Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399664.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2910.0, 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: 4047
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.30
Warning! 730 characters in sequence are not A, C, G, or T
Found at i:1273 original size:171 final size:171
Alignment explanation
Indices: 1--1794 Score: 857
Period size: 170 Copynumber: 10.5 Consensus size: 171
* * * * * *
1 ATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAACCAGGAATAATG
1 ATGTAAAAAAATTCAACTTCAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGG
* * * * * * * * **
66 CTTTTAAAAGAATAGATGACTATAAAGGGACTTTTCTTGCCAACGAGTA-CGTTTTTCTTCACCT
66 CTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGA-AAGCCTTTTTCTTCATAT
* * * * **
130 TTCTCCAGGTAAAAATTCAATTATAGCATGTTTTAGCCAAAA
130 TTCTCTAGGTAGACATTCAATTATAGTATGTTTTAATCAAAA
* * * * * *
172 ATGAAAAAAAAATTCAACTTAAAATTAAATATGAGACTATAAAATAATTTAAAGCGAGAAATAAG
1 ATG-TAAAAAAATTCAACTTCAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAG
* * * * * * * *
237 ACTTTTGAAGGAATGGGTAATTATAATTAGACTTTTCTTACCAATGAATGTCTTTTTCTT--TAC
65 GCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAAGCCTTTTTCTTCATA-
* * * *
300 TTT-TCATGGGGTAGACATTCAATTATAATCTGTTTTAACCAAAA
129 TTTCTC-T-AGGTAGACATTCAATTATAGTATGTTTTAATCAAAA
* * * ** * * **
344 ATG-AAAAAAATTCAACTTAAAATTAATTATGAGTTTATAAAACCATTTAAA-CCATTCTTTAAG
1 ATGTAAAAAAATTCAACTTCAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGT-AATAAG
* * * * * *
407 ACTTTTGAATGAATGGGTAACCATAAATAGACTTTTCTT-CTCAATGAATAG-CTTTTT-TT-GT
65 GCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGC-CAATGAA-AGCCTTTTTCTTCAT
* * * * *
468 ACGTTTCT-TAAGGTAGGCATTCATTTATAGTCTATTTTAACCAAAA
128 A--TTTCTCT-AGGTAGACATTCAATTATAGTATGTTTTAATCAAAA
** * * * * * *
514 GGGTAAAAAAATTCAACATAAAATCAATTATGAGA-TACAAAACAATTTATAGTGAGTAATAAGG
1 ATGTAAAAAAATTCAACTTCAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGG
* * * * *** *
578 CTTTTCAAGGAATAGGTGACTATAAATGGA-TTTTGTTTCTCAATGAATTACTTTTT-TTACACA
66 CTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGC-CAATGAAAGCCTTTTTCTT-CATA
** * * * * * **
641 TTTCTGAAGGCAGGCATTCAATTAGAGTTTGTTTTAACCTTAA
129 TTTCTCTAGGTAGACATTCAATTATAGTATGTTTTAATCAAAA
* * ********** * *
684 ATGTAAAAAAATTTAACTTAAAATCAATTNNNNNNNNNNAAAACAATTTAAAGAGAGTAATAAGG
1 ATGTAAAAAAATTCAACTTCAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGG
* * * * * * *
749 CTTTT-ACAGGAATGGATGATTATAAATAGACTTTTCTTGCTAATGAATGTCTTTTT-TTCATGT
66 CTTTTGA-AGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAAGCCTTTTTCTTCATAT
* * * * * *
812 TTCT-TAAGGTAAACATTCAATTTTTGTCTATTTTAACCAAAA
130 TTCTCT-AGGTAGACATTCAATTATAGTATGTTTTAATCAAAA
* ********** * * *
854 ATATAAAAAAANNNNNNNNNNAATTAATTATGAGTTTATAAAACT-ATTTAAAGCGAGTCATAAG
1 ATGTAAAAAAATTCAACTTCAAATCAATTATGAGATTATAAAA-TAATTTAAAGCGAGTAATAAG
********** *
918 GCTTTTGAAGGAATGGGTGANNNNNNNNNNACTTTTCTT-CTCAATGAATAG-CTTTGTT-TACA
65 GCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGC-CAATGAA-AGCCTTT-TTCTTCA
* * * * ********** *
980 CATTTCTCAAGGCAGGCATTCAATNNNNNNNNNNTTTAACCAAAA
127 TATTTCTCTAGGTAGACATTCAATTATAGTATGTTTTAATCAAAA
* * * * * ******
1025 ATTTAAAAAAAGTT-GACTTAAAATCAATTTTGGGATTATAAAATAATTTAAAGCGAGTNNNNNN
1 ATGTAAAAAAA-TTCAACTTCAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAG
**** * * **
1089 NNNNTTAAAGGAATGGGTGACTATAAATGGACTTTTGTTGCCAATGATTGCCTTTTTCTTCATAT
65 GCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAAGCCTTTTTCTTCATAT
* * * *
1154 TTC-CTTAGGTAGATATTAAATTATTA-TCTGTTTTAATTAAAA
130 TTCTC-TAGGTAGACATTCAATTA-TAGTATGTTTTAATCAAAA
* * **
1196 ATGTAAAAACATTCAACTTCAAATCAATTATGAGATTATAAAATATTTTAAAATGAGTAATAAGG
1 ATGTAAAAAAATTCAACTTCAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGG
********** * * * * * * *
1261 CTTTTGAAGGAATNNNNNNNNNNAAATAGACTTTTCTTGCCAACGAATGCGTGTTCCTTCACATT
66 CTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAAGCCTTTTTCTTCATATT
* * * * *
1326 TCTCTAAGTAAAAATTCAATTATAGTTTGTTTTAGTCAAAA
131 TCTCTAGGTAGACATTCAATTATAGTATGTTTTAATCAAAA
* ********* * *
1367 ATGT-AAAAAATTCAA-TTTANNNNNNNNNNTGAGATTATAAAATAATTTAAAGCGAGTGATAAC
1 ATGTAAAAAAATTCAACTTCA-AATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAG
* * * *
1430 GCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTACTAATGAAA-CCTTTTTCTCCACT-
65 GCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAAGCCTTTTTCTTCA-TA
********** *
1493 TTTCT-TGAGGTAGACATTCAATTATANNNNNNNNNNACCAAAA
129 TTTCTCT-AGGTAGACATTCAATTATAGTATGTTTTAATCAAAA
* * * *
1536 ATGTAAAAAAATTCAACTTCAAATGAATTATGAGTTTATAAAATTATTTAAAGGGAGTAATAAGG
1 ATGTAAAAAAATTCAACTTCAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGG
* * *
1601 CTTTTGAAGAAATGGGTGACCATAAATGGAATTTTCTT-CTCAATGAAAAG-CTTTTT-TTGCAT
66 CTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGC-CAATG-AAAGCCTTTTTCTT-CAT
* * * *
1663 GTTTCTCAAGGCA-AGCATTCAATTATAATATGTTTTAATCAAAA
128 ATTTCTCTAGGTAGA-CATTCAATTATAGTATGTTTTAATCAAAA
* * * * *
1707 ATTTAAAAAAATTTAACTTAAAATCAATTTTG-GAATTATAAAACAATTTAAAGCGAGTAATAAG
1 ATGTAAAAAAATTCAACTTCAAATCAATTATGAG-ATTATAAAATAATTTAAAGCGAGTAATAAG
* * *
1771 ACTTTTAAAGAAATGGGTGACTAT
65 GCTTTTGAAGGAATGGGTGACTAT
1795 NNNNNNNNNN
Statistics
Matches: 1191, Mismatches: 381, Indels: 102
0.71 0.23 0.06
Matches are distributed among these distances:
168 1 0.00
169 54 0.05
170 521 0.44
171 477 0.40
172 138 0.12
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.34
Consensus pattern (171 bp):
ATGTAAAAAAATTCAACTTCAAATCAATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGG
CTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAAGCCTTTTTCTTCATATT
TCTCTAGGTAGACATTCAATTATAGTATGTTTTAATCAAAA
Found at i:2396 original size:171 final size:170
Alignment explanation
Indices: 1959--2396 Score: 457
Period size: 171 Copynumber: 2.6 Consensus size: 170
1949 NNNNNNNNNN
* * *
1959 AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATAATTTAAAACGAGGAATAAAGCTTT
1 AAAAAAATTCAACTTAAAATCAAATATGAGATTATAAAATAATTTAAAACGAGTAAT-AGGCTTT
* * *
2024 TGAAGGGATGGGTGACTATAAATGGACTTTTCTTACCAACGAATATGTTTTCTTCACGTTTCTCC
65 TGAAGGAATGGGTGACTATAAATGGACTTTTCTTACAAACGAATATATTTTCTTCACGTTTCTCC
* *
2089 AAGTAGAAATTGAATTATAGCATGTTTTAGCCAAAAATACA
130 AAGTAGAAATTCAATTATAGCATGTTTTAACCAAAAATACA
* * *
2130 AAAAAAATTCAACTTAAAATCAAATATAAGATTAAAAAATAATTTAAAGCGAGTAATGAGGCTTT
1 AAAAAAATTCAACTTAAAATCAAATATGAGATTATAAAATAATTTAAAACGAGTAAT-AGGCTTT
********** * *
2195 TNNNNNNNNNNGTGACTATAAATGGACTTTTCTTGCAAACGAATGCA-ATTTTCTTCTCGTTTCT
65 TGAAGGAATGGGTGACTATAAATGGACTTTTCTTACAAACGAAT--ATATTTTCTTCACGTTTCT
* * * **
2259 CCAAGTAGAAATTCAATTGTAGTATGTTTTAACTAAAAAT-GT
128 CCAAGTAGAAATTCAATTATAGCATGTTTTAACCAAAAATACA
**********
2301 AAAAAAATTCAACTNNNNNNNNNNTATGAGATTATAAAATAATTTAAAACGAGTAATATGGCTTT
1 AAAAAAATTCAACTTAAAATCAAATATGAGATTATAAAATAATTTAAAACGAGTAATA-GGCTTT
* *
2366 TGAAGGAATGGGTGACTGTAAATAGACTTTT
65 TGAAGGAATGGGTGACTATAAATGGACTTTT
2397 TTTTCTCAAT
Statistics
Matches: 211, Mismatches: 53, Indels: 6
0.78 0.20 0.02
Matches are distributed among these distances:
170 1 0.00
171 159 0.75
172 50 0.24
173 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.32
Consensus pattern (170 bp):
AAAAAAATTCAACTTAAAATCAAATATGAGATTATAAAATAATTTAAAACGAGTAATAGGCTTTT
GAAGGAATGGGTGACTATAAATGGACTTTTCTTACAAACGAATATATTTTCTTCACGTTTCTCCA
AGTAGAAATTCAATTATAGCATGTTTTAACCAAAAATACA
Found at i:2726 original size:170 final size:168
Alignment explanation
Indices: 2330--3156 Score: 515
Period size: 170 Copynumber: 4.9 Consensus size: 168
2320 NNNNNTATGA
* * * * * * *
2330 GATTATAAAATAATTTAAAACGAGTAATATGGCTTTTGAAGGAATGGGTGACTGTAAATAGACTT
1 GATTATAAAACAATTTAAAGCGAATAATAAGGCTTTTGAA-GAATGAGTGACTATAAATGGAC--
* * *
2395 TTTTTTCTCAATG--TGTAGCTTTTTTTACCTATTTCTCAAGGCAAGCATTCAATTATAGTCTGT
63 TTTTTTCTCAATGAATG-A-C-TTTTTTACATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGT
** * * * * ****
2458 TTTAATAAAAAAATGTATAAA-AATTTAACTTAAAATTAATTANNN
125 TTTAA-CCATAAATGTA-AAACAATTCAACTAAAAATCAATTTTGG
******* * * * * *
2503 NNNNNNNAAATAATTTAAAG-TAAGTAATAATGCTTTTGAAGGAATGGGTGACTATAAATTGACT
1 GATTATAAAACAATTTAAAGCGAA-TAATAAGGCTTTTGAA-GAATGAGTGACTATAAATGGACT
* * * *
2567 TTTTTCTCAATGAATGAATTTGTTTACATGTTTCTTAAGGCAGACATTTAATTATAGTCTGTTTT
64 TTTTTCTCAATGAATGACTTT-TTTACATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGTTTT
*
2632 AACCATAAATGTAAAACAATTCAACTCAAAATCAATTTTGG
128 AACCATAAATGTAAAACAATTCAACTAAAAATCAATTTTGG
*
2673 GATTATAAAACATTTTAAAGCGAATAATAAGGCTTTTGAAGAAGTGAGTGACTATAAATGGACTT
1 GATTATAAAACAATTTAAAGCGAATAATAAGGCTTTTGAAGAA-TGAGTGACTATAAATGGACTT
* * * * * *
2738 TTCTTC-CAAATGAAT-AGCTTTTTTGCACGTTTCTCAAGGTAGGTATTCAATTATAATCTATTT
65 TT-TTCTC-AATGAATGA-CTTTTTTACATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGTTT
* * * * * * *
2801 GAACAAAAAATATAAAAAAATTCAACTAAAAATCGATTAT-G
127 TAACCATAAATGTAAAACAATTCAACTAAAAATCAATTTTGG
* * * * * ********* *
2842 AAATATAAAACAATTTATAGTGAGTAATAAGGCNNNNNNNNNNAT-AGGTGACTATAAATGGATT
1 GATTATAAAACAATTTAAAGCGAATAATAAGGC-TTTTGAAGAATGA-GTGACTATAAATGGA-C
* * *
2906 TTTTTTCTCATTGAATGACTTTTTTTAC-TGATTTCTGAAGACAGGCATTCAATTATAGTCTGTT
63 TTTTTTCTCAATGAATGAC-TTTTTTACATG-TTTCTCAAGGCAGGCATTCAATTATAGTCTGTT
* * * *
2970 TTAACCATAAATGTAAAACAATTTAATTTAAAATCAATTTTGA
126 TTAACCATAAATGTAAAACAATTCAACTAAAAATCAATTTTGG
* ********** * * *
3013 GATTATAAAACAATTTAAAGCGAGTANNNNNNNNNNTAAAGGAATGAATGACTATAAATAGACTT
1 GATTATAAAACAATTTAAAGCGAATAATAAGGCTTTTGAA-GAATGAGTGACTATAAATGGACTT
* * * ** *
3078 TTCTTGCT-AATGATTGCCTTTTTT-CATGTTTCTCAAGGTAAACATTCAATTATTGTCTGTTTT
65 TT-TT-CTCAATGAATGACTTTTTTACATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGTTTT
* *
3141 AACAAAAAATGTAAAA
128 AACCATAAATGTAAAA
3157 NNNNNNNNNN
Statistics
Matches: 502, Mismatches: 129, Indels: 50
0.74 0.19 0.07
Matches are distributed among these distances:
168 1 0.00
169 105 0.21
170 229 0.46
171 113 0.23
172 5 0.01
173 49 0.10
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.36
Consensus pattern (168 bp):
GATTATAAAACAATTTAAAGCGAATAATAAGGCTTTTGAAGAATGAGTGACTATAAATGGACTTT
TTTCTCAATGAATGACTTTTTTACATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGTTTTAAC
CATAAATGTAAAACAATTCAACTAAAAATCAATTTTGG
Done.