Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402114.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5208.0, 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: 1792
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.34
Warning! 187 characters in sequence are not A, C, G, or T
Found at i:343 original size:169 final size:170
Alignment explanation
Indices: 120--544 Score: 412
Period size: 169 Copynumber: 2.5 Consensus size: 170
110 ATTTTGAATT
* * * * **
120 TTTTTTGCATTTT-GTTAAAATAGATTATAATTGAGTATCTGCCAAG-GCAAACGTGAAGCAAAA
1 TTTTTTACATTTTGGTTAAAATAAATTATAATTGAATGTCTGCCTTGAG-AAACGTGAAGCAAAA
* ** * ** * *
183 G-TCATCCATTGGA-GGGAAAAGTCCATTTACAGTTACTCATGCCTTCGAAA-CCTTATTACTTA
65 GCT-ACCCATT-GATAAGAAAAGTACATTTACAGCCACTCATGCCTTCAAAAGCATTATTAC-TA
* * *
245 -TTGTAAATGGTTTTATAATCTCATCATTGATTTTAAGTTCAAC
127 GTTGTAAATGGTTTTACAATCTCATAATTAATTTTAAGTTCAAC
* *
288 TTTTTTACATTTTGGTTAAAATATATTATAATTGAATGTCTGTCTTGAGAAACGTGAAGCAAAAG
1 TTTTTTACATTTTGGTTAAAATAAATTATAATTGAATGTCTGCCTTGAGAAACGTGAAGCAAAAG
* * * * * *
353 CTACCCATTGATAAGAAAAGTAGATTTATAGCCACTCATTCCTTTAAAAGTATTATTACTAGTTT
66 CTACCCATTGATAAGAAAAGTACATTTACAGCCACTCATGCCTTCAAAAGCATTATTACTAGTTG
* * *
418 TAAATGGTTTTACAATCTCATAATTAATTTTCAGTTGAAT
131 TAAATGGTTTTACAATCTCATAATTAATTTTAAGTTCAAC
* * * * * * *
458 TTTTTTACACTTTTGGTGAAAACAAATAATATTTGAATGTCTGCCTTTAGAAACATGAAGAAAAA
1 TTTTTTACA-TTTTGGTTAAAATAAATTATAATTGAATGTCTGCCTTGAGAAACGTGAAGCAAAA
** **
523 GCTATTCATTGGCAAGAAAAGT
65 GCTACCCATTGATAAGAAAAGT
545 CTATTTATAG
Statistics
Matches: 210, Mismatches: 40, Indels: 11
0.80 0.15 0.04
Matches are distributed among these distances:
168 14 0.07
169 78 0.37
170 54 0.26
171 64 0.30
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (170 bp):
TTTTTTACATTTTGGTTAAAATAAATTATAATTGAATGTCTGCCTTGAGAAACGTGAAGCAAAAG
CTACCCATTGATAAGAAAAGTACATTTACAGCCACTCATGCCTTCAAAAGCATTATTACTAGTTG
TAAATGGTTTTACAATCTCATAATTAATTTTAAGTTCAAC
Found at i:553 original size:171 final size:170
Alignment explanation
Indices: 235--554 Score: 417
Period size: 171 Copynumber: 1.9 Consensus size: 170
225 CTTCGAAACC
* * *
235 TTATTACTTATTGTAAATGGTTTTATAATCTCATCATTGATTTTAAGTTCAACTTTTTTACATTT
1 TTATTACTTATTGTAAATGGTTTTACAATCTCATAATTAATTTTAAGTTCAACTTTTTTACATTT
* * * * * * * *
300 TGGTTAAAATATATTATAATTGAATGTCTGTCTTGAGAAACGTGAAGCAAAAGCTACCCATTGAT
66 TGGTGAAAACAAATAATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGCTACCCATTGAC
365 AAGAAAAGTAGATTTATAGCCACTCATTCCTTTAAAAGTA
131 AAGAAAAGTAGATTTATAGCCACTCATTCCTTTAAAAGTA
* * * *
405 TTATTAC-TAGTTTTAAATGGTTTTACAATCTCATAATTAATTTTCAGTTGAATTTTTTTACACT
1 TTATTACTTA-TTGTAAATGGTTTTACAATCTCATAATTAATTTTAAGTTCAACTTTTTTACA-T
* * **
469 TTTGGTGAAAACAAATAATATTTGAATGTCTGCCTTTAGAAACATGAAGAAAAAGCTATTCATTG
64 TTTGGTGAAAACAAATAATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGCTACCCATTG
* **
534 GCAAGAAAAGTCTATTTATAG
129 ACAAGAAAAGTAGATTTATAG
555 TCACCNNNNN
Statistics
Matches: 126, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
169 2 0.02
170 52 0.41
171 72 0.57
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (170 bp):
TTATTACTTATTGTAAATGGTTTTACAATCTCATAATTAATTTTAAGTTCAACTTTTTTACATTT
TGGTGAAAACAAATAATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAAGCTACCCATTGAC
AAGAAAAGTAGATTTATAGCCACTCATTCCTTTAAAAGTA
Found at i:1025 original size:171 final size:171
Alignment explanation
Indices: 848--1792 Score: 554
Period size: 171 Copynumber: 5.5 Consensus size: 171
838 NNNNNNNNNN
* *
848 AGCCTTATTACTCGCTTTAAATGGTTTTATATCCTTC-TAACTGATTTTAAGTTAAACTTTTTTA
1 AGCCTTATTACTCGCTTTAAATGGTTTTATATCC-TCATAATTGATTTTAAGTTGAA-TTTTTTA
*
912 CATTTTTAGTTAAAATAGATTATACA-TGAATGTTTGTCTTAGGAAACATAAAGTAAAAGCCATC
64 CATTTTTAGTTAAAATAGATTATA-ATTGAATGTTTGTCTTAGGAAACATAAAGAAAAAGCCATC
*
976 CATTGAAGAGAAAAGTTTACTTT-TATTGACTCATGCCTTCGAA
128 CATTGAAGAGAAAAGTTTACTTTATATTAACTCATGCCTTCGAA
** * * *
1019 AGCCTTATTACTTACTTTAAATAGTTGTATAACCTCATAATTGATTTTAAGTTGAATTTTCTTAC
1 AGCCTTATTACTCGCTTTAAATGGTTTTATATCCTCATAATTGATTTTAAGTTGAATTTT-TTAC
* * * * * ** *
1084 ATTTTTGGTTAAAATATATTATAATTGAATGTCTGCCTTAGGAAACTTTGAGCAAAAGCCATCCA
65 ATTTTTAGTTAAAATAGATTATAATTGAATGTTTGTCTTAGGAAACATAAAGAAAAAGCCATCCA
* ** * * * * * *
1149 TTGAAAAGAAAAGTCCA-TTTGTAGTCACTTAAGCCTTTGAA
130 TTGAAGAGAAAAGTTTACTTTATATTAACTCATGCCTTCGAA
* * * *
1190 AGCATTATTACTCGTTTTAAAGGGTTTTATAAT-CTCATAATTGATTTTCAGTTGAATTTGTTTA
1 AGCCTTATTACTCGCTTTAAATGGTTTTAT-ATCCTCATAATTGATTTTAAGTTGAATTT-TTTA
* * * *
1254 CATTTTTAGTTCAAACAGATTATAATTGAATGTTT-TCCTT-GAGAAACATGAAGAAAAAACCAT
64 CATTTTTAGTTAAAATAGATTATAATTGAATGTTTGT-CTTAG-GAAACATAAAGAAAAAGCCAT
* * *
1317 TCATTGGCAG-GAAAAG-TT-CGTTTATAGTCAAC-CATGCCTTCGAA
127 CCATT-GAAGAGAAAAGTTTAC-TTTATA-TTAACTCATGCCTTCGAA
* * *********** ** * *
1361 AACCTTATTACTTGCTTTAAATGANNNNNNNNNNTCATAATTGAACTTAAGATGAATGTTTTGAC
1 AGCCTTATTACTCGCTTTAAATGGTTTTATATCCTCATAATTGATTTTAAGTTGAAT-TTTTTAC
* * * * * * * *** *
1426 ATTTTTAGTTAAATTATATTGTAATTGAATGTCTG-CTAAAGAAAACATAAAGCAAAAGTTGTTC
65 ATTTTTAGTTAAAATAGATTATAATTGAATGTTTGTCT-TAGGAAACATAAAGAAAAAGCCATCC
* * ** * * * * * ** *
1490 GTTGGCA-AGAAAAGTCCA-TCTATAGTCATTCAAGTATTTGAA
129 ATT-GAAGAGAAAAGTTTACTTTATATTAACTCATGCCTTCGAA
* * * *
1532 AG-CTCTATTACTTGCTTTAAATGGTTTCATAAT-CTTATAATTAATTTTAAGTTGAATTTTCTT
1 AGCCT-TATTACTCGCTTTAAATGGTTTTAT-ATCCTCATAATTGATTTTAAGTTGAATTTT-TT
* * * * * * *
1595 ACATTTTTTA-TTAAAA-A-ACTAATATTTGAAGGTTTG-C-CAAGAGAATATGAAGAAAAATG-
63 ACA-TTTTTAGTTAAAATAGA-TTATAATTGAATGTTTGTCTTAGGA-AACATAAAGAAAAA-GC
** *** ** ** * * **
1654 CATTTATTGCTTAGAAAAGTCCA-TTTATGGTCACTCAAGCCTTTAAA
124 CATCCATTGAAGAGAAAAGTTTACTTTATATTAACTCATGCCTTCGAA
* * * *
1701 AGCCTTATTACTGGCTTTAAATAGTTGTATAAT-CACATAATTGATTTTAAGTTGAATTTGTTTA
1 AGCCTTATTACTCGCTTTAAATGGTTTTAT-ATCCTCATAATTGATTTTAAGTTGAATTT-TTTA
1765 CATTGTTT-GTTAAAATAGATTATAATTG
64 CATT-TTTAGTTAAAATAGATTATAATTG
Statistics
Matches: 589, Mismatches: 150, Indels: 71
0.73 0.19 0.09
Matches are distributed among these distances:
168 6 0.01
169 108 0.18
170 45 0.08
171 415 0.70
172 15 0.03
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.39
Consensus pattern (171 bp):
AGCCTTATTACTCGCTTTAAATGGTTTTATATCCTCATAATTGATTTTAAGTTGAATTTTTTACA
TTTTTAGTTAAAATAGATTATAATTGAATGTTTGTCTTAGGAAACATAAAGAAAAAGCCATCCAT
TGAAGAGAAAAGTTTACTTTATATTAACTCATGCCTTCGAA
Found at i:1355 original size:342 final size:334
Alignment explanation
Indices: 851--1792 Score: 857
Period size: 342 Copynumber: 2.8 Consensus size: 334
841 NNNNNNNAGC
* *
851 CTTATTACTCGCTTTAAATGGTTTTAT-ATCCTTC-TAACTGATTTTAAGTTAAACTTTTTTACA
1 CTTATTACTCGCTTTAAATGGTTTTATAAT-C-TCATAATTGATTTTAAGTTGAA-TTTTTTACA
* * * *
914 TTTTTAGTTAAAATAGATTATACA-TGAATGTTTGT-CTT-AGGAAACATAAAGTAAAAGCCATC
63 TTTTTAGTT-AAA-AGATTATA-ATTGAATGTTT-TCCTTGA-GAAACATGAAGAAAAAACCATT
* * * *
976 CATTGAAGAGAAAAGTTTACTTT-TATTGACTCATGCCTTCGAAAGCCTTATTACTTACTTTAAA
123 CATTGCAG-GAAAAG-TT-CTTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTTGCTTTAAA
1040 TAGTTGTATAACCTCATAATTGATTTTAAGTTGAATTTTCTTACATTTTTGGTTAAAATATATTA
185 TAGTTGTATAACCTCATAATTGATTTTAAGTTGAATTTT-TTACATTTTT-GTTAAAATATATTA
* * * ** *
1105 TAATTGAATGTCTGCCT-TAGGAAACTTTGAGCAAAAGCCATCCATTGAAAAGAAAAGTCCATTT
248 TAATTGAATGTCTG-CTAAAGAAAACATAAAGCAAAAGCCATCCATTGAAAAGAAAAGTCCATCT
* *
1169 GTAGTCACTT-AAGCCTTTGAAAG
312 ATAGTCA-TTCAAGCATTTGAAAG
* * *
1192 CATTATTACTCGTTTTAAAGGGTTTTATAATCTCATAATTGATTTTCAGTTGAATTTGTTTACAT
1 C-TTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTT-TTTACAT
1257 TTTTAGTTCAAACAGATTATAATTGAATGTTTTCCTTGAGAAACATGAAGAAAAAACCATTCATT
64 TTTTAGTT-AAA-AGATTATAATTGAATGTTTTCCTTGAGAAACATGAAGAAAAAACCATTCATT
*
1322 GGCAGGAAAAGTTCGTTTATAGTCAAC-CATGCCTTCGAAAACCTTATTACTTGCTTTAAAT-GA
127 -GCAGGAAAAGTTC-TTTATAGTC-ACTCATGCCTTCGAAAGCCTTATTACTTGCTTTAAATAG-
********** ** * * * *
1385 NNNNNNNNNNTCATAATTGAACTTAAGATGAATGTTTTGACATTTTTAGTTAAATTATATTGTAA
188 TTGTATAACCTCATAATTGATTTTAAGTTGAAT-TTTTTACATTTTT-GTTAAAATATATTATAA
*** * * **
1450 TTGAATGTCTGCTAAAGAAAACATAAAGCAAAAGTTGTTCGTTGGCAAGAAAAGTCCATCTATAG
251 TTGAATGTCTGCTAAAGAAAACATAAAGCAAAAGCCATCCATTGAAAAGAAAAGTCCATCTATAG
*
1515 TCATTCAAGTATTTGAAAG
316 TCATTCAAGCATTTGAAAG
* * * *
1534 CTCTATTACTTGCTTTAAATGGTTTCATAATCTTATAATTAATTTTAAGTTGAATTTTCTTACAT
1 CT-TATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTT-TTACA-
* * * * * ** * ** *
1599 TTTTTA-TTAAAAAACTAATATTTGAAGGTTTGCCAAGAG-AATATGAAGAAAAATGCATTTATT
63 TTTTTAGTTAAAAGA-TTATAATTGAATGTTTTCCTTGAGAAACATGAAGAAAAAACCATTCATT
* * * ** *
1662 GCTTA-GAAAAGTCCATTTATGGTCACTCAAGCCTTTAAAAGCCTTATTACTGGCTTTAAATAGT
127 GC--AGGAAAAGTTC-TTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTTGCTTTAAATAGT
* * *
1726 TGTATAATCACATAATTGATTTTAAGTTGAATTTGTTTACATTGTTTGTTAAAATAGATTATAAT
189 TGTATAACCTCATAATTGATTTTAAGTTGAATTT-TTTACATT-TTTGTTAAAATATATTATAAT
1791 TG
252 TG
Statistics
Matches: 483, Mismatches: 93, Indels: 51
0.77 0.15 0.08
Matches are distributed among these distances:
339 6 0.01
340 111 0.23
341 46 0.10
342 303 0.63
343 17 0.04
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.39
Consensus pattern (334 bp):
CTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTACATTT
TTAGTTAAAAGATTATAATTGAATGTTTTCCTTGAGAAACATGAAGAAAAAACCATTCATTGCAG
GAAAAGTTCTTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTTGCTTTAAATAGTTGTATAA
CCTCATAATTGATTTTAAGTTGAATTTTTTACATTTTTGTTAAAATATATTATAATTGAATGTCT
GCTAAAGAAAACATAAAGCAAAAGCCATCCATTGAAAAGAAAAGTCCATCTATAGTCATTCAAGC
ATTTGAAAG
Done.