Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402983.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_649.0, 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: 2338
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.32
Warning! 285 characters in sequence are not A, C, G, or T
Found at i:1067 original size:173 final size:170
Alignment explanation
Indices: 292--1310 Score: 543
Period size: 171 Copynumber: 5.9 Consensus size: 170
282 TACCTTTAAC
* * ** ** ** *
292 AGCCTTATTACTCGCTTTAAATGGTTTTATAATCTAATAACAGACCTAAAGTCA-AATTTTTTT-
1 AGCCTTATTACTCGCTTTAAATAGCTTTATAATCTCTTAATTGATTTTAAGT-AGAATTTTTTTA
* * * * * * * * *
355 CATTTTTAGTTATAATAGATTATAATTAAATATCTACCTCAAGAAACATGAAGAAAAAGCTATTC
65 CATTTTTAGTTAAAACAAATAATAATTGAATGT-TACCTCAAGAAATATGAAGAAAGAGCCATTC
* * * * *
420 ATTGACAAGAAAA-CTCCATTTATAGTCACCTATGCCTTTGAA
129 ATTGACAAGAAAAGC-CTATTTATAGTCACCCATCCCTCTAAA
* ************* * *
462 AGCCTTATTACTCACTNNNNNNNNNNNNNTAATCTCATAATTGATTTTAAGTTA-AATTGTTTTA
1 AGCCTTATTACTCGCTTTAAATAGCTTTATAATCTCTTAATTGATTTTAAG-TAGAATTTTTTTA
* * * * * * * * *
526 CATTTTTGGCTAAAATAGATTATAATTAAATGTCTACCTCGAGAAACT-TGAATAAAGAGTCATT
65 CATTTTTAGTTAAAACAAATAATAATTGAATGT-TACCTCAAGAAA-TATGAAGAAAGAGCCATT
** * *
590 CATTGGTAAGAAAAGCCTATTTACT-GTCACCTATACCT-TGAAA
128 CATTGACAAGAAAAGCCTATTTA-TAGTCACCCATCCCTCT-AAA
* ********** * ** * **
633 AGCCTTATTACTCCCTTTAANNNNNNNNNNAACCTGATAATTGATTTTAAGTTGAATTGGTTTAC
1 AGCCTTATTACTCGCTTTAAATAGCTTTATAATCTCTTAATTGATTTTAAGTAGAATTTTTTTAC
* * * ** ** **
698 ATTTTTGGTTAAAACAGATAATAATTAAATGTCTGTCTTGAGAAAGGTGAAGAAA-AGCCATTCA
66 ATTTTTAGTTAAAACAAATAATAATTGAATGT-TACCTCAAGAAATATGAAGAAAGAGCCATTCA
* * * * * *
762 TT-ATTAAGGAAAATCC-ATTTTATAGTCACTCATGCCTTTGAA
130 TTGA-CAA-GAAAAGCCTA-TTTATAGTCACCCATCCCTCTAAA
* * * * * * * * ********** * *
804 AGACTTATTACTCACTTCAATTGGTTTTATAA-CATCATGATNNNNNNNNNNTTGAATTGTTTTA
1 AGCCTTATTACTCGCTTTAAATAGCTTTATAATC-TCTTAATTGATTTTAAGTAGAATTTTTTTA
* * * * *
868 CATTTTTTGTTAAAATAGATAATAATTGAATGCTTACCTCAAGAAACATGAAGAAAGAGCCATTT
65 CATTTTTAGTTAAAACAAATAATAATTGAATG-TTACCTCAAGAAATATGAAGAAAGAGCCATTC
933 ATTGACAAGAAAAGCCTTATTTATAGTCACCCATCCCTCTAAA
129 ATTGACAAGAAAAGCC-TATTTATAGTCACCCATCCCTCTAAA
********** *
976 AGCCTTATTACTCGCTTTANNNNNNNNNNTAATCT-TATAATTGATTTTGAGTAGAATTATTTTT
1 AGCCTTATTACTCGCTTTAAATAGCTTTATAATCTCT-TAATTGATTTTAAGTAGAATT-TTTTT
* * *
1040 ACATTTTTAGTTAAAACAAATAATAATTGAATGTCTACTTTGAA-AAATATAAAGAAAGAGCCAT
64 ACATTTTTAGTTAAAACAAATAATAATTGAATGT-TAC-CTCAAGAAATATGAAGAAAGAGCCAT
* * * *
1104 TCATTGGCAAGAAAAGCATATTTATAGTCACCCATGCCTTTAAA
127 TCATTGACAAGAAAAGCCTATTTATAGTCACCCATCCCTCTAAA
* *
1148 AGCCTTATTACTCGCTTTAAATAGCTTTATAATCTCTTATTTGATTTTAAGTTGAATTTTTTTAC
1 AGCCTTATTACTCGCTTTAAATAGCTTTATAATCTCTTAATTGATTTTAAGTAGAATTTTTTTAC
* * ** * *
1213 ATTTTTGGTTAAAACAAATAATAATTGCATGTTTACCTTGAGAAATGTGAAAGAAAGAGCAATTC
66 ATTTTTAGTTAAAACAAATAATAATTGAATG-TTACCTCAAGAAATATG-AAGAAAGAGCCATTC
1278 ATTGACAAGAAAAGCCTATTTATAGTCACCCAT
129 ATTGACAAGAAAAGCCTATTTATAGTCACCCAT
1311 GCCTNNNNNN
Statistics
Matches: 656, Mismatches: 165, Indels: 54
0.75 0.19 0.06
Matches are distributed among these distances:
170 60 0.09
171 340 0.52
172 179 0.27
173 74 0.11
174 3 0.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.35
Consensus pattern (170 bp):
AGCCTTATTACTCGCTTTAAATAGCTTTATAATCTCTTAATTGATTTTAAGTAGAATTTTTTTAC
ATTTTTAGTTAAAACAAATAATAATTGAATGTTACCTCAAGAAATATGAAGAAAGAGCCATTCAT
TGACAAGAAAAGCCTATTTATAGTCACCCATCCCTCTAAA
Found at i:1157 original size:344 final size:332
Alignment explanation
Indices: 502--1310 Score: 732
Period size: 344 Copynumber: 2.4 Consensus size: 332
492 AATCTCATAA
* * * *
502 TTGATTTTAAGTTAAATTGTTTTACATTTTTGGCTAAAATAGATTATAATTAAATGTCTACCTCG
1 TTGATTTTAAGTTGAATTGTTTTACATTTTTGGTTAAAATAGATAATAATTGAATGT-TACCTCG
* * * ** *
567 AGAAACTTGAATAAAGAGTCATTCATTGGTAAGAAAAGCCTATTTACT-GTCACCTATACCTTGA
65 AGAAACATGAAGAAAGAGCCATTCATTGACAAGAAAAGCCTATTTA-TAGTCACCCATACCTTGA
* *
631 AAAGCCTTATTACTCCCTTTAANNNNNNNNNNAACCTGATAATTGATTTTAAGTTGAATTGGTTT
129 AAAGCCTTATTACTCCCTTTAA---------TAACCTGATAATTGATTTTAAGTAGAATTGGTTT
* * * * * *
696 ACATTTTTGGTTAAAACAGATAATAATTAAATGTCTGTCTTGAGAAAGGTGAAGAAAAGCCATTC
185 ACATTTTTAGTTAAAACAAATAATAATTAAATGTCTCTCTTGAAAAAGATAAAGAAAAGCCATTC
** * * *
761 ATTATTAAGGAAAATCCATTTTATAGTCACTCATGCCTTTGAAAGACTTATTACTCACTTCAATT
250 ATTAGCAAGGAAAATCCATTTTATAGTCACCCATGCCTTTAAAAGACTTATTACTCACTTCAAAT
* *
826 GGTTTTATAA-CATCATGA-
315 AGCTTTATAATC-TC-TGAT
********** * *
844 TNNNNNNNNNNTTGAATTGTTTTACATTTTTTGTTAAAATAGATAATAATTGAATGCTTACCTCA
1 TTGATTTTAAGTTGAATTGTTTTACATTTTTGGTTAAAATAGATAATAATTGAATG-TTACCTCG
* *
909 AGAAACATGAAGAAAGAGCCATTTATTGACAAGAAAAGCCTTATTTATAGTCACCCATCCCTCT-
65 AGAAACATGAAGAAAGAGCCATTCATTGACAAGAAAAGCC-TATTTATAGTCACCCATACCT-TG
* * * * * **
973 AAAAGCCTTATTACTCGCTTTANNNNNNNNNNTAATCTTATAATTGATTTTGAGTAGAATTATTT
128 AAAAGCCTTATTACTCCCTTTA---------ATAACCTGATAATTGATTTTAAGTAGAATT-GGT
* *
1038 TTACATTTTTAGTTAAAACAAATAATAATTGAATGTCTACT-TTGAAAAATATAAAGAAAGAGCC
183 TTACATTTTTAGTTAAAACAAATAATAATTAAATGTCT-CTCTTGAAAAAGATAAAGAAA-AGCC
* * * *
1102 ATTCATTGGCAA-GAAAA-GCATATTTATAGTCACCCATGCCTTTAAAAGCCTTATTACTCGCTT
246 ATTCATTAGCAAGGAAAATCCAT-TTTATAGTCACCCATGCCTTTAAAAGACTTATTACTCACTT
* *
1165 TAAATAGCTTTATAATCTCTTAT
310 CAAATAGCTTTATAATCTCTGAT
* * * * *
1188 TTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAAATAATAATTGCATGTTTACCTTG
1 TTGATTTTAAGTTGAATTGTTTTACATTTTTGGTTAAAATAGATAATAATTGAATG-TTACCTCG
** *
1253 AGAAATGTGAAAGAAAGAGCAATTCATTGACAAGAAAAGCCTATTTATAGTCACCCAT
65 AGAAACATG-AAGAAAGAGCCATTCATTGACAAGAAAAGCCTATTTATAGTCACCCAT
1311 GCCTNNNNNN
Statistics
Matches: 371, Mismatches: 76, Indels: 38
0.76 0.16 0.08
Matches are distributed among these distances:
342 82 0.22
343 68 0.18
344 177 0.48
345 44 0.12
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.36
Consensus pattern (332 bp):
TTGATTTTAAGTTGAATTGTTTTACATTTTTGGTTAAAATAGATAATAATTGAATGTTACCTCGA
GAAACATGAAGAAAGAGCCATTCATTGACAAGAAAAGCCTATTTATAGTCACCCATACCTTGAAA
AGCCTTATTACTCCCTTTAATAACCTGATAATTGATTTTAAGTAGAATTGGTTTACATTTTTAGT
TAAAACAAATAATAATTAAATGTCTCTCTTGAAAAAGATAAAGAAAAGCCATTCATTAGCAAGGA
AAATCCATTTTATAGTCACCCATGCCTTTAAAAGACTTATTACTCACTTCAAATAGCTTTATAAT
CTCTGAT
Found at i:1819 original size:171 final size:171
Alignment explanation
Indices: 1349--2338 Score: 730
Period size: 171 Copynumber: 5.8 Consensus size: 171
1339 NNNNNNNNNN
* * *
1349 CATTTTTTGTTAAAACAGAA-TATAATTAAATGTCTACCTCAAGAAACATGAAGAAAAAACCATT
1 CATTTTTGGTTAAAACA-AATTATAATTAAATGTCTACCTGAAGAAACATGAAGAAAAAGCCATT
** * * *
1413 GATTAATAAGAAAAGTCCATTTATAGTCACCCATGCCTTCAAATA-CTTTATTACTCGCTTTAAC
65 GATTAGCAAGAAAAGTCTATTTATAGTCACCCATGCCTTCAAA-AGCCTTATTACTCGCTTTAAA
* * *
1477 TGATTTTATAATCTAATAATTAATTTTCAA-TTGAATTTTTGTA
129 TGGTTTTATAATCTAATAATTGATTTT-AAGTTGAATTTTTTTA
* * * * * * * *
1520 CATTTATAGTTAAAACTAATAATAATTGAATGTTTACCTTG-AGAAACATGAA-AGAAAGTTCAA
1 CATTTTTGGTTAAAACAAATTATAATTAAATGTCTACC-TGAAGAAACATGAAGAAAAAG--CCA
* * * *
1583 TTCG-TT-GACAAGAAAAG-CATATTTATAGTCACCCATGCCTTGAAAGGCCTTATTAATCACTT
63 TT-GATTAG-CAAGAAAAGTC-TATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCTT
* *
1645 TAAATGGTTTTAT-ATCCTCATCATTGATTTTAAGTTGAATTTTTTTA
125 TAAATGGTTTTATAAT-CTAATAATTGATTTTAAGTTGAATTTTTTTA
* * * *
1692 TATTTTTTGTTAAAAAAAATTATAATTAAATGTCTACCTGAACAAACATGAAGAAAAAGCCATTG
1 CATTTTTGGTTAAAACAAATTATAATTAAATGTCTACCTGAAGAAACATGAAGAAAAAGCCATTG
* *
1757 ATTAGCAAGAAAAGTCTATTTCTAGTTACCCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATG
66 ATTAGCAAGAAAAGTCTATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATG
***********
1822 GTTTTATAATCNNNNNNNNNNNTTTAAGTTGAATTTTTTTA
131 GTTTTATAATCTAATAATTGATTTTAAGTTGAATTTTTTTA
* * * * * *
1863 CATTTTTGGCTAAAACAGATTATAATTAAATGTCTTCCTAAAGAAACATGAAGAGAAAGCCATTN
1 CATTTTTGGTTAAAACAAATTATAATTAAATGTCTACCTGAAGAAACATGAAGAAAAAGCCATTG
********* * * *
1928 NNNNNNNNNAAAAGTCTATTTATTGTCACCCATGCCTTCAACAGCCTTATTACTCGCTTTAGATG
66 ATTAGCAAGAAAAGTCTATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATG
** *
1993 GTTTT-TAATCTAATAATTGACCTTAAGTTGAA-TTTTTTC
131 GTTTTATAATCTAATAATTGATTTTAAGTTGAATTTTTTTA
* * ** * *
2032 CATTTTTGGTTAAAACAAATCATAATTGAATGTCTGTCTTAGGAAACATG-AGAAAAAAGCCATT
1 CATTTTTGGTTAAAACAAATTATAATTAAATGTCTACCTGAAGAAACATGAAG-AAAAAGCCATT
* * *********** * **
2096 CATTGGCAAGAAAAGTCCNNNNNNNNNNACCCACGCCTTTGAAAGCCTTATTACTCG-TATTAAA
65 GATTAGCAAGAAAAGTCTATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCT-TTAAA
* * **********
2160 TAGTTTTATAA-CATCATAATTGATTTTAAGTNNNNNNNNNNTA
129 TGGTTTTATAATC-TAATAATTGATTTTAAGTTGAATTTTTTTA
* * * * * * * ** * *
2203 CATTTTTAGTTAAAATAGATAATAATTGAATGTCTGCCTTAAGAAATGTGAAGAAAGAGCCATTT
1 CATTTTTGGTTAAAACAAATTATAATTAAATGTCTACCTGAAGAAACATGAAGAAAAAGCCATTG
* * * ** *
2268 ATTGGCAAAAAAAGCCTTATTTATAGTCACTTATGCCTTCAAAAGCCTTATTACTAGCTTTAAAT
66 ATTAGCAAGAAAAGTC-TATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCTTTAAAT
2333 GGTTTT
130 GGTTTT
Statistics
Matches: 627, Mismatches: 168, Indels: 47
0.74 0.20 0.06
Matches are distributed among these distances:
168 3 0.00
169 101 0.16
170 40 0.06
171 310 0.49
172 166 0.26
173 7 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.35
Consensus pattern (171 bp):
CATTTTTGGTTAAAACAAATTATAATTAAATGTCTACCTGAAGAAACATGAAGAAAAAGCCATTG
ATTAGCAAGAAAAGTCTATTTATAGTCACCCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATG
GTTTTATAATCTAATAATTGATTTTAAGTTGAATTTTTTTA
Done.