Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398870.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2152.0, 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: 9087
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.29
Warning! 1884 characters in sequence are not A, C, G, or T
Found at i:2226 original size:73 final size:73
Alignment explanation
Indices: 2054--2238 Score: 210
Period size: 73 Copynumber: 2.5 Consensus size: 73
2044 CAGACAGAAT
* * * * *
2054 GCTCTTAGTCGACTAACATTGCTACTTAGTTGATTAAGTCGTCTCTGTCTTTAAACCTAGTTTCT
1 GCTCTTAGTTGACTAACAATGCTTCTTAGTCGATTAAGTCATCTCTGTCTTTAAACCTAGTTTCT
*
2119 GGCAGTAG
66 GGCAGTAA
* ** * * *
2127 GCTCTTGGTTGACTAACAAAACTTCTTAGTCGATTAAGTCATTTTTGT-TTCTAAACCTAGTTTT
1 GCTCTTAGTTGACTAACAATGCTTCTTAGTCGATTAAGTCATCTCTGTCTT-TAAACCTAGTTTC
2191 TGGCAGTAA
65 TGGCAGTAA
* * * *
2200 GCTCTTAGTTGACTAACACTGTTTCTTGGTCGACTAAGT
1 GCTCTTAGTTGACTAACAATGCTTCTTAGTCGATTAAGT
2239 GTTCGCTGTA
Statistics
Matches: 92, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
72 2 0.02
73 90 0.98
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.39
Consensus pattern (73 bp):
GCTCTTAGTTGACTAACAATGCTTCTTAGTCGATTAAGTCATCTCTGTCTTTAAACCTAGTTTCT
GGCAGTAA
Found at i:4852 original size:21 final size:21
Alignment explanation
Indices: 4828--4872 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4818 AGGGTTTTCC
*
4828 TTTTTCTTTCTTTT-TCTCTGA
1 TTTTTCTTCCTTTTCTCTCT-A
*
4849 TTTTTGTTCCTTTTCTCTCTA
1 TTTTTCTTCCTTTTCTCTCTA
4870 TTT
1 TTT
4873 CTTCCCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.04, C:0.20, G:0.04, T:0.71
Consensus pattern (21 bp):
TTTTTCTTCCTTTTCTCTCTA
Found at i:6632 original size:170 final size:170
Alignment explanation
Indices: 6429--6756 Score: 405
Period size: 171 Copynumber: 1.9 Consensus size: 170
6419 NNNNNNNNNN
* * * *
6429 GAATTTTTTTATATGTTTTGTTCAAATAGATTATAT-TGAATGTTTGCCTTGGAAAACATGAA-G
1 GAATTTTTTTATATGTTTTGTTAAAAGAGATTATATGTGAATGTTTACCTTGGAAAACATGAACA
* * * * * *
6492 AAAACCTATTCA-TGGGAAAGAAAAG-CGCATGTATAGTTACTCATTTCTTCAAAAGCCTTATTA
66 AAAACC-ATTCACT-AGAAAGAAAAGTC-CATCTATAGTCACCCATTCCTTCAAAAGCCTTACTA
* *
6555 CTCATTTTAAATAGTTTTATAATCTGATAATTTATTTTAAGTT
128 CTCACTTTAAATAGTTTTATAATCTCATAATTTATTTTAAGTT
* *
6598 GAATTTCTTTTATAT-TTTTAGTTAAAAGAGATTATATGTGTATGTTTACCTTGGAAAATATGAA
1 GAATTT-TTTTATATGTTTT-GTTAAAAGAGATTATATGTGAATGTTTACCTTGGAAAACATGAA
* *
6662 CAAAAACCATTCACTAGCAAGAAAAGTCCATCTATAGTCACCCATTCCTTCGAAAGCCTTACTAC
64 CAAAAACCATTCACTAGAAAGAAAAGTCCATCTATAGTCACCCATTCCTTCAAAAGCCTTACTAC
** *
6727 TTGCTTTAAATGGTTTTATAATCTCATAAT
129 TCACTTTAAATAGTTTTATAATCTCATAAT
6757 NNNNNNNNNN
Statistics
Matches: 134, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
169 10 0.07
170 23 0.17
171 93 0.69
172 8 0.06
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (170 bp):
GAATTTTTTTATATGTTTTGTTAAAAGAGATTATATGTGAATGTTTACCTTGGAAAACATGAACA
AAAACCATTCACTAGAAAGAAAAGTCCATCTATAGTCACCCATTCCTTCAAAAGCCTTACTACTC
ACTTTAAATAGTTTTATAATCTCATAATTTATTTTAAGTT
Found at i:7226 original size:171 final size:170
Alignment explanation
Indices: 6904--7236 Score: 386
Period size: 171 Copynumber: 1.9 Consensus size: 170
6894 GTTACTCAAT
* * *
6904 CCTTCGAAAGTCGTATTACTCGCTTTAGATGGTTTTACAATCTCATAATTGATTTTAAGTTGAAT
1 CCTTCAAAAGTCGTATTACTCGCTTTAAACGGTTTTACAATCTCA-AATTGATTTTAAGTTGAAT
* * * *
6969 TGTTTTGTATTTTTCATTGAAATATACTATAATTGAATACCTACCTAGGAAATTGTGAAGCAAAA
65 TGTTTTGTATTTTTCATTAAAATATACTAGAATTGAATACCTACCTAAGAAAATGTGAAGCAAAA
** * *
7034 GCCATTTATCGGTAAAAAAAGTCCATTTATAGTCACCCATG
130 GCCATCCATCAGCAAAAAAAGTCCATTTATAGTCACCCATG
*
7075 CCTTCAAAAG-CGTTATTACTCAGC-TTAAACGGTTTTATAATCTC-AATTGATTTTAAGTTGAA
1 CCTTCAAAAGTCG-TATTACTC-GCTTTAAACGGTTTTACAATCTCAAATTGATTTTAAGTTGAA
** * *** *
7137 TTTGTTTT-TCATTTTTTCATTAAAATATTTTAGGATTGAATTTTTATCTAAGAAAATGTGAAGC
64 -TTGTTTTGT-A-TTTTTCATTAAAATATACTAGAATTGAATACCTACCTAAGAAAATGTGAAGC
* * *
7201 AAAAGCCATCCATTAGCACAAAAAGTTCATTTATAG
126 AAAAGCCATCCATCAGCAAAAAAAGTCCATTTATAG
7237 NNNNNNNNNN
Statistics
Matches: 135, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
169 19 0.14
170 10 0.07
171 104 0.77
172 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (170 bp):
CCTTCAAAAGTCGTATTACTCGCTTTAAACGGTTTTACAATCTCAAATTGATTTTAAGTTGAATT
GTTTTGTATTTTTCATTAAAATATACTAGAATTGAATACCTACCTAAGAAAATGTGAAGCAAAAG
CCATCCATCAGCAAAAAAAGTCCATTTATAGTCACCCATG
Found at i:7469 original size:171 final size:169
Alignment explanation
Indices: 7281--8125 Score: 477
Period size: 170 Copynumber: 4.9 Consensus size: 169
7271 NNNNNNNNNN
*
7281 TCATAATTAATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAATAGATTATATTTGAATGTTT
1 TCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAATAGATTATATTTGAATGTTT
* * * *
7346 ACCTCAAGAACCATGAAGAAAAGGTCAGAAATTGATAGGAAAAGTCTATTTATAGTCACCCAAGC
66 ACCTCAAGAACCGTGAAGAAAA-AT-AGAAATTGATAAGAAAAGTCTATTTATAGTCACCCATGC
*
7411 CTTCTAAAGCCTTATTACTTGCTTTAAATGGTTTTATAATG
129 CTTCTAAAGCCTTATTACTTGCTTTAAATGGTTTTATAATC
* * ** * * * * *
7452 TCATAATTGATTTTAAGTAGGA-TTTTTTACATTTTTGGCTAAAATTGGTTATAATTGAAAGTCT
1 TCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAATAGATTATATTTGAATGTTT
* * * * *
7516 GCCTCAAGAACCGTGAAGACAAAATTGATTATTGATAAAAAAAGTCCATTTATAGTCACCCATTG
66 ACCTCAAGAACCGTGAAGA-AAAATAGA-AATTGATAAGAAAAGTCTATTTATAGTCACCCA-TG
* * * *******
7581 -CTTCTAAAGCCTTATTACTCGTTTTAAATAGTTTNNNNNNN
128 CCTTCTAAAGCCTTATTACTTGCTTTAAATGGTTTTATAATC
*** * * * * * *
7622 NNNTAATTGATTTTAAGTTAAATTTTTTAATATTTTT-AGTTCAAACAGATTATATTTGAATGCT
1 TCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGA-TTAAAATAGATTATATTTGAATGTT
* * * * * * *
7686 TACCTTAGGAAACGTGAGGAAAAA-A-TAATTCACTGGCAAGAAAAGTCTATTTATAGTCACTCA
65 TACCTCAAGAACCGTGAAGAAAAATAGAAATTGA-T---AAGAAAAGTCTATTTATAGTCACCCA
* * * * *
7749 TTCATTCGAAAGCCTTATTGCTTGCTTTAAATGGTTTTCTAATC
126 TGCCTTCTAAAGCCTTATTACTTGCTTTAAATGGTTTTATAATC
* * * * * * * * *
7793 TCATAATTGATTTGGAA-TTGAA-TTTTTTGCATTCTTCATTAAACTATACTATAATTGAATGTC
1 TCATAATTGATTT-TAAGTTGAATTTTTTTACATTTTTGATTAAAATAGATTATATTTGAATGTT
* * ** *** ** * * * * *
7856 T-GCTTAGAGAAATGTGAAGCAAAAGATATCCATTGGCATGAAAAGTCCATTTATACTCACTCAA
65 TACCTCA-AGAACCGTGAAG-AAAA-ATAGAAATTGATAAGAAAAGTCTATTTATAGTCACCCAT
* * **********
7920 GCCTTCGAAAGCCTTATTACTCGCTTNNNNNNNNNNTATAATC
127 GCCTTCTAAAGCCTTATTACTTGCTTTAAATGGTTTTATAATC
* * ** ** * * *
7963 TCATAATTGATTTTAAGTTGATTTTTTTTTGCATTTTCAATTCGAACAGATTATAATTGAATGTG
1 TCATAATTGATTTTAAGTTGA-ATTTTTTTACATTTTTGATTAAAATAGATTATATTTGAATGTT
* ** * * *** * * *
8028 TACCTCAGGAAATGTGATGAAAAAGCCATTCATT-AGTAAGAAAAGTGC-ATTTATAATCATCTA
65 TACCTCAAGAACCGTGAAGAAAAA--TAGAAATTGA-TAAGAAAAGT-CTATTTATAGTCACCCA
* *
8091 TGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGT
126 TGCCTTCTAAAGCCTTATTACTTGCTTTAAATGGT
8126 NNNNNNNNNN
Statistics
Matches: 496, Mismatches: 153, Indels: 49
0.71 0.22 0.07
Matches are distributed among these distances:
167 4 0.01
168 1 0.00
169 8 0.02
170 240 0.48
171 140 0.28
172 95 0.19
173 5 0.01
174 3 0.01
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.38
Consensus pattern (169 bp):
TCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAATAGATTATATTTGAATGTTT
ACCTCAAGAACCGTGAAGAAAAATAGAAATTGATAAGAAAAGTCTATTTATAGTCACCCATGCCT
TCTAAAGCCTTATTACTTGCTTTAAATGGTTTTATAATC
Done.