Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402357.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5437.0, 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: 1907
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.29
Warning! 374 characters in sequence are not A, C, G, or T
Found at i:1450 original size:171 final size:171
Alignment explanation
Indices: 493--1639 Score: 551
Period size: 171 Copynumber: 6.7 Consensus size: 171
483 NNNNNNNNNN
* * * * * ** ** *
493 TTCTTCATGTTTCTCAAGGTAAACATTCAATTATAGTCTGTTTTAACAAAAAATTTAAAAAAACT
1 TTCTACATGTTTCTCAGGGCAAGCATTCAATTATAGCCTGTTTTAATGAAAAATGAAAAAAAATT
* * ** * * *
558 CAACTTAAAATCAAATATAAGTTTATAAAATAATTTAAAACGAGTAATGAGGCTT-TCGTAGGAA
66 CAACTTAAAATCAAGTATGAGTTTATAAAACCATTTAAAGCGAGTAATAAGGCTTCT-GAAGGAA
* * * * *
622 TAGGTGACTATAAATGGACTTTTCTTCCCAATGGATGTCTTT
130 TGGGTGACTCTAAATGGACTTTTCTTCTCAATGAATGGCTTT
* * * * ********** * *
664 TTCTTCATATTTCTCAAGG-TAGACATTCAATTANNNNNNNNNNTAATAAAAAATGTAAAAAAAT
1 TTCTACATGTTTCTCAGGGCAAG-CATTCAATTATAGCCTGTTTTAATGAAAAATGAAAAAAAAT
** * ** * * * **
728 TCAACTTAAAAT-TGGTTATGAGATTATAAAATAATTTAAAGCGGGTAATAAGGCTTTTTAAAAA
65 TCAACTTAAAATCAAG-TATGAGTTTATAAAACCATTTAAAGCGAGTAATAAGGCTTCTGAAGGA
* * * ***********
792 ATGGGAGACTATAAAGGGACTATTT-TT-GNNNNNNNNNNCGTTT
129 ATGGGTGACTCTAAATGGACT-TTTCTTCTCAATGAATGGC-TTT
* * * * * ** *
835 TTCTTCATGTTTCTCTA--ACTAGACATTGAATTATTA-TCTGTTTTAACCAAAAATGTAAAAAA
1 TTCTACATGTTTCTC-AGGGCAAG-CATTCAATTA-TAGCCTGTTTTAATGAAAAATGAAAAAAA
* * * * * * * * ** *
897 ACTCAACTTAAAACCAATTATGAGATAATAAAACCATTTAACGCAAGTTATAATACTTTTGAAGG
63 ATTCAACTTAAAATCAAGTATGAGTTTATAAAACCATTTAAAGCGAGTAATAAGGCTTCTGAAGG
********** * *
962 AATNNNNNNNNNNAAATGGACTTTTTTTTTCAATGAAT-GCTTTT
128 AATGGGTGACTCTAAATGGACTTTTCTTCTCAATGAATGGC-TTT
* * * * * * * *
1006 TTTTTCATGTTTCTCAAGGTATA-CATTCAATTATAGTCTGTATTAA-GTAAAAT-ATAAAAACA
1 TTCTACATGTTTCTCAGGGCA-AGCATTCAATTATAGCCTGTTTTAATGAAAAATGA-AAAAAAA
* ********** * * *
1068 TTCAACTTAAAATCAATTATGNNNNNNNNNNACAATTTAAATCGAGTAATAAGGCTTTTGAAGGA
64 TTCAACTTAAAATCAAGTATGAGTTTATAAAACCATTTAAAGCGAGTAATAAGGCTTCTGAAGGA
** * *
1133 AAAGGTGACTCTAAATGGACTTTTCTTCTCAATAAATGACTTT
129 ATGGGTGACTCTAAATGGACTTTTCTTCTCAATGAATGGCTTT
* * * * *
1176 TTCTACATGTTTCTTTA-GGTAAGCATTCAATTATAGCTTGTTTTAATGAAAAATGTAAACAAAT
1 TTCTACATGTTTC-TCAGGGCAAGCATTCAATTATAGCCTGTTTTAATGAAAAATGAAAAAAAAT
********** * * *
1240 TCAACTTAAANNNNNNNNNNAGATTATAAAACAATTTAAAGCGATTAATAAGGCTTCTGAAGGAA
65 TCAACTTAAAATCAAGTATGAGTTTATAAAACCATTTAAAGCGAGTAATAAGGCTTCTGAAGGAA
** * *
1305 TGGGTGACTCTAAATGGGTTTTTTTTCTCAATGAATGGTTTT
130 TGGGTGACTCTAAATGGACTTTTCTTCTCAATGAATGGCTTT
*
1347 TTCTACATGTTTCTCAGGGCAAGCATTCAATTATAGCCTGTTTTAATGAAAAATGAAAAAAAAAT
1 TTCTACATGTTTCTCAGGGCAAGCATTCAATTATAGCCTGTTTTAATGAAAAATGAAAAAAAATT
* * * *********
1412 CAATTTAAAATCAATTATGAGTTTACAAAACCATTTAAAGCGAGTAATAAGG-TTNNNNNNNNNN
66 CAACTTAAAATCAAGTATGAGTTTATAAAACCATTTAAAGCGAGTAATAAGGCTT-CTGAAGGAA
* * **
1476 TGAGTGACTATAAATGGACTTTTCTTCTTGATGAATGGCTTT
130 TGGGTGACTCTAAATGGACTTTTCTTCTCAATGAATGGCTTT
** * * * *
1518 TTCTACACATTTCTC-GACGCAAGCATTCAATTATAGTCTATTTTAATAAAAAAATGTAAAAAAA
1 TTCTACATGTTTCTCAG-GGCAAGCATTCAATTATAGCCTGTTTTAAT-GAAAAATG-AAAAAAA
* *
1582 ATTCAACTTAAAATCAAGTATGAGTTTATAGAACCGTTTAAAGCGAGTAATAAGGCTT
63 ATTCAACTTAAAATCAAGTATGAGTTTATAAAACCATTTAAAGCGAGTAATAAGGCTT
1640 NNNNNNNNNN
Statistics
Matches: 719, Mismatches: 230, Indels: 51
0.72 0.23 0.05
Matches are distributed among these distances:
169 1 0.00
170 131 0.18
171 516 0.72
172 12 0.02
173 57 0.08
174 2 0.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.34
Consensus pattern (171 bp):
TTCTACATGTTTCTCAGGGCAAGCATTCAATTATAGCCTGTTTTAATGAAAAATGAAAAAAAATT
CAACTTAAAATCAAGTATGAGTTTATAAAACCATTTAAAGCGAGTAATAAGGCTTCTGAAGGAAT
GGGTGACTCTAAATGGACTTTTCTTCTCAATGAATGGCTTT
Found at i:1675 original size:173 final size:162
Alignment explanation
Indices: 1329--1766 Score: 378
Period size: 173 Copynumber: 2.6 Consensus size: 162
1319 TGGGTTTTTT
* * * *
1329 TTCTCAATGAATGGTTTTTTCTACATGTTTCTCAGGGCAAGCATTCAATTATAGCCTGTTTTAAT
1 TTCTCAATGAATGGCTTTTTCTACACGTTTCTC-GAGCAAGCATTCAATTATAGTCTGTTTTAAT
* * * *
1394 GAAAAATG-AAAAAAAAATCAATTTAAAATCAATTATGAGTTTACAAAACCATTTAAAGCGAGTA
65 AAAAAATGTAAAAAAAATTCAACTTAAAATCAAGTATGAGTTTACAAAACCATTTAAAGCGAGTA
* * *
1458 ATAAGGTTNNNNNNNNNNTGAGTGACTATAAATGGACTTTTC
130 ATAAGGTT---------ATGAGTGACTATAAATGAACGTTTC
** * *
1500 TTCTTGATGAATGGCTTTTTCTACACATTTCTCGACGCAAGCATTCAATTATAGTCTATTTTAAT
1 TTCTCAATGAATGGCTTTTTCTACACGTTTCTCGA-GCAAGCATTCAATTATAGTCTGTTTTAAT
* * *
1565 AAAAAAATGTAAAAAAAATTCAACTTAAAATCAAGTATGAGTTTATAGAACCGTTTAAAGCGAGT
65 -AAAAAATGTAAAAAAAATTCAACTTAAAATCAAGTATGAGTTTACAAAACCATTTAAAGCGAGT
** *
1630 AATAAGGCTTNNNNNNNNNNGGGTGACTATAAATGAACGTTTC
129 AATAAGG-TT--------ATGAGTGACTATAAATGAACGTTTC
* * ** * *
1673 TTCTCAATAAATCGCTTTTTCTATGCGTTTCTTGAG-ATAGGCATTAAATTATAGTCTGTTTTAA
1 TTCTCAATGAATGGCTTTTTCTACACGTTTCTCGAGCA-A-GCATTCAATTATAGTCTGTTTTAA
** *
1737 CCAAAAATGT-TAAAAAATTCAACTTAAAAT
64 TAAAAAATGTAAAAAAAATTCAACTTAAAAT
1767 NNNNNNNNNN
Statistics
Matches: 229, Mismatches: 32, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
170 1 0.00
171 75 0.33
172 17 0.07
173 134 0.59
174 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.34
Consensus pattern (162 bp):
TTCTCAATGAATGGCTTTTTCTACACGTTTCTCGAGCAAGCATTCAATTATAGTCTGTTTTAATA
AAAAATGTAAAAAAAATTCAACTTAAAATCAAGTATGAGTTTACAAAACCATTTAAAGCGAGTAA
TAAGGTTATGAGTGACTATAAATGAACGTTTC
Done.