Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400358.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3559.0, 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: 2687
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.33
Warning! 242 characters in sequence are not A, C, G, or T
Found at i:323 original size:171 final size:171
Alignment explanation
Indices: 1--1512 Score: 1063
Period size: 171 Copynumber: 8.8 Consensus size: 171
* * * * *
1 AATCAATTGTG-AGATTATATAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGTTGAC
1 AATCAATTATGAAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAACGTATGGGTGAC
* * * * *
65 TATAAATGGACTTTTCATGCCAACGGATATATTTTTGTTCATGTTTCTCGAGGTAGACATTCAAT
66 TATAAATGGACTTTTCTTG-CAATGGATATCTTTTTCTTCATGTTTCTCGAGATAGACATTCAAT
* * *
130 TATATTCTATTTTACA-AAAAAATATAAAAAAACTCAAATTAA
130 TATATTCTGTTTTA-ATAAAAAATATAAAAAAATTCAACTTAA
* * * *
172 AATTAATTATGAAG-TTATAAAATCGTTTAAAGTAAGTAATAAGGCTTTTGAACCTATGGGTGAC
1 AATCAATTATGAAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAACGTATGGGTGAC
* * * * *
236 TATATATGGACTTTTTTTGTCAATGGATATCTTTTTCTGCATGTTTCTTGAGTTAGACATTCAAT
66 TATAAATGGACTTTTCTTG-CAATGGATATCTTTTTCTTCATGTTTCTCGAGATAGACATTCAAT
*
301 TATATTTTGTTTTAATAAAAAATATAAAAAAATTCAACTTAA
130 TATATTCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAA
** * * * * *
343 ACCCAATTATG-AGATCACAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAACGTATTGGTGAC
1 AATCAATTATGAAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAACGTATGGGTGAC
* * * * *
407 TATAAATGAACTTTTCTTGCTAATGGATACCTTTTTCTTCAAGTTTCTCAAGATACACATTCAAT
66 TATAAATGGACTTTTCTTGC-AATGGATATCTTTTTCTTCATGTTTCTCGAGATAGACATTCAAT
* * *
472 TATAATCTGTTTTAGTAAAAAA-AGTAAAAATATTCAACTTAA
130 TATATTCTGTTTTAATAAAAAATA-TAAAAAAATTCAACTTAA
*********** * * *** * * *
514 AATCAATTATG-AGCNNNNNNNNNNATTTAAACTGATTAATAAGGCTTCCAAAGGCATGAGTGAC
1 AATCAATTATGAAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAACGTATGGGTGAC
* * * * * **
578 TATAAATGCACTTTTCTTGCCAATGGGTATCTTTTTCTTCATATTTTTCAAGGCAGACATTCAAT
66 TATAAATGGACTTTTCTTG-CAATGGATATCTTTTTCTTCATGTTTCTCGAGATAGACATTCAAT
* * * *
643 TATAATT-TGTTTTAATAACAAATGTAAAAACATTCAACTTGA
130 TAT-ATTCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAA
* * *
685 AATCAATTATG-AGGTTATAAAA-CTATTTAAAGTGAGTAATAAGG-TTTTCGAAGGCATGGGT-
1 AATCAATTATGAAGATTATAAAATC-ATTTAAAGTGAGTAATAAGGCTTTT-GAACGTATGGGTG
********* * ** *
746 ANNNNNNNNNNGACTTTTCTTGCCAATGGATATCTTTTACTTCACATTTCTCATAGA-AGACATT
64 A-CTATAAATGGACTTTTCTTG-CAATGGATATCTTTTTCTTCATGTTTCTC-GAGATAGACATT
* *
810 CAATTATATTCTGTTTTAATGAAAAATAAAAAAAAATTCAACTTAA
126 CAATTATATTCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAA
* * * * * **********
856 ACA-CAATTATG-AGATTACAAAACCATATAAAGCGAGTAATAAAG-TTTTCGANNNNNNNNNNG
1 A-ATCAATTATGAAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTT-GAACGTATGGGTG
* * * * * * * *
918 ACTATAAATGGACTTTTCTTGCCGATGGA-AGCCTTTTTTTTCACGTTTCTCAAGGTAAAAATTC
64 ACTATAAATGGACTTTTCTTG-CAATGGATA-TCTTTTTCTTCATGTTTCTCGAGATAGACATTC
** * *
982 AATTATAGCCTATTTTAATAAAAACTATAAAAAAATTCAACTTAA
127 AATTATATTCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAA
* ********** * * * *
1027 AACCAATTATG-AGATTNNNNNNNNNNTTAAAGTGAGTAATAAGGC-TTTCAAAGCCATGGCTGA
1 AATCAATTATGAAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAACG-TATGGGTGA
* * * * * * * * * *
1090 CTATAAATGGACTTCTCTTGCTAATGAATATATTTTTCTTCACGTTTCTTGGGAAAGGCTTTTAA
65 CTATAAATGGACTTTTCTTGC-AATGGATATCTTTTTCTTCATGTTTCTCGAGATAGACATTCAA
* * * **
1155 TTTTAATCTGTTTTAATAAAAAATGTAAAAAAATTTTACTTAA
129 TTATATTCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAA
** * *
1198 AGA-CAATTATG-AGATTATAAAAAT-ATTTAAAGCAAGTAATAAGGCTTTTGAAGGTAAGGGTG
1 A-ATCAATTATGAAGATTAT-AAAATCATTTAAAGTGAGTAATAAGGCTTTTGAACGTATGGGTG
* * * *
1260 ACTATAAATGGACTATTCTTGCAAATGAATATCTTTTTCTTCACGTTTCTCGAGGTAGACATTCA
64 ACTATAAATGGACTTTTCTTGC-AATGGATATCTTTTTCTTCATGTTTCTCGAGATAGACATTCA
**********
1325 ATTATAATT-TGTNNNNNNNNNNNAATATAAAAAAATTCAACTTAA
128 ATTAT-ATTCTGT-TTTAATAAAAAATATAAAAAAATTCAACTTAA
* * * *
1370 AATCAATTATGAA-ATTATAAAACCATTTAAGGTGAGTAATAAGGCTTTTGAAGGCATGGGTGAC
1 AATCAATTATGAAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAACGTATGGGTGAC
* * ** * * * **
1434 TGTAAATGGACTTTTCTTACCCGTGGATATCCTTTTCTTCACGTTTCTCAAGGCAGACATTCAAT
66 TATAAATGGACTTTTCTT-GCAATGGATATCTTTTTCTTCATGTTTCTCGAGATAGACATTCAAT
* *
1499 TATAATCTATTTTA
130 TATATTCTGTTTTA
1513 NNNNNNNNNN
Statistics
Matches: 1036, Mismatches: 272, Indels: 66
0.75 0.20 0.05
Matches are distributed among these distances:
170 17 0.02
171 870 0.84
172 147 0.14
173 2 0.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (171 bp):
AATCAATTATGAAGATTATAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAACGTATGGGTGAC
TATAAATGGACTTTTCTTGCAATGGATATCTTTTTCTTCATGTTTCTCGAGATAGACATTCAATT
ATATTCTGTTTTAATAAAAAATATAAAAAAATTCAACTTAA
Found at i:1281 original size:513 final size:502
Alignment explanation
Indices: 25--1512 Score: 1249
Period size: 513 Copynumber: 2.9 Consensus size: 502
15 TTATATAATC
* ** * * *
25 ATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGTTGACTATAAATGGACTTTTCATGCCAACG
1 ATTTAAAGTGAGTAATAAGGCTTTCAAAGGCATGG-TGACTATAAATGGACTTTTCTTGCCAATG
* * * * * *
90 GATATATTTTTGTTCATGTTTCTCGAGGTAGACATTCAATTATATTCTATTTTACA-AAAAAATA
65 GATATATTTTTCTTCATGTTTCTTG-GGAAGACATTCAATTATAATCTGTTTTA-ATAAAAAATG
* * * *
154 TAAAAAAACTCAAATTAAAATTAATTATGA-AGTTAT-AAAATCGTTTAAAGTAAGTAATAAGGC
128 TAAAAAAATTCAACTTAAAA-CAATTATGAGA-TTATAAAAAT-ATTTAAAGTAAGTAATAAGGC
** * * * * *
217 TTTTGAACCTATGGGTGACTATATATGGACTTTTTTTGTCAATGGATATCTTTTTCTGCATGTTT
190 TTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTT
* *
282 CT--TGAGTTAGACATTCAATTATATTTTGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAC
255 CTCAT-AG-TAGACATTCAATTATATTCTGTTTTAATAAAAAATAAAAAAAAATTCAACTTAAAC
* * * *
345 CCAATTATGAGATCACAAAACCATTTAAAGTGAGTAATAAGGCTTTCGAACGTATTGGTGACTAT
318 ACAATTATGAGATCACAAAACCATATAAAGCGAGTAATAAAGCTTTCGAACGTATTGGTGACTAT
* * *
410 AAATGAACTTTTCTTGCTAATGGATACCTTTTTCTTCAAGTTTCTCAAGATACACATTCAATTAT
383 AAATGAACTTTTCTTGCCAATGGATACCTTTTTCTTCAAGTTTCTCAAGATAAAAATTCAATTAT
* * * * * ***
475 AATCTGTTTTAGTAAAAAAAGTAAAAATATTCAACTTAAAATCAATTATGAGCNNNNNNNNNN
448 AACCTATTTTAATAAAAAAAGTAAAAAAATTCAACTTAAAACCAATTATGAG--------ATT
* * * *
538 ATTTAAACTGATTAATAAGGCTTCCAAAGGCATGAGTGACTATAAATGCACTTTTCTTGCCAATG
1 ATTTAAAGTGAGTAATAAGGCTTTCAAAGGCATG-GTGACTATAAATGGACTTTTCTTGCCAATG
* * * * * * *
603 GGTATCTTTTTCTTCATATTT-TTCAAGGCAGACATTCAATTATAATTTGTTTTAATAACAAATG
65 GATATATTTTTCTTCATGTTTCTT--GGGAAGACATTCAATTATAATCTGTTTTAATAAAAAATG
* * * * *
667 TAAAAACATTCAACTTGAAATCAATTATGAGGTTATAAAACTATTTAAAGTGAGTAATAAGG-TT
128 TAAAAAAATTCAACTT-AAAACAATTATGAGATTATAAAAATATTTAAAGTAAGTAATAAGGCTT
* ********* * *
731 TTCGAAGGCATGGGT-ANNNNNNNNNNGACTTTTCTTGCCAATGGATATCTTTTACTTCACATTT
192 TT-GAAGGTATGGGTGA-CTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTT
* *
795 CTCATAGAAGACATTCAATTATATTCTGTTTTAATGAAAAATAAAAAAAAATTCAACTTAAACAC
255 CTCATAGTAGACATTCAATTATATTCTGTTTTAATAAAAAATAAAAAAAAATTCAACTTAAACAC
* * **********
860 AATTATGAGATTACAAAACCATATAAAGCGAGTAATAAAGTTTTCGANNNNNNNNNNGACTATAA
320 AATTATGAGATCACAAAACCATATAAAGCGAGTAATAAAGCTTTCGAACGTATTGGTGACTATAA
* * * * *
925 ATGGACTTTTCTTGCCGATGGA-AGCCTTTTTTTTCACGTTTCTCAAGGTAAAAATTCAATTATA
385 ATGAACTTTTCTTGCCAATGGATA-CCTTTTTCTTCAAGTTTCTCAAGATAAAAATTCAATTATA
* *
989 GCCTATTTTAATAAAAACTA-TAAAAAAATTCAACTTAAAACCAATTATGAGATT
449 ACCTATTTTAATAAAAA-AAGTAAAAAAATTCAACTTAAAACCAATTATGAGATT
** * *
1043 NNNNNNNNNNTTAAAGTGAGTAATAAGGCTTTCAAAGCCATGGCTGACTATAAATGGACTTCTCT
1 --------ATTTAAAGTGAGTAATAAGGCTTTCAAAGGCATGG-TGACTATAAATGGACTTTTCT
* * * * * * *
1108 TGCTAATGAATATATTTTTCTTCACGTTTCTTGGGAAAGGCTTTTAATTTTAATCTGTTTTAATA
57 TGCCAATGGATATATTTTTCTTCATGTTTCTTGGG-AAGACATTCAATTATAATCTGTTTTAATA
** *
1173 AAAAATGTAAAAAAATTTTACTTAAAGACAATTATGAGATTATAAAAATATTTAAAGCAAGTAAT
121 AAAAATGTAAAAAAATTCAACTTAAA-ACAATTATGAGATTATAAAAATATTTAAAGTAAGTAAT
* * * *
1238 AAGGCTTTTGAAGGTAAGGGTGACTATAAATGGACTATTCTTGCAAATGAATATCTTTTTCTTCA
185 AAGGCTTTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCA
* ********** *
1303 CGTTTCTCGA-GGTAGACATTCAATTATAATT-TGTNNNNNNNNNNNAATATAAAAAAATTCAAC
250 CGTTTCTC-ATAGTAGACATTCAATTAT-ATTCTGT-TTTAATAAAAAATAAAAAAAAATTCAAC
* * * * * * * * * * *
1366 TTAAA-ATCAATTATGAAATTATAAAACCATTTAAGGTGAGTAATAAGGCTTTTGAAGGCATGGG
312 TTAAACA-CAATTATGAGATCACAAAACCATATAAAGCGAGTAATAAAGCTTTCGAACGTATTGG
* * * ** * ** * *
1430 TGACTGTAAATGGACTTTTCTTACCCGTGGATATCC-TTTTCTTCACGTTTCTCAAGGCAGACAT
376 TGACTATAAATGAACTTTTCTTGCCAATGGATA-CCTTTTTCTTCAAGTTTCTCAAGATAAAAAT
*
1494 TCAATTATAATCTATTTTA
440 TCAATTATAACCTATTTTA
1513 NNNNNNNNNN
Statistics
Matches: 768, Mismatches: 175, Indels: 63
0.76 0.17 0.06
Matches are distributed among these distances:
512 14 0.02
513 599 0.78
514 151 0.20
515 4 0.01
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (502 bp):
ATTTAAAGTGAGTAATAAGGCTTTCAAAGGCATGGTGACTATAAATGGACTTTTCTTGCCAATGG
ATATATTTTTCTTCATGTTTCTTGGGAAGACATTCAATTATAATCTGTTTTAATAAAAAATGTAA
AAAAATTCAACTTAAAACAATTATGAGATTATAAAAATATTTAAAGTAAGTAATAAGGCTTTTGA
AGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCACGTTTCTCATA
GTAGACATTCAATTATATTCTGTTTTAATAAAAAATAAAAAAAAATTCAACTTAAACACAATTAT
GAGATCACAAAACCATATAAAGCGAGTAATAAAGCTTTCGAACGTATTGGTGACTATAAATGAAC
TTTTCTTGCCAATGGATACCTTTTTCTTCAAGTTTCTCAAGATAAAAATTCAATTATAACCTATT
TTAATAAAAAAAGTAAAAAAATTCAACTTAAAACCAATTATGAGATT
Found at i:2131 original size:170 final size:169
Alignment explanation
Indices: 1667--2155 Score: 461
Period size: 170 Copynumber: 2.9 Consensus size: 169
1657 NNNNNNNAAC
* * ** * * * * ** *
1667 CAATTATGAGATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTCAAAGGTAGGGTTGACTATA
1 CAATTATGAGATTATAAAATCATTTAAACCGAGTAACAAGGCTTCCAAATGCATCGATGACTATA
*
1732 AAT-AGGCTTTTCTTGT-CAATGAATATCTTTTTCTTTACATTTCTCAAGGTAAGCATTCAATTA
66 AATGA-ACTTTTCTT-TCCAATGAATATCTTTTTCTTTACATTTCTCAAGGTAA-CATTCAATTA
* *
1795 TAATCTGTTTTAATTAAAAATATAAAATAATTCAACATAGAAT
128 TAATCTGTTTTAA-TAAAAATATAAAATAACTCAACATAAAAT
* * ** *
1838 CAATTATGAGATTATAAAATTATTTAAAGCGAGTATTAAGGCTTTCAAATGCATCGATGA-TAAT
1 CAATTATGAGATTATAAAATCATTTAAACCGAGTAACAAGGCTTCCAAATGCATCGATGACT-AT
* * * ***********
1902 AAATGGACTTTTCTTGCCAATGGATATCTTTTTCTTCNNNNNNNNNNAGGTAAACATTCAATTAT
65 AAATGAACTTTTCTTTCCAATGAATATCTTTTTCTTTACATTTCTCAAGGT-AACATTCAATTAT
* *
1967 AATCTGTTTTAAGAAAAATATGAAAA-AACTCGACATAAAAT
129 AATCTGTTTTAATAAAAATAT-AAAATAACTCAACATAAAAT
* * *
2008 TAATTATGA-AGTTATAAAATCATTTAAACCTAGTAACAAGGCTTCCGAA-GACAT-GAGTGACT
1 CAATTATGAGA-TTATAAAATCATTTAAACCGAGTAACAAGGCTTCCAAATG-CATCGA-TGACT
* *
2070 ATAAATGAACTTTTCTTTCCAATAAATATCTTTTTCTTTACATTTCTCGAGGTAGACATTCAATT
63 ATAAATGAACTTTTCTTTCCAATGAATATCTTTTTCTTTACATTTCTCAAGGTA-ACATTCAATT
*
2135 ATAATATGTTTTAATAAAAAT
127 ATAATCTGTTTTAATAAAAAT
2156 GTACAAAANN
Statistics
Matches: 254, Mismatches: 54, Indels: 21
0.77 0.16 0.06
Matches are distributed among these distances:
169 5 0.02
170 133 0.52
171 114 0.45
172 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.36
Consensus pattern (169 bp):
CAATTATGAGATTATAAAATCATTTAAACCGAGTAACAAGGCTTCCAAATGCATCGATGACTATA
AATGAACTTTTCTTTCCAATGAATATCTTTTTCTTTACATTTCTCAAGGTAACATTCAATTATAA
TCTGTTTTAATAAAAATATAAAATAACTCAACATAAAAT
Done.