Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403129.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_797.0, 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: 2740
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.29
Warning! 522 characters in sequence are not A, C, G, or T
Found at i:2008 original size:170 final size:169
Alignment explanation
Indices: 1360--2428 Score: 996
Period size: 170 Copynumber: 6.3 Consensus size: 169
1350 NNNNNNNNNN
* * * * * * *
1360 CTATAAATAGACTTTTCTTCTTAATGAATGGCTTTTAT-TGCACGTTCCCCTAGGTAGACATTCA
1 CTATAAATGGACTTTTCTTCTCAATGAAT-GCTTTT-TCTACATGTTTCTCGAGGTAGACATTCA
* * * ********** *
1424 ATTATTGTCTGTTTTAATAAAAATGTAAAAAAANNNNNNNNNNAATCAATTATGGGATTATAAAA
64 ATTATAGTCTGTTTTAACAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
*
1489 CTGTTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTGA
129 CTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTGA
* ********** * *
1530 CTCTAAATGGACTTTTNNNNNNNNNNAATGCTTGTTTCTTCATGTTTCTCAAGGTAGACATTCAA
1 CTATAAATGGACTTTTCTTCTCAATGAATGCTT-TTTCTACATGTTTCTCGAGGTAGACATTCAA
* * * *
1595 TTATAGTATGTTTTTAATCAAAAATATAAAAAAATTCAACTTAAAATAAATTATGAGATTGTAAN
65 TTATAGTCTG-TTTTAA-CAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
********* *
1660 NNNNNNNNNAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGA
128 ACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTGA
* * *** * * * * *
1702 CTATAAATAGACCTTTCTTCTCAGCCAATAGCTTTTTCTAC-TCCTTTCTTGAGGCAGGCTTTCA
1 CTATAAATGGACTTTTCTTCTCAATGAAT-GCTTTTTCTACAT-GTTTCTCGAGGTAGACATTCA
* ** *
1766 ATTATAGTCTGTTCTAA-AGAAAA-ATGTAAAACTTCAACTTAAAATCAATTATGAGATTATAAA
64 ATTATAGTCTGTTTTAACA-AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * *
1829 ACCATTTAAATCGGGTAATAA-CGCTTTTTAAGGAATGAGTGA
128 ACTATTTAAAGCGAGTAATAAGC-CTTTTGAAGGAATGAGTGA
* *
1871 CTATAAATAGACTTTT-TTCTCAATGAATGGCTTTTTCTACATGTTTCTCGAGATAGACATTCAA
1 CTATAAATGGACTTTTCTTCTCAATGAAT-GCTTTTTCTACATGTTTCTCGAGGTAGACATTCAA
* *
1935 TTATAGTCTGTTTTAACAAAATATGTAAAACAATTCAACTTAAAATCAATTATGAGATTATAAAA
65 TTATAGTCTGTTTTAACAAAA-ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
* *
2000 CTATTTAAAGCAAGTGATAAGCCTTTTGAAGGAAT-AGATGA
129 CTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAG-TGA
* * * *
2041 CTCTAAATGGACTTTTCTTTTCAATGAATGCTTGTTTCT-CTACGTTTCTTGAGGTAGACATTCA
1 CTATAAATGGACTTTTCTTCTCAATGAATGCTT-TTTCTAC-ATGTTTCTCGAGGTAGACATTCA
* *
2105 ATTATAGTATGTTTTAATCAAAAATATAAAAAAATTCAACTTAAAATTAATTATGAGATT-TAAA
64 ATTATAGTCTGTTTTAA-CAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * *
2169 ACCATTTAAAGCAAGTAATAAGCCTTTTGAAGGAATGGGTGA
128 ACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTGA
** * *
2211 CTATAAATGGACTTTTCTTC-CTAACAAATGCTTTTTTCTTA-ATGTTTCTAGAGATAGACATTC
1 CTATAAATGGACTTTTCTTCTC-AATGAATGC-TTTTTC-TACATGTTTCTCGAGGTAGACATTC
* * * *
2274 AAATATAGTCTATTTTAATAAAAAATATAAAAAAATTCAA-TCTAAAATTAATTATGAGA-TATA
63 AATTATAGTCTGTTTTAA-CAAAAATATAAAAAAATTCAACT-TAAAATCAATTATGAGATTATA
* *
2337 AAA-TCATTTAAAGCGAGTAATAAGCGTTTTGAAGGAATGGGTGA
126 AAACT-ATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTGA
* *
2381 CTCTAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTACTTGTTTC
1 CTATAAATGGACTTTTCTTCTCAATGAAT-GCTTTTTCTACATGTTTC
2429 AAAGGGTAGA
Statistics
Matches: 730, Mismatches: 140, Indels: 58
0.79 0.15 0.06
Matches are distributed among these distances:
168 55 0.08
169 92 0.13
170 358 0.49
171 106 0.15
172 115 0.16
173 4 0.01
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (169 bp):
CTATAAATGGACTTTTCTTCTCAATGAATGCTTTTTCTACATGTTTCTCGAGGTAGACATTCAAT
TATAGTCTGTTTTAACAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACT
ATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTGA
Found at i:2217 original size:340 final size:336
Alignment explanation
Indices: 1467--2422 Score: 1073
Period size: 341 Copynumber: 2.8 Consensus size: 336
1457 NNNNNNNNNN
* **
1467 AATCAATTATGGGATTATAAAACTGTTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTGACT
1 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTGACT
* ********* * * *
1532 CTAAATGGACTTTTNNNNNNNNNNAATGCTTGTTTCTTCATGTTTCTCAAGGTAGACATTCAATT
66 ATAAATGGACTTTT-CTTCCAACAAATGCTT-TTTCTACATGTTTCTCGAGATAGACATTCAATT
* * **
1597 ATAGTATGTTTTTAATCAAAAATATAAAAAAATTCAACTTAAAATAAATTATGAGATTGTAANNN
129 ATAGTCTG-TTTTAA-CAAAAATATAAAAAAATTCAACTTAAAATAAATTATGAGATTATAA-AA
******* * * * **
1662 NNNNNNNAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATAGACCTTTCTTCTCAGC
191 TATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTCTAAATGGACTTTTCTTCTCAAT
* * * * * *
1727 CAATAGCTTTTTCTACTCCTTTCTTGAGGCAGGCTTTCAATTATAGTCTGTTCTAAAGAAAAATG
256 GAATAGCTTTTTCTACTCCTTTCTTGAGGCAGACATTCAATTATAGTATGTTCTAAACAAAAATA
*
1792 TAAAACTTCAACTTAA
321 TAAAAATTCAACTTAA
* * *
1808 AATCAATTATGAGATTATAAAACCATTTAAATCGGGTAATAA-CGCTTTTTAAGGAATGAGTGAC
1 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGC-CTTTTGAAGGAATGAGTGAC
* **
1872 TATAAATAGACTTTT-TTCTCAATGAATGGCTTTTTCTACATGTTTCTCGAGATAGACATTCAAT
65 TATAAATGGACTTTTCTTC-CAACAAAT-GCTTTTTCTACATGTTTCTCGAGATAGACATTCAAT
* * *
1936 TATAGTCTGTTTTAACAAAATATGTAAAACAATTCAACTTAAAATCAATTATGAGATTATAAAAC
128 TATAGTCTGTTTTAACAAAA-ATATAAAAAAATTCAACTTAAAATAAATTATGAGATTATAAAA-
* * * * *
2001 TATTTAAAGCAAGTGATAAGCCTTTTGAAGGAATAGATGACTCTAAATGGACTTTTCTTTTCAAT
191 TATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTCTAAATGGACTTTTCTTCTCAAT
* * * *
2066 GAAT-GCTTGTTTCT-CTACGTTTCTTGAGGTAGACATTCAATTATAGTATGTTTTAATCAAAAA
256 GAATAGCTT-TTTCTACT-CCTTTCTTGAGGCAGACATTCAATTATAGTATGTTCTAAACAAAAA
2129 TATAAAAAAATTCAACTTAA
319 TAT--AAAAATTCAACTTAA
* * *
2149 AATTAATTATGAGATT-TAAAACCATTTAAAGCAAGTAATAAGCCTTTTGAAGGAATGGGTGACT
1 AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTGACT
* *
2213 ATAAATGGACTTTTCTTCCTAACAAATGCTTTTTTCTTA-ATGTTTCTAGAGATAGACATTCAAA
66 ATAAATGGACTTTTCTTCC-AACAAATGC-TTTTTC-TACATGTTTCTCGAGATAGACATTCAAT
* * *
2277 TATAGTCTATTTTAATAAAAAATATAAAAAAATTCAA-TCTAAAATTAATTATGAGA-TATAAAA
128 TATAGTCTGTTTTAA-CAAAAATATAAAAAAATTCAACT-TAAAATAAATTATGAGATTATAAAA
*
2340 TCATTTAAAGCGAGTAATAAGCGTTTTGAAGGAATGGGTGACTCTAAATGGACTTTTCTTCTCAA
191 T-ATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTCTAAATGGACTTTTCTTCTCAA
*
2405 TGAATGGCTTTTTCTACT
255 TGAATAGCTTTTTCTACT
2423 TGTTTCAAAG
Statistics
Matches: 520, Mismatches: 76, Indels: 38
0.82 0.12 0.06
Matches are distributed among these distances:
338 11 0.02
339 140 0.27
340 173 0.33
341 190 0.37
342 6 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.35
Consensus pattern (336 bp):
AATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTGACT
ATAAATGGACTTTTCTTCCAACAAATGCTTTTTCTACATGTTTCTCGAGATAGACATTCAATTAT
AGTCTGTTTTAACAAAAATATAAAAAAATTCAACTTAAAATAAATTATGAGATTATAAAATATTT
AAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTCTAAATGGACTTTTCTTCTCAATGAATA
GCTTTTTCTACTCCTTTCTTGAGGCAGACATTCAATTATAGTATGTTCTAAACAAAAATATAAAA
ATTCAACTTAA
Found at i:2329 original size:511 final size:510
Alignment explanation
Indices: 1360--2428 Score: 1271
Period size: 511 Copynumber: 2.1 Consensus size: 510
1350 NNNNNNNNNN
* * * * * *
1360 CTATAAATAGACTTTTCTTCTTAATGAATGGCTTTTAT-TGCACGTTCCCCTAGGTAGACATTCA
1 CTATAAATAGACTTTTCTTCTCAATGAATGGCTTTT-TCTACATGTTTCCCGAGATAGACATTCA
* * ********** *
1424 ATTATTGTCTGTTTTAATAAAAATGTAAAAAAANNNNNNNNNNAATCAATTATGGGATTATAAAA
65 ATTATAGTCTGTTTTAACAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
* * ********
1489 CTGTTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGAGTGACTCTAAATGGACTTTTNNNNNNNN
130 CTATTTAAAGCAAGTAATAAGCCTTTTGAAGGAATGAGTGACTCTAAATGGACTTTTCTTTTCAA
** *
1554 NNAATGCTTGTTTCTTCATGTTTCTCAAGGTAGACATTCAATTATAGTATGTTTTTAATCAAAAA
195 TGAATGCTTGTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAGTATGTTTTTAATCAAAAA
********** *
1619 TATAAAAAAATTCAACTTAAAATAAATTATGAGATTGTAANNNNNNNNNNAGCGAGTAATAAGCC
260 TATAAAAAAATTCAACTTAAAATAAATTATGAGATTGTAAAACCATTTAAAGCAAGTAATAAGCC
* * *
1684 TTTTGAAGGAATGGGTGACTATAAATAGACCTTTCTTCTCAGCCAATAGCTTTTTCTACTCCTTT
325 TTTTGAAGGAATGGGTGACTATAAATAGACCTTTCTTCTCAACAAATAGCTTTTTCTAATCCTTT
* * * * * * * *
1749 CTTGAGGCAGGCTTTCAATTATAGTCTGTTCTAAAGAAAAATGTAAAACTTCAACTTAAAATCAA
390 CTAGAGACAGACATTCAAATATAGTCTATTCTAAAGAAAAATATAAAAATTCAACTTAAAATCAA
* * *
1814 TTATGAGATTATAAAACCATTTAAATCGGGTAATAA-CGCTTTTTAAGGAATGAGTGA
455 TTATGAGA-TATAAAACCATTTAAAGCGAGTAATAAGCG-TTTTGAAGGAATGAGTGA
*
1871 CTATAAATAGACTTTT-TTCTCAATGAATGGCTTTTTCTACATGTTTCTCGAGATAGACATTCAA
1 CTATAAATAGACTTTTCTTCTCAATGAATGGCTTTTTCTACATGTTTCCCGAGATAGACATTCAA
*
1935 TTATAGTCTGTTTTAACAAAATATGTAAAACAATTCAACTTAAAATCAATTATGAGATTATAAAA
66 TTATAGTCTGTTTTAACAAAA-ATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
*
2000 CTATTTAAAGCAAGTGATAAGCCTTTTGAAGGAAT-AGATGACTCTAAATGGACTTTTCTTTTCA
130 CTATTTAAAGCAAGTAATAAGCCTTTTGAAGGAATGAG-TGACTCTAAATGGACTTTTCTTTTCA
**
2064 ATGAATGCTTGTTTC-TCTACGTTTCTTGAGGTAGACATTCAATTATAGTATG-TTTTAATCAAA
194 ATGAATGCTTGTTTCTTC-ACGTTTCTCAAGGTAGACATTCAATTATAGTATGTTTTTAATCAAA
*
2127 AATATAAAAAAATTCAACTTAAAATTAATTATGAGATT-TAAAACCATTTAAAGCAAGTAATAAG
258 AATATAAAAAAATTCAACTTAAAATAAATTATGAGATTGTAAAACCATTTAAAGCAAGTAATAAG
* *
2191 CCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTC-CTAACAAAT-GCTTTTTTCTTAAT
323 CCTTTTGAAGGAATGGGTGACTATAAATAGACCTTTCTTCTC-AACAAATAGC-TTTTTC-TAAT
* * *
2254 -GTTTCTAGAGATAGACATTCAAATATAGTCTATTTTAATA-AAAAATATAAAAAAATTCAA-TC
385 CCTTTCTAGAGACAGACATTCAAATATAGTCTATTCTAA-AGAAAAATAT--AAAAATTCAACT-
* * *
2316 TAAAATTAATTATGAGATATAAAATCATTTAAAGCGAGTAATAAGCGTTTTGAAGGAATGGGTGA
446 TAAAATCAATTATGAGATATAAAACCATTTAAAGCGAGTAATAAGCGTTTTGAAGGAATGAGTGA
* * *
2381 CTCTAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTACTTGTTTC
1 CTATAAATAGACTTTTCTTCTCAATGAATGGCTTTTTCTACATGTTTC
2429 AAAGGGTAGA
Statistics
Matches: 471, Mismatches: 74, Indels: 26
0.82 0.13 0.05
Matches are distributed among these distances:
508 3 0.01
509 101 0.21
510 169 0.36
511 198 0.42
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (510 bp):
CTATAAATAGACTTTTCTTCTCAATGAATGGCTTTTTCTACATGTTTCCCGAGATAGACATTCAA
TTATAGTCTGTTTTAACAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
TATTTAAAGCAAGTAATAAGCCTTTTGAAGGAATGAGTGACTCTAAATGGACTTTTCTTTTCAAT
GAATGCTTGTTTCTTCACGTTTCTCAAGGTAGACATTCAATTATAGTATGTTTTTAATCAAAAAT
ATAAAAAAATTCAACTTAAAATAAATTATGAGATTGTAAAACCATTTAAAGCAAGTAATAAGCCT
TTTGAAGGAATGGGTGACTATAAATAGACCTTTCTTCTCAACAAATAGCTTTTTCTAATCCTTTC
TAGAGACAGACATTCAAATATAGTCTATTCTAAAGAAAAATATAAAAATTCAACTTAAAATCAAT
TATGAGATATAAAACCATTTAAAGCGAGTAATAAGCGTTTTGAAGGAATGAGTGA
Done.