Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403308.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_980.0, 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: 24916
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.20
Warning! 11397 characters in sequence are not A, C, G, or T
Found at i:13572 original size:20 final size:20
Alignment explanation
Indices: 13547--13597 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
13537 AATTCAACTT
*
13547 AAAATCATTTATGAGTCTAC
1 AAAATCATTTATGAGTCTAA
*
13567 AAAATCATTTATTAGTCTAA
1 AAAATCATTTATGAGTCTAA
13587 AAAATCATTTA
1 AAAATCATTTA
13598 AAGCGAGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (20 bp):
AAAATCATTTATGAGTCTAA
Found at i:15012 original size:166 final size:169
Alignment explanation
Indices: 14840--15184 Score: 428
Period size: 166 Copynumber: 2.0 Consensus size: 169
14830 NNNNNNNNNN
* * *
14840 CAAAATTGATTTCAG-GTTAAATTTTTTTACATTTTTCAAAAAAATAGACTATAATTGAATGTTT
1 CAAAATTGA-TTCAGAGTTAAATATTTTTACATTTTTCAAAAAAACAGACTATAATTGAATGCTT
* * * * * *
14904 ACTTAGAGAAACATGTAGAATAAGCCATTGATT-G-AG-AAGTCCATTTATAGGCACCTATTCTT
65 ACCTACAGAAACATGTAGAATAAGCCATTCATTAGAAGAAAGTCCATTTAGAGGCACCTAGTCCT
*
14966 TCAAAACCCTTATTACTCGCTTTAAATTATTTTATAATCT
130 TCAAAACCCTTATTACTCACTTTAAATTATTTTATAATCT
* * ** *
15006 CAAAATTGATTCTGAGTTAAATATTTTTATATTTTTCATTAAAACAGACTATAATTGAATGCTTG
1 CAAAATTGATTCAGAGTTAAATATTTTTACATTTTTCAAAAAAACAGACTATAATTGAATGCTTA
* ** * * *
15071 CCTCCAGAAATGTTTAGAATAAGCCATTCATTGAGAAGAAAAGTCCATTTAGAGTCACTTAGTCC
66 CCTACAGAAACATGTAGAATAAGCCATTCATT-AGAAG-AAAGTCCATTTAGAGGCACCTAGTCC
*
15136 TTCAAAAGCCTTATTACTCACTTTAAATTATTTTATAATCT
129 TTCAAAACCCTTATTACTCACTTTAAATTATTTTATAATCT
*
15177 CATAATTG
1 CAAAATTG
15185 NNNNNNNNNN
Statistics
Matches: 150, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
165 4 0.03
166 77 0.51
168 1 0.01
169 2 0.01
171 66 0.44
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (169 bp):
CAAAATTGATTCAGAGTTAAATATTTTTACATTTTTCAAAAAAACAGACTATAATTGAATGCTTA
CCTACAGAAACATGTAGAATAAGCCATTCATTAGAAGAAAGTCCATTTAGAGGCACCTAGTCCTT
CAAAACCCTTATTACTCACTTTAAATTATTTTATAATCT
Found at i:19263 original size:171 final size:160
Alignment explanation
Indices: 19086--19413 Score: 320
Period size: 171 Copynumber: 2.0 Consensus size: 160
19076 ATTATAAAAC
*
19086 AATTTAAATAGAGTAATAAGGCTTTTGAAAGAATAGATGACTACAAATGGACTTTTCTTCTCAAT
1 AATTTAAAGAGAGTAATAAGGCTTTTGAAAGAATAGATGACTACAAATGGACTTTTCTTCTCAAT
* * * *
19151 GAATAACTTTTTCTAAATG-TTTCTCG-GGTCAGGCGTTAACTTATAGTCAGTTTTAACT-AAAA
66 GAATAAC-TTTTCTAAACGTTTTCT-GAGAT-AGACATTAACTTATAGTCAGTTTTAA-TAAAAA
*
19213 ATGTAAAAAAATTCAACTTAAAATCAATTANNNNNNNNNNTAAT
127 AAGTAAAAAAATTCAACTTAAAATCAATTA----------TAAT
* * * * * * * *
19257 AATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAGATTGACTTTTCTTCTCATT
1 AATTTAAAGAGAGTAATAAGGCTTTTGAAAGAATAGATGACTACAAATGGACTTTTCTTCTCAAT
** * * *
19322 GAATGGCTTTTCTATACGTTTTCTGAGATAGACATTCACTTATAGTCTGTTTTAATAAAAAAAGT
66 GAATAACTTTTCTAAACGTTTTCTGAGATAGACATTAACTTATAGTCAGTTTTAATAAAAAAAGT
* *
19387 AAAAAAATTTAACTTAAAATCATTTAT
131 AAAAAAATTCAACTTAAAATCAATTAT
19414 GAGTTTATAA
Statistics
Matches: 133, Mismatches: 21, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
160 1 0.01
169 1 0.01
170 63 0.47
171 68 0.51
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.36
Consensus pattern (160 bp):
AATTTAAAGAGAGTAATAAGGCTTTTGAAAGAATAGATGACTACAAATGGACTTTTCTTCTCAAT
GAATAACTTTTCTAAACGTTTTCTGAGATAGACATTAACTTATAGTCAGTTTTAATAAAAAAAGT
AAAAAAATTCAACTTAAAATCAATTATAAT
Found at i:19407 original size:170 final size:169
Alignment explanation
Indices: 19011--19617 Score: 551
Period size: 170 Copynumber: 3.6 Consensus size: 169
19001 CTTGGAACTG
* * ** * * **
19011 GACATTCAATTATTGTCTGTTTTGTCTAAATATGTAAAAAAATTCAACTTAAAATTTATTATGAG
1 GACATTCACTTATAGTCTGTTTTAACTAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGAG
* * * ** * * * * * *
19076 ATTATAAAACAATTTAAATAGAGTAATAAGGCTTTTGAAAGAATAGATGACTACAAATGGACTTT
66 TTTATAACATAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAGATAGACTTT
* *
19141 TCTTCTCAATGAATAACTTTTTCTAAATGTTTCTCG-GGTCA
131 TCTTCTCAATGAATGAC-TTTTCTAAACGTTTCT-GAGGT-A
* * * * * **
19182 GGCGTTAACTTATAGTCAGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTANNNN
1 GACATTCACTTATAGTCTGTTTTAACTAAAAAAGTAAAAAAATTCAACTTAAAATCAATTA--TG
****** *
19247 NNNNNNT-A-ATAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAGATTGACT
64 AGTTTATAACATAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAGATAGACT
* * * *
19310 TTTCTTCTCATTGAATGGCTTTTCTATACGTTTTCTGAGATA
129 TTTCTTCTCAATGAATGACTTTTCTAAACG-TTTCTGAGGTA
* *
19352 GACATTCACTTATAGTCTGTTTTAA-TAAAAAAAGTAAAAAAATTTAACTTAAAATCATTTATGA
1 GACATTCACTTATAGTCTGTTTTAACT-AAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGA
* * *
19416 GTTTATAACATCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGGGTGTCTATAGATAGACTT
65 GTTTATAACATAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAGATAGACTT
* *********
19481 TTCTTGC-CAATGAATGTCTTTTCTNNNNNNNNNNTGAGGTA
130 TTCTT-CTCAATGAATGACTTTTCT-AAACGTTTCTGAGGTA
* * *
19522 GACATTCAATTATAGTCTGTTTTAACTAAAAACGTAAAAAAGTTCAACTTAAAATCAATTATGAG
1 GACATTCACTTATAGTCTGTTTTAACTAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGAG
* *
19587 ATTATATA-ATAATTTAAAGTGAGTAATAAGG
66 TTTATA-ACATAATTTAAAGCGAGTAATAAGG
19618 NNNNNNNNNN
Statistics
Matches: 352, Mismatches: 73, Indels: 23
0.79 0.16 0.05
Matches are distributed among these distances:
168 1 0.00
169 2 0.01
170 225 0.64
171 122 0.35
172 1 0.00
173 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.35
Consensus pattern (169 bp):
GACATTCACTTATAGTCTGTTTTAACTAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGAG
TTTATAACATAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAGATAGACTTT
TCTTCTCAATGAATGACTTTTCTAAACGTTTCTGAGGTA
Done.