Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402318.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_54.0, 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: 8213
ACGTcount: A:0.20, C:0.06, G:0.07, T:0.18
Warning! 4044 characters in sequence are not A, C, G, or T
Found at i:972 original size:188 final size:188
Alignment explanation
Indices: 653--1025 Score: 622
Period size: 188 Copynumber: 2.0 Consensus size: 188
643 GACTATAAAT
653 AGACTTTTCTTGCCAATGAATTCTTTTTTCTTCACATTTCACGAGGCAAACATTCAATTAATATA
1 AGACTTTTCTTGCCAATGAATTCTTTTTTCTTCACATTTCACGAGGCAAACATTCAATTAATATA
*
718 TGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAATCAATTATGAGATTACAAAACCACTTAAA
66 TATTTTAACCAAAAATGTAAAAAAATTTAACTTAAATCAATTATGAGATTACAAAACCACTTAAA
** * *
783 GCGAGTAGTAAGACTTTTAAAGGAGTAGGTAACTAGAAGTAGACTTTTCTTGCCACTA
131 GCGAGTAACAAAACTTTTAAAGGAATAGGTAACTAGAAGTAGACTTTTCTTGCCACTA
*
841 AGACTTTTCTTGCCAATGAATTCTTTTTTCTTCACATTTCACG-GGTAAACATTCAATTAATATA
1 AGACTTTTCTTGCCAATGAATTCTTTTTTCTTCACATTTCACGAGGCAAACATTCAATTAATATA
* * * * *
905 TATTTTAACTAAAAATGTATAAAAATTTAACTTAAAATCAATTATGAGATTAGAAAACTATTTAA
66 TATTTTAACCAAAAATGTAAAAAAATTTAACTT-AAATCAATTATGAGATTACAAAACCACTTAA
*
970 AGCGAGTAACAAAACTTTTGAAGGAATAGGTAACTAGAAGTAGACTTTTCTTGCCA
130 AGCGAGTAACAAAACTTTTAAAGGAATAGGTAACTAGAAGTAGACTTTTCTTGCCA
1026 ATAAACAACA
Statistics
Matches: 172, Mismatches: 12, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
187 50 0.29
188 122 0.71
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (188 bp):
AGACTTTTCTTGCCAATGAATTCTTTTTTCTTCACATTTCACGAGGCAAACATTCAATTAATATA
TATTTTAACCAAAAATGTAAAAAAATTTAACTTAAATCAATTATGAGATTACAAAACCACTTAAA
GCGAGTAACAAAACTTTTAAAGGAATAGGTAACTAGAAGTAGACTTTTCTTGCCACTA
Found at i:1136 original size:172 final size:171
Alignment explanation
Indices: 841--1963 Score: 887
Period size: 171 Copynumber: 6.6 Consensus size: 171
831 CTTGCCACTA
* * * * * * *
841 AGACTTTTCTTGCCAATGAAT-TCTTTTTTCTTCACATTTCACG-GGTAAACATTCAATTA-ATA
1 AGACTTTTCTTACCAATGAATAGC-TTTTTCTTCACGTTTCTCGAGGCAGACAATCAATTATA-A
* * * *
903 TATATTTTAACTAAAAATGTATAAAAATTTAACTTAAAATCAATTATGAGATTAG-AAAACTATT
64 TCTGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATT-GTAAAACTATT
* ** * *
967 TAAAGCGAGTAACAAAACTTTTGAAGGAATAGGTAACTAGAAGT
128 TAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTAACTATAAAT
* * * * * * *
1011 AGACTTTTCTTGCCAATAAACAACATTTTCTTCATGTTTCTCGAGGCAGACAATCAATTATAATT
1 AGACTTTTCTTACCAATGAATAGCTTTTTCTTCACGTTTCTCGAGGCAGACAATCAATTATAATC
* *
1076 TGTTTTAACCAAAAATGTAAACAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTA
66 TGTTTTAACCAAAAATGTAAA-AAAATTTAACTTAAAATCAATTATGAGATTGTAAAACTATTTA
* * * * * *
1141 GAGCTAGTAATAAGGCTTTTAAAGGATTGGGTGACTATAAAT
130 AAGCGAGTAATAAGGCTTTTGAAGGAATAGGTAACTATAAAT
* * * * * * *
1183 ACACTTTTTTTACCAACT-AATGGCTTTTTCTTCATGTCTT-TCGAGGCAAATAATCAATTATAG
1 AGACTTTTCTTACCAA-TGAATAGCTTTTTCTTCACGT-TTCTCGAGGCAGACAATCAATTATAA
* * * * * * *
1246 CCTGTTTTAACCAAAAATATCAAAAACTTTAACTTAAAATCAATTATGAGTTTGCAAAACCATTT
64 TCTGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTGTAAAACTATTT
* * * **
1311 AAAGCGAGTAATATGGCTTTT-AAAGAAGTGGGTAGGTATAAAT
129 AAAGCGAGTAATAAGGCTTTTGAAGGAA-TAGGTAACTATAAAT
* * * * *
1354 AGACTTTTCTTACCAATGAATAGCTTTTTCTTTACGTTTCTTGATGTAGATAATCAATTATAAT-
1 AGACTTTTCTTACCAATGAATAGCTTTTTCTTCACGTTTCTCGAGGCAGACAATCAATTATAATC
* ** **
1418 TCATTTTAACCAAAAATGTAAAAATGTTTAACTTAAAATCAATTACAAGATTGTAAAA-TCATTT
66 T-GTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTGTAAAACT-ATTT
* * *
1482 AAAGCGAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAAT
129 AAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTAACTATAAAT
* * ** * * * * * * *
1525 AGAATATT-TTAGTAATGAATGGCTTTTTCATCACATTTCTCAAGGTAGACATTCAATTGTAATC
1 AGACTTTTCTTACCAATGAATAGCTTTTTCTTCACGTTTCTCGAGGCAGACAATCAATTATAATC
**
1589 TGTTTTAATCCAAAAA-GTAAAAAAATTTAACTTAAAATCAATTATGAGATTGTAAAACCGTTTA
66 TGTTTTAA-CCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTGTAAAACTATTTA
* * ** * ** * * *
1653 AAACGAGTAATATGGCTTTCAAAGGGAGGGGTGATTATAATT
130 AAGCGAGTAATAAGGCTTTTGAAGGAATAGGTAACTATAAAT
* * * * ** * * * * *
1695 GGGCTTTTC-TAGTCAATGAAT-GACTTTTTCTTTATAATTTC-CAAGGTAAACATTCAATTATG
1 AGACTTTTCTTA-CCAATGAATAG-CTTTTTCTTCA-CGTTTCTCGAGGCAGACAATCAATTATA
* * * ** * *
1757 ATCTGATTTAACCAAAAATCTAAAAAAATTCAACTTAAAATGGATTATGAGATTATAAAACCATT
63 ATCTGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTGTAAAACTATT
* * * * * *
1822 TAAAGTGAGAAATAAGGCTTTGGAAGGAAT-GAGTCATTACAAAT
128 TAAAGCGAGTAATAAGGCTTTTGAAGGAATAG-GTAACTATAAAT
* * ** * * * *
1866 -GAACTTTTCTCACCAATAAATTCCTTTTTCTTCACATTT-TCAAAG-ATTGACAATCTATTATA
1 AG-ACTTTTCTTACCAATGAATAGCTTTTTCTTCACGTTTCTCGAGGCA--GACAATCAATTATA
* *
1928 GTCTGTTTTAACCAAAAATGTAAAAAAATTCAACTT
63 ATCTGTTTTAACCAAAAATGTAAAAAAATTTAACTT
1964 NNNNNNNNNN
Statistics
Matches: 767, Mismatches: 158, Indels: 55
0.78 0.16 0.06
Matches are distributed among these distances:
169 1 0.00
170 190 0.25
171 424 0.55
172 149 0.19
173 3 0.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (171 bp):
AGACTTTTCTTACCAATGAATAGCTTTTTCTTCACGTTTCTCGAGGCAGACAATCAATTATAATC
TGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTGTAAAACTATTTAA
AGCGAGTAATAAGGCTTTTGAAGGAATAGGTAACTATAAAT
Found at i:1806 original size:512 final size:514
Alignment explanation
Indices: 906--1842 Score: 1097
Period size: 512 Copynumber: 1.8 Consensus size: 514
896 ATTAATATAT
* **
906 ATTTTAACTAAAAATGTATAAAAATTTAACTTAAAATCAATTATGAGATTAGAAAACTATTTAAA
1 ATTTTAACCAAAAATGTATAAAAATTTAACTTAAAATCAATTACAAGATTAGAAAACTATTTAAA
* * * *
971 GCGAGTAACAAAACTTTTGAAGGAATAGGTAACTAGAAGTAGACTTTTCTTGCCAATAAACAACA
66 GCGAGTAACAAAACTTTCGAAGGAATAGGTAACTAGAAATAGAATTTTCTAGCCAATAAACAACA
* ** * *
1036 TTTTCTTCATGTTTCTCGAGGCAGACAATCAATTATAATTTGTTTTAACCAAAAATGTAAACAAA
131 TTTTCATCACATTTCTCAAGGCAGACAATCAATTATAATCTGTTTTAACCAAAAATGTAAACAAA
* * * * *
1101 ATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAGAGCTAGTAATAAGGCTTTTAAAGG
196 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAACGAGTAATAAGGCTTTCAAAGG
* * * * * *
1166 ATTGGGTGACTATAAATACACTTTTTTTACCAACTAATGGCTTTTTCTTCATGTCTTTCGAGGCA
261 ATGGGGTGACTATAAATACACTTTTTCTACCAACTAATGACTTTTTCTTCATATCTTCCAAGGCA
* * * * *
1231 AATAATCAATTATAGCCTGTTTTAACCAAAAATATCAAAAACTTTAACTTAAAATCAATTATGAG
326 AACAATCAATTATAGCCTGATTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
* * * *
1296 TTTGCAAAACCATTTAAAGCGAGTAATATGGCTTTTAAAGAAGTGGGTAGGTATAAATAGACTTT
391 ATTACAAAACCATTTAAAGCGAGAAATAAGGCTTTTAAAGAAGTGGGTAGGTATAAATAGACTTT
1361 TCTTACCAATGAATAGCTTTTTCTTTACGTTTCTTGATGTAGATAATCAATTATAATTC
456 TCTTACCAATGAATAGCTTTTTCTTTACGTTTCTTGATGTAGATAATCAATTATAATTC
*
1420 ATTTTAACCAAAAATGTA-AAAATGTTTAACTTAAAATCAATTACAAGATT-GTAAAA-TCATTT
1 ATTTTAACCAAAAATGTATAAAA-ATTTAACTTAAAATCAATTACAAGATTAG-AAAACT-ATTT
* ** * * * * * *
1482 AAAGCGAGTAATAAGGCTTTCGAAGGCATAGGTGACTATAAATAGAATATTT-TAG-TAATGAAT
63 AAAGCGAGTAACAAAACTTTCGAAGGAATAGGTAACTAGAAATAGAAT-TTTCTAGCCAATAAAC
** * * * *
1545 GGCTTTTTCATCACATTTCTCAAGGTAGACATTCAATTGTAATCTGTTTTAATCCAAAAA-GTAA
127 AACATTTTCATCACATTTCTCAAGGCAGACAATCAATTATAATCTGTTTTAA-CCAAAAATGTAA
* * * *
1609 A-AAAATTTAACTTAAAATCAATTATGAGATTGTAAAACCGTTTAAAACGAGTAATATGGCTTTC
191 ACAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAACGAGTAATAAGGCTTTC
* * *** * *
1673 AAAGGGA-GGGGTGATTATAATTGGGC-TTTTCTAGTCAA-TGAATGACTTTTTCTTTATAAT-T
256 AAA-GGATGGGGTGACTATAAATACACTTTTTCTA-CCAACT-AATGACTTTTTCTTCAT-ATCT
* * * *
1734 TCCAAGGTAAACATTCAATTAT-GATCTGATTTAACCAAAAATCTAAAAAAATTCAACTTAAAAT
317 TCCAAGGCAAACAATCAATTATAG-CCTGATTTAACCAAAAATATAAAAAAATTCAACTTAAAAT
** * *
1798 GGATTATGAGATTATAAAACCATTTAAAGTGAGAAATAAGGCTTT
381 CAATTATGAGATTACAAAACCATTTAAAGCGAGAAATAAGGCTTT
1843 GGAAGGAATG
Statistics
Matches: 346, Mismatches: 67, Indels: 22
0.80 0.15 0.05
Matches are distributed among these distances:
511 8 0.02
512 177 0.51
513 61 0.18
514 97 0.28
515 3 0.01
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (514 bp):
ATTTTAACCAAAAATGTATAAAAATTTAACTTAAAATCAATTACAAGATTAGAAAACTATTTAAA
GCGAGTAACAAAACTTTCGAAGGAATAGGTAACTAGAAATAGAATTTTCTAGCCAATAAACAACA
TTTTCATCACATTTCTCAAGGCAGACAATCAATTATAATCTGTTTTAACCAAAAATGTAAACAAA
ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAACGAGTAATAAGGCTTTCAAAGG
ATGGGGTGACTATAAATACACTTTTTCTACCAACTAATGACTTTTTCTTCATATCTTCCAAGGCA
AACAATCAATTATAGCCTGATTTAACCAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAG
ATTACAAAACCATTTAAAGCGAGAAATAAGGCTTTTAAAGAAGTGGGTAGGTATAAATAGACTTT
TCTTACCAATGAATAGCTTTTTCTTTACGTTTCTTGATGTAGATAATCAATTATAATTC
Found at i:1945 original size:341 final size:335
Alignment explanation
Indices: 907--1963 Score: 907
Period size: 341 Copynumber: 3.1 Consensus size: 335
897 TTAATATATA
* * *
907 TTTTAACTAAAAATGTATAAAAATTTAACTTAAAATCAATTATGAGATTAG-AAAACTATTTAAA
1 TTTTAACCAAAAA-GTAAAAAAATTTAACTTAAAATCAATTATGAGATT-GCAAAACCATTTAAA
* * *** * * * ** * * * * * *
971 GCGAGTAACAAAACTTTTGAAGGAA-TAGGTAACTAGAAGTAGACTTTTCTTGCCAATAAACAAC
64 ACGAGTAATATGGC-TTTCAAAGAAGTGGGTAGGTATAAATAGACTTTTCTTACCAATGAATAGC
* * ** * * * *
1035 ATTTTCTTCATGTTTCTCGAGGCAGACAATCAATTATAATTTGTTTTAACCAAAAATGTAAACAA
128 TTTTTCTTTAAATTTCTCAAGGTAAACAATCAATTATAA-TTGATTTAACCAAAAATGTAAA-AA
* * **
1100 AATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAGAGCT-AGTAATAAGGCTTTTAAA
191 AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG-TGAGTAATAAGGCTTTCGAA
* * ** *
1164 GGATTGGGTGACTATAAAT-ACACTTTTTTTACCAACTAATGGCTTTTTCTTCATGTCTTTCGAG
255 GGAATGAGTGACTATAAATGA-AC--TTTTTACCAA-TAATGGCTTTTTCTTCACAT-TTTC-AA
* * *
1228 GCA-AATAATCAATTATAGCCTG
314 G-ATGACAATCAATTATAGTCTG
* *
1250 TTTTAACCAAAAA-TATCAAAAACTTTAACTTAAAATCAATTATGAGTTTGCAAAACCATTTAAA
1 TTTTAACCAAAAAGTA--AAAAAATTTAACTTAAAATCAATTATGAGATTGCAAAACCATTTAAA
* *
1314 GCGAGTAATATGGCTTTTAAAGAAGTGGGTAGGTATAAATAGACTTTTCTTACCAATGAATAGCT
64 ACGAGTAATATGGCTTTCAAAGAAGTGGGTAGGTATAAATAGACTTTTCTTACCAATGAATAGCT
** ** * * * * **
1379 TTTTCTTTACGTTTCTTGATGTAGATAATCAATTATAATTCATTTTAACCAAAAATGTAAAAATG
129 TTTTCTTTAAATTTCTCAAGGTAAACAATCAATTATAATTGA-TTTAACCAAAAATGTAAAAAAA
* ** * * * *
1444 TTTAACTTAAAATCAATTACAAGATTGTAAAATCATTTAAAGCGAGTAATAAGGCTTTCGAAGGC
193 TTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAGGA
** * *
1509 AT-AGGTGACTATAAATAGAA-TATTTTAGTAATGAATGGCTTTTTCATCACATTTCTCAAGGTA
258 ATGA-GTGACTATAAAT-GAACT-TTTTACCAAT-AATGGCTTTTTCTTCACATTT-TCAAGAT-
* * *
1572 GACATTCAATTGTAATCTG
317 GACAATCAATTATAGTCTG
* *
1591 TTTTAATCCAAAAAGTAAAAAAATTTAACTTAAAATCAATTATGAGATTGTAAAACCGTTTAAAA
1 TTTTAA-CCAAAAAGTAAAAAAATTTAACTTAAAATCAATTATGAGATTGCAAAACCATTTAAAA
* * * * * *
1656 CGAGTAATATGGCTTTCAAAGGGAG-GGGT-GATTATAATTGGGCTTTTC-TAGTCAATGAAT-G
65 CGAGTAATATGGCTTTCAAA-GAAGTGGGTAG-GTATAAATAGACTTTTCTTA-CCAATGAATAG
* * *
1717 ACTTTTTCTTTATAATTTC-CAAGGTAAACATTCAATTATGATCTGATTTAACCAAAAATCTAAA
127 -CTTTTTCTTTA-AATTTCTCAAGGTAAACAATCAATTATAAT-TGATTTAACCAAAAATGTAAA
** * *
1781 AAAATTCAACTTAAAATGGATTATGAGATTATAAAACCATTTAAAGTGAGAAATAAGGCTTTGGA
189 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGA
* * * **
1846 AGGAATGAGTCATTACAAATGAACTTTTCTCACCAATAAATTCCTTTTTCTTCACATTTTCAAAG
254 AGGAATGAGTGACTATAAATGAACTTTT-T-ACCAAT-AATGGCTTTTTCTTCACATTTTC-AAG
*
1911 ATTGACAATCTATTATAGTCTG
315 A-TGACAATCAATTATAGTCTG
*
1933 TTTTAACCAAAAATGTAAAAAAATTCAACTT
1 TTTTAACCAAAAA-GTAAAAAAATTTAACTT
1964 NNNNNNNNNN
Statistics
Matches: 577, Mismatches: 108, Indels: 59
0.78 0.15 0.08
Matches are distributed among these distances:
340 16 0.03
341 255 0.44
342 158 0.27
343 147 0.25
344 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (335 bp):
TTTTAACCAAAAAGTAAAAAAATTTAACTTAAAATCAATTATGAGATTGCAAAACCATTTAAAAC
GAGTAATATGGCTTTCAAAGAAGTGGGTAGGTATAAATAGACTTTTCTTACCAATGAATAGCTTT
TTCTTTAAATTTCTCAAGGTAAACAATCAATTATAATTGATTTAACCAAAAATGTAAAAAAATTC
AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAAGGAATG
AGTGACTATAAATGAACTTTTTACCAATAATGGCTTTTTCTTCACATTTTCAAGATGACAATCAA
TTATAGTCTG
Done.