Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399884.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3117.0, 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: 2043
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.37
Warning! 161 characters in sequence are not A, C, G, or T
Found at i:791 original size:21 final size:22
Alignment explanation
Indices: 761--801 Score: 59
Period size: 20 Copynumber: 1.9 Consensus size: 22
751 CTTAGGAACC
761 GTAAGGAAAAAGCT-ATTTATTG
1 GTAAGG-AAAAGCTCATTTATTG
783 GTAA-GAAAAGCTCATTTAT
1 GTAAGGAAAAGCTCATTTAT
802 AGTAACCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (22 bp):
GTAAGGAAAAGCTCATTTATTG
Found at i:806 original size:20 final size:20
Alignment explanation
Indices: 768--806 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
758 ACCGTAAGGA
*
768 AAAAGCTATTTATTGGTAAG
1 AAAAGCTATTTATTAGTAAG
788 AAAAGCTCATTTA-TAGTAA
1 AAAAGCT-ATTTATTAGTAA
807 CCCAAGCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (20 bp):
AAAAGCTATTTATTAGTAAG
Found at i:1307 original size:171 final size:171
Alignment explanation
Indices: 1--1320 Score: 1195
Period size: 171 Copynumber: 7.7 Consensus size: 171
* * *
1 TCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTAGTTAAAATAGATTACAATTGAATAT
1 TCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAATAGATTATAATTGAATGT
** * * * *
66 CTGTCTTCG-GAAACATGAAAAAAAAGCCATTCATTGATAAGAAAAGTCCATTGATAGTCACCCA
66 CTACCTT-GAAAAACATGAAGAAAAAGCCATTCATTGATAAGAAAAGTTCATTTATAGTCACCCA
* * * *
130 TACCCTTGAAAACCTTATTACTCGCTTTAAATGGTTTTATAA
130 TGCCTTTGAAAGCCTTATTACTAGCTTTAAATGGTTTTATAA
* * * * **
172 TCTCATAATTAATTTTAGGTTGAATATTTTTATATTTTTCATTAAAATAGATTATAATTGAATGT
1 TCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAATAGATTATAATTGAATGT
* * * * * * * *
237 TTTCCTT-AGGAAACGTGAAGAAAAAACCATTCATTGATAAGAAAA-ATCGATTTATAGTTATCC
66 CTACCTTGA-AAAACATGAAGAAAAAGCCATTCATTGATAAGAAAAGTTC-ATTTATAGTCACCC
* *
300 ATACCTTTGAAAGCCTTATAACTCA-CTTTAAATGGTTTTATAA
129 ATGCCTTTGAAAGCCTTATTACT-AGCTTTAAATGGTTTTATAA
* * * *
343 TCTCATAATTGATTTTAGGTTGAA-TTTTTTACATTTTTGGTTCAAGTAGATTATAATTGAATGT
1 TCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAATAGATTATAATTGAATGT
* * * * * *
407 TTGCCTT-AGAAAACAT-AAGAGAAAAGCCATTTATT-AGTAAGTAAAGTCCATCTATAGTCACC
66 CTACCTTGA-AAAACATGAAGA-AAAAGCCATTCATTGA-TAAGAAAAGTTCATTTATAGTCACC
* * *
469 CATACCTTTGGAAGCCTTATTACTAGC-CTAAAGTGGTTTTATAA
128 CATGCCTTTGAAAGCCTTATTACTAGCTTTAAA-TGGTTTTATAA
* * * * * **
513 TCTCATAATTGACTTTAAGTTGAATTTTTTTACATTTTTTGTTCAAATATATTGT-ATTTATACC
1 TCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAATAGATTATAATTGA-ATG
* * * * * * * **
577 TCTACCTTGGAAAACGTGAAGAAAGAGCTATTTATTG-TCAA-AAAAGTTTATTTATAATCACTT
65 TCTACCTTGAAAAACATGAAGAAAAAGCCATTCATTGAT-AAGAAAAGTTCATTTATAGTCACCC
* ** * * *
640 AAGCCTTCAAAAGTCTCATTACTCGCTTTAAATGGTTTTAT-A
129 ATGCCTTTGAAAGCCTTATTACTAGCTTTAAATGGTTTTATAA
* *
682 TCTCATAATTAATTTTAAGTTGAATTTTTTTAGA-TTTTTGATTAAAATAGATTATAATTGAATG
1 TCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTG-TTAAAATAGATTATAATTGAATG
* ** * * * * * *
746 TCTATCTT-AGGAAC-CGTAAGGAAAAAGCTATTTATTGGTAAGAAAAGCTCATTTATAGTAACC
65 TCTACCTTGAAAAACATG-AA-GAAAAAGCCATTCATTGATAAGAAAAGTTCATTTATAGTCACC
* * **
809 CAAGCCTTTGAAAGCCTTATTACTCGCTTTAAATTATTTTATAA
128 CATGCCTTTGAAAGCCTTATTACTAGCTTTAAATGGTTTTATAA
* * * * * * *
853 TTTCATAATTGATTTTAGGTTAAATTTTTTTATATTGTTAGTTAAAATATATTATAATTGAATGT
1 TCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAATAGATTATAATTGAATGT
** * ** *
918 CTGTCTTGAGAAACATG-AGAGAAAAGCCATTCATTGGCAGGAAAA-TTACATTTATAGTCACCC
66 CTACCTTGAAAAACATGAAGA-AAAAGCCATTCATTGATAAGAAAAGTT-CATTTATAGTCACCC
* * *
981 ATGCCTTCGAAAGCCTAATTACTTGCTTTAAATGGTTTTATAA
129 ATGCCTTTGAAAGCCTTATTACTAGCTTTAAATGGTTTTATAA
* * *
1024 TCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTCGTTAAAATATATTATAATTAAATGT
1 TCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAATAGATTATAATTGAATGT
* * * ** * * * * * * *
1089 CTATCTTTG-AAAACGTAAAGTGAAAGCTAATCATTAGAGAA-AAAAGTTCACTCATAATCACTC
66 CTA-CCTTGAAAAACATGAAGAAAAAGCCATTCATT-GATAAGAAAAGTTCATTTATAGTCACCC
* * * *
1152 ATGCCTTTGAAAGCATTATTACTAGCCTGAAATAGTTTTATAA
129 ATGCCTTTGAAAGCCTTATTACTAGCTTTAAATGGTTTTATAA
* * * * * * * *
1195 TCTCATAATTGACTTTAAGTTGAATTTTTTTATATTTTTTGCTCAAATAGATTGTATTTAAATCT
1 TCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAATAGATTATAATTGAATGT
* * ** * *
1260 CTACCTTGAAAAACATGAAGAAAGAGCTATTCATTGCCAAGAAAAGTTTATTTATACTCAC
66 CTACCTTGAAAAACATGAAGAAAAAGCCATTCATTGATAAGAAAAGTTCATTTATAGTCAC
1321 TTAAGNNNNN
Statistics
Matches: 937, Mismatches: 178, Indels: 68
0.79 0.15 0.06
Matches are distributed among these distances:
167 1 0.00
168 11 0.01
169 79 0.08
170 246 0.26
171 577 0.62
172 22 0.02
173 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (171 bp):
TCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGTTAAAATAGATTATAATTGAATGT
CTACCTTGAAAAACATGAAGAAAAAGCCATTCATTGATAAGAAAAGTTCATTTATAGTCACCCAT
GCCTTTGAAAGCCTTATTACTAGCTTTAAATGGTTTTATAA
Found at i:1857 original size:171 final size:170
Alignment explanation
Indices: 1490--2043 Score: 512
Period size: 171 Copynumber: 3.3 Consensus size: 170
1480 NNNNNNNTTG
* * * *
1490 AAAGCCTTATTACTCACTTTAAATGGTTTTATAATATCATAATTGATTTTATA-TTGAATTTTTT
1 AAAGTCTTATTACTCGCTTCAAATGGTTTTATAATCTCATAATTGATTTTA-AGTTGAATTTTTT
* * * * *
1554 ATATTTTT-GTTTCAAACAGATTATAATTGAATGTTTGCCTTGGAAAACATGAGAGAAAAGCCAT
65 ATATTTTTAG-TTCAAATAGATTATAATTAAATCTTTACCTTGAAAAACATGAGAGAAAAGCCAT
* * * **
1618 TTATTGGCAAATAAAGTTCATCTATAGTCACCCATGCCTTTG
129 TCATTGGCAAATAAAGTTCATCTATACTCACCCAAGCCTTCA
** * * *
1660 AAAGTCTTATTACAAGCTTGAAATGGTTTTATAATCTCATAATTAACTTTAAGTTGAATTTTTTT
1 AAAGTCTTATTACTCGCTTCAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTT
* * * * * *
1725 ACATTTTTAGTTCAAATAGATTGTATTTAAATCTTTACCTTGAAAAACGTGA-AGAAAGGGCTAT
65 ATATTTTTAGTTCAAATAGATTATAATTAAATCTTTACCTTGAAAAACATGAGAGAAA-AGCCAT
* * * **
1789 TCATTGGTAAGA-AAAGTTCCTTTATACTCACTTAAGCCTTCA
129 TCATTGGCAA-ATAAAGTTCATCTATACTCACCCAAGCCTTCA
*
1831 AAAGTCTTATTACTCGCTTCAAATGGTTTTAT-ATCTCATAATTGATTTTAAGTTAAATTTTTTA
1 AAAGTCTTATTACTCGCTTCAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTA
* * * * * * *
1895 TAGTTTTAGTTTAAATAGATTATAATTGAATGTCTACCTT-AGGAACCATGAG-GAAAAAGCCAT
66 TATTTTTAGTTCAAATAGATTATAATTAAATCTTTACCTTGA-AAAACATGAGAG-AAAAGCCAT
** * ** * * * *
1958 TTGTTAGCAAGA-AAAGCCCATTTATAGTAACCCAAGCCTTCG
129 TCATTGGCAA-ATAAAGTTCATCTATACTCACCCAAGCCTTCA
* ** * *
2000 AAAGCCTTATTACTTACTTTAAATGATTTTATAATCTCATAATT
1 AAAGTCTTATTACTCGCTTCAAATGGTTTTATAATCTCATAATT
Statistics
Matches: 310, Mismatches: 65, Indels: 18
0.79 0.17 0.05
Matches are distributed among these distances:
168 1 0.00
169 108 0.35
170 89 0.29
171 110 0.35
172 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (170 bp):
AAAGTCTTATTACTCGCTTCAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTA
TATTTTTAGTTCAAATAGATTATAATTAAATCTTTACCTTGAAAAACATGAGAGAAAAGCCATTC
ATTGGCAAATAAAGTTCATCTATACTCACCCAAGCCTTCA
Done.