Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402984.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_65.0, 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: 1760
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.30
Warning! 324 characters in sequence are not A, C, G, or T
Found at i:1634 original size:172 final size:170
Alignment explanation
Indices: 879--1760 Score: 902
Period size: 172 Copynumber: 5.2 Consensus size: 170
869 NNNNNNNNNN
* * * * * *** *
879 AATTCAACTAAAAATCAATTACGAGTTTACAAAACCATTTAAAATGAGTAATAAAATTTTTAAAG
1 AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAG
* * ** *
944 GAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACCTTTTTCTTCCCGTTTCTCGATA-
66 GAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAAT-GCTTTTTTTTCATGTTTCTC-AAAG
* * * * *
1008 TAGACATTCAATTACAATCTATTTTAACCTAAACA-GTATAAAG
129 TAGACATTCAATTATAGTCTGTTTTAACC-AAAAATGTA-AAAA
* * *
1051 AATTCAACTAAAAATCAATTTTGAGATTTTAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAG
1 AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAG
* * * * * *
1116 GAATAGTTGACTATAAATAGACTTTTGTTGCTAATGAATG-TAATTTTTTAATGTTTCTC-AAGA
66 GAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCT-TTTTTTTCATGTTTCTCAAAG-
** * * *
1179 TAGACATTCAATTATAGTCTACTTTAACAAAAAATATTAAAA
129 TAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAA
* * * *
1221 AATTCAACTTAAATTC-ATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTGGAAG
1 AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAG
** * * * * * * *
1285 GAATGGAAGACTATAAATGGACTTTT-TTTCAAATGAATATCTTTTTTTACATGTTTCCCAAAGA
66 GAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAAT-GCTTTTTTTTCATGTTTCTCAAAGT
* **** *
1349 AGGCATTCAATTATAGTCTGTTTTGGTGAAAAATGCAAAAA
130 AGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAA
* * * ** * * *
1390 AAGTCAACTTAAAATCAAATATGAGATTAGAAAACCATTTAAAACGAATAATATA-GTTTTTAAA
1 AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATA-AGGCTTTTGAA
*
1454 GGAATGGGTGACTATAAATAGATTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCTCAAAG
65 GGAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTT-TTCATGTTTCTCAAAG
* * * *
1519 TAGACGTTCAATTATAATCTGTTTTAACCAAAACTGTACAAAG
129 TAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTA-AAAA
* *
1562 AATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTGAAAGTGAGTAATAAGGCTTTTGAAG
1 AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAG
* * * * * *
1627 AAATGGGTGACTATAAAT-GAAATTTTCTTGCTAATGAATGC-TTTTTTTCTATGATTCTCGAGG
66 GAATGGGTGACTATAAATAG-ACTTTTCTTGCCAATGAATGCTTTTTTTTC-ATGTTTCTCAAAG
*
1690 TAAACATTCAATTATAGTCTGTTTTAGA-CAAAAATGTAAAAA
129 TAGACATTCAATTATAGTCTGTTTTA-ACCAAAAATGTAAAAA
*
1732 AATTCAACTTAAAATCAATTTTGAGATTA
1 AATTCAACTTAAAATCAATTATGAGATTA
Statistics
Matches: 585, Mismatches: 109, Indels: 34
0.80 0.15 0.05
Matches are distributed among these distances:
168 10 0.02
169 124 0.21
170 128 0.22
171 140 0.24
172 183 0.31
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (170 bp):
AATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAG
GAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTTTCATGTTTCTCAAAGTA
GACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAA
Found at i:1702 original size:342 final size:339
Alignment explanation
Indices: 1054--1760 Score: 843
Period size: 342 Copynumber: 2.1 Consensus size: 339
1044 TATAAAGAAT
* ** ** * *
1054 TCAACTAAAAATCAATTTTGAGATTTTAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAA
1 TCAACTTAAAATCAATTTTGAGATTAGAAAACCATTTAAAACGAATAATAAGGCTTTTAAAGGAA
* * *
1119 TAGTTGACTATAAATAGACTTTTGTTGCTAATGAATGTAATTTTTTAATGTTTCTCAAGATAGAC
66 TAGGTGACTATAAATAGACTTTTCTTGCCAATGAATGTAATTTTTTAATGTTTCTCAAGATAGAC
* * *
1184 ATTCAATTATAGTCTACTTTAACAAAAAATATTAAAAAATTCAACTTAAATTCATTATGAGATTA
131 ATTCAATTATAATCTACTTTAACAAAAAATAGTAAAAAATTCAACTTAAAATCATTATGAGATTA
* * * * * *
1249 TAAAACTATTTAAAGCGAGTAATAAGGCTTTGGAAGGAATGGAAGACTATAAATGGACTTTTTTT
196 TAAAACCATTGAAAGCGAGTAATAAGGCTTTGGAAGAAATGGAAGACTATAAATGAAATTTTTTG
* * * * **
1314 CAAATGAATATCTTTTTTTACATGTTTCCCAAAGAAGGCATTCAATTATAGTCTGTTTTGGTGAA
261 CAAATGAATAGCTTTTTTTACATGATTCCCAAAGAAGACATTCAATTATAGTCTGTTTTAGACAA
1379 AAATGCAAAAAAAG
326 AAATGCAAAAAAAG
* * *
1393 TCAACTTAAAATCAAATATGAGATTAGAAAACCATTTAAAACGAATAATATA-GTTTTTAAAGGA
1 TCAACTTAAAATCAATTTTGAGATTAGAAAACCATTTAAAACGAATAATA-AGGCTTTTAAAGGA
* * * *
1457 ATGGGTGACTATAAATAGATTTTTCTTGCCAATGAATGCT-TTTTTCTTCATGTTTCTCAA-AGT
65 ATAGGTGACTATAAATAGACTTTTCTTGCCAATGAATG-TAATTTT-TTAATGTTTCTCAAGA-T
* ** * * *
1520 AGACGTTCAATTATAATCTGTTTTAACCAAAACT-GTACAAAGAATTCAACTTAAAATCAATTTT
127 AGACATTCAATTATAATCTACTTTAACAAAAAATAGTA-AAA-AATTCAACTTAAAATC-ATTAT
* * **
1584 GAGATTATAAAACCATTGAAAGTGAGTAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGAAA
189 GAGATTATAAAACCATTGAAAGCGAGTAATAAGGCTTTGGAAGAAATGGAAGACTATAAATGAAA
* * * *
1649 TTTTCTTGCTAATGAAT-GCTTTTTTT-CTATGATTCTCGAGGTAA-ACATTCAATTATAGTCTG
254 TTTT-TTGCAAATGAATAGCTTTTTTTAC-ATGATTCCCAAAG-AAGACATTCAATTATAGTCTG
* *
1711 TTTTAGACAAAAATGTAAAAAAAT
316 TTTTAGACAAAAATGCAAAAAAAG
1735 TCAACTTAAAATCAATTTTGAGATTA
1 TCAACTTAAAATCAATTTTGAGATTA
Statistics
Matches: 308, Mismatches: 50, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
339 92 0.30
340 47 0.15
341 16 0.05
342 141 0.46
343 12 0.04
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (339 bp):
TCAACTTAAAATCAATTTTGAGATTAGAAAACCATTTAAAACGAATAATAAGGCTTTTAAAGGAA
TAGGTGACTATAAATAGACTTTTCTTGCCAATGAATGTAATTTTTTAATGTTTCTCAAGATAGAC
ATTCAATTATAATCTACTTTAACAAAAAATAGTAAAAAATTCAACTTAAAATCATTATGAGATTA
TAAAACCATTGAAAGCGAGTAATAAGGCTTTGGAAGAAATGGAAGACTATAAATGAAATTTTTTG
CAAATGAATAGCTTTTTTTACATGATTCCCAAAGAAGACATTCAATTATAGTCTGTTTTAGACAA
AAATGCAAAAAAAG
Done.