Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397947.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1251.0, 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: 2062
ACGTcount: A:0.24, C:0.09, G:0.10, T:0.26
Warning! 637 characters in sequence are not A, C, G, or T
Found at i:1476 original size:171 final size:168
Alignment explanation
Indices: 1155--2062 Score: 827
Period size: 171 Copynumber: 5.3 Consensus size: 168
1145 NNNNNNNNNN
** * *
1155 CTTTTCTTGCCAATGAATGTTTTTTTCT-TCATGTTTCTCATGGTAGACATTCAAGTCTAGTCTA
1 CTTTTCTTGCCAATGAATGCCTTTTTCTAT-A-GTTTCTCATGGTAGACATTCAATTCTAGTCTG
* * *
1219 TTTTACCTAAAAATGTACAA-AGAATTCAAATTTAAATCAATTTTGAGATTATAAAACTATTTAA
64 TTTTAACTAAAAATGTA-AAGA-AATTC-AATTAAAATCAATTTTGAGATTATAAAACCATTTAA
* *
1283 ACTGAGTAATAAGCTCTTGAAGGAATGGGTGACTATAAATGGA
126 AGTGAGTAATAAGCTTTTGAAGGAATGGGTGACTATAAATGGA
*
1326 CTTTTCTTGCCAATGAATGCCTTTTTCTATACGTTTCTCGA-GGTAGACATTCAATTCTAGTCTA
1 CTTTTCTTGCCAATGAATGCCTTTTTCTATA-GTTTCTC-ATGGTAGACATTCAATTCTAGTCTG
* * * * * * *
1390 TTTAAACTAAAAATGTAGAGAAATTCAATTCAAAATAAATTATG-GCCTTACAAAACCGTTTAAA
64 TTTTAACTAAAAATGTAAAGAAATTCAATT-AAAATCAATTTTGAG-ATTATAAAACCATTTAAA
* * * * *
1454 GTAAATAGTACAGCTTTTGAAGGCATGGGTGACCATAAATGGA
127 GTGAGTAATA-AGCTTTTGAAGGAATGGGTGACTATAAATGGA
* * * * * * * * *
1497 TTTTTCTTGTCAATGAACGCATTTTTCCTCAT-GATTCTTAAGGTAGACATTTAATCCTAGTCTG
1 CTTTTCTTGCCAATGAATGCCTTTTT-CT-ATAGTTTCTCATGGTAGACATTCAATTCTAGTCTG
* * * *
1561 TTTTAACCAAAAATGTGCAAAGAATTTAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAA
64 TTTTAACTAAAAATGT--AAAGAAATTCAATTAAAATCAATTTTGAGATTATAAAACCATTTAAA
*
1626 GTGAGTAATAAGCCTTTT-AAAGAAGTGGGTGACTATAAATGGA
127 GTGAGTAATAAG-CTTTTGAAGGAA-TGGGTGACTATAAATGGA
* * * * * * *
1669 CTTCTCTTGCGAATGAATGCTCTTTTCTTTATA-TTTCTCAGGGTAGACATTCAATTATAATATG
1 CTTTTCTTGCCAATGAATGC-CTTTT-TCTATAGTTTCTCATGGTAGACATTCAATTCTAGTCTG
* * * * * *
1733 TTTTAACTAGAAAA-CTAAAGAAGTTGAACTTAAAATTAATTTTGAGAATATAAAACTATTTAAA
64 TTTTAACTA-AAAATGTAAAGAAATTCAA-TTAAAATCAATTTTGAGATTATAAAACCATTTAAA
* * * * *
1797 GTGATTAATTAGGCTTTTGAAGTAATAGGTGACTATAAATAGA
127 GTGAGTAA-TAAGCTTTTGAAGGAATGGGTGACTATAAATGGA
* * *
1840 CTTTTCTTTCCAATGAATACTCTTTCCTTC-AT-GTTTCTCAAGGTAGACATTCAATTCTAGTCT
1 CTTTTCTTGCCAATGAATGC-CTTT--TTCTATAGTTTCTCATGGTAGACATTCAATTCTAGTCT
* * ** * *
1903 G-TTTAACCAAAAATGTAAAAACAATTCAACTTAAAATCAATTACG-GCATTACAAAATCATTTA
63 GTTTTAACTAAAAATGTAAAGA-AATTCAA-TTAAAATCAATTTTGAG-ATTATAAAACCATTTA
* * *
1966 AAGCGAGTAATAATGCTTTTGAA-GATATGGGTTACTATAAATAGA
125 AAGTGAGTAATAA-GCTTTTGAAGGA-ATGGGTGACTATAAATGGA
**
2011 CTTTTCTTGCCAATGAATGTTTTTTTCT-TCATGTTTCTCATGGTAGACATTC
1 CTTTTCTTGCCAATGAATGCCTTTTTCTAT-A-GTTTCTCATGGTAGACATTC
Statistics
Matches: 596, Mismatches: 108, Indels: 66
0.77 0.14 0.09
Matches are distributed among these distances:
168 4 0.01
169 9 0.02
170 66 0.11
171 377 0.63
172 115 0.19
173 24 0.04
174 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (168 bp):
CTTTTCTTGCCAATGAATGCCTTTTTCTATAGTTTCTCATGGTAGACATTCAATTCTAGTCTGTT
TTAACTAAAAATGTAAAGAAATTCAATTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGA
GTAATAAGCTTTTGAAGGAATGGGTGACTATAAATGGA
Found at i:2050 original size:342 final size:338
Alignment explanation
Indices: 1155--2062 Score: 997
Period size: 342 Copynumber: 2.6 Consensus size: 338
1145 NNNNNNNNNN
* * * * * *
1155 CTTTTCTTGCCAATGAATGTTTTTTTCTTCATGTTTCTCATGGTAGACATTCAAGTCTAGTCTAT
1 CTTTTCTTTCCAATGAATGCTTTTTCCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCTGT
*
1220 TTTACCTAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACTATTTAAA-
66 TTAACC-AAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAAC-ATTTAAAG
* *
1284 CTGAGTAATAAGCTCTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCCTT
129 C-GAGTAATAAGCTTTTGAA-GAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTT
* * * * * *
1349 TTTCTATACGTTTCTC-GAGGTAGACATTCAATTCTAGTCTATTTAAACTAAAAATGTAGAGAAA
192 TTTCT-TATGTTTCTCAG-GGTAGACATTCAATTATAATATATTTAAACTAAAAATCTAAAGAAA
** * *
1413 TTCAATTCAAAATAAATTATGGCCTTACAAAACCGTTTAAAGTAAATAGTACAGCTTTTGAAGGC
255 TTCAATTCAAAATAAATTATGGCAATACAAAACCATTTAAAGTAAATAGTACAGCTTTTGAAGGA
* *
1478 ATGGGTGACCATAAATGGA
320 ATAGGTGACCATAAATAGA
* * * * * *
1497 TTTTTCTTGT-CAATGAACGCATTTTTCC-TCATGATTCTTAAGGTAGACATTTAATCCTAGTCT
1 CTTTTCTT-TCCAATGAATGC-TTTTTCCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCT
* *
1560 GTTTTAACCAAAAATGTGCAAAGAATTTAAATTTAAATCAATTTTGAGATTATAAAACCATTTAA
64 G-TTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAA-CATTTAA
* * * *
1625 AGTGAGTAATAAGCCTTTTAAAGAAGTGGGTGACTATAAATGGACTTCTCTTGCGAATGAATGCT
127 AGCGAGTAATAAG-CTTTTGAAGAA-TGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCT
* * * *
1690 CTTTTCTTTATATTTCTCAGGGTAGACATTCAATTATAATATGTTTTAACTAGAAAA-CTAAAGA
190 TTTTTC-TTATGTTTCTCAGGGTAGACATTCAATTATAATATATTTAAACTA-AAAATCTAAAGA
* * * * * * * * * *
1754 AGTTGAACTT-AAAATTAATTTTGAG-AATATAAAACTATTTAAAGTGATTAATTA-GGCTTTTG
253 AATTCAA-TTCAAAATAAATTATG-GCAATACAAAACCATTTAAAGTAAAT-AGTACAGCTTTTG
* *
1816 AAGTAATAGGTGACTATAAATAGA
315 AAGGAATAGGTGACCATAAATAGA
* *
1840 CTTTTCTTTCCAATGAATACTCTTTCCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCTGT
1 CTTTTCTTTCCAATGAATGCTTTTTCCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCTGT
* * * * ** *
1905 TTAACCAAAAATGTAAAAACAATTCAACTTAAAATCAATTACG-GCATTACAAAATCATTTAAAG
66 TTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAG-ATTATAAAA-CATTTAAAG
* * *
1969 CGAGTAATAATGCTTTTGAAGATATGGGTTACTATAAATAGACTTTTCTTGCCAATGAATGTTTT
129 CGAGTAATAA-GCTTTTGAAGA-ATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTT
*
2034 TTTCTTCATGTTTCTCATGGTAGACATTC
192 TTTCTT-ATGTTTCTCAGGGTAGACATTC
Statistics
Matches: 470, Mismatches: 77, Indels: 38
0.80 0.13 0.06
Matches are distributed among these distances:
341 3 0.01
342 247 0.53
343 208 0.44
344 12 0.03
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (338 bp):
CTTTTCTTTCCAATGAATGCTTTTTCCTTCATGTTTCTCAAGGTAGACATTCAATTCTAGTCTGT
TTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACATTTAAAGCG
AGTAATAAGCTTTTGAAGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTTTTTC
TTATGTTTCTCAGGGTAGACATTCAATTATAATATATTTAAACTAAAAATCTAAAGAAATTCAAT
TCAAAATAAATTATGGCAATACAAAACCATTTAAAGTAAATAGTACAGCTTTTGAAGGAATAGGT
GACCATAAATAGA
Done.