Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399025.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2301.0, 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: 5222
ACGTcount: A:0.25, C:0.07, G:0.09, T:0.23
Warning! 1805 characters in sequence are not A, C, G, or T
Found at i:2559 original size:171 final size:171
Alignment explanation
Indices: 2248--2559 Score: 412
Period size: 171 Copynumber: 1.8 Consensus size: 171
2238 NNNNNNNGAC
* * * * * *
2248 ATTCAATTATAAATTGTTCTAATTAAAAATGTAAAACAATTCTACTTAAAAATAATTTTGAGGTT
1 ATTCAATTATAAATCGTTCTAATAAAAAATATAAAAAAATTCAACTTAAAAATAATTTTGAGATT
* * * * * *
2313 CTAAAACTATTTAAAGTGAGTAATAAGTCTTCTAAAAGAATGGGTGACTATAAATGGACTGTTCT
66 ATAAAACCATTGAAAGTGAGCAAAAAGGCTTCTAAAAGAATGGGTGACTATAAATGGACTGTTCT
*
2378 TGTCAATGAATACCTTTTTCTTCATGTTTCTCAGCGTAGAT
131 CGTCAATGAATACCTTTTTCTTCATGTTTCTCAGCGTAGAT
* * *
2419 ATTCAATTAT-AATCGATTTTAATAAAAAATATAAAAAAATTGAACTTAAAATTAATTTTGAGAT
1 ATTCAATTATAAATCG-TTCTAATAAAAAATATAAAAAAATTCAACTTAAAAATAATTTTGAGAT
* * * *
2483 TATAAAACCATTGAAAGTGAGCAAAAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTC
65 TATAAAACCATTGAAAGTGAGCAAAAAGGCTTCTAAAAGAATGGGTGACTATAAATGGACTGTTC
2548 TCG-CTAATGAAT
130 TCGTC-AATGAAT
2560 GTNNNNNNNN
Statistics
Matches: 119, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
170 5 0.04
171 114 0.96
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (171 bp):
ATTCAATTATAAATCGTTCTAATAAAAAATATAAAAAAATTCAACTTAAAAATAATTTTGAGATT
ATAAAACCATTGAAAGTGAGCAAAAAGGCTTCTAAAAGAATGGGTGACTATAAATGGACTGTTCT
CGTCAATGAATACCTTTTTCTTCATGTTTCTCAGCGTAGAT
Found at i:2912 original size:21 final size:21
Alignment explanation
Indices: 2888--2930 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2878 AAAGAATGGG
*
2888 TGACTATAAATAGATTTTTCT
1 TGACAATAAATAGATTTTTCT
* **
2909 TGACAATGAATATCTTTTTCT
1 TGACAATAAATAGATTTTTCT
2930 T
1 T
2931 CATATTTCTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (21 bp):
TGACAATAAATAGATTTTTCT
Found at i:4142 original size:171 final size:170
Alignment explanation
Indices: 3545--5222 Score: 1727
Period size: 171 Copynumber: 9.8 Consensus size: 170
3535 NNNNNNNNNN
* * * *
3545 TAAAATCAATTTTGAGGTAATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAGGGAACGGGTG
1 TAAAATCAA-TTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * **
3610 ATTATAAATAGACTTTTATTGCCAATGAATGTGTTTTTCTTCATGTTTCTTC-AGGTAGACATTC
65 ACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTC-TCGAGGTAGACATTC
* * * *
3674 AATTATAGTCTGTTTTAACCAAAAATATAAAAAAAATTTAACT
129 AATTATAATCTATTTTAACCAAAAATGT-AAAAAAATTGAACT
* * *
3717 TAAAATCAATAATGAGATTATAAAACAATTAAAAGTGCA-TAATAAGGCTTTTGAAGGAATGGGT
1 TAAAATCAAT-TTGAGATTATAAAACCATTTAAAGTG-AGTAATAAGGCTTTTGAAGGAATGGGT
* * * *
3781 GACTATAAATAAACTTTTCTTGCCAATGAATGCCTTTGTCTTCATGTTTCTTGATGTAGACATTC
64 GACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCGAGGTAGACATTC
* **
3846 AATTATAATCGATTTTAACCAAAAATACAAAAAAAATTGAACT
129 AATTATAATCTATTTTAACCAAAAAT-GTAAAAAAATTGAACT
* *
3889 TAAAATCAATTTTGAGATTATAAAACCATTGAAAATGAGTAATAAGGCTTTTGAAGGAATGGGTG
1 TAAAATCAA-TTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * *
3954 AC-AGTAAATACACTTTTCTTACCAATGAAT-CCATTTTTCTTTACGTTTCTCGAGGTAGACATT
65 ACTA-TAAATAGACTTTTCTTGCCAATGAATGCC-TTTTTCTTCATGTTTCTCGAGGTAGACATT
*
4017 CCATTATAATCT-TTCTTAACCAAAAATGTAAAAAAATTGAACT
128 CAATTATAATCTATT-TTAACCAAAAATGTAAAAAAATTGAACT
* * * * * **
4060 TAAAATCAATTTGAAGATTATAAAATCATGTAAAGTGAGTGATAAGGCTTTTGCAGGAATAGGCA
1 TAAAATCAATTTG-AGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * * * ** * *
4125 ACAATAAATGGACTTTTCTTGCCAATAAATACCTTTTTCTTCATATTGCTTAAGGTAAACAATCA
65 ACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCGAGGTAGACATTCA
* * * *** *
4190 ATTATAAACTATTCTAACTAAAAATGTAAAAGTGTTTAACT
130 ATTATAATCTATTTTAACCAAAAATGTAAAAAAATTGAACT
* * ** *
4231 TAAAATCAATTATGAGATTATAAAATCATTTGAAGTGAGTAATAACTCTTTTGAAGGAATGGATG
1 TAAAATCAATT-TGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * * * *
4296 ACTATAAATAAACTTTTCTTACCAATGAATGCCTTTTTCTTCACGTTTCACGAAGTGGACTTTCA
65 ACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCGAGGTAGACATTCA
* * * *
4361 ATTATAATCTATTTGAAGCAAAAATATAAAAAAATTTAACT
130 ATTATAATCTATTTTAACCAAAAATGTAAAAAAATTGAACT
* *
4402 TAAAATCGATACTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
1 TAAAATCAAT-TTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * *
4467 ACTATAAATGGACTTTTCTCGCCAATGAAAGCCTTGTTT-TT-ATGTTTCTCAAGGTAGACATTC
65 ACTATAAATAGACTTTTCTTGCCAATGAATGCCTT-TTTCTTCATGTTTCTCGAGGTAGACATTC
* * *
4530 AACTATAATCTGTTCTAA--AAAAAGTGTAAAAAAATTGAACT
129 AATTATAATCTATTTTAACCAAAAA-TGTAAAAAAATTGAACT
* *
4571 TCAAATCAATTTGAGATTATAAAACCATTTAAAGT-AGGTAATAAGGCTTTTGAAGGAATGAGTG
1 TAAAATCAATTTGAGATTATAAAACCATTTAAAGTGA-GTAATAAGGCTTTTGAAGGAATGGGTG
* * * ** *
4635 ACTACAAATGGACTTTTTTTGCCAATGAATGCCTTTCTT-TTCACATTTCTTGAGGTAGACATTC
65 ACTATAAATAGACTTTTCTTGCCAATGAATGCCTTT-TTCTTCATGTTTCTCGAGGTAGACATTC
* * * * * * * *
4699 AATTATAAACTGTTGTATCAAAAAACGTAAAAAAATTCAACC
129 AATTATAATCTATTTTAACCAAAAATGTAAAAAAATTGAACT
* * *
4741 TAAAATCAACTATGAGATTATAAAATCATTTAAAGTGAGTAATAATGCTTTTGAAGGAATGGGTG
1 TAAAATCAA-TTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * * *
4806 AGTATAAACAGACTTTTCTTGTCAATGAAT-ACTTTTTCCTTTATGTTTCTTGAGGTAGACATTC
65 ACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTT-CTTCATGTTTCTCGAGGTAGACATTC
* * * * *
4870 TATTATAATCTATTTTAACTAAAAATATTAACAAAATT-ACACC
129 AATTATAATCTATTTTAACCAAAAAT-GTAAAAAAATTGA-ACT
* * *
4913 AAAAATCAATTATGAGATTATAAAACCATTTAAAATGAGTAATAAGGCTTTTGAAGGAATGGGAG
1 TAAAATCAATT-TGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * * ** *
4978 ACTATAAATGGACTTTTCTTGCCAATGAATGTCTTTTT-TTACATATTT-TCTAAATACAC-TAT
65 ACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTT-CATGTTTCTCGAGGTAGACAT-T
* * * * ***
5040 CAATTATAATATGTTTTAACAAAAAATATAAAAAAAAATTGATGA
128 CAATTATAATCTATTTTAACCAAAAATGT--AAAAAAATTGAACT
* * * *
5085 TAAAATCAATTTTGAGATTGTAATACCATTTAAAGTGAGTAATAAGGCTTTTAAAGGAATGAGTG
1 TAAAATCAA-TTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTG
* * * ** * * *
5150 ACTAGAAATGGACTTTTTCTAT--CAATAAATATCTTTCTCTTCATGTTTCTCAAGGTAAACATT
65 ACTATAAATAGAC-TTTTCT-TGCCAATGAATGCCTTTTTCTTCATGTTTCTCGAGGTAGACATT
*
5213 CCATTATAAT
128 CAATTATAAT
Statistics
Matches: 1253, Mismatches: 212, Indels: 81
0.81 0.14 0.05
Matches are distributed among these distances:
167 2 0.00
168 90 0.07
169 57 0.05
170 62 0.05
171 525 0.42
172 479 0.38
173 36 0.03
174 2 0.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (170 bp):
TAAAATCAATTTGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGA
CTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCTCGAGGTAGACATTCAA
TTATAATCTATTTTAACCAAAAATGTAAAAAAATTGAACT
Done.