Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400476.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3672.0, 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: 2098
ACGTcount: A:0.25, C:0.09, G:0.10, T:0.26
Warning! 637 characters in sequence are not A, C, G, or T
Found at i:1231 original size:172 final size:170
Alignment explanation
Indices: 933--1257 Score: 404
Period size: 172 Copynumber: 1.9 Consensus size: 170
923 NNNNNNNNNN
* * * * *
933 TTGAAGGAATGGGTGACTATAAATGGAATTTTTTTGCTAATGAATGCTTTTTTTCTAGGTTTCTC
1 TTGAAAGAATGGGTGACTATAAATGGAATTTTCTTGCCAATGAAAGCTTTTTTTCTAAGTTTCTC
* ** ** * * * *
998 GAGGTAGACATTCAATTATTGTCTATTTTCGTCAAAAATGTAAAAAAATTCAACTTAAAATCAAT
66 GAGGCAGACATTCAACAATAATCTATTTTCGCCAAAAATGCAAAAAAAATCAACCTAAAATCAAT
1063 TATGAAATTATAAAACCATTTAAAGCGTGTAATAAGGCTT
131 TATGAAATTATAAAACCATTTAAAGCGTGTAATAAGGCTT
*
1103 TTGAAAGAATGGGTTACTATAAATGGACA-TTTCTTGCCAATGAAAGCCTTTTTCTT-TAAGTTT
1 TTGAAAGAATGGGTGACTATAAATGGA-ATTTTCTTGCCAATGAAAG-CTTTTT-TTCTAAGTTT
* *
1166 CTTGAGGCAGACATTCAACAATAATCTGTTTTAC-CCAAAAAATGCAAAAAAAATCAACCTAAAA
63 CTCGAGGCAGACATTCAACAATAATCTATTTT-CGCC-AAAAATGCAAAAAAAATCAACCTAAAA
* * *
1230 TCAATTTTGAGATTATAAAACTATTTAA
126 TCAATTATGAAATTATAAAACCATTTAA
1258 CCATTCCTTC
Statistics
Matches: 130, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
170 39 0.30
171 39 0.30
172 52 0.40
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (170 bp):
TTGAAAGAATGGGTGACTATAAATGGAATTTTCTTGCCAATGAAAGCTTTTTTTCTAAGTTTCTC
GAGGCAGACATTCAACAATAATCTATTTTCGCCAAAAATGCAAAAAAAATCAACCTAAAATCAAT
TATGAAATTATAAAACCATTTAAAGCGTGTAATAAGGCTT
Found at i:1781 original size:172 final size:171
Alignment explanation
Indices: 1263--2098 Score: 688
Period size: 172 Copynumber: 4.9 Consensus size: 171
1253 TTTAACCATT
* * * * * * * *
1263 CCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATATTCTCCAAATTGATTTCAATTTCAAT
1 CCTTCAAAAGCCTTATTACTTACTTTAAATGGTTTTATAATCTCAAAATTAATTTTAAGTTGAAT
* ** * * * * * * *
1328 TCTTTGTACATTTTTCATTAAAACAGATTAGAATAGAATGTCCACCTTGAGAAA-AGTGAAAAAA
66 T-TTTTTACATTTTTGGTTAAAAAAGACTATAATTGAATGTCTACCATGAGAAACA-TG-AAGAA
* * * **
1392 AAAAG-AATTCATTGGCAAGAAAAGTCCATTTATATTCACCCATT
128 AAAAGCAA-CCATTGGCAAGAAAAGTCCATTTATAGTCACTCAAG
** ** * ** * * *
1436 ATTTCCAAAA-TTTTATTACTCACTTTAAAAAGTTTTATAACCTCATAATTGATTTT-AGATTGA
1 CCTT-CAAAAGCCTTATTACTTACTTTAAATGGTTTTATAATCTCAAAATTAATTTTAAG-TTGA
* ** ** * * * * * *
1499 A-TTTTTGATGTTTTTGG-TAAGAATTGATTATAATTGAATGTTTGCCTTGGGAAACGTGAAGAA
64 ATTTTTTTACATTTTTGGTTAA-AAAAGACTATAATTGAATGTCTACCATGAGAAACATGAAGAA
* * * ** *
1562 AAATG-TACTCATTGGCAAGAAAAGTCTATTTATAGTTGCTTAAG
128 AAAAGCAAC-CATTGGCAAGAAAAGTCCATTTATAGTCACTCAAG
* * * * *
1606 CCTTCAAAAGCCTTATTACTCACTTTAAATGGCTTTATAATTTCAAAATTGATTTTAAGTTGAGT
1 CCTTCAAAAGCCTTATTACTTACTTTAAATGGTTTTATAATCTCAAAATTAATTTTAAGTTGAAT
* * * * * *
1671 TTTTTTAACATTTTTGGTTAAAAAAGTCTATAATTGAGT-TTTGACCATGGGGAACATGAAG-CA
66 TTTTTT-ACATTTTTGGTTAAAAAAGACTATAATTGAATGTCT-ACCATGAGAAACATGAAGAAA
*
1734 AAGGCCAACCATTGGCATAG-AAAGTCCATTTATAGTCACTCAAG
129 AAAG-CAACCATTGGCA-AGAAAAGTCCATTTATAGTCACTCAAG
* * * *
1778 CCTTCAAAAGCCCTATTACTTGCTTTAAATGGTTTTATAAACT-AATAATTTATTTTAAGTTGAA
1 CCTTCAAAAGCCTTATTACTTACTTTAAATGGTTTTATAATCTCAA-AATTAATTTTAAGTTGAA
* * * *
1842 TTTTTTTACATTTTTGGTTAAAACAGACTAGAATTGAATGTCTACCTTGAGAAACGTGAAGAAAA
65 TTTTTTTACATTTTTGGTTAAAAAAGACTATAATTGAATGTCTACCATGAGAAACATGAAGAAAA
** * *
1907 AAGCATTCATTAGCAAGAAAAGTCCCTTTATAGTCACTCATA-
130 AAGCAACCATTGGCAAGAAAAGTCCATTTATAGTCACTCA-AG
* * *
1949 CCTTCAAACAGCCTTATTAGTTACTTTAAATGGTTTTATAATGTCATAATTAATTTTAAGTTGAA
1 CCTTCAAA-AGCCTTATTACTTACTTTAAATGGTTTTATAATCTCAAAATTAATTTTAAGTTGAA
* * * * * *
2014 TTTTTTTATATTTTTGGCTAAAATAGACTATAATTGAATGCCTACCTTGAGAAACATAAAGAAAA
65 TTTTTTTACATTTTTGGTTAAAAAAGACTATAATTGAATGTCTACCATGAGAAACATGAAGAAAA
**
2079 AAGCATTCATTGGCAAGAAA
130 AAGCAACCATTGGCAAGAAA
Statistics
Matches: 535, Mismatches: 107, Indels: 43
0.78 0.16 0.06
Matches are distributed among these distances:
169 5 0.01
170 85 0.16
171 132 0.25
172 256 0.48
173 52 0.10
174 5 0.01
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (171 bp):
CCTTCAAAAGCCTTATTACTTACTTTAAATGGTTTTATAATCTCAAAATTAATTTTAAGTTGAAT
TTTTTTACATTTTTGGTTAAAAAAGACTATAATTGAATGTCTACCATGAGAAACATGAAGAAAAA
AGCAACCATTGGCAAGAAAAGTCCATTTATAGTCACTCAAG
Found at i:2092 original size:343 final size:339
Alignment explanation
Indices: 1263--2098 Score: 815
Period size: 343 Copynumber: 2.4 Consensus size: 339
1253 TTTAACCATT
* * * * *
1263 CCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATATTCTCCAAATTGATTTCAATTTCAAT
1 CCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCT-CAAATTGATTTTAAGTTGAAT
* ** * * * * *
1328 TCTTTGTACATTTTTCATTAAAACAGATTAGAATAGAATGTCC-ACCTTGAGAAA-AGTGAAAAA
65 T-TTTTTACATTTTTGGTTAAAAAAGACTATAATTGAATG-CCTACCTTGAGAAACA-T-AAAGA
* * ** * ***
1391 AAAAAGAATTCATTGGCAAGAAAAGTCCATTTATATTCACCCATTATTTCCAAAATTTTATTACT
126 AAAAAGCATTCATTGGCAAG-AAAGTCCATTTATAGTCACCCAAGACTTCCAAAACCCTATTACT
* * **
1456 CACTTTAAAAAGTTTTATAACCTCATAATTGATTTTAGATTGAATTTTTGATGTTTTTGGTAAGA
190 CACTTTAAAAAGTTTTATAAACTAATAATTGATTTTAGATTGAATTTTTGACATTTTTGGTAAGA
** * * * * * * * *
1521 ATTGATTATAATTGAATGTTTGCCTTGGGAAACGTGAAGAAAAATGTACTCATTGGCAAGAAAAG
255 ACAGACTAGAATTGAATGTCTACCTTGAGAAACGTGAAGAAAAAAGCACTCATTAGCAAGAAAAG
* ** *
1586 TCTATTTATAGTTGCTTAAG
320 TCCATTTATAGTCACTCAAG
* * *
1606 CCTTCAAAAGCCTTATTACTCACTTTAAATGGCTTTATAATTTCAAAATTGATTTTAAGTTGAGT
1 CCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTC-AAATTGATTTTAAGTTGAAT
* * ** * * * * *
1671 TTTTTTAACATTTTTGGTTAAAAAAGTCTATAATTGAGT-TTTGACCATGGGGAACATGAAG-CA
65 TTTTTT-ACATTTTTGGTTAAAAAAGACTATAATTGAATGCCT-ACCTTGAGAAACATAAAGAAA
* ** * *
1734 AAGGCCAACCATTGGCATAGAAAGTCCATTTATAGTCACTCAAGCCTT-CAAAAGCCCTATTACT
128 AAAG-CATTCATTGGCA-AGAAAGTCCATTTATAGTCACCCAAGACTTCCAAAA-CCCTATTACT
** ** * *
1798 TGCTTTAAATGGTTTTATAAACTAATAATTTATTTTA-AGTTGAATTTTTTTACATTTTTGGTTA
190 CACTTTAAAAAGTTTTATAAACTAATAATTGATTTTAGA-TTGAA-TTTTTGACATTTTTGG-TA
*
1862 A-AACAGACTAGAATTGAATGTCTACCTTGAGAAACGTGAAGAAAAAAGCATTCATTAGCAAGAA
252 AGAACAGACTAGAATTGAATGTCTACCTTGAGAAACGTGAAGAAAAAAGCACTCATTAGCAAGAA
*
1926 AAGTCCCTTTATAGTCACTCATA-
317 AAGTCCATTTATAGTCACTCA-AG
* * * *
1949 CCTTCAAACAGCCTTATTAGTTACTTTAAATGGTTTTATAATGTCATAATTAATTTTAAGTTGAA
1 CCTTCAAA-AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCA-AATTGATTTTAAGTTGAA
* * *
2014 TTTTTTTATATTTTTGGCTAAAATAGACTATAATTGAATGCCTACCTTGAGAAACATAAAGAAAA
64 TTTTTTTACATTTTTGGTTAAAAAAGACTATAATTGAATGCCTACCTTGAGAAACATAAAGAAAA
2079 AAGCATTCATTGGCAAGAAA
129 AAGCATTCATTGGCAAGAAA
Statistics
Matches: 392, Mismatches: 85, Indels: 33
0.77 0.17 0.06
Matches are distributed among these distances:
341 10 0.03
342 85 0.22
343 232 0.59
344 65 0.17
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (339 bp):
CCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAAATTGATTTTAAGTTGAATT
TTTTTACATTTTTGGTTAAAAAAGACTATAATTGAATGCCTACCTTGAGAAACATAAAGAAAAAA
GCATTCATTGGCAAGAAAGTCCATTTATAGTCACCCAAGACTTCCAAAACCCTATTACTCACTTT
AAAAAGTTTTATAAACTAATAATTGATTTTAGATTGAATTTTTGACATTTTTGGTAAGAACAGAC
TAGAATTGAATGTCTACCTTGAGAAACGTGAAGAAAAAAGCACTCATTAGCAAGAAAAGTCCATT
TATAGTCACTCAAG
Done.