Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402608.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5679.0, 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: 3757
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.26
Warning! 805 characters in sequence are not A, C, G, or T
Found at i:1415 original size:170 final size:170
Alignment explanation
Indices: 1044--1436 Score: 398
Period size: 170 Copynumber: 2.3 Consensus size: 170
1034 NNNCATGTTC
* * * *
1044 TCTTCATGTTTCTTGAGGAAAACACTCTATTATAATTGATCTGAACCAAAAAAGTAAACAGATTC
1 TCTTCATGTTTCCTGAGGAAAACACTCAATTATAATTG-TTTTAACCAAAAAAGTAAACAGATTC
* * *
1109 AACTTAAAATCAATTATAAGATAGTAAAACCATTTAATGCAAGTAATAAGGCTTTGGAAGGCATG
65 AACTTAAAATCAATAATAAGATAGTAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATG
* **********
1174 GGTGACTATAANNNNNNNNNNCTTGCCAATGAATGGCTTTT
130 GGTGACTACAATTGGACTTTTCTTGCCAATGAATGGCTTTT
** ** ** *
1215 TCTTCACATTTCCCAAGGAAAATGCTCAATTATAATCTGTTTTAACC-AAAATGTAAAACA-ATT
1 TCTTCATGTTTCCTGAGGAAAACACTCAATTATAAT-TGTTTTAACCAAAAAAGT-AAACAGATT
** * *
1278 CAACTTAAAATCAATAATGGGAGTA-TAAAACTATTTAAAGCAAGTAGTAAGGCTTTCGAAGGCA
64 CAACTTAAAATCAATAATAAGA-TAGTAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCA
1342 TGGGTGACTACAATTGGACTTTTCTTGCCAATGAATGGCTTTT
128 TGGGTGACTACAATTGGACTTTTCTTGCCAATGAATGGCTTTT
** * * *
1385 T-TCTCATGTTTCCTGAGGCCAACACTCAATTCTAATTTGTTTTGACGAAAAA
1 TCT-TCATGTTTCCTGAGGAAAACACTCAATTATAA-TTGTTTTAACCAAAAA
1437 TATAAAAAAA
Statistics
Matches: 176, Mismatches: 40, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
169 1 0.01
170 127 0.72
171 46 0.26
172 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.31
Consensus pattern (170 bp):
TCTTCATGTTTCCTGAGGAAAACACTCAATTATAATTGTTTTAACCAAAAAAGTAAACAGATTCA
ACTTAAAATCAATAATAAGATAGTAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAGGCATGG
GTGACTACAATTGGACTTTTCTTGCCAATGAATGGCTTTT
Found at i:2927 original size:341 final size:339
Alignment explanation
Indices: 2265--3015 Score: 822
Period size: 341 Copynumber: 2.2 Consensus size: 339
2255 NNNNNNNNNC
* * *
2265 TTTCGAAGACATGGGTGACTATAAATGGACTTTTCTTGCTAATGAATGGCTTTTTCCTATCGATT
1 TTTCGAAGACAT-GGTGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTAT-GTTT
* **
2330 CCCAAGGCAAACATTCTAATATAATCTGTTTTAACCAAAATATAAAAGAATTAAACTTAAAATCA
64 CCCAAAGCAAACATTAAAATATAATCTGTTTTAACCAAAATATAAAAGAATTAAACTTAAAATCA
* * * * * *** * *
2395 AATATGCGCTTATAAAACTATTTAAAGCGAGTAATAAGGCTTTGGAAGGTATGGATGACTATAAA
129 AATATGAGCCTATAAAACGATTTAAAGAGAGCAATAAGGCTTCCAAAAGTATGGATGACTACAAA
* * ** * * *
2460 TGGACTTCTCTTGCCAATGAATCATGTTCTCTTTATGTTTCTTGAGGAAAGCACTCAATTATAAT
194 CGAACTTCTCTTGCCAATGAATCACCTTCTCATCAAGTTTCTTGAGGAAAGCACTCAATTATAAT
** * * * ** * *
2525 CTATTTTAACCAAAAATACAAAAACATTCATGTTAAAATCAATTGTGAGATTTTTAAACCATTTC
259 CTATTTTAACCAAAAATACAAAAACATTCAACTCAAAATCAAGTATGAGATAATGAAACCATTTA
* *
2590 AACCAAGTTATAAGGT
324 AACCAAGTAATAAGGA
* * * * *
2606 TTTCGAAGGCATGAGTGACTATGAATGGACTTTTCTTGCCAATGAATAGTTTTTTCTTCATTTTT
1 TTTCGAAGACATG-GTGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTT-ATGTTT
* * *
2671 CCCAAAGTAGACATTAAAATATAATCTGTTTTAGA-CAAAATATAAAAGAATTGAACTTAAAATC
64 CCCAAAGCAAACATTAAAATATAATCTGTTTTA-ACCAAAATATAAAAGAATTAAACTTAAAATC
* * *
2735 AAATATGAGCCTATAAAACGATTTAAAGATAGCAATAAGGCTTCCAAAAGTGTGGGTGACTACAA
128 AAATATGAGCCTATAAAACGATTTAAAGAGAGCAATAAGGCTTCCAAAAGTATGGATGACTACAA
* * ** * * *
2800 ACGAACTTTTCTTGCCAATGAATCACCTTTTCATCAAGTTTCTTGAGG-TGGACATTGAATTTTA
193 ACGAACTTCTCTTGCCAATGAATCACCTTCTCATCAAGTTTCTTGAGGAAAG-CACTCAATTATA
* ** ** * * *
2864 ATCTGTTTTAATTAAAAATGTAAACAGATTCAACTCAAAATCTAGTATGAGATAATGAAACCATT
257 ATCTATTTTAACCAAAAATACAAAAACATTCAACTCAAAATCAAGTATGAGATAATGAAACCATT
* *
2929 TAAAGCGAGTAATAAGGA
322 TAAACCAAGTAATAAGGA
* * * * *
2947 TTTGGAAGTCATGGATAACTATAAATAGACTTCTCTTGCCAATGAATGGCTTTTTCTTATGTTTC
1 TTTCGAAGACATGG-TGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTATGTTTC
3012 CCAA
65 CCAA
3016 GGAAAACACT
Statistics
Matches: 334, Mismatches: 71, Indels: 11
0.80 0.17 0.03
Matches are distributed among these distances:
340 13 0.04
341 318 0.95
342 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (339 bp):
TTTCGAAGACATGGTGACTATAAATGGACTTTTCTTGCCAATGAATGGCTTTTTCTTATGTTTCC
CAAAGCAAACATTAAAATATAATCTGTTTTAACCAAAATATAAAAGAATTAAACTTAAAATCAAA
TATGAGCCTATAAAACGATTTAAAGAGAGCAATAAGGCTTCCAAAAGTATGGATGACTACAAACG
AACTTCTCTTGCCAATGAATCACCTTCTCATCAAGTTTCTTGAGGAAAGCACTCAATTATAATCT
ATTTTAACCAAAAATACAAAAACATTCAACTCAAAATCAAGTATGAGATAATGAAACCATTTAAA
CCAAGTAATAAGGA
Found at i:3098 original size:171 final size:172
Alignment explanation
Indices: 2877--3270 Score: 384
Period size: 171 Copynumber: 2.3 Consensus size: 172
2867 TGTTTTAATT
* * * * * * * *
2877 AAAAATGTAAACAGATTCAACTCAAAATCTAGT-ATGAGATAATGAAACCATTTAAAGCGAGTAA
1 AAAAATGTAAAAAAATTTAACTTAAAATC-AATAATGAGATTATAAAACCATTTAAAGCAAGTAA
* ** * * *
2941 TAAGGATTTGGAAGTCATGGAT-AACTATAAATAGACTTCTCTTGCCAATGAATGGCTTTTT-CT
65 CAAGGATTCCGAAGGCATGGATGAA-AACAAATAGACTTCTCTTGCCAATGAATGGCTTTTTCCT
* **********
3004 TATGTTTCCCA-AGGAAAACACTCAA-NNNNNNNNNNTTTTGACC
129 CATGTTTCCCATA-GAAAACACTCAATTCTAATTTTTTTTTGACC
* *
3047 AAAAATGTAAAAAAAATTTAACTTAAAATCAATAATGGGATTATAAAACCATTTAAAGCAAGTAG
1 AAAAATGT-AAAAAAATTTAACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGCAAGTAA
* * * * * *
3112 CAAGGCTTCCGAAGGCATGGGTGAAAACAAATGGACTTTTGTTGCCGATGAATGGCTTTTTCCTC
65 CAAGGATTCCGAAGGCATGGATGAAAACAAATAGACTTCTCTTGCCAATGAATGGCTTTTTCCTC
**
3177 ATGTTTCCCATAGCCAACACTCAATTCTAATTTTTTTTTGACC
130 ATGTTTCCCATAGAAAACACTCAATTCTAATTTTTTTTTGACC
* *
3220 AAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTGTAAAACCAT
1 AAAAATGTAAAAAAATTTAACTTAAAATCAATAATGAGATTATAAAACCAT
3271 NNNNNNNNNN
Statistics
Matches: 180, Mismatches: 38, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
170 10 0.06
171 89 0.49
172 64 0.36
173 17 0.09
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.30
Consensus pattern (172 bp):
AAAAATGTAAAAAAATTTAACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGCAAGTAAC
AAGGATTCCGAAGGCATGGATGAAAACAAATAGACTTCTCTTGCCAATGAATGGCTTTTTCCTCA
TGTTTCCCATAGAAAACACTCAATTCTAATTTTTTTTTGACC
Done.