Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397770.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1069.0, 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: 5076
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.31
Warning! 992 characters in sequence are not A, C, G, or T
Found at i:1620 original size:341 final size:330
Alignment explanation
Indices: 973--2336 Score: 814
Period size: 341 Copynumber: 4.0 Consensus size: 330
963 AAGCCTTCGA
* * * * **
973 AAGCCTTATTACACGCTTTAAATGGTTTTATAATTTAATTATTGATTTTAATTTGAATTTTTTTT
1 AAGCCTTATTACACGCTTTAAATAGTTTTATAATCTAACTATTGATTTTAAATTGAATTTTTTAC
* *
1038 ATTTTTGATTAAAATATATTATAACTGAATATCTGCCTCAAATACATGAAGCAAAAGCCATCAAT
66 ATTTTTGATTAAAATATATCATAACTGAATATCTGCCTCAAAAACATGAAGCAAAAGCCATCAAT
* * *
1103 TTGTCAGATAAGTCGATTTATAGTCACTCAAGCCCTATGACAAACTATTACTAGCTTTAAATAGT
131 TTGTCAGAAAAGTCGATTTATAGTCACTCAAGCCCTATAAAAAACTATTACTAGCTTTAAATAGT
* * *
1168 TTTATAATCATGTAATGGATTTTAAGTTGAATTTTTTTATATTTTTATTTAAAATAGATTATATT
196 TTTATAATCATATAATGGATTTTAAGTTCAATTTTTTTATATTTTTATTGAAAATAGATTATATT
* * *
1233 TGATTGTTTACCTTGAGAAATGTGAACTAAAAGCCATCCGTTGGCAA-AACAAGTCTATTTATAG
261 TGACTGTTTACCTTGAGAAATGTGAACTAAAAGCCATCCATTGGCAAGAA-AAGTCCATTTATAG
1297 TCACTC
325 TCACTC
*
1303 AAGNNNNNNNNNNCCTTATTACTCGCTTTAAATAGTTTTATAATCTAACTATTGATTTTAAATTG
1 AAG----------CCTTATTACACGCTTTAAATAGTTTTATAATCTAACTATTGATTTTAAATTG
* * *
1368 AATTTTTTACATTTTTTG-TTAAAATATATCATAGCTGAATATCTTCCT-AGGAAAACATGAAGT
56 AATTTTTTACA-TTTTTGATTAAAATATATCATAACTGAATATCTGCCTCA--AAAACATGAAGC
* * * * *
1431 AAAAGTCATCTATTTGT-AGGAAAAGTTGATTTATTTGT-ACTCAAGCTCTA-AAAAAACTTATT
118 AAAAGCCATCAATTTGTCA-GAAAAGTCGATTTA-TAGTCACTCAAGCCCTATAAAAAAC-TATT
* * *
1493 ACTAGTTTTAAATAGTTTTATAATCATATAATTGATTTTAAGTTCAATTTTTTTTATATTTTTGC
180 ACTAGCTTTAAATAGTTTTATAATCATATAATGGATTTTAAGTTCAA-TTTTTTTATATTTTT-A
* *
1558 TTGAAAA-AGATTATATTTGACTGTTTGCCTT-AGGAAAT-TGAAAC-AAAAGCCATCTATTGGC
243 TTGAAAATAGATTATATTTGACTGTTTACCTTGA-GAAATGTG-AACTAAAAGCCATCCATTGGC
*
1619 AAGAAAAGTCCATTTCTAGTTACTTAAGCCTTC
306 AAGAAAAGTCCATTTATAG-T-C---A--C-TC
* *** * * ** * *
1652 AAAAACCTTATTATTTGCTTTGAAT-GATTTTATATTCCCATTATTGATTTTAAGTTGAATTTTT
1 --AAGCCTTATTACACGCTTTAAATAG-TTTTATAATCTAACTATTGATTTTAAATTGAA-TTTT
** * * * *************
1716 TTATGTTTTTGATTAAAATATGTTATAACTGAATGTCTG-CTNNNNNNNNNNNNNNNNNNNNNNN
62 TTACATTTTTGATTAAAATATATCATAACTGAATATCTGCCT----------CAAAAACATGAAG
***************************** * * *
1780 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNATTTATAGTCACTCAAGCCTTACAAAAAATTATTAC
117 CAAAAGCCATCAATTTGTCAGAAAAGTCGATTTATAGTCACTCAAGCCCTATAAAAAACTATTAC
** * * * * *
1845 TAGCTTTAAAT-GATTTTATAATCGCATAATTGATTTTAAGTTAAATTTTTTAATATTTTTGTTT
182 TAGCTTTAAATAG-TTTTATAATCATATAATGGATTTTAAGTTCAATTTTTTTATATTTTTATTG
* * * *
1909 AAAATAGATTATATTTGACTGTTTACCTTGAAAAACGTGAAGC-AAAAGCCATCCGTTGGTAAGA
246 AAAATAGATTATATTTGACTGTTTACCTTGAGAAATGTGAA-CTAAAAGCCATCCATTGGCAAGA
* *
1973 CAAGTCTATTTATAAGTCACTCAAGCCTTC
310 AAAGTCCATTTAT-AG----TC-A--C-TC
* * *
2003 AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAA-CATAACTATTGATTTTAAATTGGATTTTT
1 --AAGCCTTATTACACGCTTTAAATAGTTTTATAATC-TAACTATTGATTTTAAATTGAATTTTT
** *
2067 TTTATTTTTTG-TTAAAATATATCATAACTGAATGTCTG-C-CAAGGAAACATGAAGCAAAAGCC
63 TACA-TTTTTGATTAAAATATATCATAACTGAATATCTGCCTCAA--AAACATGAAGCAAAAGCC
* * * * *
2129 ATCCATTTAT-AGGAAAAGTCAATTTAT-TTACACTTAAGCCCTA-AAAAAACTTATTACTAGCT
125 ATCAATTTGTCA-GAAAAGTCGATTTATAGT-CACTCAAGCCCTATAAAAAAC-TATTACTAGCT
* * * *
2191 TTAAATAGTTTTATAATCGTATAA-GTGATTTTAAGTTAAATGTTTTTATATTTTTCCTT-AAAA
187 TTAAATAGTTTTATAATCATATAATG-GATTTTAAGTTCAATTTTTTTATATTTTT-ATTGAAAA
* * ** * *
2254 CAGATTATATTTGACTATTTACCTCAAGAAACGTGAAAC-AAAAGCCATCCATTGACAAGAAAAG
250 TAGATTATATTTGACTGTTTACCTTGAGAAATGTG-AACTAAAAGCCATCCATTGGCAAGAAAAG
* *
2318 TCCATTTCTAGTTACTC
314 TCCATTTATAGTCACTC
2335 AA
1 AA
2337 NNNNNNNNNN
Statistics
Matches: 780, Mismatches: 185, Indels: 138
0.71 0.17 0.13
Matches are distributed among these distances:
330 5 0.01
332 2 0.00
333 1 0.00
335 1 0.00
336 1 0.00
339 1 0.00
340 99 0.13
341 324 0.42
342 85 0.11
343 7 0.01
346 1 0.00
348 7 0.01
349 48 0.06
350 126 0.16
351 69 0.09
352 1 0.00
353 1 0.00
354 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.39
Consensus pattern (330 bp):
AAGCCTTATTACACGCTTTAAATAGTTTTATAATCTAACTATTGATTTTAAATTGAATTTTTTAC
ATTTTTGATTAAAATATATCATAACTGAATATCTGCCTCAAAAACATGAAGCAAAAGCCATCAAT
TTGTCAGAAAAGTCGATTTATAGTCACTCAAGCCCTATAAAAAACTATTACTAGCTTTAAATAGT
TTTATAATCATATAATGGATTTTAAGTTCAATTTTTTTATATTTTTATTGAAAATAGATTATATT
TGACTGTTTACCTTGAGAAATGTGAACTAAAAGCCATCCATTGGCAAGAAAAGTCCATTTATAGT
CACTC
Found at i:2051 original size:172 final size:166
Alignment explanation
Indices: 1809--2336 Score: 508
Period size: 171 Copynumber: 3.1 Consensus size: 166
1799 NNNNNNNNNN
* *
1809 ATTTATAGTCACTCAAGCCTTACAAAAAATTATTACTAGCTTTAAATGATTTTATAATCGCATA-
1 ATTTATAGTCACTCAAGCCTT-CAAAAACTTATTACTAGCTTTAAATGGTTTTATAAT--CATAT
1873 ATTGATTTTAAGTTAAATTTTTTAATATTTTTGTTTAAAATAGATTATATTTGACTGTTTACCTT
63 ATTGATTTTAAGTTAAATTTTTT-ATATTTTT-TTTAAAATAGATTATATTTGACTGTTTACC-T
* * * *
1938 GAAAAACGTGAAGCAAAAGCCATCCGTTGGTAAGACAAGTCT
125 GAAAAACGTGAAGCAAAAGCCATCCATTGATAAGAAAAGTCA
* *
1980 ATTTATAAGTCACTCAAGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAA-CATAAC
1 ATTTAT-AGTCACTCAAGCCTTCAAAA-ACTTATTACTAGCTTTAAATGGTTTTATAATCAT-A-
* ** * * * ** * * *
2044 TATTGATTTTAAATTGGATTTTTTTTATTTTTTGTTAAAATATATCATAACTGAATGTCTGCC--
62 TATTGATTTTAAGTTAAATTTTTTATATTTTTT-TTAAAATAGATTATATTTGACTGTTTACCTG
* * *
2107 AAGGAAACATGAAGCAAAAGCCATCCATTTATAGGAAAAGTCA
126 AA--AAACGTGAAGCAAAAGCCATCCATTGATAAGAAAAGTCA
* * ** * *
2150 ATTTAT-TTACACTTAAGCCCTAAAAAAACTTATTACTAGCTTTAAATAGTTTTATAATCGTATA
1 ATTTATAGT-CACTCAAG-CCTTCAAAAACTTATTACTAGCTTTAAATGGTTTTATAATCATAT-
* * * * *
2214 AGTGATTTTAAGTTAAATGTTTTTATATTTTTCCTTAAAACAGATTATATTTGACTATTTACCTC
63 ATTGATTTTAAGTTAAAT-TTTTTATATTTTT-TTTAAAATAGATTATATTTGACTGTTTACCTG
* * *
2279 AAGAAACGTGAAACAAAAGCCATCCATTGACAAGAAAAGTCC
126 AA-AAACGTGAAGCAAAAGCCATCCATTGATAAGAAAAGTCA
* *
2321 ATTTCTAGTTACTCAA
1 ATTTATAGTCACTCAA
2337 NNNNNNNNNN
Statistics
Matches: 285, Mismatches: 55, Indels: 34
0.76 0.15 0.09
Matches are distributed among these distances:
168 4 0.01
169 52 0.18
170 81 0.28
171 84 0.29
172 64 0.22
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (166 bp):
ATTTATAGTCACTCAAGCCTTCAAAAACTTATTACTAGCTTTAAATGGTTTTATAATCATATATT
GATTTTAAGTTAAATTTTTTATATTTTTTTTAAAATAGATTATATTTGACTGTTTACCTGAAAAA
CGTGAAGCAAAAGCCATCCATTGATAAGAAAAGTCA
Found at i:3122 original size:22 final size:22
Alignment explanation
Indices: 3079--3123 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3069 CCCATTATTG
* * *
3079 ATTTTAAGTTAAATTTTTTTAT
1 ATTTTAAGTTAAAATATATTAT
*
3101 ATTTTTAGTTAAAATATATTAT
1 ATTTTAAGTTAAAATATATTAT
3123 A
1 A
3124 ACTGAATGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
ATTTTAAGTTAAAATATATTAT
Found at i:3369 original size:342 final size:342
Alignment explanation
Indices: 2732--3385 Score: 764
Period size: 342 Copynumber: 1.9 Consensus size: 342
2722 NNNATCTAAC
* **
2732 TATTGATTTTAGATTAAATTTTTTTATATTTTTTGTTAAAATATATCATAACTAAATGTCTGTCT
1 TATTGATTTTAGATTAAATTTTTTTATATTTTTAGTTAAAATATATCATAACTAAATGTCTACCT
*
2797 AGGGAAACATGAAGCAAAAGCCATCCATTTGTAGAAAAAGTCAATTTATTTGCACTCAAGTCCTA
66 AGGGAAACATGAAGCAAAAGCCATCCATTTGTAGAAAAAGTCAATTTATTTGCACTCAAGCCCTA
********** * * *
2862 AAAAAACTTATTACTAGCTTTAAATNNNNNNNNNNTCGTATAATTGATTTTAAGTTAAATTTTTG
131 AAAAAACTTATTACTAGCTTTAAATGGTTTGAAAATCGCAGAATTGATTTTAAGCTAAATTTTTG
* * *
2927 TACATTTTTACTTAAAAGAGATTATATTTGACTGTTTGGCTCAAGAAACGTGAAACAAAAGCCAT
196 TACATTTTTACTTAAAACAGATTATATTTGACTATTTGCCTCAAGAAACGTGAAACAAAAGCCAT
********** * * * **
2992 NNNNNNNNNNGAAAAGTCTATTTCTAGTTACTTAAGCCATCGAAAGCCTTATCATTCGCTTTGAA
261 CCATTAGTAAGAAAAGTCCATTTATAGTCACTTAAGCCATAAAAAGCCTTATCATTCGCTTTGAA
3057 TGGTTCTATATTCCCAT
326 TGGTTCTATATTCCCAT
* * *
3074 TATTGATTTTA-AGTTAAATTTTTTTATATTTTTAGTTAAAATATATTATAACTGAATGTGTACC
1 TATTGATTTTAGA-TTAAATTTTTTTATATTTTTAGTTAAAATATATCATAACTAAATGTCTACC
* * * ** *
3138 TTGGGAAACGTGAAGCAAAAGCCATTCATTTG-AGAGAAAAGTTGATTTCTTAT-CAC-CTAAGC
65 TAGGGAAACATGAAGCAAAAGCCATCCATTTGTAGA-AAAAGTCAATTTATT-TGCACTC-AAGC
*
3200 CCTAAAAAAACTTATTACTAGCTTTAAATGGTTTGAAAATCGCAGAATTGATTTTAAGCTGAATA
127 CCTAAAAAAACTTATTACTAGCTTTAAATGGTTTGAAAATCGCAGAATTGATTTTAAGCTAAAT-
* *
3265 TTTT-TACATTTTTTA-TTAAAACAGATTATATTTGACTATTTGCCTCGAGTAACGT-AAAGCAA
191 TTTTGTACA-TTTTTACTTAAAACAGATTATATTTGACTATTTGCCTCAAGAAACGTGAAA-CAA
*
3327 AAGCCATCCATTAGTAAGAAAAGTCCATTTATAGTCACTTAAGCCTTAAAAAGCCTTAT
254 AAGCCATCCATTAGTAAGAAAAGTCCATTTATAGTCACTTAAGCCATAAAAAGCCTTAT
3386 TTCTCGCTTT
Statistics
Matches: 257, Mismatches: 48, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
341 8 0.03
342 238 0.93
343 11 0.04
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.37
Consensus pattern (342 bp):
TATTGATTTTAGATTAAATTTTTTTATATTTTTAGTTAAAATATATCATAACTAAATGTCTACCT
AGGGAAACATGAAGCAAAAGCCATCCATTTGTAGAAAAAGTCAATTTATTTGCACTCAAGCCCTA
AAAAAACTTATTACTAGCTTTAAATGGTTTGAAAATCGCAGAATTGATTTTAAGCTAAATTTTTG
TACATTTTTACTTAAAACAGATTATATTTGACTATTTGCCTCAAGAAACGTGAAACAAAAGCCAT
CCATTAGTAAGAAAAGTCCATTTATAGTCACTTAAGCCATAAAAAGCCTTATCATTCGCTTTGAA
TGGTTCTATATTCCCAT
Done.