Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401303.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4444.0, 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: 2176
ACGTcount: A:0.26, C:0.09, G:0.08, T:0.28
Warning! 640 characters in sequence are not A, C, G, or T
Found at i:845 original size:167 final size:167
Alignment explanation
Indices: 590--894 Score: 443
Period size: 167 Copynumber: 1.8 Consensus size: 167
580 AATAGTTTTA
* *
590 TAATCTCATAATTGATTTTAAGTTGATTTTTTTACATTTCTCATTAAAACAGATTATAATTAAAT
1 TAATCTCATAATTAATTTTAAGTTGATTTTTTTA-ATTTCTCATTAAAACAGACTATAATTAAAT
* * * *
655 GCTTGCCTCGAGAAACATGTAGAAAAACCCATTTATTTGGA-AGAAAAGTCCATTTGTAGTCTCT
65 GCCTGCCTCAAAAAACATGTAGAAAAACCCATTTATTT-GATAGAAAAGTCCATTTATAGTCTCT
719 CATTCCTTCAAAAACTTTATTATTGCTTTAAATGAATTT
129 CATTCCTTCAAAAACTTTATTATTGCTTTAAATGAATTT
* * *
758 TAATCTCATAATTAATTTTAAGTTGGATTTTTTT-ATTTTTTATTAAAACAGACTATAATTGAAT
1 TAATCTCATAATTAATTTTAAGTT-GATTTTTTTAATTTCTCATTAAAACAGACTATAATTAAAT
* * * * *
822 GCCTGCCTTAAAAAACTTGTAGAAAAACCTATTTATTTGATAGAAAAGTCCATTTATATTCTTTC
65 GCCTGCCTCAAAAAACATGTAGAAAAACCCATTTATTTGATAGAAAAGTCCATTTATAGTCTCTC
887 ATTCCTTC
130 ATTCCTTC
895 GAAAGCCTTA
Statistics
Matches: 121, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
166 2 0.02
167 87 0.72
168 23 0.19
169 9 0.07
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (167 bp):
TAATCTCATAATTAATTTTAAGTTGATTTTTTTAATTTCTCATTAAAACAGACTATAATTAAATG
CCTGCCTCAAAAAACATGTAGAAAAACCCATTTATTTGATAGAAAAGTCCATTTATAGTCTCTCA
TTCCTTCAAAAACTTTATTATTGCTTTAAATGAATTT
Found at i:1760 original size:170 final size:169
Alignment explanation
Indices: 1316--1842 Score: 501
Period size: 170 Copynumber: 3.1 Consensus size: 169
1306 NNNNNNNNNN
* * *
1316 TAATTGATTTTGAGTTGAATTTTTTACATTTTTTATTAAAATAGACTAAAATT-AATTGCCTACC
1 TAATTGATTTTAAGTTGAATTTTTTACATTTTTGATTAAAATAGACTATAATTGAA-TGCCTACC
* * *
1380 TTAGGAAACGTGT--AAAAATCTCATTGT-TTTAAAAGAAAAGTCCATTTATAGTTTCCCATTCC
65 TTAGGAAACGTATAGAAAAAACT-ATT-TATTTGAAAGAAAAGTCCATTTATAG-TTCCCATTCC
* *
1442 TTCAAAAGTCTTATTAGTTACTTTAAATGATTTTACAATCTCA
127 TTCAAAAGCCTTATTACTTACTTTAAATGATTTTACAATCTCA
* * * * * **
1485 TAATTGATTGTAAGTTAAATTTTTTTTACATTTTTGATTAAAACAAAATATAATTGAATGTTTAC
1 TAATTGATTTTAAGTTGAA--TTTTTTACATTTTTGATTAAAATAGACTATAATTGAATGCCTAC
** * ** * * * * *****
1550 CCAATGAAACGTGA-AGAAAAAAGAATTCATTAGCAAGAAAAGTTCATTTATA-TTCACNNNNNN
64 CTTAGGAAACGT-ATAGAAAAAACTATTTATTTGAAAGAAAAGTCCATTTATAGTTC-C-CATTC
**** * * *
1613 NNNNAAAAGCCTTATTACTTGCTTTAAATGATTTTAGAATCTTA
126 CTTCAAAAGCCTTATTACTTACTTTAAATGATTTTACAATCTCA
*
1657 TAATTGATTTTAAGTTGAATGTTTTACATTTTTGATTAAAATAGACTATAATTGAATGCCTACCT
1 TAATTGATTTTAAGTTGAATTTTTTACATTTTTGATTAAAATAGACTATAATTGAATGCCTACCT
* *
1722 T-GAGAAACGTATAGAAAAACCTATTTATTTGAAAGAAAAGTCCATTTACAGTCTCCCATTCCTT
66 TAG-GAAACGTATAGAAAAAACTATTTATTTGAAAGAAAAGTCCATTTATAGT-TCCCATTCCTT
* ** * *
1786 CAAAAGCCTTATTACTCACGCTAAATGGTTTTATAATCTCA
129 CAAAAGCCTTATTACTTACTTTAAATGATTTTACAATCTCA
*
1827 TAATTGATTCTAAGTT
1 TAATTGATTTTAAGTT
1843 NNNNNNNNNN
Statistics
Matches: 273, Mismatches: 72, Indels: 25
0.74 0.19 0.07
Matches are distributed among these distances:
169 17 0.06
170 127 0.47
171 46 0.17
172 78 0.29
173 5 0.02
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (169 bp):
TAATTGATTTTAAGTTGAATTTTTTACATTTTTGATTAAAATAGACTATAATTGAATGCCTACCT
TAGGAAACGTATAGAAAAAACTATTTATTTGAAAGAAAAGTCCATTTATAGTTCCCATTCCTTCA
AAAGCCTTATTACTTACTTTAAATGATTTTACAATCTCA
Found at i:1932 original size:172 final size:170
Alignment explanation
Indices: 1412--1964 Score: 511
Period size: 172 Copynumber: 3.2 Consensus size: 170
1402 ATTGTTTTAA
** * *
1412 AAGAAAAGTCCATTTATAGTTTCCCATTCCTTCAAAAGTCTTATTAGTTACTTTAAATGATTTTA
1 AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTTACTTTAAATGATTTTA
* *
1477 CAATCTCATAATTGATTGTAAGTTAAATTTTTTTTACATTTTTGATTAAAACAAAATATAATTGA
66 CAATCTCATAATTGATTCTAAGTTAAA--TGTTTTACATTTTTGATTAAAACAAAATATAATTGA
* * * *
1542 ATGTTTACCCAATGAAACGTGAAGAAAAAAGAATTCATTAGC
129 ATGTCTACCTAATGAAAAGTGAAGAAAAAAGCATTCATTAGC
* * ********** *
1584 AAGAAAAGTTCATTTATATTCACNNNNNNNNNNAAAAGCCTTATTACTTGCTTTAAATGATTTTA
1 AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTTACTTTAAATGATTTTA
* * * * * * *
1649 GAATCTTATAATTGATTTTAAGTTGAATGTTTTACATTTTTGATTAAAATAGACTATAATTGAAT
66 CAATCTCATAATTGATTCTAAGTTAAATGTTTTACATTTTTGATTAAAACAAAATATAATTGAAT
* * * * *
1714 GCCTACCT--TGAGAAACGT-ATAG-AAAAACCTATTTATTTGA
131 GTCTACCTAATGA-AAA-GTGA-AGAAAAAAGC-ATTCATTAGC
* * * ** *
1754 AAGAAAAGTCCATTTACAGTCTCCCATTCCTTCAAAAGCCTTATTACTCACGCTAAATGGTTTTA
1 AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTTACTTTAAATGATTTTA
* ******** **
1819 TAATCTCATAATTGATTCTAAGTTNNNNNNNNNNTACATTTTTGGCTAAAACAAAATATAATTGA
66 CAATCTCATAATTGATTCTAAGTT--AAATGTTTTACATTTTTGATTAAAACAAAATATAATTGA
*
1884 ATGTCTACCTAATGAAAAGTGGAGAAAAAAGCATTCATTAGC
129 ATGTCTACCTAATGAAAAGTGAAGAAAAAAGCATTCATTAGC
* *
1926 AAGAAAAGTCTATTTATATTCACCCATTCCTTCAAAAGC
1 AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGC
1965 TTTTATAATC
Statistics
Matches: 292, Mismatches: 79, Indels: 20
0.75 0.20 0.05
Matches are distributed among these distances:
168 3 0.01
169 8 0.03
170 117 0.40
172 152 0.52
173 9 0.03
174 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.35
Consensus pattern (170 bp):
AAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTTACTTTAAATGATTTTA
CAATCTCATAATTGATTCTAAGTTAAATGTTTTACATTTTTGATTAAAACAAAATATAATTGAAT
GTCTACCTAATGAAAAGTGAAGAAAAAAGCATTCATTAGC
Found at i:1943 original size:342 final size:331
Alignment explanation
Indices: 1316--1948 Score: 781
Period size: 342 Copynumber: 1.9 Consensus size: 331
1306 NNNNNNNNNN
* * *
1316 TAATTGATTTTGAGTTGAATTTTTTACATTTTTTATTAAAATAGACTAAAATTAATTGCCTACCT
1 TAATTGATTTTAAGTTGAATGTTTTACATTTTTGATTAAAATAGACTAAAATTAATTGCCTACCT
* * * *
1381 TAGGAAACGTGTAAAAATCTCATTGTTTTAAAAGAAAAGTCCATTTATAGTTTCCCATTCCTTCA
66 TAGGAAACGTATAAAAACCTCATTGTTTTAAAAGAAAAGTCCATTTACAGTCTCCCATTCCTTCA
* * * ** *
1446 AAAGTCTTATTAGTTACTTTAAATGATTTTACAATCTCATAATTGATTGTAAGTTAAATTTTTTT
131 AAAGCCTTATTACTCACGCTAAATGATTTTACAATCTCATAATTGATTCTAAGTTAAATTTTTTT
* * *
1511 TACATTTTTGATTAAAACAAAATATAATTGAATGTTTACCCAATGAAACGTGAAGAAAAAAGAAT
196 TACATTTTTGACTAAAACAAAATATAATTGAATGTCTACCCAATGAAAAGTGAAGAAAAAAGAAT
1576 TCATTAGCAAGAAAAGTTCATTTATATTCACNNNNNNNNNNAAAAGCCTTATTACTTGCTTTAAA
261 TCATTAGCAAGAAAAGTTCATTTATATTCAC----------AAAAGCCTTATTACTTGCTTTAAA
1641 TGATTTTAGAATCTTA
316 TGATTTTAGAATCTTA
*
1657 TAATTGATTTTAAGTTGAATGTTTTACATTTTTGATTAAAATAGACTATAATTGAA-TGCCTACC
1 TAATTGATTTTAAGTTGAATGTTTTACATTTTTGATTAAAATAGACTAAAATT-AATTGCCTACC
*
1721 TT-GAGAAACGTATAGAAAAACCT-ATT-TATTTGAAAGAAAAGTCCATTTACAGTCTCCCATTC
65 TTAG-GAAACGTAT--AAAAACCTCATTGT-TTTAAAAGAAAAGTCCATTTACAGTCTCCCATTC
* * *****
1783 CTTCAAAAGCCTTATTACTCACGCTAAATGGTTTTATAATCTCATAATTGATTCTAAGTTNNNNN
126 CTTCAAAAGCCTTATTACTCACGCTAAATGATTTTACAATCTCATAATTGATTCTAAGTTAAATT
***** * * *
1848 NNNNNTACATTTTTGGCTAAAACAAAATATAATTGAATGTCTACCTAATGAAAAGTGGAGAAAAA
191 TTTTTTACATTTTTGACTAAAACAAAATATAATTGAATGTCTACCCAATGAAAAGTGAAGAAAAA
*
1913 AGCATTCATTAGCAAGAAAAG-TCTATTTATATTCAC
256 AGAATTCATTAGCAAGAAAAGTTC-ATTTATATTCAC
1949 CCATTCCTTC
Statistics
Matches: 252, Mismatches: 34, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
340 1 0.00
341 70 0.28
342 174 0.69
343 7 0.03
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.37
Consensus pattern (331 bp):
TAATTGATTTTAAGTTGAATGTTTTACATTTTTGATTAAAATAGACTAAAATTAATTGCCTACCT
TAGGAAACGTATAAAAACCTCATTGTTTTAAAAGAAAAGTCCATTTACAGTCTCCCATTCCTTCA
AAAGCCTTATTACTCACGCTAAATGATTTTACAATCTCATAATTGATTCTAAGTTAAATTTTTTT
TACATTTTTGACTAAAACAAAATATAATTGAATGTCTACCCAATGAAAAGTGAAGAAAAAAGAAT
TCATTAGCAAGAAAAGTTCATTTATATTCACAAAAGCCTTATTACTTGCTTTAAATGATTTTAGA
ATCTTA
Done.