * *
2089 TCCGTTTTAACCAAAACTGTAAAAGAGTACAACTTAAAATTA
130 TATATTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCA
* * * * * * * *
2131 ATTATAAGATTATAAAACCATTAAAAGCGAGTAATAAGACTTTC-AAAG-ACTAAAGCGGCTACA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAACGCA-T-GAGTGACTATA
* * * * * * * *
2194 AATAGATTTTTCTTATCAATGGATGACTTTTGCTTTATGTTTCCTGAGGTAAACATTCAGTTATA
64 GATGGACTTTTCTTACCAATGAATGACTTTTGCTTCATGTTTCCTGAGGTAGACATTCAATTATA
* *
2259 ATATATTTTAATAAAAAATAT--AAAAATTAAACTTAAAATC-
129 ATATATTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCA
* * * *
2299 ATATATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTCAAATGCATGAGTTACTATAG
1 AT-TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAACGCATGAGTGACTATAG
* ** * ** * * * * *
2364 ATGGACTTTTCTTACCAATAAATGGTTTTTTCTTCATGTTTCCCCATGCAAACATTCAAATATTA
65 ATGGACTTTTCTTACCAATGAATGACTTTTGCTTCATGTTTCCTGAGGTAGACATTCAATTATAA
* ** * * * * * *
2429 TCTGCGTTGACCAAAAAA-GTAAAACAATTCAATTTAACATCA
130 TAT-ATTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCA
* * * * * * *
2471 ATTATGAGATTATAAAGCCGTTTAAAGTGAGTCATAAGGCTTACGAA-G-ACTCAAGCGACTATA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAACGCA-T-GAGTGACTATA
* * * * * * * * * * *
2534 AATGGACTTTTCTTGCCAATGGATAACTTTCGTTTTAAGTTTTCAGAGGCAGACATTCAATTATA
64 GATGGACTTTTCTTACCAATGAATGACTTTTGCTTCATGTTTCCTGAGGTAGACATTCAATTATA
* * ***
2599 ATATACTTTAA-TAAAAATATAAAAAAATTTTGCTTAAAATCA
129 ATATATTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCA
* * * * * * *
2641 ATTATGACATTATAAAACCATTTAAAGCAAGTGATAAAGCTTTTGAACGCATGGGTGACTATGGA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAACGCATGAGTGACTATAGA
*** * * ** **** * *
2706 TGGACTTTTCTTGGTAATGAATGGCTTTTTCTTCACATTTCCCCTCGTAGACATTCAAATATTAT
66 TGGACTTTTCTTACCAATGAATGACTTTTGCTTCATGTTTCCTGAGGTAGACATTCAATTATAAT
* * * * * * *
2771 CTGTTTTATCAAAAAATGTAAGAAAATTTAACTTAAAATGA
131 ATATTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCA
* * * * * *
2812 ATTATGAGATTATAATACCATTTAAAACGAGTAATAAGGATTTCGAA-GACTTAAGTGACTATAA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAACG-CATGAGTGACTATAG
* ** * * * * *
2876 ATAGACTTTTCTTGTCAATGGATGACTTTTGCTTCACGTTTCTTGAGGCAGACATTCAATTAAAA
65 ATGGACTTTTCTTACCAATGAATGACTTTTGCTTCATGTTTCCTGAGGTAGACATTCAATTATAA
* *
2941 TATATTTTAACAAAAAATATAAAAAAATTTAACTTAGAATCA
130 TATATTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCA
* * * * *
2983 ATTATAAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTCAAACGCATGGGTGACTGTAGA
1 ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAACGCATGAGTGACTATAGA
**
3048 TAAACTTTTCTT
66 TGGACTTTTCTT
3060 CTCGTTTTTC
Statistics
Matches: 1476, Mismatches: 426, Indels: 98
0.74 0.21 0.05
Matches are distributed among these distances:
167 1 0.00
168 15 0.01
169 333 0.23
170 220 0.15
171 876 0.59
172 23 0.02
173 7 0.00
174 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (171 bp):
ATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTCGAACGCATGAGTGACTATAGA
TGGACTTTTCTTACCAATGAATGACTTTTGCTTCATGTTTCCTGAGGTAGACATTCAATTATAAT
ATATTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCA
Done.