Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400392.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3591.0, 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: 1683
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.26
Warning! 449 characters in sequence are not A, C, G, or T
Found at i:1287 original size:171 final size:171
Alignment explanation
Indices: 721--1679 Score: 968
Period size: 171 Copynumber: 5.6 Consensus size: 171
711 CTGAGGCAAG
* * * * * * * *
721 CATTCAATTATCGTCTGTTGTAACTAAAAATTTGAAAAAATTCAGCTTAATATCAATTATGAGAT
1 CATTCAATTATAGTATGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * * * * * *
786 TATAAAATAATTTATAGCAAGTAATAAGGCTTTTGAAGGAATAAGAGATTATAAATTGACTTTT-
66 TATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGACTTTTC
* * *
850 TCTGCAAATGAATGCCTTTTTCTTAACT-TTTCTCAAGGTAAA
131 T-TGCCAATGAATGCCTTTTTCTTCA-TGTTTCTCGAGGTAAA
** * * ** * * *
892 TGTTCAATTATCGTCTGTTGAAAACAAAAATGTGAAAAAATTCAACTTAAAATCAATAATGAGAT
1 CATTCAATTATAGTATGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * * **
957 TATAAAA-CAATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAGGAGACTATAAA-AGGAC-CG
66 TATAAAATC-ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATA-GACTTT
* * *
1019 TCTTGCTAATAAATG-CTTGTTTCTTCATGTTTCTCGAGGTAGA
129 TCTTGCCAATGAATGCCTT-TTTCTTCATGTTTCTCGAGGTAAA
* * * * * * *
1062 CATTTAATTGTAGTTTATTTTAACCAAAAATGCAAAACAATTCAACTGAAAATCAATTATGAG-T
1 CATTCAATTATAGTATGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * * *
1126 TCATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAGGGAATGGGTGACTATAAATTGACTTTT
66 T-ATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGACTTTT
* * * **
1191 CTTACCAATGAATG-CTTGTTTCTTCATGTTTCT-TATGCTGGA
130 CTTGCCAATGAATGCCTT-TTTCTTCATGTTTCTCGA-GGTAAA
* * * * * *
1233 CATTCAATTATAGTGTGTTTTAGCCAAAAATGTCAAACAATTTAACTTAAAATCAACTATGAGAT
1 CATTCAATTATAGTATGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * * * *
1298 CATAAAATCATTTAAAGCGAGGAATAAGGCTTATGAAGAAAT-GGATGACTATAAGTAGACTTTT
66 TATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGG-TGACTATAAATAGACTTTT
**
1362 CTTGCCAATGAATGCCTTTTTCTTTTTGTTTCTCGAGGTAAA
130 CTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCGAGGTAAA
* * * * * *
1404 CATTCAATTATAGTATGTTTTAGCAAAAAAATATAAAAAAATTCTACTTAAAAAT-GATAATGAG
1 CATTCAATTATAGTATGTTTTAAC-CAAAAATGTAAAAAAATTCAACTT-AAAATCAATTATGAG
* * *
1468 ATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTAAAGGGATAGGTGACTATAAATAGACATT
64 ATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGACTTT
* * *
1533 TCTTGTCAATGAATGCCTTTTTCTTTATGTTTCTCTAGGTAAA
129 TCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCGAGGTAAA
* * * * ** * *
1576 CAGTCAACTATAGTATGTTTTAACCCAAAATATAAAAAAATTCTGCTTAAAAACGATTATGAGAT
1 CATTCAATTATAGTATGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
* *
1641 TATAAAATCATTTAAAGTGAGTAATAAGGCTTTTAAAGG
66 TATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGG
1680 GATG
Statistics
Matches: 661, Mismatches: 109, Indels: 36
0.82 0.14 0.04
Matches are distributed among these distances:
169 6 0.01
170 134 0.20
171 370 0.56
172 144 0.22
173 7 0.01
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (171 bp):
CATTCAATTATAGTATGTTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
TATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGACTTTTC
TTGCCAATGAATGCCTTTTTCTTCATGTTTCTCGAGGTAAA
Found at i:1597 original size:343 final size:338
Alignment explanation
Indices: 755--1672 Score: 924
Period size: 341 Copynumber: 2.7 Consensus size: 338
745 TAAAAATTTG
* * * * * * *
755 AAAAAATTCAGCTTAATATCAATTATGAGATTATAAAATAATTTATAGCAAGTAATAAGGCTTTT
1 AAAAAATTCAACTAAAAATCAATAATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTT
* * * * *
820 GAAGGAATAAGAGATTATAAATTGACTTT-TTCTGCAAATGAATGCCTTTTTCTTAACT-TTTCT
66 -AAGGGATAGGTGACTATAAATTGACTTTCTTAT-C-AATGAATGCCTTTTTCTTAA-TGTTTCT
* * * * ** * * *
883 CAAGGTAAA-TGTTCAATTATCGTCTGTTGAAAACAAAAATGTGAAAAAATTCAACTTAAAATCA
127 CTAGGTAAACAG-TCAATTATAGTATGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCA
* *
947 ATAATGAGATTATAAAA-CAATTTAAAACGAGTAATAAGGCTTTTGAAGAAATAGGAGACTATAA
191 AT-ATGAGATTATAAAATC-ATTTAAAGCGAGTAATAAGGCTTATGAAGAAATAGGAGACTATAA
* * * *
1011 AAGGACCGTCTTGCTAATAAATGCTTGTTTCTTCATGTTTCTCGAGGTAGACATTTAATTGTAGT
254 AAGGACCGTCTTGCCAATAAATGCTTGTTTCTTCATGTTTCTCGAGGTAAACATTCAATTATAGT
* * *
1076 TTATTTTAACCAAAAATGCA
319 ATATTTTAACAAAAAATACA
* * * *
1096 AAACAATTCAACTGAAAATCAATTATGAG-TTCATAAAATCATTTAAAGTGAGTAATAAGGCTTT
1 AAAAAATTCAACTAAAAATCAATAATGAGATT-ATAAAATCATTTAAAGCGAGTAATAAGGCTTT
* * * *
1160 TGAGGGAATGGGTGACTATAAATTGACTTTTCTTACCAATGAATG-CTTGTTTCTTCATGTTTCT
65 TAAGGG-ATAGGTGACTATAAATTGAC-TTTCTTATCAATGAATGCCTT-TTTCTTAATGTTTCT
* ** * * * * *
1224 -TATGCTGGACATTCAATTATAGTGTGTTTTAGCCAAAAATGTCAAACAATTTAACTTAAAATCA
127 CTA-GGTAAACAGTCAATTATAGTATGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCA
* *
1288 ACTATGAGATCATAAAATCATTTAAAGCGAGGAATAAGGCTTATGAAGAAAT-GGATGACTATAA
191 A-TATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTATGAAGAAATAGGA-GACTATAA
* ** * **
1352 GTA-GACTTTTCTTGCCAATGAATGCCTT-TTTCTTTTTGTTTCTCGAGGTAAACATTCAATTAT
254 -AAGGAC-CGTCTTGCCAATAAATG-CTTGTTTCTTCATGTTTCTCGAGGTAAACATTCAATTAT
* * *
1415 AGTATGTTTTAGCAAAAAAATATA
316 AGTATATTTTAAC-AAAAAATACA
* *
1439 AAAAAATTCTACTTAAAAAT-GATAATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTT
1 AAAAAATTCAAC-TAAAAATCAATAATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTT
* * *
1503 TAAAGGGATAGGTGACTATAAATAGACATTTCTTGTCAATGAATGCCTTTTTCTTTATGTTTCTC
65 T-AAGGGATAGGTGACTATAAATTGAC-TTTCTTATCAATGAATGCCTTTTTCTTAATGTTTCTC
* * * * *
1568 TAGGTAAACAGTCAACTATAGTATGTTTTAACCCAAAATATAAAAAAATTCT-GCTTAAAAACGA
128 TAGGTAAACAGTCAATTATAGTATGTTTTAACCAAAAATGTAAAAAAATT-TAACTTAAAATC-A
* *
1632 TTATGAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTT
191 ATATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTT
1673 TTAAAGGGAT
Statistics
Matches: 473, Mismatches: 82, Indels: 42
0.79 0.14 0.07
Matches are distributed among these distances:
340 13 0.03
341 191 0.40
342 60 0.13
343 190 0.40
344 19 0.04
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (338 bp):
AAAAAATTCAACTAAAAATCAATAATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTT
AAGGGATAGGTGACTATAAATTGACTTTCTTATCAATGAATGCCTTTTTCTTAATGTTTCTCTAG
GTAAACAGTCAATTATAGTATGTTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATATG
AGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTATGAAGAAATAGGAGACTATAAAAGGACC
GTCTTGCCAATAAATGCTTGTTTCTTCATGTTTCTCGAGGTAAACATTCAATTATAGTATATTTT
AACAAAAAATACA
Done.