Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401374.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4505.0, 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: 4746
ACGTcount: A:0.27, C:0.09, G:0.10, T:0.26
Warning! 1301 characters in sequence are not A, C, G, or T
Found at i:1876 original size:171 final size:171
Alignment explanation
Indices: 1512--1888 Score: 393
Period size: 171 Copynumber: 2.2 Consensus size: 171
1502 NNNNTGAACC
* * *
1512 TAAAATCAATTTTAAGATTATAAAACCATTTAAAGTGAGTAATAAGGCCTTTAAAGGAATGGGTA
1 TAAAATCAATTATAAGATTATAAAACAATTTAAAGTGAGTAATAAGGCCTTTAAAGGAATAGGTA
* * * * **
1577 ACTATAAATGGACTTTTCTTGCCAATTAATACCTTGTTCTTCACATTTCTTGAGGTAGGCATTCA
66 ACTAAAAATGGACTTTTCTTGCCAATGAATACCTTGTTCTTCACATTTCTTAAAGTAAACATTCA
* *
1642 ATTATAGTATGTTTTAACCAAAAATGTAAAAAAATTCAACN
131 ATTATAGTATGTTTTAACCAAAAATCTAAAAAAATTCAACT
********* * * *
1683 NNNNNNNNNTTATGAGATTATAAAATAATTTAAAGTGAGTAATAAGG-CTTTCGAAGGAATAGG-
1 TAAAATCAATTATAAGATTATAAAACAATTTAAAGTGAGTAATAAGGCCTTT-AAAGGAATAGGT
* * * * **
1746 AGACTAAAAATGGACTTTTCTTGCCAATGAAT-GCTTTTTTTGTTATGTTTCTTAAAGTAAACAT
65 A-ACTAAAAATGGACTTTTCTTGCCAATGAATACCTTGTTCT-TCACATTTCTTAAAGTAAACAT
* **
1810 TCAATTATAGT-TTTTTCTAATGAAAAATCTAAAAAAATTCAACT
128 TCAATTATAGTATGTTT-TAACCAAAAATCTAAAAAAATTCAACT
*
1854 TAAAATCAATTATAAAATTATAAAACAATTTAAAG
1 TAAAATCAATTATAAGATTATAAAACAATTTAAAG
1889 CGAGNNNNNN
Statistics
Matches: 158, Mismatches: 44, Indels: 8
0.75 0.21 0.04
Matches are distributed among these distances:
170 15 0.09
171 143 0.91
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.35
Consensus pattern (171 bp):
TAAAATCAATTATAAGATTATAAAACAATTTAAAGTGAGTAATAAGGCCTTTAAAGGAATAGGTA
ACTAAAAATGGACTTTTCTTGCCAATGAATACCTTGTTCTTCACATTTCTTAAAGTAAACATTCA
ATTATAGTATGTTTTAACCAAAAATCTAAAAAAATTCAACT
Found at i:3428 original size:171 final size:170
Alignment explanation
Indices: 3117--4610 Score: 1293
Period size: 171 Copynumber: 8.7 Consensus size: 170
3107 NNNNNNNNNN
* * * * * *
3117 AAAGCGAGTGATAAGGCTTTTGAAGGAAT-AGGAGACTATAAATGGACTTTTTTTACCAATGAAT
1 AAAGCGAGTAATAAGGCTTTTAAAGGAATGA-GTGACTATAAATGGACTTTTCTTGCTAATGAAT
* * * * * *
3181 GGTTTTTCTTTACATTTCTTGAGGTAAACATTCAATTATAGTATGTTTTAACTAAAAAAACTAAA
65 GCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATAC-AAA
* * * *
3246 AAAAATCAACTTAAAATCAATTATCAGATTGTAAAACTATTT
129 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTT
* * *
3288 AAAGCGAGTAATAAGGCTTTTAAAGGAATGAGTTACTATAAATGGACTTGTT-TTGCTAGTAAAT
1 AAAGCGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTT-TTCTTGCTAATGAAT
* ** * *
3352 GTCTTTTTCTTCATGTTTCTCAAGGTAGACCTTCAATTATAGTCTGTTCTAACTAAAAATACAAA
65 G-CTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATACAAA
* * * *
3417 AGAATTCAACTTAAAATCAATTAAGAGATTGTAAAACCATTT
129 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTT
* * * ** * * *
3459 AATGTGAGTAATATGGCTTTTGGAGGAATGAGTGACTACAAATGGACTTTTCTTGCCAAAGAATG
1 AAAGCGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGCTAATGAATG
* * *
3524 TCTTTTTCTTC-CAGTTACTTGAGCTAGACATTCAATTATTA-TCTGTTTTAACCAATAATATA-
66 -CTTTTTCTTCAC-GTTTCTTGAGGTAGACATTCAATTA-TAGTCTGTTTTAACTAA-AA-ATAC
* *
3586 AAAAAAATTGAACCTAAAATGGACTTAAAATCAATTATTAGATTATCAAACAATTT
126 AAAAAAATT----C----A---ACTTAAAATCAATTATGAGATTATAAAACAATTT
* * *
3642 AAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTT-CTAAATGAAT
1 AAAGCGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGCT-AATGAAT
* * * * * *
3706 GACTTTCTT-TACATGTTTTCCTTGA--CAGACATTTAACTATAGTTTGTTTTAACTAAAAAAGT
65 G-CTTT-TTCTTCACG-TTT-CTTGAGGTAGACATTCAATTATAGTCTGTTTTAACT-AAAAA-T
* *
3768 A-AAAAAAATTCAACTTAAAATCAATTATGATATTATAAAAGAATTT
124 ACAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTT
* * * * * *
3814 AAAGCGAGTAGTAAGGCTTTTGAAGGAATGGGTGACTATAAATGG-GTTTTCTTCCTTATGAATG
1 AAAGCGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGCTAATGAAT-
* * * * **
3878 GCTTTTTCTACACGTTTCTCGAGGTAGACATTCAATTATAGTCTGTTTTAGCCAAAAATGTAAAA
65 GCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATACAAAA
* * *
3943 ACATTCAACTTAAAATTAATTATGAGTTTATAAAACAATTT
130 AAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTT
* * * * *
3984 AAA-CTGAGTAATAAAGTTTTTAAAGGAAT-AGGAGACTATAAATAGACTTTTCTTGCCAATGAA
1 AAAGC-GAGTAATAAGGCTTTTAAAGGAATGA-GTGACTATAAATGGACTTTTCTTGCTAATGAA
* * * * *
4047 TGCTTTTTTCTTTATGTTTCTTAAGGTAAACATTCAATTATAGTCTATTTTAACTAAAAAT-CTA
64 TGC-TTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATAC-A
* *
4111 AAAACATTCAAC-TAAAATCAATTATGAGATTATAAAACCATTT
127 AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTT
* * * * * * * *
4154 AAAGCAAGTACA-AAGGCTTTT-GAGAGATTGGGTGACTATAAATGGACTTTTTTTGCCAGTTAA
1 AAAGCGAGTA-ATAAGGCTTTTAAAG-GAATGAGTGACTATAAATGGACTTTTCTTGCTAATGAA
* * * * *
4217 TGTCTGTTTCTTCACGTTTCTTGAGGTAGACATTTAATTATACTCTGTTTTAACTAATAATGTAA
64 TG-CTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTAA-AA-ATAC
* * * * *
4282 AAAAACAATTGAACCTAAAATCAATTTTTAGATTATAAAACCATTT
126 AAAAA-AATTCAACTTAAAATCAATTATGAGATTATAAAACAATTT
* * * * *
4328 AAAGCGTGTAATAAGGCTTTTAAAGGAATGGGTAACTATAAATGGACTTCTCTTG-TCAATTAAT
1 AAAGCGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGCT-AATGAAT
* ** * * * *
4392 ACCTTTTTCTTCACAATCCTTGGGGTAGACATTCAAATATAGTCTGTTTTAACTAAAAATATAAA
65 -GCTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATACAAA
********** *
4457 AAAATTCAACNNNNNNNNNNTTATGAGATTATAAAATAATTT
129 AAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTT
* *
4499 AAAGCAAGTAATAAGGCTTTTAAAGGAAT-AG-GAGCCTATAAATGGACTTTTCTTACTAATGAA
1 AAAGCGAGTAATAAGGCTTTTAAAGGAATGAGTGA--CTATAAATGGACTTTTCTTGCTAATGAA
** ** * *
4562 TGCTTTTTTCGTT-GTGTTTCTCAAGGTAAACATTCAATTATAGTTTGTT
64 TGC-TTTTTC-TTCACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTT
4611 CTAATAAGGC
Statistics
Matches: 1074, Mismatches: 192, Indels: 114
0.78 0.14 0.08
Matches are distributed among these distances:
169 9 0.01
170 210 0.20
171 418 0.39
172 156 0.15
173 12 0.01
174 124 0.12
175 3 0.00
176 1 0.00
179 1 0.00
180 1 0.00
182 4 0.00
183 124 0.12
184 6 0.01
185 5 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (170 bp):
AAAGCGAGTAATAAGGCTTTTAAAGGAATGAGTGACTATAAATGGACTTTTCTTGCTAATGAATG
CTTTTTCTTCACGTTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAACTAAAAATACAAAAA
AATTCAACTTAAAATCAATTATGAGATTATAAAACAATTT
Done.