Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397507.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_915.0, 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: 11317
ACGTcount: A:0.19, C:0.07, G:0.09, T:0.18
Warning! 5265 characters in sequence are not A, C, G, or T
Found at i:1336 original size:8 final size:8
Alignment explanation
Indices: 1312--1353 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
1302 CTCTTTCTAT
1312 TTTCTT-C
1 TTTCTTCC
1319 TTTC-TCC
1 TTTCTTCC
1326 TTTCTTCC
1 TTTCTTCC
1334 TTTCTTCC
1 TTTCTTCC
1342 TTTCTTCC
1 TTTCTTCC
1350 TTTC
1 TTTC
1354 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 1 0.03
7 9 0.27
8 23 0.70
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTCTTCC
Found at i:4485 original size:23 final size:23
Alignment explanation
Indices: 4457--4512 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
4447 GCTAGAAAGC
4457 AAAGGAAGAAAGAAAGA-AAGGAG
1 AAAGGAAGAAAGAAAGAGAA-GAG
*
4480 AAAGGAAGAAAGGAAGAGAAGAG
1 AAAGGAAGAAAGAAAGAGAAGAG
4503 AAA-GAAGAAA
1 AAAGGAAGAAA
4513 CTAGAAAGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
22 7 0.23
23 22 0.71
24 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (23 bp):
AAAGGAAGAAAGAAAGAGAAGAG
Found at i:4490 original size:19 final size:19
Alignment explanation
Indices: 4463--4512 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
4453 AAGCAAAGGA
4463 AGAAAGAAAGAAAGGAGAA-
1 AGAAAGAAAGAAA-GAGAAG
* *
4482 AGGAAGAAAGGAAGAGAAG
1 AGAAAGAAAGAAAGAGAAG
4501 AGAAAG-AAGAAA
1 AGAAAGAAAGAAA
4513 CTAGAAAGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (19 bp):
AGAAAGAAAGAAAGAGAAG
Found at i:7802 original size:343 final size:340
Alignment explanation
Indices: 6731--7893 Score: 1444
Period size: 342 Copynumber: 3.4 Consensus size: 340
6721 AGAAGTAAAC
*
6731 ATCAAATTGTGATCT-GTTTTAACAAAAAATGAGAAAAAAGAATTCAACTTAAAATCATTTATAA
1 ATCAAATTGTGA-CTAGTTTTAACAAAAAATGA-AAGAAA-AA-TCAACTTAAAATCATTTATAA
* ** * *
6795 GATTATAAAAACCTTTTAAAATGAGTAAGAAAGCTTTTGAAGGCATGACTGAATATAAATAGACT
62 GATTAT-AAAACCTTTTCAAGCGAGTAAGAAAGCTTTCGAAGGCATGAGTGAATATAAATAGACT
* * * *
6860 TTTCTCATCAATAGGGGGCTTTTGCTTCATGATTCCTGATGAATACAGTAAATTAT-ACTGTGTT
126 TTTCTCATCAATAGGTGGCTTTTGCTTCATGATTCC-AATGAA-ATAGTAAATTATGA-TATGTT
** * * * * *
6924 TTAATTAAAAATGAAAAAAAAAATTCAATTGAAAAGCATTTAGAAGATTATAAAATTATTTAAAG
188 TTAA-CCAAAATGGAAAAACAAATTCAATTGAAAATCATTTATAAGATTATAAAACTATTTAAA-
* * * ** * ** *
6989 CAAGTAATCAGGCTTTCAAAGGAACGAGTGACTATAAGTGGACTTTTCTTGCCAATTGATTACTT
251 AAAGTAATCAGGCTTTCGAAGGCATAAGTGACTATAAATGGACTTTTCTTGCTGATCGA-TACTT
7054 TT-GCTTCACGTTTCCCAATGCAAAT
315 TTCGCTTCACGTTTCCCAATGCAAAT
* * * * * *
7079 ATCAAATTGTAATTAGGTTTAACCAAAACTGAAAGAAAAATCCACTTAAAATCATTTATAAGATT
1 ATCAAATTGTGACTAGTTTTAACAAAAAATGAAAGAAAAATCAACTTAAAATCATTTATAAGATT
* * * * ** ** *
7144 ATAAAACCCTTCCAAGCGAATAAGAAAGTTTTCGAAGAAATGAGCAAATATAAACAGACTTTTCT
66 ATAAAACCTTTTCAAGCGAGTAAGAAAGCTTTCGAAGGCATGAGTGAATATAAATAGACTTTTCT
* *
7209 CATCAATAAGTGGCTTATGCTTCATGATTCCCAATGTAAATAGTAAATTATGATATGTTTTAACC
131 CATCAATAGGTGGCTTTTGCTTCATGATT-CCAATG-AAATAGTAAATTATGATATGTTTTAACC
*
7274 AAAA-GTG-AAAACAAATTCAATTGAAAATCATTTATAAAATTATAAAACTATTTAAAGAAAGTA
194 AAAATG-GAAAAACAAATTCAATTGAAAATCATTTATAAGATTATAAAACTATTTAAA-AAAGTA
* * * *
7337 ATCAGGCTTTCGAAGGCATAAGTGACTATAAATAGACTTTTTTTGCTGATCGCTTGC-TTTCGCT
257 ATCAGGCTTTCGAAGGCATAAGTGACTATAAATGGACTTTTCTTGCTGATCG-ATACTTTTCGCT
* *
7401 TCACGTTTCTCAATGCAGAT
321 TCACGTTTCCCAATGCAAAT
* *
7421 ATCAAATTGTGACTAGTTTTAACAAAAAATGAAAGAAAAAGCAACCTAAAATCATTTATAAGATT
1 ATCAAATTGTGACTAGTTTTAACAAAAAATGAAAGAAAAATCAACTTAAAATCATTTATAAGATT
* *
7486 ATAAAACCTTTTCAAGTGAGTAAGAAAGCTTTCGAAGGCATGAGTGAATATAAATAGACTTTTGT
66 ATAAAACCTTTTCAAGCGAGTAAGAAAGCTTTCGAAGGCATGAGTGAATATAAATAGACTTTTCT
*
7551 CATCAATAGGTGGCTTTTGCTTCATGGTTCTCAATGCAAATAGTAAATTATGATATGTTTTAACC
131 CATCAATAGGTGGCTTTTGCTTCATGATTC-CAATG-AAATAGTAAATTATGATATGTTTTAACC
* *
7616 AAAATGGAAAAACAAATTCAATTAAAAATTATTTATAAGATTATAAAACTATTTAAAATAAGTAA
194 AAAATGGAAAAACAAATTCAATTGAAAATCATTTATAAGATTATAAAACTATTTAAAA-AAGTAA
* * ** * *
7681 TTAGGC-TTCGGAACGCATAAGTGACTATAAATGGACTTTTCTTATTGATCGAAACTTTTCGTTT
258 TCAGGCTTTC-GAAGGCATAAGTGACTATAAATGGACTTTTCTTGCTGATCGATACTTTTCGCTT
* *
7745 CATGATTCCCAATGCAAAT
322 CACGTTTCCCAATGCAAAT
* *
7764 ATCAAATTGTGACTAGTTTTAACCAAAAATGAAAGAAAAATCAACTTAAACTCATTTATAAGATT
1 ATCAAATTGTGACTAGTTTTAACAAAAAATGAAAGAAAAATCAACTTAAAATCATTTATAAGATT
* *
7829 ATAAAA-CTATTTCAAGCGAGTAAGAAAGCTTTCGAAGGCATGAATGACTATAAAT-GAACTTTT
66 ATAAAACCT-TTTCAAGCGAGTAAGAAAGCTTTCGAAGGCATGAGTGAATATAAATAG-ACTTTT
7892 CT
129 CT
7894 TGTCAATGGA
Statistics
Matches: 702, Mismatches: 98, Indels: 35
0.84 0.12 0.04
Matches are distributed among these distances:
341 4 0.01
342 299 0.43
343 237 0.34
344 98 0.14
345 31 0.04
346 2 0.00
347 6 0.01
348 25 0.04
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (340 bp):
ATCAAATTGTGACTAGTTTTAACAAAAAATGAAAGAAAAATCAACTTAAAATCATTTATAAGATT
ATAAAACCTTTTCAAGCGAGTAAGAAAGCTTTCGAAGGCATGAGTGAATATAAATAGACTTTTCT
CATCAATAGGTGGCTTTTGCTTCATGATTCCAATGAAATAGTAAATTATGATATGTTTTAACCAA
AATGGAAAAACAAATTCAATTGAAAATCATTTATAAGATTATAAAACTATTTAAAAAAGTAATCA
GGCTTTCGAAGGCATAAGTGACTATAAATGGACTTTTCTTGCTGATCGATACTTTTCGCTTCACG
TTTCCCAATGCAAAT
Found at i:7892 original size:171 final size:171
Alignment explanation
Indices: 6731--7900 Score: 914
Period size: 171 Copynumber: 6.8 Consensus size: 171
6721 AGAAGTAAAC
* *
6731 ATCAAATTGTGATCT-GTTTTAACAAAAAATGAGAAAAAAGAATTCAACTTAAAATCATTTATAA
1 ATCAAATTGTGA-CTAGTTTTAACCAAAAATGA-AAGAAA-AA-TCAACTTAAAATCATTTATAA
** * * *
6795 GATTATAAAAACCT-TTTAAAATGAGTAAGAAAGCTTTTGAAGGCATGACTGAATATAAATAGAC
62 GATTAT-AAAA-CTATTTAAAGCGAGTAAGAAAGCTTTCGAAGGCATGAATGACTATAAATAGAC
* * * ** *
6859 TTTTCTCATCAATAGGGGGCTTTTGCTTCATGATTCCTGATG-AATAC
125 TTTTCTTATCAATACGTGGCTTTTGCTTCATGATTCCCAATGCAA-AT
* * ** * * *
6906 AGT-AAATTAT-ACTGTGTTTTAATTAAAAATGAAAAAAAAAATTCAA-TTGAAAAGCATTTAGA
1 A-TCAAATTGTGACT-AGTTTTAACCAAAAATG-AAAGAAAAA-TCAACTT-AAAATCATTTATA
* * ** * * * * * * *
6968 AGATTATAAAATTATTTAAAGCAAGTAATCAGGCTTTCAAAGGAACGAGTGACTATAAGTGGACT
61 AGATTATAAAACTATTTAAAGCGAGTAAGAAAGCTTTCGAAGGCATGAATGACTATAAATAGACT
** * ** * *
7033 TTTCTTGCCAAT-TGATTACTTTTGCTTCACGTTTCCCAATGCAAAT
126 TTTCTTATCAATACG-TGGCTTTTGCTTCATGATTCCCAATGCAAAT
* * * * *
7079 ATCAAATTGTAATTAGGTTTAACCAAAACTGAAAGAAAAATCCACTTAAAATCATTTATAAGATT
1 ATCAAATTGTGACTAGTTTTAACCAAAAATGAAAGAAAAATCAACTTAAAATCATTTATAAGATT
** ** * * ** *** * *
7144 ATAAAACCCTTCCAAGCGAATAAGAAAGTTTTCGAAGAAATGAGCAAATATAAACAGACTTTTCT
66 ATAAAACTATTTAAAGCGAGTAAGAAAGCTTTCGAAGGCATGAATGACTATAAATAGACTTTTCT
* * * *
7209 CATCAATAAGTGGCTTATGCTTCATGATTCCCAATGTAAAT
131 TATCAATACGTGGCTTTTGCTTCATGATTCCCAATGCAAAT
* * *
7250 AGT-AAATTATGA-TATGTTTTAACCAAAAGTGAAA-ACAAATTCAA-TTGAAAATCATTTATAA
1 A-TCAAATTGTGACTA-GTTTTAACCAAAAATGAAAGA-AAAATCAACTT-AAAATCATTTATAA
* ** ** *
7311 AATTATAAAACTATTTAAAGAAAGTAATCAGGCTTTCGAAGGCAT-AAGTGACTATAAATAGACT
62 GATTATAAAACTATTTAAAGCGAGTAAGAAAGCTTTCGAAGGCATGAA-TGACTATAAATAGACT
* * * * * * *
7375 TTT-TT-TGCTGAT-CGCTTGCTTTCGCTTCACGTTTCTCAATGCAGAT
126 TTTCTTAT-C-AATACG-TGGCTTTTGCTTCATGATTCCCAATGCAAAT
* * *
7421 ATCAAATTGTGACTAGTTTTAACAAAAAATGAAAGAAAAAGCAACCTAAAATCATTTATAAGATT
1 ATCAAATTGTGACTAGTTTTAACCAAAAATGAAAGAAAAATCAACTTAAAATCATTTATAAGATT
* * * * *
7486 ATAAAACCT-TTTCAAGTGAGTAAGAAAGCTTTCGAAGGCATGAGTGAATATAAATAGACTTTTG
66 ATAAAA-CTATTTAAAGCGAGTAAGAAAGCTTTCGAAGGCATGAATGACTATAAATAGACTTTTC
* * * *
7550 TCATCAATAGGTGGCTTTTGCTTCATGGTTCTCAATGCAAAT
130 TTATCAATACGTGGCTTTTGCTTCATGATTCCCAATGCAAAT
* *
7592 AGT-AAATTATGA-TATGTTTTAACC-AAAATGGAAA-AACAAATTCAA-TTAAAAATTATTTAT
1 A-TCAAATTGTGACTA-GTTTTAACCAAAAAT-GAAAGAA-AAA-TCAACTT-AAAATCATTTAT
*** ** * * *
7652 AAGATTATAAAACTATTTAAAATAAGTAATTAGGC-TTCGGAACGCAT-AAGTGACTATAAATGG
60 AAGATTATAAAACTATTTAAAGCGAGTAAGAAAGCTTTC-GAAGGCATGAA-TGACTATAAATAG
** *** *
7715 ACTTTTCTTATTGAT-CGAAACTTTTCGTTTCATGATTCCCAATGCAAAT
123 ACTTTTCTTATCAATACGTGGCTTTT-GCTTCATGATTCCCAATGCAAAT
*
7764 ATCAAATTGTGACTAGTTTTAACCAAAAATGAAAGAAAAATCAACTTAAACTCATTTATAAGATT
1 ATCAAATTGTGACTAGTTTTAACCAAAAATGAAAGAAAAATCAACTTAAAATCATTTATAAGATT
*
7829 ATAAAACTATTTCAAGCGAGTAAGAAAGCTTTCGAAGGCATGAATGACTATAAAT-GAACTTTTC
66 ATAAAACTATTTAAAGCGAGTAAGAAAGCTTTCGAAGGCATGAATGACTATAAATAG-ACTTTTC
*
7893 TTGTCAAT
130 TTATCAAT
7901 GGATGGGTTT
Statistics
Matches: 776, Mismatches: 172, Indels: 98
0.74 0.16 0.09
Matches are distributed among these distances:
169 1 0.00
170 20 0.03
171 446 0.57
172 147 0.19
173 103 0.13
174 30 0.04
175 27 0.03
176 2 0.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (171 bp):
ATCAAATTGTGACTAGTTTTAACCAAAAATGAAAGAAAAATCAACTTAAAATCATTTATAAGATT
ATAAAACTATTTAAAGCGAGTAAGAAAGCTTTCGAAGGCATGAATGACTATAAATAGACTTTTCT
TATCAATACGTGGCTTTTGCTTCATGATTCCCAATGCAAAT
Done.