Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400461.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3658.0, 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: 2978
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.30
Warning! 497 characters in sequence are not A, C, G, or T
Found at i:714 original size:172 final size:170
Alignment explanation
Indices: 63--787 Score: 639
Period size: 170 Copynumber: 4.3 Consensus size: 170
53 AAACGAGTAC
* ** * **** * ** *
63 AAAAA-GTCATTCATTGTGAAAAAAAGTCCATTTATAGTGTTTCATTTCTTCGGAAGCCTAATTA
1 AAAAAGGTAATTCATTGCAAAAAAAAGTCCACTTATAGTCACCCATTCCTTCAAAAGCCTTATTA
* * *
127 CTCGCTTTAAATAGTTTTATAATCT-AATAATTGATTTTAAGTTGAATTTTTTTACATTTTCGTT
66 CTC-ATTTAAATAGTTTTATAATCTCAA-AATTGATTTTAAGTTGAATTTTTTCACATTTTAGTT
* * *
191 AAAACAGACTATAATTGAATGTCTACCTTGAGAAACAT-ATGG
129 AAAACAGATTATAATTGAATGTCTACCTCGAGAAACATGA-AG
* * * * * *
233 AAAAAGCT-ATTCATTG-ATAAGAAATTACCAAC-TATAGTCTCTCATTCCTT-AGAAAGCCTTA
1 AAAAAGGTAATTCATTGCAAAAAAAAGT-CC-ACTTATAGTCACCCATTCCTTCA-AAAGCCTTA
* * * *
294 TTACTCACTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTGAATTTCTTCTACATTTTA
63 TTACTCA-TTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTGAATTTTTTC-ACATTTTA
* * * * * * *
359 GTAAAAACATATTATAATTAAATGTTTACTTTGAGAAACGTG-AG
126 GTTAAAACAGATTATAATTGAATGTCTACCTCGAGAAACATGAAG
* * ** * * * *
403 AAAAAGG-CATTTATTGGTAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTG
1 AAAAAGGTAATTCATTGCAAAAAAAAGTCCACTTATAGTCACCCATTCCTTCAAAAGCCTTATTA
* * * * * *** *
467 TTTATTTAAATGGTTTTATAATCTCATAATTCATTTTAAGTTGAATTTCTTTTGTA-TTTATGGT
66 CTCATTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTGAATTT-TTTCACATTTTA-GTT
*
531 AAAAGTAGATTATAATTGAATGTCTACCTCGAGAAACATGAAG
129 AAAA-CAGATTATAATTGAATGTCTACCTCGAGAAACATGAAG
* * *
574 AAAAAGGTAATT-ACTGACAAAAAAAAGTCCACTTATAGTCACCCATTCTTTCAAAAGCCTTATC
1 AAAAAGGTAATTCATTG-CAAAAAAAAGTCCACTTATAGTCACCCATTCCTTCAAAAGCCTTATT
* * **
638 ACTCATTTTAAATAGTTTTGTAATCTCAAAAATGATTTTAAGTTGAATGGTTTCACATTTTTAGT
65 ACTCA-TTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTGAATTTTTTCACA-TTTTAGT
* *
703 TAAAATAGATTATAATTGAATGTCTACCTCAAGAAACATGAAG
128 TAAAACAGATTATAATTGAATGTCTACCTCGAGAAACATGAAG
* * *
746 AAAAAGG-CATTCATTGGC-AAAAAAAGTTCATTTATAGTCACC
1 AAAAAGGTAATTCATT-GCAAAAAAAAGTCCACTTATAGTCACC
788 AATTNNNNNN
Statistics
Matches: 449, Mismatches: 83, Indels: 45
0.78 0.14 0.08
Matches are distributed among these distances:
168 4 0.01
169 56 0.12
170 158 0.35
171 87 0.19
172 96 0.21
173 44 0.10
174 4 0.01
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (170 bp):
AAAAAGGTAATTCATTGCAAAAAAAAGTCCACTTATAGTCACCCATTCCTTCAAAAGCCTTATTA
CTCATTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTGAATTTTTTCACATTTTAGTTAA
AACAGATTATAATTGAATGTCTACCTCGAGAAACATGAAG
Found at i:717 original size:342 final size:340
Alignment explanation
Indices: 132--787 Score: 792
Period size: 342 Copynumber: 1.9 Consensus size: 340
122 AATTACTCGC
* *
132 TTTAAATAGTTTTATAATCTAATAATTGATTTTAAGTTGAATTTTTTTACATTTTCGTTAAAACA
1 TTTAAATAGTTTTATAATCTAATAATTCATTTTAAGTTGAATTTTTTTACATTTTCGGTAAAACA
* * * * * *
197 GACTATAATTGAATGTCTACCTTGAGAAACATATGGAAAAAGCTATTCATTGATAAGAAATTACC
66 GACTATAATTGAATGTCTACCTCGAGAAACATATAGAAAAAGCTATTCACTGAAAAAAAAGTACC
* * * * *
262 AACTATAGTCTCTCATTCCTTAGAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAA
131 AACTATAGTCACCCATTCCTTAGAAAGCCTTATCACTCACTTTAAATAGTTTTATAATCTCAAAA
* * * * * **
327 TTAATTTTAAGTTGAATTTCTTCTACATTTTAGTAAAAACATATTATAATTAAATGTTTACTTTG
196 ATAATTTTAAGTTGAATGTCTTCTACATTTTAGTAAAAACAGATTATAATTAAATGTCTACCTCA
* * * *
392 AGAAACGTG-AGAAAAAGGCATTTATTGGTAAGAAAAG-TCTATTTATAGTCACCCATTCCTTCA
261 AGAAACATGAAGAAAAAGGCATTCATTGGCAAAAAAAGTTC-ATTTATAGTCACCCATTCCTTCA
455 AAAGCCTTATTGTTTA
325 AAAGCCTTATTGTTTA
* * **
471 TTTAAATGGTTTTATAATCTCATAATTCATTTTAAGTTGAATTTCTTTTGTATTTAT-GGTAAAA
1 TTTAAATAGTTTTATAATCTAATAATTCATTTTAAGTTGAATTT-TTTTACATTT-TCGGTAAAA
* * *
535 GTAGATTATAATTGAATGTCTACCTCGAGAAACATGA-AGAAAAAGGTAATT-ACTGACAAAAAA
64 -CAGACTATAATTGAATGTCTACCTCGAGAAACAT-ATAGAAAAAGCT-ATTCACTG--AAAAAA
* * *
598 AAGT-CC-ACTTATAGTCACCCATTCTTTCA-AAAGCCTTATCACTCATTTTAAATAGTTTTGTA
124 AAGTACCAAC-TATAGTCACCCATTCCTT-AGAAAGCCTTATCACTCACTTTAAATAGTTTTATA
* * * *
660 ATCTCAAAAATGATTTTAAGTTGAATGGT-TTC-ACATTTTTAGTTAAAATAGATTATAATTGAA
187 ATCTCAAAAATAATTTTAAGTTGAAT-GTCTTCTACA-TTTTAGTAAAAACAGATTATAATTAAA
723 TGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAAAAAAGTTCATTTATAGTCACC
250 TGTCTACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAAAAAAGTTCATTTATAGTCACC
788 AATTNNNNNN
Statistics
Matches: 266, Mismatches: 38, Indels: 22
0.82 0.12 0.07
Matches are distributed among these distances:
339 41 0.15
340 14 0.05
341 48 0.18
342 114 0.43
343 47 0.18
344 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (340 bp):
TTTAAATAGTTTTATAATCTAATAATTCATTTTAAGTTGAATTTTTTTACATTTTCGGTAAAACA
GACTATAATTGAATGTCTACCTCGAGAAACATATAGAAAAAGCTATTCACTGAAAAAAAAGTACC
AACTATAGTCACCCATTCCTTAGAAAGCCTTATCACTCACTTTAAATAGTTTTATAATCTCAAAA
ATAATTTTAAGTTGAATGTCTTCTACATTTTAGTAAAAACAGATTATAATTAAATGTCTACCTCA
AGAAACATGAAGAAAAAGGCATTCATTGGCAAAAAAAGTTCATTTATAGTCACCCATTCCTTCAA
AAGCCTTATTGTTTA
Found at i:1438 original size:169 final size:173
Alignment explanation
Indices: 1155--1465 Score: 445
Period size: 170 Copynumber: 1.8 Consensus size: 173
1145 NNNATCATTT
*
1155 AAAGTGAGTAATAAGGCTTTTGAAAGAATGAGTGACTATAAATGAACGTTTCTTACCAACGAATG
1 AAAGTGAGTAATAACGCTTTTGAAAGAATGAGTGACTATAAATGAACGTTTCTTACCAACGAATG
* * * * *
1220 CCTTTTCCTTCATGTTTCACAAGTTAGACATTCAATTAGAGTTTATTTTAACT-AAAATGAAAAA
66 ACTTTTCCATCATGTTTCACAAGGTAGACATTCAATTAGAATCTATTTTAACTAAAAATGAAAAA
*
1284 TAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAA
131 CAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAA
* * * *
1327 AAAGTG-G-AATAACGCTTTTGAAGGAATG-GATGACTATAAATGAACTTTTCTTGCCAATGAAT
1 AAAGTGAGTAATAACGCTTTTGAAAGAATGAG-TGACTATAAATGAACGTTTCTTACCAACGAAT
* *
1389 -ACTATTT-CATCATGTTTCACAAGGTAGACATTCAATTATAATCTATTTTAACTAAAAATGTAA
65 GACT-TTTCCATCATGTTTCACAAGGTAGACATTCAATTAGAATCTATTTTAACTAAAAATGAAA
1452 AACAATTCAACTTA
129 AACAATTCAACTTA
1466 NNNNNNNNNN
Statistics
Matches: 123, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
169 44 0.36
170 72 0.59
171 1 0.01
172 6 0.05
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.34
Consensus pattern (173 bp):
AAAGTGAGTAATAACGCTTTTGAAAGAATGAGTGACTATAAATGAACGTTTCTTACCAACGAATG
ACTTTTCCATCATGTTTCACAAGGTAGACATTCAATTAGAATCTATTTTAACTAAAAATGAAAAA
CAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAA
Found at i:2013 original size:171 final size:170
Alignment explanation
Indices: 1698--2073 Score: 391
Period size: 171 Copynumber: 2.2 Consensus size: 170
1688 NNNNNNNNNN
* *
1698 AAATGGACTTTTCTTACCAATGAATGCCTTATTCTTCACATTTCTCAAAGTAGACATTTAATTAT
1 AAATGGACTTTTCTTACCAATGAATGGCTT-TT-TTCACATTTCTCAAAGTAGACATTCAATTAT
* * * * **
1763 CATATGTTTTTACAAAAAATGTAGAAGAAATTCAATTTAAAATCAATTATGAGATTATAAAACNN
64 CATATGTTTTAACAAAAAATATAGAACAAATTCAATGTAAAATCAATTATGAGATTATAAAACTA
******** * *
1828 NNNNNNNNGAGTAATAAAGCTTTTGAAGGAAT-AGGAGACTAT
129 TCTAAAGCGAGTAATAAAGCTTTTGAAGAAATGA-GACACTAT
** * *
1870 AGTTGGACATTTCTTACCAATGAATGGCTTTTTTTACATGTTTCTCAAAGGTAGACATTCAATTA
1 AAATGGACTTTTCTTACCAATGAATGGCTTTTTTCACA--TTTCTCAAA-GTAGACATTCAATTA
* **
1935 T-AGTTTGTTTTAATGAAAAATATA-AACAAATT-AATGTAAAATCAATTATGAGATTATAAAAC
63 TCA-TATGTTTTAACAAAAAATATAGAACAAATTCAATGTAAAATCAATTATGAGATTATAAAAC
* *
1997 TATCTAAAGCGAGTAATTAGGCTTTTGAAGAAATGAGACACTAT
127 TATCTAAAGCGAGTAATAAAGCTTTTGAAGAAATGAGACACTAT
* * *
2041 AAATAGACTTTTCTTCCCAATAAATGGCTTTTT
1 AAATGGACTTTTCTTACCAATGAATGGCTTTTT
2074 ATACTCATTT
Statistics
Matches: 166, Mismatches: 33, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
170 5 0.03
171 86 0.52
172 44 0.27
173 31 0.19
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (170 bp):
AAATGGACTTTTCTTACCAATGAATGGCTTTTTTCACATTTCTCAAAGTAGACATTCAATTATCA
TATGTTTTAACAAAAAATATAGAACAAATTCAATGTAAAATCAATTATGAGATTATAAAACTATC
TAAAGCGAGTAATAAAGCTTTTGAAGAAATGAGACACTAT
Done.