Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401809.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4916.0, 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, 745
Length: 1242
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Found at i:553 original size:170 final size:170
Alignment explanation
Indices: 1--706 Score: 708
Period size: 171 Copynumber: 4.1 Consensus size: 170
* * * *
1 AATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGACTTTTGAAAGCATGGGTGACT
1 AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGTATGGGTGACT
* * * ** * * * * * * *
66 ATAAATGGACTTTTCTT-ACCAATAAATACCTTTTTTTTTTCACATTTCTTAACGCAAACAATCA
66 ATAAATGGACTTTTCTTGTCTAATGAATGGC--TTTTTCTTCACTTTTC-CAAGGTAGACATTC-
* * ** * * *
130 ATTAGAATATGTGCTCACAAAAAATGTAGAAAAATTCAACCTAA
127 ATTATAATCTGTTTTAATAAAAAATGTAAAAAAATTCAACCTAA
* *
174 AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGCT-TGGGTGAT
1 AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTG-AAGGTATGGGTGAC
* * * * * * *
238 TAGAAATAGACTTTTCTTCT-TAATCAATGGCTTTTTCTTCACGTTTCTCGAGATAGACATTCAC
65 TATAAATGGACTTTTCTTGTCTAATGAATGGCTTTTTCTTCACTTTTC-CAAGGTAGACATTCA-
* * *
302 TTATAATCTATTTTAATGAAAAATGTAAAAAAATTCTACCTAA
128 TTATAATCTGTTTTAATAAAAAATGTAAAAAAATTCAACCTAA
* * * * *
345 AATCAATTATGAGATTATAAAATCATTTAAAATGAGTAATTACGCTTTTGAAGGTATGGGTAACT
1 AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGTATGGGTGACT
*
410 ATAAATGGACTTTACTTGTCT-ATGAATGGCTTTTTCTTCACATTTTCCAAGGTAGACATTCATT
66 ATAAATGGACTTTTCTTGTCTAATGAATGGCTTTTTCTTCAC-TTTTCCAAGGTAGACATTCATT
* *
474 ATAATCTGTTTTAATAAAAAATGTAAAAACATTCAACTTAA
130 ATAATCTGTTTTAATAAAAAATGTAAAAAAATTCAACCTAA
* * * **
515 AATCATTTATCAGATTATAAAACCATTTTAAGTGAGTAATAAGGCTTTCAAAGGTATGGGTGACT
1 AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGTATGGGTGACT
* * * * *
580 ATAAA-GGAAATTTTCTTG-CTCATG-ATAGCCTTTTTCCTCA-TGTTTCCCAAGGTAAACATTC
66 ATAAATGG-ACTTTTCTTGTCTAATGAAT-GGCTTTTTCTTCACT-TTT-CCAAGGTAGACATTC
* ** * *
641 AACTATAATCTGTTTTAACCAAAAATGTAAAAAAATTTAACTTAA
127 -ATTATAATCTGTTTTAATAAAAAATGTAAAAAAATTCAACCTAA
*
686 AATCAATTATGAGGTTATAAA
1 AATCAATTATGAGATTATAAA
707 TGTTAGCTCC
Statistics
Matches: 446, Mismatches: 75, Indels: 26
0.82 0.14 0.05
Matches are distributed among these distances:
168 1 0.00
169 9 0.02
170 139 0.31
171 212 0.48
172 5 0.01
173 78 0.17
174 2 0.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.36
Consensus pattern (170 bp):
AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGTATGGGTGACT
ATAAATGGACTTTTCTTGTCTAATGAATGGCTTTTTCTTCACTTTTCCAAGGTAGACATTCATTA
TAATCTGTTTTAATAAAAAATGTAAAAAAATTCAACCTAA
Found at i:641 original size:341 final size:343
Alignment explanation
Indices: 1--706 Score: 797
Period size: 341 Copynumber: 2.1 Consensus size: 343
* *
1 AATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGACTTTTGAAAGCATGGGTGACT
1 AATCAATTATGAGATTATAAAACTATTTAAAATGAGTAATAAGACTTTTGAAAGCATGGGTAACT
* * *
66 ATAAATGGACTTTTCTTACCAATAAATACCTTTTTTTTTTCACATTTCTTAACGCAAACAATCAA
66 ATAAATGGACTTTACTTACCAATAAATACC-TTTTTTCTTCACATTTCTCAACGCAAACAATCAA
* *
131 TTAGAATATGTGCTCACAAAAAATGTAGAAAAATTCAACCTAAAATCAATTATGAGATTATAAAA
130 TTAGAATATGTGCTAACAAAAAATGTAGAAAAATTCAACCTAAAATCAATTATCAGATTATAAAA
* * * *
196 CCATTTAAAGTGAGTAATAAGGCTTTTGAAAGCTTGGGTGATTAGAAATAGACTTTTCTTCTTAA
195 CCATTTAAAGTGAGTAATAAGGCTTTTCAAAGCTTGGGTGACTAGAAAGAGAATTTTCTTCTTAA
* * * * * **
261 TCAATGGCTTTTTCTTCACGTTTCTCGAGATAGACATTC-ACTTATAATCTATTTTAATGAAAAA
260 TCAATGCCTTTTTCCTCACGTTTCCCAAGATAAACATTCAAC-TATAATCTATTTTAACCAAAAA
325 TGTAAAAAAATTCT-ACCTAA
324 TGTAAAAAAATT-TAACCTAA
* * *
345 AATCAATTATGAGATTATAAAA-TCATTTAAAATGAGTAATTACG-CTTTTGAAGGTATGGGTAA
1 AATCAATTATGAGATTATAAAACT-ATTTAAAATGAGTAA-TAAGACTTTTGAAAGCATGGGTAA
** * * ** * * * *
408 CTATAAATGGACTTTACTTGTCTATGAATGGC-TTTTTCTTCACATTT-TCCAAGGTAGACATTC
64 CTATAAATGGACTTTACTTACCAATAAATACCTTTTTTCTTCACATTTCT-CAACGCAAACAATC
* * ** * * *
471 -ATTATAATCTGTTTTAATAAAAAATGTA-AAAACATTCAACTTAAAATCATTTATCAGATTATA
128 AATTAGAATATGTGCTAACAAAAAATGTAGAAAA-ATTCAACCTAAAATCAATTATCAGATTATA
* * *
534 AAACCATTTTAAGTGAGTAATAAGGC-TTTCAAAGGTATGGGTGACTATAAAG-GAAATTTTCTT
192 AAACCATTTAAAGTGAGTAATAAGGCTTTTCAAAGCT-TGGGTGACTAGAAAGAG-AATTTTCTT
* * * * *
597 GC-TCAT-GATAGCCTTTTTCCTCATGTTTCCCAAGGTAAACATTCAACTATAATCTGTTTTAAC
255 -CTTAATCAAT-GCCTTTTTCCTCACGTTTCCCAAGATAAACATTCAACTATAATCTATTTTAAC
*
660 CAAAAATGTAAAAAAATTTAACTTAA
318 CAAAAATGTAAAAAAATTTAACCTAA
*
686 AATCAATTATGAGGTTATAAA
1 AATCAATTATGAGATTATAAA
707 TGTTAGCTCC
Statistics
Matches: 304, Mismatches: 48, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
340 16 0.05
341 181 0.60
342 26 0.09
343 1 0.00
344 77 0.25
345 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.36
Consensus pattern (343 bp):
AATCAATTATGAGATTATAAAACTATTTAAAATGAGTAATAAGACTTTTGAAAGCATGGGTAACT
ATAAATGGACTTTACTTACCAATAAATACCTTTTTTCTTCACATTTCTCAACGCAAACAATCAAT
TAGAATATGTGCTAACAAAAAATGTAGAAAAATTCAACCTAAAATCAATTATCAGATTATAAAAC
CATTTAAAGTGAGTAATAAGGCTTTTCAAAGCTTGGGTGACTAGAAAGAGAATTTTCTTCTTAAT
CAATGCCTTTTTCCTCACGTTTCCCAAGATAAACATTCAACTATAATCTATTTTAACCAAAAATG
TAAAAAAATTTAACCTAA
Found at i:1065 original size:73 final size:73
Alignment explanation
Indices: 988--1222 Score: 253
Period size: 73 Copynumber: 3.2 Consensus size: 73
978 AGAGACAACA
** *
988 TTAGTCGACTAAGAGCTTAC-TGTCAAAAACTGGGTTTAGAGACAGAAACAACTTAATCGACTAA
1 TTAGTCGACTAAGAGCTTACAACT-AAAAACTGGGTTCAGAGACAGAAACAACTTAATCGACTAA
1052 GA-AGTTTTG
65 GACA-TTTTG
* * * *
1061 TTAGTCGACTAAAAGCTTACAACTAGAAATTGGGTTCAGAGACAGAAACGACTTAATCGACTAAG
1 TTAGTCGACTAAGAGCTTACAACTAAAAACTGGGTTCAGAGACAGAAACAACTTAATCGACTAAG
1126 ACATTTTG
66 ACATTTTG
* * * ** *
1134 TTAGTCGACTAAGAG-TCTACTACTAAAAATTGGGTTCAGAGGCA-AAGATGACTTAGTCGACTA
1 TTAGTCGACTAAGAGCT-TACAACTAAAAACTGGGTTCAGAGACAGAA-ACAACTTAATCGACTA
** **
1197 AGTGATAATG
64 AGACATTTTG
1207 TTAGTCGACTAAGAGC
1 TTAGTCGACTAAGAGC
1223 ATTCTATCTG
Statistics
Matches: 140, Mismatches: 17, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
72 3 0.02
73 135 0.96
74 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (73 bp):
TTAGTCGACTAAGAGCTTACAACTAAAAACTGGGTTCAGAGACAGAAACAACTTAATCGACTAAG
ACATTTTG
Done.