Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398451.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_175.0, 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: 2968
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.26
Warning! 821 characters in sequence are not A, C, G, or T
Found at i:1844 original size:172 final size:171
Alignment explanation
Indices: 1475--2569 Score: 813
Period size: 171 Copynumber: 6.4 Consensus size: 171
1465 NNNNNNNNNN
** * * **
1475 ATAAGGCTTTTGAAGGCTTGGGTGACTATAAAAGGGCTTTTCTTGCCAATGAATGTGTTTTGATT
1 ATAAGGCTTTTGAAGGCTTGGGTGACTATAATTGGACTTTTCTTGCAAATGAATG-GTTTTTCTT
* * * * * *
1540 CATGTTTCCCAAGGTAAACATTCAATTATAATTTTTTTTAAC-TAAAAATGTAAAAAAGTTTAAC
65 CATGTTTCTCAAGGAAAACATTCAATTATAATTTGTTTTAACAAAAAAACGTAAAAAAGTTCAAC
* * *
1604 TTAAAATGAATTATGAGGTTATGAAACCATTTAAAGTGAGTA
130 TTAAAATCAATTATGAGGTTATAAAACCATTTAAAGAGAGTA
* * *
1646 ATAAGGCTTTTGAAGGATTTGGTGACTATAATTGGACTTTTAGTT-CAAATGAATGGCTTTTTCT
1 ATAAGGCTTTTGAAGGCTTGGGTGACTATAATTGGACTTTT-CTTGCAAATGAATGG-TTTTTCT
* * * * *
1710 TC-TCATTTCTCAATGCAAACATTTAATTATAATCTGTTTTAACAAAAAAACGTAAGAAAA-TTC
64 TCAT-GTTTCTCAAGGAAAACATTCAATTATAATTTGTTTTAACAAAAAAACGTAA-AAAAGTTC
* * * *
1773 AATTTAAAATCAATTGTGAGGTTATAAAATCGTTTAAAGAGAGTA
127 AACTTAAAATCAATTATGAGGTTATAAAACCATTTAAAGAGAGTA
* * *
1818 ATAAGGCTTGTGAAGGCTTGGGTGACTATAATTGTACTTGTCTTGCAAATGAATTGGTTTTTCTT
1 ATAAGGCTTTTGAAGGCTTGGGTGACTATAATTGGACTTTTCTTGCAAATGAA-TGGTTTTTCTT
********** * *
1883 CATGTTTCTCAAGGAAAACATTCAATTATAATTTGTTTTAACANNNNNNNNNNAACAA-TTAAAC
65 CATGTTTCTCAAGGAAAACATTCAATTATAATTTGTTTTAACAAAAAAACGTAAAAAAGTTCAAC
* * * *
1947 TTAAAATCAATTTTGA-GTCTATGAAATCGTTTAAAGAGAGTA
130 TTAAAATCAATTATGAGGT-TATAAAACCATTTAAAGAGAGTA
* ** * * * * *********
1989 ATAAGACTTTTGAAGGCTTAAGTGACAATAAATGGGCTTTTCTTGCCAATGANNNNNNNNNNCTT
1 ATAAGGCTTTTGAAGGCTTGGGTGACTATAATTGGACTTTTCTTGCAAATGA-ATGGTTTTTCTT
* * *
2054 CATGTTTCCCAAGGTAAACATTCAATTATAATTT-TTTTAAC-AAAAAATGTAAGAAAA-TTCAA
65 CATGTTTCTCAAGGAAAACATTCAATTATAATTTGTTTTAACAAAAAAACGTAA-AAAAGTTCAA
********** *
2116 CTTAAAATCAATTNNNNNNNNNNAAAACCATTTAAAGGGAGTA
129 CTTAAAATCAATTATGAGGTTATAAAACCATTTAAAGAGAGTA
** * * * * *
2159 ATAAGGCTTTTGAAGGCTTGGACGACTATAAATGGGCTTTTCTTGCCAAGGAATGGCTTTTTC-C
1 ATAAGGCTTTTGAAGGCTTGGGTGACTATAATTGGACTTTTCTTGCAAATGAATGG-TTTTTCTT
* ** * * * *
2223 CTATGTTT-TAAAAGGAAAACATTCAATTATAACCTATTTTAATCAAAAATA--TAAAAAAATTT
65 C-ATGTTTCT-CAAGGAAAACATTCAATTATAATTTGTTTTAA-CAAAAAAACGTAAAAAAGTTC
** * *
2285 AACTTAAAATTGATTTTGAGGTTATAAAACCATTTAAAGAGAGTG
127 AACTTAAAATCAATTATGAGGTTATAAAACCATTTAAAGAGAGTA
* * * *
2330 ATAAGGCTTTTAAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGGC-AATGAACAGGTTTTTCT
1 ATAAGGCTTTTGAAGGCTTGGGTGACTATAATTGGACTTTTCTT-GCAAATGAA-TGGTTTTTCT
* * * * * * * *
2394 TCAGGTTTC-CTAGGGTAAACATTCAATTATAATCTATTTTAAC-TAAAAATGTAAAAAAAATTC
64 TCATGTTTCTC-AAGGAAAACATTCAATTATAATTTGTTTTAACAAAAAAACGT-AAAAAAGTTC
* * * * * *
2457 TACTTAAAATCAATTATGAGATTAAAAAACCATTTCAAGGGAGTT
127 AACTTAAAATCAATTATGAGGTTATAAAACCATTTAAAGAGAGTA
* * * ** * *
2502 GTATGGCTTTGGAAGGAATGGGTGACTATAATTAGAC-TTT-TTGTAACAATGAATGGCTTTTTC
1 ATAAGGCTTTTGAAGGCTTGGGTGACTATAATTGGACTTTTCTTG-CA-AATGAATGG-TTTTTC
2565 TTCAT
63 TTCAT
2570 ATTTTCCAAG
Statistics
Matches: 722, Mismatches: 171, Indels: 61
0.76 0.18 0.06
Matches are distributed among these distances:
169 7 0.01
170 127 0.18
171 340 0.47
172 235 0.33
173 13 0.02
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.35
Consensus pattern (171 bp):
ATAAGGCTTTTGAAGGCTTGGGTGACTATAATTGGACTTTTCTTGCAAATGAATGGTTTTTCTTC
ATGTTTCTCAAGGAAAACATTCAATTATAATTTGTTTTAACAAAAAAACGTAAAAAAGTTCAACT
TAAAATCAATTATGAGGTTATAAAACCATTTAAAGAGAGTA
Done.