Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401971.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5069.0, 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, 891
Length: 1486
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.35
Warning! 214 characters in sequence are not A, C, G, or T
Found at i:399 original size:171 final size:171
Alignment explanation
Indices: 1--430 Score: 521
Period size: 171 Copynumber: 2.5 Consensus size: 171
*
1 AGCCTTATTACTCACTATAAATAGTTTTATAATCTCATAATTGATTTTAAGTT--ATATTTTTTA
1 AGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAAT-TTTTTTA
* * * *
64 CATTTTTGGTTAAAACAAACTATAATTGAATGTCTATCTCGAGAAACCTAAAGAAAAAGACATTC
65 AATTTTTGGTTAAAACAAACTATAATTGAATGTCTACCTCAAGAAAACTAAAGAAAAAGACATTC
* *
129 ATTGGTATGAAAAGTCTATTTATAATCACTCATTCTCTCAAA
130 ATTGGAAAGAAAAGTCTATTTATAATCACTCATTCTCTCAAA
** * * *
171 AGCCTTATTACTCTTTTTAAATAATTTTATAATCTCGTAAATGATTTTAAGTTGAATTTTTTTAA
1 AGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTT-A
* ** * * * *
236 AATTTTTGGTTAAAACAGACTATTGTTGAATGTCTACCTTAAGAAAAGTGAAGAAAAAGGCATTC
65 AATTTTTGGTTAAAACAAACTATAATTGAATGTCTACCTCAAGAAAACTAAAGAAAAAGACATTC
* * * *
301 ATTGGAAAGAAAATTC-ATTTGTAGTCA-TCCATTCTTTCAAA
130 ATTGGAAAGAAAAGTCTATTTATAATCACT-CATTCTCTCAAA
* * *
342 AGCCTTATTTCTCGCTTTAAA-AGGTTTCATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTA
1 AGCCTTATTACTCACTTTAAATA-GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTA
* * *
405 TATTTTTCGTTAAAACATACTATAAT
65 AATTTTTGGTTAAAACAAACTATAAT
431 NNNNNNNNNN
Statistics
Matches: 220, Mismatches: 35, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
169 22 0.10
170 55 0.25
171 73 0.33
172 70 0.32
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.41
Consensus pattern (171 bp):
AGCCTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAA
ATTTTTGGTTAAAACAAACTATAATTGAATGTCTACCTCAAGAAAACTAAAGAAAAAGACATTCA
TTGGAAAGAAAAGTCTATTTATAATCACTCATTCTCTCAAA
Found at i:1418 original size:170 final size:170
Alignment explanation
Indices: 794--1486 Score: 530
Period size: 170 Copynumber: 4.1 Consensus size: 170
784 NNNNNNNNNT
* * * * ** * * * *
794 TTTTTTACTTTTTTGGTTAAAACAAATTATAATTGAATGTCTACATTGAGAAA-GATGAGGAAAA
1 TTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATACCTGC-CTCAGAAACG-TGAAGAAAA
* * * * *
858 AG-GTATTCATGGACAAGAAAAG-TCTATTTATTGTCACCCATTCTTTTAAAAGTCTTATTACTC
64 AGACTATTCATGGACAAGAAAAGTTC-ATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTT
* * * * *
921 GCTTTAAATGATTTTGTAATCTCATAATTGATTATAAGTTAAA
128 GCTTTAAATGGTTTTATAATCTCATAATCGATTTTAAGTTATA
** ** * * * **
964 TTTTTTTTATTTTTCTTTAAAACAGACTTTAATTGAATATCTAGCTTGGGAAACGTGTAA-AAAA
1 TTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATACCT-GCCTCAGAAACGTG-AAGAAAA
* ** ** * * *
1028 TGAC-ATTTTTTAAGAAGAAAAGTTCATTTATAGACACCCATTCTTTCAAAAGCATTATTACTTG
64 AGACTATTCATGGACAAGAAAAGTTCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTTG
* *
1092 CTTTAAATGGTTTTATAATATCATAATTC-ACTTTAAGTCTACT-
129 CTTTAAATGGTTTTATAATCTCATAA-TCGATTTTAAGT-TA-TA
***********
1135 TTTTTTACATTTTTAGTT-AAACAGACTATAANNNNNNNNNNACCTCAAGAAACGTGAAGAAAAA
1 TTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATACCTGCCTC-AGAAACGTGAAGAAAAA
* * * * **
1199 -AATATTCATGGGCAAGAAAAGTCCATTTATAGTTACTTATTCTTTCAAAAGCCTTATTACTTGC
65 GACTATTCATGGACAAGAAAAGTTCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTTGC
* *
1263 TTTAAATGGTGTTATAATCTCATAATCGATTTTTAGTTATA
130 TTTAAATGGTTTTATAATCTCATAATCGATTTTAAGTTATA
* * * *
1304 TTTATTTATATTTTTAGTTAAAACAGACAATAATTGAATGCCTGCCTCAGAAAGGGTGAAGAAAA
1 TTT-TTTACATTTTTAGTTAAAACAGACTATAATTGAATACCTGCCTCAGAAA-CGTGAAGAAAA
* * * * * *
1369 AGGCT-TTCATTGACAAGAAAAGTTCATTTATACTCACTCACTC-TTCAAAAGCTTTATTA-TT-
64 AGACTATTCATGGACAAGAAAAGTTCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTTG
* * *
1430 CATTGTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGTA
129 C-TT-TAAATGGTTTTATAATCTCATAATCGATTTTAAGTTATA
1474 TTTTTTTACATTT
1 -TTTTTTACATTT
Statistics
Matches: 404, Mismatches: 99, Indels: 40
0.74 0.18 0.07
Matches are distributed among these distances:
168 2 0.00
169 16 0.04
170 302 0.75
171 83 0.21
172 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (170 bp):
TTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATACCTGCCTCAGAAACGTGAAGAAAAAG
ACTATTCATGGACAAGAAAAGTTCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTTGCT
TTAAATGGTTTTATAATCTCATAATCGATTTTAAGTTATA
Found at i:1418 original size:340 final size:330
Alignment explanation
Indices: 861--1486 Score: 672
Period size: 340 Copynumber: 1.9 Consensus size: 330
851 AGGAAAAAGG
* * * *
861 TATTCATGGACAAGAAAAGTCTATTTATTGTCACCCATTCTTTTAAAAGTCTTATTACTCGCTTT
1 TATTCATGGACAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCGCTTT
* * * * **
926 AAATGATTTTGTAATCTCATAATTGATTATAAGTTAAATTTTTTTTATTTTTCTTTAAAACAGAC
66 AAATGATGTTATAATCTCATAATCGATTATAAGTTAAATTTTTTATATTTTTAGTTAAAACAGAC
** * * ** * * *
991 TTTAATTGAATATCTAGCTTGGGAAACGTGTAAAAAATGACATTTTTTAAGAAGAAAAGTTCATT
131 AATAATTGAATACCTAGCCTCAGAAACGTGTAAAAAAAGACATTTATTAACAAGAAAAGTTCATT
* * *
1056 TATAGACACCCATTCTTTCAAAAGCATTATTACTTGC-TT-TAAATGGTTTTATAATATCATAAT
196 TATACACACCCACTCTTTCAAAAGCATTATTA-TT-CATTGTAAATAGTTTTATAATATCATAAT
1119 TCACTTTAAG-TCTACTTTTTTTACATTTTTAGTTAAACAGACTATAANNNNNNNNNNACCTCAA
259 TCACTTTAAGTTCTA-TTTTTTTACATTTTTAGTTAAACAGACTATAA----------ACCTCAA
1183 GAAACGTGAAGAAAAAAA
313 GAAACGTGAAGAAAAAAA
* * ** *
1201 TATTCATGGGCAAGAAAAGTCCATTTATAGTTACTTATTCTTTCAAAAGCCTTATTACTTGCTTT
1 TATTCATGGACAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCGCTTT
* * * *
1266 AAATGGTGTTATAATCTCATAATCGATTTTTAGTTATATTTATTTATATTTTTAGTTAAAACAGA
66 AAATGATGTTATAATCTCATAATCGATTATAAGTTAAATTT-TTTATATTTTTAGTTAAAACAGA
* * * *
1331 CAATAATTGAATGCCT-GCCTCAGAAA-GGGTGAAGAAAAAGGC-TTTCATTGACAAGAAAAGTT
130 CAATAATTGAATACCTAGCCTCAGAAACGTGT-AA-AAAAAGACATTT-ATTAACAAGAAAAGTT
* * * *
1393 CATTTATACTCACTCACTC-TTCAAAAGCTTTATTATTCATTGTAAATAGTTTTATAATCTCATA
192 CATTTATACACACCCACTCTTTCAAAAGCATTATTATTCATTGTAAATAGTTTTATAATATCATA
* * *
1457 ATTGATTTTAAGTTGTATTTTTTTACATTT
257 ATTCACTTTAAGTTCTATTTTTTTACATTT
Statistics
Matches: 237, Mismatches: 42, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
338 1 0.00
339 7 0.03
340 160 0.68
341 69 0.29
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.40
Consensus pattern (330 bp):
TATTCATGGACAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCGCTTT
AAATGATGTTATAATCTCATAATCGATTATAAGTTAAATTTTTTATATTTTTAGTTAAAACAGAC
AATAATTGAATACCTAGCCTCAGAAACGTGTAAAAAAAGACATTTATTAACAAGAAAAGTTCATT
TATACACACCCACTCTTTCAAAAGCATTATTATTCATTGTAAATAGTTTTATAATATCATAATTC
ACTTTAAGTTCTATTTTTTTACATTTTTAGTTAAACAGACTATAAACCTCAAGAAACGTGAAGAA
AAAAA
Done.