Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398557.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_185.0, 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: 12903
ACGTcount: A:0.21, C:0.07, G:0.08, T:0.20
Warning! 5716 characters in sequence are not A, C, G, or T
Found at i:1530 original size:171 final size:161
Alignment explanation
Indices: 1224--1556 Score: 343
Period size: 171 Copynumber: 2.0 Consensus size: 161
1214 NNNTAAGCTT
* * * **
1224 TTTGAAAGAATGAATGACTCTAAATGGACTTTTCTTGTCAATAAATGTTTGTTTCTTCACGTTTC
1 TTTGAAAGAATGAATGACTATAAATGGACTTTTCTTCTCAATAAATGTTTGTTACAACACGTTTC
* * *
1289 TCTAGATAGACATTCAGTTATAGTATGTTTTAATAAAAAATGTAAAGAAATTCAACTAAAAATCA
66 TCTAGATAGACATTCAATTATAGTATATTTTAATAAAAAATATAAAGAAATTCAACTAAAAATCA
1354 ATTATAAGATTATAAAA-CTATTTAAACCGAG
131 ATTATAAGATTATAAAATC-ATTTAAACCGAG
* ** *
1385 NNNNNNNNNNTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATCAATGGTTT-TTA
1 ----------TTTGAAAGAATGAATGACTATAAATGGACTTTTCTTCTCAATAAAT-GTTTGTTA
* * *
1449 CAACACGTTTCT-TGAGTTAGACATTCAATTATTGTCTATTTTAA-AGAAAAATATAAA-AAATT
55 CAACACGTTTCTCT-AGATAGACATTCAATTATAGTATATTTTAATA-AAAAATATAAAGAAA-T
* *
1511 TCAACTCAAAATTAATTATAAGATTATAAAATCATTTAAACCGAG
117 TCAACTAAAAATCAATTATAAGATTATAAAATCATTTAAACCGAG
1556 T
1 T
1557 AATAAGGCTT
Statistics
Matches: 140, Mismatches: 17, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
161 1 0.01
170 5 0.04
171 129 0.92
172 5 0.04
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.36
Consensus pattern (161 bp):
TTTGAAAGAATGAATGACTATAAATGGACTTTTCTTCTCAATAAATGTTTGTTACAACACGTTTC
TCTAGATAGACATTCAATTATAGTATATTTTAATAAAAAATATAAAGAAATTCAACTAAAAATCA
ATTATAAGATTATAAAATCATTTAAACCGAG
Found at i:4575 original size:172 final size:170
Alignment explanation
Indices: 4229--4780 Score: 459
Period size: 171 Copynumber: 3.2 Consensus size: 170
4219 NNNTTTGAAG
* * * * * * *
4229 GAATGGGTGACTCTCAATGGACTTTTCTTGTCAATGAATGCTTGTTTCTTCACATTTGTCAAGGT
1 GAAT-GGTGACTATAAATGGACTTTTCTTCTCAATGAACGATTGTTTATTCACATTTCTCAAGGT
* * * ** * * * ** ***
4294 AGACATTCAATTATAGTATGTCTTAATTAAAAATATAAAAAAATTTAATTTAAAATCAATTANNN
65 ACACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAATCAACATAAAATCAATTATGA
******* * * *
4359 NNNNNNNAAACCATTCAAAGCGAGTAATAAGCCTTTTGAAA
130 CATTAAAAAACCATTTAAACCGAGTAATAAGCCTTTTAAAA
* * * **
4400 GAATGTGTGACTATAAATGGACTTTTCTTCTCAATGAACGATT-TTTTTTACACGTTTTTTGA-G
1 GAATG-GTGACTATAAATGGACTTTTCTTCTCAATGAACGATTGTTTATT-CACATTTCTCAAGG
* *
4463 -ACACGTATTTAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAATCAACTTAAAA-CGAATT
64 TACAC--ATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAATCAACATAAAATC-AATT
*
4526 ATGACATTATAAAAACCATTTAAATCGAGTAATAAGCCTTTTAAAA
126 ATGACATTA-AAAAACCATTTAAACCGAGTAATAAGCCTTTTAAAA
** * * *
4572 GAATGAGTGACTCCAAATGGGA-TTTTCTTATCAATGAATGCTTGTTTATTCACATTTCTCAAGG
1 GAATG-GTGACTATAAAT-GGACTTTTCTTCTCAATGAACGATTGTTTATTCACATTTCTCAAGG
* * * * *
4636 TAGACATTCACTTATAGTCTGTTTTAACCAAAAATGTAAAACAATTCAACATAAAATCAATTATT
64 TACACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAATCAACATAAAATCAATTATG
* * * *
4701 AGATTACAAAACCATTTAAACCGAGTAATAAAG-TTTTTAAAG
129 ACATTAAAAAACCATTTAAACCGAGTAAT-AAGCCTTTTAAAA
** * *
4743 GAATAGGTGACTATAAATAAACTTTTATTCTCTATGAA
1 GAAT-GGTGACTATAAATGGACTTTTCTTCTCAATGAA
4781 TAAGCTTTCT
Statistics
Matches: 304, Mismatches: 63, Indels: 28
0.77 0.16 0.07
Matches are distributed among these distances:
169 3 0.01
170 9 0.03
171 146 0.48
172 133 0.44
173 10 0.03
174 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.35
Consensus pattern (170 bp):
GAATGGTGACTATAAATGGACTTTTCTTCTCAATGAACGATTGTTTATTCACATTTCTCAAGGTA
CACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAATCAACATAAAATCAATTATGAC
ATTAAAAAACCATTTAAACCGAGTAATAAGCCTTTTAAAA
Found at i:4825 original size:172 final size:171
Alignment explanation
Indices: 4467--4840 Score: 377
Period size: 172 Copynumber: 2.2 Consensus size: 171
4457 TTTGAGACAC
* *
4467 GTATTTAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAATCAACTTAAAACGAATTATGACA
1 GTATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAATCAACATAAAACGAATTATGACA
* * **
4532 TTATAAAAACCATTTAAATCGAGTAATAAGCCTTTTAAAAGAATGAGTGACTCCAAATGGGATTT
66 TTATAAAAACCATTTAAACCGAGTAATAAGCCTTTTAAAAGAATGAGTGACTACAAATGAAATTT
* * * * * *
4597 TCTTATCAATGAATGCTTGTTTATTCACATTTCTCAAGGTA
131 TATTATCAATGAATGCTTGTCTATGCACATTCCCCAAGGCA
* * * * *
4638 GACATTCACTTATAGTCTGTTTTAACCAAAAATGTAAAACAATTCAACATAAAATC-AATTATTA
1 G-TATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAATCAACATAAAA-CGAATTATGA
* * * * *
4702 GATTA-CAAAACCATTTAAACCGAGTAATAAAG-TTTTTAAAGGAAT-AGGTGACTATAAAT-AA
64 CATTATAAAAACCATTTAAACCGAGTAAT-AAGCCTTTTAAAAGAATGA-GTGACTACAAATGAA
* * *
4763 ACTTTTATTCTCTATGAATAAGCTT-TCTCTGCA-AGTTCCCCAAGGCA
127 A-TTTTATTATCAATGAAT--GCTTGTCTATGCACA-TTCCCCAAGGCA
*
4810 TGTATTCAATTATAGTCTATTTTAA-CAAAAA
1 -GTATTCAATTATAGTCTGTTTTAACCAAAAA
4841 CTACAAAAAA
Statistics
Matches: 166, Mismatches: 28, Indels: 18
0.78 0.13 0.08
Matches are distributed among these distances:
170 2 0.01
171 64 0.39
172 94 0.57
173 6 0.04
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (171 bp):
GTATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAATCAACATAAAACGAATTATGACA
TTATAAAAACCATTTAAACCGAGTAATAAGCCTTTTAAAAGAATGAGTGACTACAAATGAAATTT
TATTATCAATGAATGCTTGTCTATGCACATTCCCCAAGGCA
Found at i:11957 original size:16 final size:16
Alignment explanation
Indices: 11936--11977 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
11926 ATAATCTCAT
11936 AATTGATTTTATGTTG
1 AATTGATTTTATGTTG
11952 AATTGATTTTATGTTG
1 AATTGATTTTATGTTG
11968 AATTG-TTTTA
1 AATTGATTTTA
11978 CATCTTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 5 0.19
16 21 0.81
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (16 bp):
AATTGATTTTATGTTG
Done.