Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397931.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1236.0, 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: 14088
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.23
Warning! 5539 characters in sequence are not A, C, G, or T
Found at i:865 original size:171 final size:162
Alignment explanation
Indices: 628--952 Score: 307
Period size: 172 Copynumber: 2.0 Consensus size: 162
618 TTTGAAGTCT
* ** *
628 AATTGTTTTACATTTTTTATTAAAACAGACCATAATTGATTGTCTACTTGCAGAAACCTCCAAAA
1 AATTGTTTTACATTTTTTATTAAAACAGACCATAATTGAATACCTACTTGCAGAAACATCCAAAA
** * * *
693 AAAGT-C-ATTCATTGAGAAGAAAAGTTCATTTATAGTTAC-TCATTTCTTCAAAAGGCTTGTTA
66 AAA-TCCTATTCATTGAGAAGAAAAGTTCATTTATAGGCACAT-ATTCCTTCAAAAGCCTTATTA
* * *
755 CCCGCTTTTAATGGTTTTATAATCTNNNNNNNNNNTTTATGTTG
129 CCCGATTTAAATAGTTTTATAATCT----------TTTATGTTG
* * * * * *
799 AATTTTTTTATATTTTTTGTTAAAACAGACTATAATTGAATACCTATCTTG-GGAAACATGCAAA
1 AATTGTTTTACATTTTTTATTAAAACAGACCATAATTGAATACCTA-CTTGCAGAAACATCCAAA
* **
863 AAAATCCTGTTCATTGAGAAGAAAAGTTTGTTTATAGGCACATATTCCTTCAAAAGCCTTATTAC
65 AAAATCCTATTCATTGAGAAGAAAAGTTCATTTATAGGCACATATTCCTTCAAAAGCCTTATTAC
*
928 TCGATTTAAATAGTTTTATAATCTT
130 CCGATTTAAATAGTTTTATAATCTT
953 ATAATTGATT
Statistics
Matches: 128, Mismatches: 22, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
162 1 0.01
170 1 0.01
171 54 0.42
172 71 0.55
173 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.39
Consensus pattern (162 bp):
AATTGTTTTACATTTTTTATTAAAACAGACCATAATTGAATACCTACTTGCAGAAACATCCAAAA
AAATCCTATTCATTGAGAAGAAAAGTTCATTTATAGGCACATATTCCTTCAAAAGCCTTATTACC
CGATTTAAATAGTTTTATAATCTTTTATGTTG
Found at i:1028 original size:172 final size:170
Alignment explanation
Indices: 543--1028 Score: 458
Period size: 171 Copynumber: 2.8 Consensus size: 170
533 NNNNNNNNNN
* * * * *
543 AAGTCCATTTAGAGTCACCCATTCCTTCAAAAGGCTTATTACTC-ATTTTAAATACTTTTATAAT
1 AAGTTCATTTATAGGCACTCATTCCTTCAAAAGGCTTATTACTCGA-TTTAAATAGTTTTATAAT
* * * * * *
607 CTTATAATTGATTTGAAGTCTAATTGTTTTACATTTTTTATTAAAACAGACCATAATTGATTGTC
65 CTTATAATTGATTTTAAGT-TAAATATTTTATATTTTTTGTTAAAACAGACTATAATTGATTGTC
* *
672 TACTTGCA-GAAACCTCCAAAAAAAGTCATTCATTGAGAAGAA
129 TACCT-CAGGAAACATCCAAAAAAAGTCATTCATTGAGAAGAA
** * * * * * *
714 AAGTTCATTTATAGTTACTCATTTCTTCAAAAGGCTTGTTACCCGCTTTTAATGGTTTTATAATC
1 AAGTTCATTTATAGGCACTCATTCCTTCAAAAGGCTTATTACTCGATTTAAATAGTTTTATAATC
********** * * * * **
779 TNNNNNNNNNNTTTATGTTGAATTTTTTTATATTTTTTGTTAAAACAGACTATAATTGAATACCT
66 TTATAATTGATTTTAAGTT-AAATATTTTATATTTTTTGTTAAAACAGACTATAATTGATTGTCT
* ** * *
844 ATCTTGGGAAACATGCAAAAAAA-TCCTGTTCATTGAGAAGAA
130 ACCTCAGGAAACATCCAAAAAAAGT-C-ATTCATTGAGAAGAA
** *
886 AAGTTTGTTTATAGGCACAT-ATTCCTTCAAAAGCCTTATTACTCGATTTAAATAGTTTTATAAT
1 AAGTTCATTTATAGGCAC-TCATTCCTTCAAAAGGCTTATTACTCGATTTAAATAGTTTTATAAT
950 CTTATAATTGATTTTAAGTTAAATATTTCTATATTTTTTGTTAAAACAGACTATAATTGATTGTC
65 CTTATAATTGATTTTAAGTTAAATATTT-TATATTTTTTGTTAAAACAGACTATAATTGATTGTC
*
1015 TGCCTCAGGAAACA
129 TACCTCAGGAAACA
1029 ANNNNNNNNN
Statistics
Matches: 240, Mismatches: 68, Indels: 13
0.75 0.21 0.04
Matches are distributed among these distances:
170 2 0.01
171 120 0.50
172 117 0.49
173 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.40
Consensus pattern (170 bp):
AAGTTCATTTATAGGCACTCATTCCTTCAAAAGGCTTATTACTCGATTTAAATAGTTTTATAATC
TTATAATTGATTTTAAGTTAAATATTTTATATTTTTTGTTAAAACAGACTATAATTGATTGTCTA
CCTCAGGAAACATCCAAAAAAAGTCATTCATTGAGAAGAA
Found at i:13414 original size:172 final size:171
Alignment explanation
Indices: 13129--13516 Score: 462
Period size: 172 Copynumber: 2.3 Consensus size: 171
13119 NNNNNNNNNN
* * * * *
13129 TTAAGTTGAATTTTTTTATATTTTTTA-TTAAAATAGACTATAATTGAATACCTATCTTGGGAAA
1 TTAAGTTGAATTTTTTTA-AATTTTTAGTTAAAACAGACTATAATTAAATACCTACCTTGAGAAA
* * * * *
13193 TGTGCAAAAAAAGCCTATTCATTTAGAAAAAAATCCATTTATAGTCACCCAATCCTTCAAAAGCT
65 CGTACAAAAAAAGCCTATTCATTGAGAAAAAAATCCATTTACAGTCACCCAATCCTACAAAAGCT
13258 TTATTACTCAG-TTTAAATAGTTTTATAATC-TCATAATTAATT
130 TTATTACTC-GCTTTAAATAGTTTTATAATCTTC-TAATTAATT
** *
13300 TTAAGTTGAATTTTTTTTAAATTTTTAGTTAAAACAGACTATAATTAAATGTCTACCTTGATAAA
1 TTAAGTTGAA-TTTTTTTAAATTTTTAGTTAAAACAGACTATAATTAAATACCTACCTTGAGAAA
* * * * *
13365 CGTACAAAAAAAGCC-ATTCATTGAGAAGAAAAGTTCATTTACAGTCACCCATTCCTACAAATGG
65 CGTACAAAAAAAGCCTATTCATTGAGAA-AAAAATCCATTTACAGTCACCCAATCCTACAAAAGC
* *
13429 TTTATTACTCGCTTTAAATGGTTTTATAATCTTCTAATTGATT
129 TTTATTACTCGCTTTAAATAGTTTTATAATCTTCTAATTAATT
* * * * *
13472 TTAAGTAGAGTATTTTTACATTTTT-GATTAAAACATACTATAATT
1 TTAAGTTGAATTTTTTTAAATTTTTAG-TTAAAACAGACTATAATT
13517 NNNNNNNNNN
Statistics
Matches: 186, Mismatches: 25, Indels: 12
0.83 0.11 0.05
Matches are distributed among these distances:
170 1 0.01
171 59 0.32
172 124 0.67
173 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (171 bp):
TTAAGTTGAATTTTTTTAAATTTTTAGTTAAAACAGACTATAATTAAATACCTACCTTGAGAAAC
GTACAAAAAAAGCCTATTCATTGAGAAAAAAATCCATTTACAGTCACCCAATCCTACAAAAGCTT
TATTACTCGCTTTAAATAGTTTTATAATCTTCTAATTAATT
Done.