Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398897.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2179.0, 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, 665
Length: 1109
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Found at i:427 original size:172 final size:171
Alignment explanation
Indices: 1--1109 Score: 830
Period size: 172 Copynumber: 6.5 Consensus size: 171
* * * *** * * * *
1 TAAAACCAATTTTGAGA-TTATAAAACCATTTAAATTGAGTAATAAGGCTTCCGAAGGAATGGGG
1 TAAAATCAATTATGAGACTTATAAAACAATTTAAAGCAAGTAATAAGGCTTTCGAAAGAATAGTG
* * * * * * * ** * ** **
65 CATTATAAATGGAATTTTCATCCCAAAGAATGACTTTTTCTACATGTTTCCTGAGACAGGCATTC
66 -ACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACATTTCTTGAGGTAAACATTC
* * * ** *
130 AATTATAATATGTTTTAACCAAAAACGTAAAAAAAATTGAACT
130 AATTATAGTCTGTTTTAAACAAAAAAAT-AAAAAAATTCAACT
* * * ** * * * *
173 TAAAATTAATTATGAGA-TAATAAAAGC-ATTTGAAGTGAGTGATAAGGCTTTTGAAGGAATGGA
1 TAAAATCAATTATGAGACTTATAAAA-CAATTTAAAGCAAGTAATAAGGCTTTCGAAAGAATAG-
* * ** * * *
236 TGACTATAAATGAACTTTTCTTACCAACAAATACCTTTTTCTTCACATTTCTTGAGGTAGACTTT
64 TGACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACATTTCTTGAGGTAAACATT
* ** *
301 TAATTATAGTCTGTTTTAAACAAAAAAATAAAAATCTTCTACT
129 CAATTATAGTCTGTTTTAAACAAAAAAATAAAAAAATTCAACT
* * * **
344 TAAAATCAATTATTAG-CTTATAAAATAATTTAGAGCAAGTAATAAGGCTTTCGAAAGCTTCAGT
1 TAAAATCAATTATGAGACTTATAAAACAATTTAAAGCAAGTAATAAGGCTTTCGAAAGAAT-AGT
* * * * * *
408 GACTATGAAATGGACTTTTCGTGCCAAT-AGATGGCTTTTTCTTCACGTTCCCTAAGGTAAACAT
65 GACTAT-AAATGGACTTTTCTTGCCAATGA-ATGCCTTTTTCTTCACATTTCTTGAGGTAAACAT
* * ** *
472 TCAATTATAGCCT-TTTTTAACTAAAAATTTTAAAAAAATTTAACT
128 TCAATTATAGTCTGTTTTAAAC-AAAAA-AATAAAAAAATTCAACT
* * **
517 TAAAATCAATTTTGACA-TTATAAAACTAA-TTAAAGTGAGTAATAAGGCTTTC-AAAGGAATAG
1 TAAAATCAATTATGAGACTTATAAAAC-AATTTAAAGCAAGTAATAAGGCTTTCGAAA-GAATAG
* * *** ** * *
579 AAGACTATAAATAGACTGTTT-TTGCCAATGAATGCCTTTTTCTTCATGCTTCCCGAGGCAAGCA
64 -TGACTATAAATGGACT-TTTCTTGCCAATGAATGCCTTTTTCTTCACATTTCTTGAGGTAAACA
*
643 TTCAATTATAGTTTGTTTT-AACAAAAAATATAAAAAAAATTCAACT
127 TTCAATTATAGTCTGTTTTAAACAAAAAA-AT-AAAAAAATTCAACT
* ** * * **
689 TAAAATCAATTATGAGAC-TATAAAACCATTTAAAGTGAGTGATAAGGCTTTTGAGGGAATGAGT
1 TAAAATCAATTATGAGACTTATAAAACAATTTAAAGCAAGTAATAAGGCTTTCGAAAGAAT-AGT
* * * *
753 GGCTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTCCTTCAAATTTCTTGAGGTAGACATTC
65 GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACATTTCTTGAGGTAAACATTC
* * * ** * *
818 AATTATATTTTGTTTTAACCAAAAATTTAATAAAATTGAACT
130 AATTATAGTCTGTTTTAAACAAAAAAATAAAAAAATTCAACT
* * * * * *
860 TAAAATCAATTATGAGA-TTATAAAACCATTTAAAGCAAGT--TATGACTTTTGAAGGAATTGGT
1 TAAAATCAATTATGAGACTTATAAAACAATTTAAAGCAAGTAATAAGGCTTTCGAAAGAA-TAGT
* * *
922 GACTATAAATGGACTTTTCTTGCTAATGAATGCTTTTTTCTTCACATTTCTTGAGGCAAACATTC
65 GACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACATTTCTTGAGGTAAACATTC
* ** * *
987 AATTATAATCTGTTTT-AACTAAAACTATAAAAAAAATCAATT
130 AATTATAGTCTGTTTTAAAC-AAAAAAATAAAAAAATTCAACT
* * ** ** * * *
1029 TAAAATCAATTTTGAGA-TTATAAAACCATTTATTGTGAGCAATAAGGCTTTTGAAAGAATGAGA
1 TAAAATCAATTATGAGACTTATAAAACAATTTAAAGCAAGTAATAAGGCTTTCGAAAGAAT-AGT
*
1093 GACTATAAATAGACTTT
65 GACTATAAATGGACTTT
Statistics
Matches: 751, Mismatches: 156, Indels: 61
0.78 0.16 0.06
Matches are distributed among these distances:
168 2 0.00
169 138 0.18
170 2 0.00
171 160 0.21
172 367 0.49
173 80 0.11
174 2 0.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (171 bp):
TAAAATCAATTATGAGACTTATAAAACAATTTAAAGCAAGTAATAAGGCTTTCGAAAGAATAGTG
ACTATAAATGGACTTTTCTTGCCAATGAATGCCTTTTTCTTCACATTTCTTGAGGTAAACATTCA
ATTATAGTCTGTTTTAAACAAAAAAATAAAAAAATTCAACT
Found at i:765 original size:344 final size:340
Alignment explanation
Indices: 1--1109 Score: 1106
Period size: 344 Copynumber: 3.2 Consensus size: 340
* * * * * * *
1 TAAAACCAATTTTGAGATTATAAAACCATTTAAATTGAGTAATAAGGCTTCCGAAGGAATG-GGG
1 TAAAATCAATTATGAGACTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAAGAATGAGTG
* * * * * ** *
65 CATTATAAATGGAATTTTCATCCCAA-AGAATGACTTTTTCTACATGTTTCCTGAGACAGGCATT
66 -ACTATAAATGGACTTTTCATGCCAATAGAATGACTTTTTCTTCAAGTTTCCTGAGGTAGACATT
* * * * *
129 CAATTATAATATGTTTTAACCAAAAACGTAAAAAAAATTGAACTTAAAATTAATTATGAGATAAT
130 CAATTAT-ATATTTTTTAACCAAAAA-TTTAAAAAAATTGAACTTAAAATCAATTATGAGATTAT
* * *
194 AAAAGCATTTGAAGTGAGTGATAAGGCTTTTGAAGGAATGGATGACTATAAATGAACTTTTCTTA
193 AAAA-CATTTAAAGTGAGT-ATAAGGCTTTTGAAGGAATAGATGACTATAAATG-ACTTTTCTTG
** * * * *
259 CCAACAAATACCTTTTTCTTCACATTTCTTGAGG-TAGACTTTTAATTATAGTCTGTTTTAAACA
255 CCAATGAATGCCTTTTTCTTCACATTTCTTGAGGCAAG-CATTCAATTATAGTCTGTTTT-AACA
** *
323 AAAAA-AT-AAAAATCTTCTACT
318 AAAAATATAAAAAAAATTCAACT
* ** * ** ** *
344 TAAAATCAATTATTAG-CTTATAAAATAATTTAGAGCAAGTAATAAGGCTTTCGAAAGCTTCAGT
1 TAAAATCAATTATGAGAC-TATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAAGAATGAGT
* * * * * *
408 GACTATGAAATGGACTTTTCGTGCCAATAG-ATGGCTTTTTCTTCACGTTCCCTAAGGTAAACAT
65 GACTAT-AAATGGACTTTTCATGCCAATAGAATGACTTTTTCTTCAAGTTTCCTGAGGTAGACAT
** * * * *
472 TCAATTATAGCCTTTTTTAACTAAAAATTTTAAAAAAATTTAACTTAAAATCAATTTTGACATTA
129 TCAATTATA-TATTTTTTAACCAAAAA-TTTAAAAAAATTGAACTTAAAATCAATTATGAGATTA
* ** *
537 TAAAACTAATTAAAGTGAGTAATAAGGCTTTCAAAGGAATAGAAGACTATAAATAGACTGTTT-T
192 TAAAAC-ATTTAAAGTGAGT-ATAAGGCTTTTGAAGGAATAGATGACTATAAAT-GACT-TTTCT
*** ** *
601 TGCCAATGAATGCCTTTTTCTTCATGCTTCCCGAGGCAAGCATTCAATTATAGTTTGTTTTAACA
253 TGCCAATGAATGCCTTTTTCTTCACATTTCTTGAGGCAAGCATTCAATTATAGTCTGTTTTAACA
666 AAAAATATAAAAAAAATTCAACT
318 AAAAATATAAAAAAAATTCAACT
* * **
689 TAAAATCAATTATGAGACTATAAAACCATTTAAAGTGAGTGATAAGGCTTTTGAGGGAATGAGTG
1 TAAAATCAATTATGAGACTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAAGAATGAGTG
* * * * * *
754 GCTATAAATGGACTTTTCTTGCCAAT-GAATGCCTTTTCCTTCAAATTTCTTGAGGTAGACATTC
66 ACTATAAATGGACTTTTCATGCCAATAGAATGACTTTTTCTTCAAGTTTCCTGAGGTAGACATTC
* *
818 AATTATATTTTGTTTTAACCAAAAATTTAATAAAATTGAACTTAAAATCAATTATGAGATTATAA
131 AATTATATATT-TTTTAACCAAAAATTTAAAAAAATTGAACTTAAAATCAATTATGAGATTATAA
** * * * * *
883 AACCATTTAAAGCAAGT-TATGACTTTTGAAGGAATTGGTGACTATAAATGGACTTTTCTTGCTA
195 AA-CATTTAAAGTGAGTATAAGGCTTTTGAAGGAATAGATGACTATAAAT-GACTTTTCTTGCCA
* * * * *
947 ATGAATGCTTTTTTCTTCACATTTCTTGAGGCAAACATTCAATTATAATCTGTTTTAACTAAAAC
258 ATGAATGCCTTTTTCTTCACATTTCTTGAGGCAAGCATTCAATTATAGTCTGTTTTAACAAAAAA
*
1012 TATAAAAAAAA-TCAATT
323 TATAAAAAAAATTCAACT
* * ** * * *
1029 TAAAATCAATTTTGAGATTATAAAACCATTTATTGTGAGCAATAAGGCTTTTGAAAGAATGAGAG
1 TAAAATCAATTATGAGACTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAAGAATGAGTG
*
1094 ACTATAAATAGACTTT
66 ACTATAAATGGACTTT
Statistics
Matches: 621, Mismatches: 129, Indels: 35
0.79 0.16 0.04
Matches are distributed among these distances:
340 78 0.13
341 99 0.16
343 111 0.18
344 259 0.42
345 73 0.12
346 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (340 bp):
TAAAATCAATTATGAGACTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAAGAATGAGTG
ACTATAAATGGACTTTTCATGCCAATAGAATGACTTTTTCTTCAAGTTTCCTGAGGTAGACATTC
AATTATATATTTTTTAACCAAAAATTTAAAAAAATTGAACTTAAAATCAATTATGAGATTATAAA
ACATTTAAAGTGAGTATAAGGCTTTTGAAGGAATAGATGACTATAAATGACTTTTCTTGCCAATG
AATGCCTTTTTCTTCACATTTCTTGAGGCAAGCATTCAATTATAGTCTGTTTTAACAAAAAATAT
AAAAAAAATTCAACT
Done.