Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400323.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3526.1, 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: 2428
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.33
Warning! 240 characters in sequence are not A, C, G, or T
Found at i:351 original size:171 final size:156
Alignment explanation
Indices: 141--466 Score: 296
Period size: 171 Copynumber: 2.0 Consensus size: 156
131 NNNNNNNNNN
* *
141 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAACGGGTGACTATAAATAGACTTTTATTGC-CAATG
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAACAGGTGACTATAAATAGACTCTTATT-CTCAATG
* * * ** ** * *
205 AAT-GATTTTTTTTTCACATTTCTTGAGGTTGACATTCGATTATAATCTATTTTAGCAAAAAAAG
65 AATAG-CTTTTTTTGCAAATTTCTCAAGGTAAACATTCAATTATAATCTATTTTAACAAAAAAAG
269 TAAAAAAATTCAACTTAAAATCAATTATNNNNNNNNNNNNNNA
129 T-AAAAAATTCAACTTAAAATCAATTAT--------------A
** *
312 TTTAAAGCGAGTAATAAGGCTTTTGAAGGATTAGGTGACTATAAATAGACTCTTCTTCTCAATGA
1 TTTAAAGCGAGTAATAAGGCTTTTGAAGGAACAGGTGACTATAAATAGACTCTTATTCTCAATGA
* * * * * *
377 ATAGCTTTTTTTGCAAATTTCTCAAGGTAAACATTTAATTATTATTTGTTTTAACTAAAAATGTA
66 ATAGCTTTTTTTGCAAATTTCTCAAGGTAAACATTCAATTATAATCTATTTTAACAAAAAAAGTA
*
442 AAAAATTTAACTTAAAATCAATTAT
131 AAAAATTCAACTTAAAATCAATTAT
467 GAGATTATAN
Statistics
Matches: 132, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
170 26 0.20
171 105 0.80
172 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.36
Consensus pattern (156 bp):
TTTAAAGCGAGTAATAAGGCTTTTGAAGGAACAGGTGACTATAAATAGACTCTTATTCTCAATGA
ATAGCTTTTTTTGCAAATTTCTCAAGGTAAACATTCAATTATAATCTATTTTAACAAAAAAAGTA
AAAAATTCAACTTAAAATCAATTATA
Found at i:1093 original size:170 final size:159
Alignment explanation
Indices: 906--1234 Score: 317
Period size: 171 Copynumber: 2.0 Consensus size: 159
896 CGAGTAATAA
* * ** **
906 GGCTTTGGAAGGAATGGGTGACTATAAATGGACTTTTTT-CTCAATGAGTAGCGTTTTGTGTATG
1 GGCTTTGGAAAGAATGGGTGACTATAAATGGACTTTTTTCCTCAATGAATAGCGTTTTGTACACA
*
970 TTTCTCAAGGCAGGCATTCAATTATAGTCTGTTTTAA-CA-AAAAATGAAAATAAAATCAACTTA
66 TTTCTCAAGGCAAGCATTCAATTATAGTC--TTTTAACCATAAAAAT-AAAA-AAAATCAACTTA
1033 AAATCA-ATTATGA-GATTATAAAACAATTTAAAG
127 AAAT-AGATT-TGAGGATTATAAAACAATTTAAAG
* * **
1066 NNNNNNNNNNGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTTTCCTCAATGAATTGTTT
1 ----------GGCTTTGGAAAGAATGGGTGACTATAAATGGACTTTTTTCCTCAATGAATAGCGT
* ** * * *
1131 TTTTTACACATTTCTTGAGGCAAGCATTCGATTATAGTCTTTTAACCATAAATATAAAAAAATTC
56 TTTGTACACATTTCTCAAGGCAAGCATTCAATTATAGTCTTTTAACCATAAAAATAAAAAAAATC
*
1196 AACTTAAAATAGATTTTAGGATTATAAAACAATTTAAAG
121 AACTTAAAATAGATTTGAGGATTATAAAACAATTTAAAG
1235 CAAGTAATAA
Statistics
Matches: 136, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
168 3 0.02
169 44 0.32
170 43 0.32
171 46 0.34
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.35
Consensus pattern (159 bp):
GGCTTTGGAAAGAATGGGTGACTATAAATGGACTTTTTTCCTCAATGAATAGCGTTTTGTACACA
TTTCTCAAGGCAAGCATTCAATTATAGTCTTTTAACCATAAAAATAAAAAAAATCAACTTAAAAT
AGATTTGAGGATTATAAAACAATTTAAAG
Found at i:1613 original size:171 final size:169
Alignment explanation
Indices: 585--2428 Score: 1073
Period size: 170 Copynumber: 10.8 Consensus size: 169
575 NNNNNNNNGG
** *
585 CTATAAATGGACTTTTCTTCTCAATGAATAGCTTTTTTTGCACGTTTCTC-AGAGCAGGCATTCA
1 CTATAAATGGACTTTT-TTCTCAATGAATA-CTTTTTTTGCATATTTCTCAAG-GCAGACATTCA
* * * * *
649 ATTATAGTCTGTTGTAACAAAAAATGTAAACAAATTCAACTTAAAATGAATTATTAGATTATAAA
63 ATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
** * *
714 ACAATTTAAAGTAAGTAATAAGGCTTTTGAAGGACTGAGTGA
128 ACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGA
* *
756 CTATAAATGGACTCTTCTTCTCAATGAATAGCTTTTTTTGCATATTTCTCAAGGTA-AGCATTCA
1 CTATAAATGGACT-TTTTTCTCAATGAATA-CTTTTTTTGCATATTTCTCAAGGCAGA-CATTCA
* ************************
820 ATTATAGTCTGTTTTAACAAAAAATTTAAAAAAATTCAACTNNNNNNNNNNNNNNNNNNNNNNNN
63 ATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
**** * *
885 NNNNTTTAAAACGAGTAATAAGGCTTTGGAAGGAATGGGTGA
128 ACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGA
* * * * * *
927 CTATAAATGGACTTTTTTCTCAATGAGTAGCGTTTTGTGTATGTTTCTCAAGGCAGGCATTCAAT
1 CTATAAATGGACTTTTTTCTCAATGAATA-CTTTTTTTGCATATTTCTCAAGGCAGACATTCAAT
992 TATAGTCTGTTTTAACAAAAAATGA-AAATAAAA-TCAACTTAAAATCAATTATGAGATTATAAA
65 TATAGTCTGTTTTAACAAAAAAT-ATAAA-AAAATTCAACTTAAAATCAATTATGAGATTATAAA
********** *
1055 ACAATTTAAAGNNNNNNNNNNGGCTTTTGAAAGAATGGGTGA
128 ACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGA
** * * ** *
1097 CTATAAATGGACTTTTTTCCTCAATGAATTGTTTTTTTTACACATTTCTTGAGGCA-AGCATTCG
1 CTATAAATGGACTTTTTT-CTCAATGAA-TACTTTTTTTGCATATTTCTCAAGGCAGA-CATTCA
* * *
1161 ATTATAGTC--TTTTAACCATAAATATAAAAAAATTCAACTTAAAAT-AGATT-TTAGGATTATA
63 ATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCA-ATTATGA-GATTATA
* ** * *
1222 AAACAATTTAAAGCAAGTAATAAAACTTTTAAAGGAATAGGTGA
126 AAACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGA
* * * * * * *
1266 CTATAAATGAACTTTTTT-TACAAATGAATGCCTTTTTTTTCATGTTTTTCAAGGTAAACATTCA
1 CTATAAATGGACTTTTTTCT-C-AATGAAT-ACTTTTTTTGCATATTTCTCAAGGCAGACATTCA
* * * * * * **
1330 ATTATTGTCTATTTTAAC-CAAAATGTATAACAATTCAACTTAAAATCAATTATGAGATTATANN
63 ATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
******** *
1394 NNNNNNNNAAGCGAGTAATACGGCTTTTGAAGGAATGGGTGA
128 ACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGA
**
1436 CTATAAATCAACTTTTCTTCTCAATGAATCACTTTTTTTGCATATTTCTCAAGGCAGACATTCAA
1 CTATAAATGGACTTTT-TTCTCAATGAAT-ACTTTTTTTGCATATTTCTCAAGGCAGACATTCAA
* * * * * *
1501 TCATAGTCTATTTTAATAAAAAATATAAACAAATTCATCTTAAAATCAATTATGATATTATAAAA
64 TTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
* * *
1566 CAATTTAATGTGAGTAATAAGGCTTCTGAAGGAATGGGTGA
129 CAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGA
********* * * * * *
1607 CTATAAATGNNNNNNNNNNCTCAATGAATGATTTTTTTTACACATTTCTAAAGGCAGAAATTCAA
1 CTATAAATG-GACTTTTTTCTCAATGAAT-ACTTTTTTTGCATATTTCTCAAGGCAGACATTCAA
* * * *
1672 TTATAGTCTGTTTTAATAAAAAATA-AAAAAAATTCAATTTAAAATCATTTATGAGATTATGAAA
64 TTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
* * *****
1736 CAATTTAAAGTGAATAATAAGGCTTTTGAAGGAATGNNNNN
129 CAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGA
***** * ** * * * * * *
1777 NNNNNAATGGAATTTTTTCCTCAATGAATGGTTTTTTTTACACATTTCTCGA-GAAAATCATTCG
1 CTATAAATGGACTTTTTT-CTCAATGAAT-ACTTTTTTTGCATATTTCTCAAGGCAGA-CATTCA
* * * * * * *
1841 ATTATAGTCT-TTTTAACCATAAATGTAAAAAAATTTAACTTCAAATTAATTTTGAGATTATAAA
63 ATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
*********** * * *
1905 ATNNNNNNNNNNGAGTAATAAGGCTTTTAAAAGAATTGGTGA
128 ACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGA
* * * * * *
1947 CTATAAATGGACTTTTCTTAC-CAATAAATGTCTTTGTTT-CTTGTTTCTCAAGGTA-ACATTCA
1 CTATAAATGGACTTTT-TT-CTCAATGAAT-ACTTTTTTTGCATATTTCTCAAGGCAGACATTCA
* ** * * * * *
2009 ATTATTGTCTACTTTAACCAAAAATGTAAAAAACATTTAACTTTAAATTAATTATGAGATTATAA
63 ATTATAGTCTGTTTTAACAAAAAATATAAAAAA-ATTCAACTTAAAATCAATTATGAGATTATAA
********** * * *
2074 AACANNNNNNNNNNAGTAATAAGGCTTTTGAAGAAATTGGTAA
127 AACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGA
* * * ** * **
2117 CTATAATTAGACTTTTTTTCTCAATGAATAGCTTTTTGTGCACGTTTCTCAAGGTATTCATTCAA
1 CTATAAATGGAC-TTTTTTCTCAATGAATA-CTTTTTTTGCATATTTCTCAAGGCAGACATTCAA
* * *
2182 TTATAGTCTATTTTAACAATAAATGTAAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
64 TTATAGTCTGTTTTAACAAAAAATAT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* ********** *
2247 ATAANNNNNNNNNNGTAATAAGGCTTTTAAAGGAATGGGTGA
128 ACAATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGA
* ** * * ** * **
2289 CTATAAATGGACTTTTTTCCTTAATGAATGGTTTTTTTTACACATTTCTTGAGG-AAAGCATTTG
1 CTATAAATGGACTTTTTT-CTCAATGAAT-ACTTTTTTTGCATATTTCTCAAGGCAGA-CATTCA
* * * * * * * *
2353 ATTATTGTCT-TTTTAA-ACATATATGTGAAAAAATTCAACTCAAAATAAATTTTGAGATTATAA
63 ATTATAGTCTGTTTTAACA-AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
2416 AACAATTTAAAGC
127 AACAATTTAAAGC
Statistics
Matches: 1277, Mismatches: 354, Indels: 85
0.74 0.21 0.05
Matches are distributed among these distances:
167 1 0.00
168 24 0.02
169 163 0.13
170 566 0.44
171 369 0.29
172 148 0.12
173 6 0.00
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.35
Consensus pattern (169 bp):
CTATAAATGGACTTTTTTCTCAATGAATACTTTTTTTGCATATTTCTCAAGGCAGACATTCAATT
ATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACA
ATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGA
Done.