Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400385.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3585.0, 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: 2832
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.27
Warning! 758 characters in sequence are not A, C, G, or T
Found at i:314 original size:171 final size:161
Alignment explanation
Indices: 100--441 Score: 323
Period size: 171 Copynumber: 2.1 Consensus size: 161
90 NNNNNNNATT
* * * *
100 TAAAACGAGTAATAAGGCTTTTAAATAAATAGGTGAGTATAAATGGTCTTTTCTTT-TCAATAAA
1 TAAAACAATTAATAAGGCTTTTAAAGAAATAGGTGAGTATAAATGGACTTTT-TTTATCAATAAA
* * * * *
164 T-AGCTTTTTTCACACGTTTCTCAAGGTAGGCATTCAATTATAGTCCGTTTTAACAAAAAATGAA
65 TGA-CTTTTTTCACACATTTCTAAAGGCAGACATTCAATTATAATCCGTTTTAACAAAAAATGAA
228 AAA-ACATTCAATTTAAAATCAATTATGAGATTA
129 AAACA-ATTCAATTTAAAATCAATTATGAGATTA
* * *
261 TAAAACAATNNNNNNNNNNTAATAAGGCTTTTGAAGGAAT-GAGTGATTATAAATGGACTTTTTT
1 TAAAACAAT----------TAATAAGGCTTTTAAAGAAATAG-GTGAGTATAAATGGACTTTTTT
* * * * * *
325 TATCAATGAATGATTTTTTTTACATATTTCTAAAGGCAGACATTCAATTATAATCTGTTTTAACT
55 TATCAATAAATGACTTTTTTCACACATTTCTAAAGGCAGACATTCAATTATAATCCGTTTTAACA
* * * * *
390 ATAAATGTAAAACAATTTAATTTAAAATCAATTTTGGGATTA
120 AAAAATGAAAAACAATTCAATTTAAAATCAATTATGAGATTA
432 TAAAACAATT
1 TAAAACAATT
442 TAAAGTGAGT
Statistics
Matches: 144, Mismatches: 23, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
161 8 0.06
170 4 0.03
171 130 0.90
172 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.37
Consensus pattern (161 bp):
TAAAACAATTAATAAGGCTTTTAAAGAAATAGGTGAGTATAAATGGACTTTTTTTATCAATAAAT
GACTTTTTTCACACATTTCTAAAGGCAGACATTCAATTATAATCCGTTTTAACAAAAAATGAAAA
ACAATTCAATTTAAAATCAATTATGAGATTA
Found at i:1044 original size:172 final size:161
Alignment explanation
Indices: 724--1046 Score: 337
Period size: 172 Copynumber: 1.9 Consensus size: 161
714 TAAAACCATT
* * * * * *
724 TAAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACCGTAAATGGACTTTTCTTCTCAATGAAT
1 TAAAACAAGTAATAAGGCTTTTAAAGGAATAGGTGACCATAAATAGACTTTTATTCTCAATGAAT
* * * *
789 AGCTTTTTTTGCATGTTTCTCTAGGCAAGCATTCAATTATAGTTTGTTTTAACCAAAATTTTAAA
66 AGCTTTTTTTGCATGTTTCTCTAGGCAAGCATTCAATTATAGTCTGTTTTAACAAAAAATATAAA
854 AAAATTTAACTTAAAATCAATTTTGAGATTA
131 AAAATTTAACTTAAAATCAATTTTGAGATTA
*
885 TAAAANNNNNNNNNNCAAGTAATAAGGCTTTTAAAGGAATAGGTGACTATAAATAGACTTTTATT
1 TAAAA----------CAAGTAATAAGGCTTTTAAAGGAATAGGTGACCATAAATAGACTTTTATT
** * * *
950 GC-CAATGAATGATTTTTTTTTTCATGTTTCT-TGAGG-TAGACATTCGATTATAGTCTGTTTTA
56 -CTCAATGAAT-AGCTTTTTTTGCATGTTTCTCT-AGGCAAG-CATTCAATTATAGTCTGTTTTA
**
1012 GTAAAAAATATAAAAAAATTTAACTTAAAATCAAT
117 ACAAAAAATATAAAAAAATTTAACTTAAAATCAAT
1047 NNNNNNNNNN
Statistics
Matches: 130, Mismatches: 18, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
161 4 0.03
171 55 0.42
172 71 0.55
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.37
Consensus pattern (161 bp):
TAAAACAAGTAATAAGGCTTTTAAAGGAATAGGTGACCATAAATAGACTTTTATTCTCAATGAAT
AGCTTTTTTTGCATGTTTCTCTAGGCAAGCATTCAATTATAGTCTGTTTTAACAAAAAATATAAA
AAAATTTAACTTAAAATCAATTTTGAGATTA
Found at i:1505 original size:170 final size:160
Alignment explanation
Indices: 1267--1580 Score: 306
Period size: 170 Copynumber: 1.9 Consensus size: 160
1257 NNNNNNNNNN
* * * * ** * * *
1267 AGTGACTATAAATGGACTTTTTTTCTCAATTAGTAGCTTTTTGTGCATGTTTCTCAAGGTAGGCA
1 AGTGACTATAAATGGACTTTTTTTCTCAATGAATAACTTTTTGTACACATATCTCAAGGCAAGCA
1332 TTCAATTATAGTCTGTTTTAACAAAAAATGAAAAAAAATCGACA-TAAAATCAATTATAAGATTA
66 TTCAATTATAGTCTGTTTTAACAAAAAATGAAAAAAAATCGA-ATTAAAATCAATTATAAGATTA
1396 TAAAACAATTTAAAGTAAGTAATAAGGCTNNNNNNNNNNTG
130 TAAAACAATTTAAAGTAAGTAATAAGGCT----------TG
* * * *
1437 AGTGACTATAAATGGACTTTTTTTCTGAATGAATAATTTTTTTTACACATATCTGAAGGCAAGCA
1 AGTGACTATAAATGGACTTTTTTTCTCAATGAATAACTTTTTGTACACATATCTCAAGGCAAGCA
* * * * ** * **
1502 TTCAATTATAGTCTGTTTTAGCCATAAATGGAAAAAAATTTAATTTAAAATCAATTTTGGGATTA
66 TTCAATTATAGTCTGTTTTAACAAAAAATGAAAAAAAATCGAA-TTAAAATCAATTATAAGATTA
*
1567 TAAAATAATTTAAA
130 TAAAACAATTTAAA
1581 ACGAGTAATA
Statistics
Matches: 119, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
169 1 0.01
170 88 0.74
171 30 0.25
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.36
Consensus pattern (160 bp):
AGTGACTATAAATGGACTTTTTTTCTCAATGAATAACTTTTTGTACACATATCTCAAGGCAAGCA
TTCAATTATAGTCTGTTTTAACAAAAAATGAAAAAAAATCGAATTAAAATCAATTATAAGATTAT
AAAACAATTTAAAGTAAGTAATAAGGCTTG
Done.