Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399367.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2633.1, 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: 2293
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.26
Warning! 603 characters in sequence are not A, C, G, or T
Found at i:467 original size:172 final size:173
Alignment explanation
Indices: 20--845 Score: 1090
Period size: 172 Copynumber: 4.8 Consensus size: 173
10 ACTTGTTTTG
* *
20 AATGGTTTTACAGTCTCAAAATTGATTTAAATTTGAATTCTTTGTA-TATTTTTGGTTAAAACAG
1 AATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACTATTTTTGGTTAAAACAG
* * * *
84 ATTATAATTGAATCTCAACCTCAAGAAATATGAAGAAAAAGGCATTCTTTGGCAAGAAAAGTCCA
66 ATTATAATTGAATGTCAACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTTCA
* * * *
149 TTTACAGTCACCCGTTCCTTCAAAAGCCTTATTACCCTCTTTA
131 TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTA
** * * * * *
192 AATAATTTTATAATCTC-AAATTTACTTAAATTTGAATCCTTTGTAC-ATTTTTGGTTAGAACTG
1 AATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACTATTTTTGGTTAAAACAG
* ** * *
255 ATTATAATTGAATGTCAACATTGAGAAACATGAAGAAAAAGGAATTCATTTGCAAGAAAAGTTCA
66 ATTATAATTGAATGTCAACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTTCA
* ** *
320 TTTATCGTCACCCATTCCTTCAAAAGCCTTAACACTCGCTTTA
131 TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTA
363 AATGGTTTT-TCAATCTCAAAATTGATTTAAATTTGAATTCTTTGT-CTATTTTTGGTTAAAACA
1 AATGGTTTTAT-AATCTCAAAATTGATTTAAATTTGAATTCTTTGTACTATTTTTGGTTAAAACA
**
426 GATTATAATTGAATGTCAACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGTTAGAAAAG-TC
65 GATTATAATTGAATGTCAACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTTC
*
490 TATTTATAGTCACCCATTCCTTCAAAAACCTTATTACTCACTTTA
130 -ATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTA
* * * *
535 AATGGTTTTATAATCTCATAATTGATTTAAATTTGAATTCGTTGTAC-ATTTTTAGTTAAAAAAG
1 AATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACTATTTTTGGTTAAAACAG
* * * ** * *
599 ACTAGAATTGAACGTTTACCTCGAGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTTCA
66 ATTATAATTGAATGTCAACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTTCA
* * *
664 TTTATAGCCAACCAATCCTTCAAAAGCCTTATTACTCACTTTA
131 TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTA
* *
707 AATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACTTTTTTTGATTAAAACAG
1 AATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACTATTTTTGGTTAAAACAG
* * * ** * * * * *
772 ACTAGAATTGAATGTCTATATTAGGAAACATGAAGAAAAAGGCATTCACTGGCAAGAAAACTCCA
66 ATTATAATTGAATGTCAACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTTCA
837 TTTATAGTC
131 TTTATAGTC
846 NNNNNNNNNN
Statistics
Matches: 566, Mismatches: 79, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
170 1 0.00
171 148 0.26
172 338 0.60
173 79 0.14
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (173 bp):
AATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACTATTTTTGGTTAAAACAG
ATTATAATTGAATGTCAACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTTCA
TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTA
Found at i:750 original size:344 final size:343
Alignment explanation
Indices: 20--845 Score: 1150
Period size: 343 Copynumber: 2.4 Consensus size: 343
10 ACTTGTTTTG
* * *
20 AATGGTTTTACAGTCTCAAAATTGATTTAAATTTGAATTCTTTGTATATTTTTGGTTAAAACAGA
1 AATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTCTATTTTTGGTTAAAACAGA
* * *
85 TTATAATTGAATCTCAACCTCAAGAAATATGAAGAAAAAGGCATTCTTTGGCAAGAAAAGTCCAT
66 TTATAATTGAATGTCAACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCAT
* * * * *
150 TTACAGTCACCCGTTCCTTCAAAAGCCTTATTACCCTCTTTAAATAATTTTATAATCTCAAATTT
131 TTATAGTCACCCATTCCTTCAAAAACCTTATTACCCACTTTAAATAATTTTATAATCTCAAATTG
* * * ** * * * *
215 ACTTAAATTTGAATCCTTTGTACATTTTTGGTTAGAACTGATTATAATTGAATGTCAACATTGAG
196 ACTTAAATTTGAATCCGTTGTACATTTTTAGTTAAAAAAGACTAGAATTGAACGTCAACATCGAG
* * * * * *
280 AAACATGAAGAAAAAGGAATTCATTTGCAAGAAAAGTTCATTTATCGTCACCCATTCCTTCAAAA
261 AAACATGAAGAAAAAAGAATTCATTGGCAAGAAAAGTTCATTTATAGCCAACCAATCCTTCAAAA
*
345 GCCTTAACACTCGCTTTA
326 GCCTTAACACTCACTTTA
363 AATGGTTTT-TCAATCTCAAAATTGATTTAAATTTGAATTCTTTGTCTATTTTTGGTTAAAACAG
1 AATGGTTTTAT-AATCTCAAAATTGATTTAAATTTGAATTCTTTGTCTATTTTTGGTTAAAACAG
** *
427 ATTATAATTGAATGTCAACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGTTAGAAAAGTCTA
65 ATTATAATTGAATGTCAACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCA
* **
492 TTTATAGTCACCCATTCCTTCAAAAACCTTATTACTCACTTTAAATGGTTTTATAATCTCATAAT
130 TTTATAGTCACCCATTCCTTCAAAAACCTTATTACCCACTTTAAATAATTTTATAATCTCA-AAT
* * ** *
557 TGATTTAAATTTGAATTCGTTGTACATTTTTAGTTAAAAAAGACTAGAATTGAACGTTTACCTCG
194 TGACTTAAATTTGAATCCGTTGTACATTTTTAGTTAAAAAAGACTAGAATTGAACGTCAACATCG
*
622 AGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTTCATTTATAGCCAACCAATCCTTCAA
259 AGAAACATGAAGAAAAAAGAATTCATTGGCAAGAAAAGTTCATTTATAGCCAACCAATCCTTCAA
**
687 AAGCCTTATTACTCACTTTA
324 AAGCCTTAACACTCACTTTA
* *
707 AATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTACTTTTTTTGATTAAAACAG
1 AATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGT-CTATTTTTGGTTAAAACAG
* * * ** * * * *
772 ACTAGAATTGAATGTCTATATTAGGAAACATGAAGAAAAAGGCATTCACTGGCAAGAAAACTCCA
65 ATTATAATTGAATGTCAACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCA
837 TTTATAGTC
130 TTTATAGTC
846 NNNNNNNNNN
Statistics
Matches: 424, Mismatches: 55, Indels: 6
0.87 0.11 0.01
Matches are distributed among these distances:
343 173 0.41
344 171 0.40
345 80 0.19
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (343 bp):
AATGGTTTTATAATCTCAAAATTGATTTAAATTTGAATTCTTTGTCTATTTTTGGTTAAAACAGA
TTATAATTGAATGTCAACCTCAAGAAACATGAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCAT
TTATAGTCACCCATTCCTTCAAAAACCTTATTACCCACTTTAAATAATTTTATAATCTCAAATTG
ACTTAAATTTGAATCCGTTGTACATTTTTAGTTAAAAAAGACTAGAATTGAACGTCAACATCGAG
AAACATGAAGAAAAAAGAATTCATTGGCAAGAAAAGTTCATTTATAGCCAACCAATCCTTCAAAA
GCCTTAACACTCACTTTA
Found at i:1875 original size:172 final size:172
Alignment explanation
Indices: 1587--2293 Score: 632
Period size: 172 Copynumber: 4.1 Consensus size: 172
1577 NNNNNNNNNA
* *
1587 ATTTAAATTTGAATTCTTTGTATATTTTTAGTTAAAACAGATTATAATTGAATCT-ACACCTCAA
1 ATTTAAATTTGAATTCTTTGTACATTTTTAGTTAAAACAGATTATAATTGAATGTCA-ACCTCAA
* * * * *
1651 TAAATATGAAGAAAAAGGCATTCCTTGGCAAGAAAAGTCCATTTACAGTCACCCATTCCTTCAAA
65 GAAACATGAAGAAAAAGGAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
** *
1716 AGCCTTATTACCCTCTTTAAATAGTTTTATAATCTCAAAATTG
130 AGCCTTATTACCAACTTTAAATGGTTTTATAATCTCAAAATTG
* * * * * * **
1759 ACTTAAATTTGAATCCTTTGTACATTTTTAGTTAGAACTGATTATAATTGAATATCAACATTGAG
1 ATTTAAATTTGAATTCTTTGTACATTTTTAGTTAAAACAGATTATAATTGAATGTCAACCTCAAG
* *
1824 AAACGTGAAGAAAAAGGAATTCATTGGCAAGAAAAGTTCATTTATAGTCACCCATTCCTTCAAAA
66 AAACATGAAGAAAAAGGAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
********** * *
1889 GCNNNNNNNNNNACTTTAAATGGTTTTACAATATCAAAATTG
131 GCCTTATTACCAACTTTAAATGGTTTTATAATCTCAAAATTG
* * *
1931 ATTTAAATTTGAATTCTTTGT-CTCTTTTTGGTTAAAACAGATTATAATTGAATGCCAACCTCAA
1 ATTTAAATTTGAATTCTTTGTAC-ATTTTTAGTTAAAACAGATTATAATTGAATGTCAACCTCAA
********** **
1995 GAAACATGAAGAAANNNNNNNNNNTTGGTTAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
65 GAAACATGAAGAAAAAGGAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
* * * * *
2060 AACCATATTACTAACTTTAAATGGTTTTATAACCTCATAATTG
130 AGCCTTATTACCAACTTTAAATGGTTTTATAATCTCAAAATTG
* * * * * * ** **
2103 ATTTAAGTTTGAATT-TGTTGTACATTTTTGGTTAAAAAAGACTAGAATTGAACGTTTACCTTGA
1 ATTTAAATTTGAATTCT-TTGTACATTTTTAGTTAAAACAGATTATAATTGAATGTCAACCTCAA
********** * * * * *
2167 GAAACATGAAGAAAANNNNNNNNNNTAGCAAGAAAAGTTCATTTATAGCCAACCAATCCTTCAAA
65 GAAACATGAAGAAAAAGGAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
**
2232 AGCCTTATTACTC-GTTTTAAATGG-TTTATAATCTCAAAATTG
130 AGCCTTATTAC-CAACTTTAAATGGTTTTATAATCTCAAAATTG
2274 ATTTAAATTTGAATTCTTTG
1 ATTTAAATTTGAATTCTTTG
Statistics
Matches: 431, Mismatches: 98, Indels: 13
0.80 0.18 0.02
Matches are distributed among these distances:
171 35 0.08
172 394 0.91
173 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.34
Consensus pattern (172 bp):
ATTTAAATTTGAATTCTTTGTACATTTTTAGTTAAAACAGATTATAATTGAATGTCAACCTCAAG
AAACATGAAGAAAAAGGAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
GCCTTATTACCAACTTTAAATGGTTTTATAATCTCAAAATTG
Done.