Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399416.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2683.0, 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: 5250
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.26
Warning! 1282 characters in sequence are not A, C, G, or T
Found at i:2044 original size:170 final size:161
Alignment explanation
Indices: 1860--2190 Score: 321
Period size: 170 Copynumber: 2.0 Consensus size: 161
1850 AATAATGAGA
* * * * *
1860 TTATAAACCCATTTAAAGCGAGTAATCACGCTTTGAAAGGCATGGGTGACCATAAATGGACTTTT
1 TTATAAAACCATTTAAAACGAGTAATAACGCTTCG-AAGGCATGAGTGACCATAAATGGACTTTT
* * ** *
1925 -TTGCCAATGAATCA-CATTTTCTTCATGTTT-CTTGAGGTAGACACTCAATTATAATCTATTTT
65 CTTACCAATGAAT-AGCATTTTCTTCAAGTTTGC-CAAGGTAGACACTCAAATATAATCTATTTT
* * *
1987 AATTAAAAATGT-AAAATAATTCT-ACTTAAAATC
128 AATGAAAAATATAAAAAAAATT-TGACTTAAAATC
* * *
2020 NNNNNNNNNNTTATAAAACCATTTAAAATGAGTAATAAGGCTTCGAAGGCATGAGTGACTATAAA
1 ----------TTATAAAACCATTTAAAACGAGTAATAACGCTTCGAAGGCATGAGTGACCATAAA
* * *
2085 TGGACTTTTCTTACCCATGAATAGCTTTTTCTTCAAGTTTGCCAAGGTAGACATTCAAATATAAT
56 TGGACTTTTCTTACCAATGAATAGCATTTTCTTCAAGTTTGCCAAGGTAGACACTCAAATATAAT
*
2150 CTGTTTTAATGAAAAATATAAAAAAAATTTGACTTAAAATC
121 CTATTTTAATGAAAAATATAAAAAAAATTTGACTTAAAATC
2191 AATTATGAGA
Statistics
Matches: 136, Mismatches: 20, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
169 28 0.21
170 89 0.65
171 19 0.14
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.34
Consensus pattern (161 bp):
TTATAAAACCATTTAAAACGAGTAATAACGCTTCGAAGGCATGAGTGACCATAAATGGACTTTTC
TTACCAATGAATAGCATTTTCTTCAAGTTTGCCAAGGTAGACACTCAAATATAATCTATTTTAAT
GAAAAATATAAAAAAAATTTGACTTAAAATC
Found at i:4278 original size:171 final size:170
Alignment explanation
Indices: 3974--5250 Score: 777
Period size: 171 Copynumber: 7.4 Consensus size: 170
3964 TATTTTAACA
* * * * *
3974 AAAAATGTAAAACAATTCAACTTAAAATTAGTTATGAGATTGTAAAACCATTTAAAGCGAGTAAT
1 AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * ** * ********** * *
4039 CAGGCTTTCGAAGATATGGGTGACTATAAATAGACTTNNNNNNNNNNTGAATAGCTTTTTCTTCA
66 AAGGCTTTGGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGGCTTTTTCTTCA
* * *
4104 TGTTT-TCCAAGGTAGACGTTTAAATATAATCTGTTTTAAT
131 TGTTTCT-CGAGGTAGACATTTAATTATAATCTGTTTTAAT
** * **
4144 GAAAAATATAAAAAAATTTGACTTAAAATCAATTACGAGATTATAAAACCATTTAAAGATAGTAA
1 -AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* *** * * *
4209 TAAGACTTCAAAAGGCATGGGTGACTACAAATGCACTTTTCTTGCCAATAAATGGCTTTTTCATC
65 TAAGGCTTTGGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGGCTTTTTCTTC
* * * *
4274 ATGTTTCTTGAGGTAGACATTGAATTTTAATCTTTTTTAAT
130 ATGTTTCTCGAGGTAGACATTTAATTATAATCTGTTTTAAT
* * * * *
4315 AAAAATTGTAAAAAAATTCAACTTAAAATCAATAATGAGATTATAAAACCATATAGAGCGGGTAA
1 AAAAA-TATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* * * *
4380 TAAGGCTTTGGAAGGCATAGGTGACTATATAAATGGACTTTTCATGCCAATGAATGGCTTGTTCT
65 TAAGGCTTTGGAAGGCATGGGTGAC--TATAAATGGACTTTTCTTGCCAATAAATGGCTTTTTCT
* * * *
4445 TCATGTTTCTCGAGGTAAAAACTTAATTATAATCTCG-TTTAACA
128 TCATGTTTCTCGAGGTAGACATTTAATTATAATCT-GTTTTAA-T
* * * * * *
4489 AAAAATAGAAAAAAACTCAACTTAAAATCAAATATGAGCTTATAAAACCAGTTAAAGCGAATAAT
1 AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * *
4554 AAGGCTTTGGAAGGCATGGGTGACTATAAATGGACTTCTCTTGCAAATGAATCAT-G-TTCTT-T
66 AAGGCTTTGGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAAT-AA--ATGGCTTTTTCT
* * * * * **
4616 TCATGTTTCTTGAGGCAAACACTCAATTATAATCAATTTTAAT
128 TCATGTTTCTCGAGGTAGACATTTAATTATAATCTGTTTTAAT
* * ********** * *
4659 CAAAAATGTAAAACAATTCAACTTAAAANNNNNNNNNNGATTGTAAAATCATTTAAAGCGAGTAA
1 -AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* * * * **
4724 TAAGGCTTTGGAAGGCTTTGGAAGGTATGGATAACTCTAAATAGACTTCTCTTGCCAACGAAT--
65 TAAGGCTTTGGAAGGC-AT-G--GG--T-G---ACTATAAATGGACTTTTCTTGCCAATAAATGG
** * * * *
4787 CATGTTTTCTTCATGTTTCTTAAGGCAAACACTCT-ATTATAAT-TGATTTGAAT
120 C-T-TTTTCTTCATGTTTCTCGAGGTAGACA-TTTAATTATAATCTG-TTTTAAT
* * * **********
4840 GAAAAATGTAAAAAAATTCAACTTAAAATTAATTATGAGATTGTAAAACCANNNNNNNNNNGTAA
1 -AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* * * * * * *
4905 TAAGGCTTTCGAAGGCGTGGGTGACTATAAATGGACTTTTCTTGCTAATGATTGGGTTTTTCCTC
65 TAAGGCTTTGGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGGCTTTTTCTTC
** * * * * * * *
4970 CCGATTC-CTAAGGCAAACATTCAAATATAATATGTTTTAACT
130 ATGTTTCTC-GAGGTAGACATTTAATTATAATCTGTTTTAA-T
* * * **
5012 -AAAATATAAAAGAATTCAATTTAAAATTAATTATGAGCCTATAAAACCATTTAAAGCGAGTAAT
1 AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
* * * * * * * * *
5076 AAGGCTCTAGAAGGTATGGATGACGATAAATAGACTTCTCTTGCCAATGAAT--CATGTTCTCTT
66 AAGGCTTTGGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGGC-T-TTTTCTT
* * * **
5139 CATGTTTCTTGA-G-ACGAACACTCAATTATAATCAATTTTAACT
129 CATGTTTCTCGAGGTA-G-ACATTTAATTATAATCTGTTTTAA-T
* * * * ** *
5182 AAAAACA-AACAAGAATTCAAGTTAAAATCAATTATGAGATTGTAAAACCATTTCGAGCAAGTAA
1 AAAAATATAA-AAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
5246 TAAGG
65 TAAGG
Statistics
Matches: 850, Mismatches: 216, Indels: 80
0.74 0.19 0.07
Matches are distributed among these distances:
168 1 0.00
169 2 0.00
170 130 0.15
171 428 0.50
172 11 0.01
173 140 0.16
174 8 0.01
175 3 0.00
177 3 0.00
178 3 0.00
179 2 0.00
180 5 0.01
181 114 0.13
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.32
Consensus pattern (170 bp):
AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAAT
AAGGCTTTGGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATAAATGGCTTTTTCTTCA
TGTTTCTCGAGGTAGACATTTAATTATAATCTGTTTTAAT
Found at i:4517 original size:173 final size:168
Alignment explanation
Indices: 3695--5233 Score: 769
Period size: 171 Copynumber: 9.0 Consensus size: 168
3685 NNNNNNNNNN
* * * * * *
3695 AAAGCGTGTAATAAAGCTTTGGAAGGCATGGGTGGCCATAAATGGACTTTTCTTGCTAATGAGTG
1 AAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG
* * * * * * * *** *
3760 ACTTTTTCTTCACGTTTTTTAAGCTAAACACTAAATTATAATCTGTTTTGACCTAAAATATAAAA
66 GCTTGTTCTTCATGTTTCTTGAGGTAAACACTTAATTATAATCTG-TTT-AAAAAAAATAGAAAA
* *
3825 AAGATTCAACTTAAAATCAATAATGAGAGTATAAAATCATTT
129 AA-ATTCAACTTAAAATCAATAATGAGATTATAAAACCA-TT
** *********** *
3867 AAAGCGAGTAATAAGGCTTTAAAAGGCATGGGTGAC-CNNNNNNNNNNTTTCTTGCCAATGAATC
1 AAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG
* * * *
3931 ACATT-CTCTTCATGTTTCTTGAGGCAAACAC-----TCT-A--T-TTTAACAAAAAAT-GTAAA
66 GC-TTGTTCTTCATGTTTCTTGAGGTAAACACTTAATTATAATCTGTTTAA-AAAAAATAG-AAA
* * * * *
3985 ACAATTCAACTTAAAATTAGTTATGAGATTGTAAAACCATTT
128 AAAATTCAACTTAAAATCAATAATGAGATTATAAAACCA-TT
* * ** * ********** *
4027 AAAGCGAGTAATCAGGCTTTCGAAGATATGGGTGACTATAAATAGACTTNNNNNNNNNNTGAATA
1 AAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG
* ** * ** * * *
4092 GCTTTTTCTTCATGTTT-TCCAAGGTAGACGTTTAAATATAATCTGTTTTAATGAAAAATATAAA
66 GCTTGTTCTTCATGTTTCT-TGAGGTAAACACTTAATTATAATCTG-TTTAA-AAAAAATAGAAA
** * *
4156 AAAATTTGACTTAAAATCAATTACGAGATTATAAAACCATTT
128 AAAATTCAACTTAAAATCAATAATGAGATTATAAAACCA-TT
** * *** * * *
4198 AAAGATAGTAATAAGACTTCAAAAGGCATGGGTGACTACAAATGCACTTTTCTTGCCAATAAATG
1 AAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG
* * * * * * *
4263 GCTTTTTCATCATGTTTCTTGAGGTAGACA-TTGAATTTTAATCTTTTTTAATAAAAATTGTAAA
66 GCTTGTTCTTCATGTTTCTTGAGGTAAACACTT-AATTATAATC-TGTTTAAAAAAAATAG-AAA
4327 AAAATTCAACTTAAAATCAATAATGAGATTATAAAACCATAT
128 AAAATTCAACTTAAAATCAATAATGAGATTATAAAACCAT-T
* * * *
4369 AGAGCGGGTAATAAGGCTTTGGAAGGCATAGGTGACTATATAAATGGACTTTTCATGCCAATGAA
1 AAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGAC--TATAAATGGACTTTTCTTGCCAATGAA
* *
4434 TGGCTTGTTCTTCATGTTTCTCGAGGTAAAAACTTAATTATAATCTCGTTTAACAAAAAATAGAA
64 TGGCTTGTTCTTCATGTTTCTTGAGGTAAACACTTAATTATAATCT-GTTTAA-AAAAAATAGAA
* *
4499 AAAAACTCAACTTAAAATCAA-ATATGAGCTTATAAAACCAGTT
127 AAAAATTCAACTTAAAATCAATA-ATGAGATTATAAAACCA-TT
* * *
4542 AAAGCGAATAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGACTTCTCTTGCAAATGAAT-
1 AAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG
* * * *
4606 -CATGTTCTTTTCATGTTTCTTGAGGCAAACACTCAATTATAATCAAT-TTTAATCAAAAAT-GT
66 GCTTGTTC--TTCATGTTTCTTGAGGTAAACACTTAATTATAATC--TGTTTAA-AAAAAATAG-
* ********** * *
4668 AAAACAATTCAACTTAAAANNNNNNNNNNGATTGTAAAATCATTT
125 AAAAAAATTCAACTTAAAATCAATAATGAGATTATAAAACCA-TT
* * * *
4713 AAAGCGAGTAATAAGGCTTTGGAAGGCTTTGGAAGGTATGGATAACTCTAAATAGACTTCTCTTG
1 AAAGCGAGTAATAAGGCTTTGGAAGGC-AT-G--GG--T-G---ACTATAAATGGACTTTTCTTG
* * * *
4778 CCAACGAAT--CATGTTTTCTTCATGTTTCTTAAGGCAAACACTCT-ATTATAAT-TGATTTGAA
56 CCAATGAATGGC-T-TGTTCTTCATGTTTCTTGAGGTAAACACT-TAATTATAATCTG-TTT-AA
* * * * **
4839 TGAAAAAT-GTAAAAAAATTCAACTTAAAATTAATTATGAGATTGTAAAACCANNN
116 -AAAAAATAG-AAAAAAATTCAACTTAAAATCAATAATGAGATTATAAAACCA-TT
******* * * * *
4894 NNNNNNNGTAATAAGGCTTTCGAAGGCGTGGGTGACTATAAATGGACTTTTCTTGCTAATGATTG
1 AAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG
* * * ** * * * * * * ** *
4959 GGTTTTTCCTCCCGATTCCTAAGGCAAACA-TTCAAATATAATATGTTTTAACTAAAATATAAAA
66 GCTTGTTCTTCATGTTTCTTGAGGTAAACACTT-AATTATAATCTG-TTTAAAAAAAATAGAAAA
* * * * **
5023 GAATTCAATTTAAAATTAATTATGAGCCTATAAAACCATTT
129 AAATTCAACTTAAAATCAATAATGAGATTATAAAACCA-TT
* * * * * * *
5064 AAAGCGAGTAATAAGGCTCTAGAAGGTATGGATGACGATAAATAGACTTCTCTTGCCAATGAAT-
1 AAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG
* *** * * *
5128 -CATGTTCTCTTCATGTTTCTTGAGACGAACACTCAATTATAATCAAT-TTTAACTAAAAACA-A
66 GCTTG-T-TCTTCATGTTTCTTGAGGTAAACACTTAATTATAATC--TGTTTAA-AAAAAATAGA
* * * *
5190 ACAAGAATTCAAGTTAAAATCAATTATGAGATTGTAAAACCATT
126 A-AAAAATTCAACTTAAAATCAATAATGAGATTATAAAACCATT
5234 TCGAGCAAGT
Statistics
Matches: 1030, Mismatches: 273, Indels: 130
0.72 0.19 0.09
Matches are distributed among these distances:
160 68 0.07
161 37 0.04
163 1 0.00
165 1 0.00
166 4 0.00
167 1 0.00
168 1 0.00
169 9 0.01
170 133 0.13
171 447 0.43
172 45 0.04
173 137 0.13
174 11 0.01
175 3 0.00
177 3 0.00
178 2 0.00
179 1 0.00
180 4 0.00
181 118 0.11
183 4 0.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.32
Consensus pattern (168 bp):
AAAGCGAGTAATAAGGCTTTGGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG
GCTTGTTCTTCATGTTTCTTGAGGTAAACACTTAATTATAATCTGTTTAAAAAAAATAGAAAAAA
ATTCAACTTAAAATCAATAATGAGATTATAAAACCATT
Found at i:4907 original size:181 final size:181
Alignment explanation
Indices: 4554--5250 Score: 451
Period size: 181 Copynumber: 4.0 Consensus size: 181
4544 AGCGAATAAT
* * * *
4554 AAGGCTTTGGAAGGCATGGGTGACTATAAATGGACTTCTCTTGCAAATGAATCATGTTCTTTTCA
1 AAGGCTTTGGAAGGCATGGATAACTATAAATAGACTTCTCTTGCAAACGAATCATGTTCTTTTCA
* * *
4619 TGTTTCTTGAGGCAAACACTCAATTATAATCAATTTTAATCAAAAATGTAAAACAATTCAACTTA
66 TGTTTCTTAAGGCAAACACTCAATTATAATCAATTTGAATCAAAAATGTAAAAAAATTCAACTTA
********** *
4684 AAANNNNNNNNNNGATTGTAAAATCATTTAAAGCGAGTAATAAGGCTTTGG
131 AAATTAATTATGAGATTGTAAAACCATTTAAAGCGAGTAATAAGGCTTTGG
* * *
4735 AAGGCTTTGGAAGGTATGGATAACTCTAAATAGACTTCTCTTGCCAACGAATCATGTT-TTCTTC
1 AAGGCTTTGGAAGGCATGGATAACTATAAATAGACTTCTCTTGCAAACGAATCATGTTCTT-TTC
* ** *
4799 ATGTTTCTTAAGGCAAACACTCTATTATAATTGATTTGAATGAAAAATGTAAAAAAATTCAACTT
65 ATGTTTCTTAAGGCAAACACTCAATTATAATCAATTTGAATCAAAAATGTAAAAAAATTCAACTT
********** *
4864 AAAATTAATTATGAGATTGTAAAACCANNNNNNNNNNGTAATAAGGCTTTCG
130 AAAATTAATTATGAGATTGTAAAACCATTTAAAGCGAGTAATAAGGCTTTGG
* * * * * ***
4916 AAGGC-GT-G--GG--T-G---ACTATAAATGGACTTTTCTTGCTAATG-ATTGGGTT-TTTCCT
1 AAGGCTTTGGAAGGCATGGATAACTATAAATAGACTTCTCTTGCAAACGAATCATGTTCTTT--T
** * * * * * * * * * *
4969 CCCGATTCCTAAGGCAAACATTCAAATATAAT-ATGTTTTAA-CTAAAATATAAAAGAATTCAAT
64 CATGTTTCTTAAGGCAAACACTCAATTATAATCA-ATTTGAATCAAAAATGTAAAAAAATTCAAC
** *
5032 TTAAAATTAATTATGAGCCTATAAAACCATTTAAAGCGAGTAATAAGGC--T--
128 TTAAAATTAATTATGAGATTGTAAAACCATTTAAAGCGAGTAATAAGGCTTTGG
* * * * * * *
5082 ----C--TAGAAGGTATGGATGACGATAAATAGACTTCTCTTGCCAATGAATCATGTTCTCTTCA
1 AAGGCTTTGGAAGGCATGGATAACTATAAATAGACTTCTCTTGCAAACGAATCATGTTCTTTTCA
* * * * * *
5141 TGTTTCTTGAGACGAACACTCAATTATAATCAATTTTAA-CTAAAAA--CAAACAAGAATTCAAG
66 TGTTTCTTAAGGCAAACACTCAATTATAATCAATTTGAATC-AAAAATGTAAA-AA-AATTCAAC
* ** *
5203 TTAAAATCAATTATGAGATTGTAAAACCATTTCGAGCAAGTAATAAGG
128 TTAAAATTAATTATGAGATTGTAAAACCATTTAAAGCGAGTAATAAGG
Statistics
Matches: 395, Mismatches: 102, Indels: 48
0.72 0.19 0.09
Matches are distributed among these distances:
161 1 0.00
162 2 0.01
164 2 0.01
166 1 0.00
167 1 0.00
168 1 0.00
169 4 0.01
170 115 0.29
171 111 0.28
172 2 0.01
174 1 0.00
175 1 0.00
177 2 0.01
179 1 0.00
180 3 0.01
181 147 0.37
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.32
Consensus pattern (181 bp):
AAGGCTTTGGAAGGCATGGATAACTATAAATAGACTTCTCTTGCAAACGAATCATGTTCTTTTCA
TGTTTCTTAAGGCAAACACTCAATTATAATCAATTTGAATCAAAAATGTAAAAAAATTCAACTTA
AAATTAATTATGAGATTGTAAAACCATTTAAAGCGAGTAATAAGGCTTTGG
Done.