Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398323.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1623.0, 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: 2260
ACGTcount: A:0.25, C:0.08, G:0.08, T:0.23
Warning! 795 characters in sequence are not A, C, G, or T
Found at i:1416 original size:171 final size:168
Alignment explanation
Indices: 1036--1902 Score: 616
Period size: 171 Copynumber: 5.1 Consensus size: 168
1026 GAAAAGAATG
* * * * * *
1036 AGTGACTATAAATAGAC-TTTAATTGTCAATAAATGCCTTTTCCTTCACATTTCTTAAAGTAGAC
1 AGTGACTATAAATAGACTTTTCA-TGTCAATGAATGACTTTTCTTTCACGTTTCTTAAAGTAGAT
* * * * * *
1100 ATTTAGTTATAATTTGTTTTAATAAAAAATA-AAAAAATATTTAACTTAAAATCGATTATTAGAT
65 A-TCAATTATAATATGTTTTAATAAAAAATATAAAAAA-ATTCAACTTAAAATCAATTA-TGGAT
* * *
1164 TATGAAACTATTTACAACGAGTAATAAGGCTTCCAAAGGCTT
127 TATAAAACTATTTAAAACGAGTAATAAGGCTTTCAAAGGCTT
* * * *
1206 GAGAGACTATAAATAGACTTTTC--GTCCTAATGCATGACTTTTCTTTTACGTTT-TCAAAGTTA
1 -AGTGACTATAAATAGACTTTTCATGT-C-AATGAATGACTTTTCTTTCACGTTTCTTAAAG-TA
* *
1268 GATATCAAATTATAATATCTTTCAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATCGG
62 GATATC-AATTATAATATGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTAT-GG
* *
1333 ATTATAAAAC-AATTAAAAGTGAGTAATAAGGCTTTCAAAGGCTT
125 ATTATAAAACTATTTAAAA-CGAGTAATAAGGCTTTCAAAGGCTT
* * *
1377 ACGTGACTATAAATAGACTTTTCATGTCAATGAATGACTTTT-TGTTCACGTTTCTTGAGGCCAG
1 A-GTGACTATAAATAGACTTTTCATGTCAATGAATGACTTTTCT-TTCACGTTTCTTAAAG-TAG
* * * * *
1441 CAT-TCAATTATAATCTGTTTTAGTAAAAAATGTAAAACAATTCAACCTAAAATCAATTATGTGA
63 -ATATCAATTATAATATGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATG-GA
* * * * *
1505 TAATAAAACTTTTTAAAACAAGTAATAAGGCTTTCAAAAGCATG
126 TTATAAAACTATTTAAAACGAGTAATAAGGCTTTCAAAGGC-TT
* * * * * *
1549 GGTGGCTATAAATGGACTTTTCTTGTCAATGAAT-AGCTTTT-TCTTCATGTTTC-TAGAGGTAG
1 AGTGACTATAAATAGACTTTTCATGTCAATGAATGA-CTTTTCT-TTCACGTTTCTTA-AAGTAG
* * ** * * * *
1611 ACATTGAATTATAATATGTTTTAACCAAAAATGTAAAATAATTTAACCTAAAATCAATTATGAGA
63 ATA-TCAATTATAATATGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATG-GA
* * * * * ** *
1676 TTATTAAACGA--TAAAAAGAAAGTAATAACGCCTTTAAAAGAATG
126 TTATAAAACTATTTAAAACG--AGTAATAA-GGCTTTCAAAGGCTT
* * * * * * * * * * *
1720 GGTAACTATAAAT-GCACTTCTCTTG-CATATGAATGCCTTTTCCTTCAAGTTTCCTGAAGCAAA
1 AGTGACTATAAATAG-ACTTTTCATGTCA-ATGAATGACTTTTCTTTCACGTTTCTTAAAGTAGA
* * ** *
1783 CATTCAATTATAATCTGTTTTAACCAGAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGAT
64 TA-TCAATTATAATATGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATG-GAT
* * ** *
1847 TATACAACCATTTAACGCAAGTAATAAGGCTTTTC-AAGGCTT
127 TATAAAACTATTTAAAACGAGTAATAAGGC-TTTCAAAGGCTT
*
1889 GGGTGACTATAAAT
1 -AGTGACTATAAAT
1903 GTACTTTCCT
Statistics
Matches: 560, Mismatches: 103, Indels: 67
0.77 0.14 0.09
Matches are distributed among these distances:
169 14 0.03
170 82 0.15
171 424 0.76
172 36 0.06
173 4 0.01
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (168 bp):
AGTGACTATAAATAGACTTTTCATGTCAATGAATGACTTTTCTTTCACGTTTCTTAAAGTAGATA
TCAATTATAATATGTTTTAATAAAAAATATAAAAAAATTCAACTTAAAATCAATTATGGATTATA
AAACTATTTAAAACGAGTAATAAGGCTTTCAAAGGCTT
Found at i:1665 original size:342 final size:341
Alignment explanation
Indices: 1106--1909 Score: 766
Period size: 342 Copynumber: 2.4 Consensus size: 341
1096 AGACATTTAG
* * * * * * * * *
1106 TTATAATTTGTTTTAATAAAAAATAAAAAAATATTTAACTTAAAATCGATTATTAGATTATGAAA
1 TTATAATCTGTTTTAACAAAAAATATAAAAA-ATTCAACCTAAAATCAATTATGAGATAATAAAA
* * * * * * * *
1171 CTATTTACAACGAGTAATAAGGC-TTCCAAAGGCTTGAGAGACTATAAATAGACTTTTC--GTCC
65 CCATTTAAAACAAGTAATAAGGCTTTTCAAA-GCATGGGTGACTATAAATGGACTTTTCTTGT-C
* * * * * * ** *
1233 TAATGCAT-GAC-TTTTCTTTTACGTTT-TCAAAGTTAGATATCAAATTATAATATCTTTCAATA
128 -AATGAATAG-CTTTTTC-TTCATGTTTCT-AGAGGTAGACATTGAATTATAATATCTTTCAACA
* * **
1295 AAAAATATAAAAAAATTCAACTTAAAATCAATTATCG-GATTATAAAACAATTAAAAGTGAGTAA
189 AAAAATATAAAAAAATTCAACCTAAAATCAATTAT-GAGATTATAAAACAATAAAAAGAAAGTAA
* * ** * * **
1359 TAA-GGCTTTCAAAGGCTTACGTGACTATAAATAG-ACTTTTCATGTCA-ATGAATGACTTTTTG
253 TAACGCCTTT-AAAAGAATACGTAACTATAAAT-GCACTTCTCATG-CATATGAATGACTTTTCC
* * * * *
1421 TTCACGTTTCTTGAGGCCAGCATTCAA
315 TTCAAGTTTCCTGAAGCAAACATTCAA
** * *
1448 TTATAATCTGTTTTAGTAAAAAATGTAAAACAATTCAACCTAAAATCAATTATGTGATAATAAAA
1 TTATAATCTGTTTTAACAAAAAATATAAAA-AATTCAACCTAAAATCAATTATGAGATAATAAAA
** *
1513 CTTTTTAAAACAAGTAATAAGGC-TTTCAAAAGCATGGGTGGCTATAAATGGACTTTTCTTGTCA
65 CCATTTAAAACAAGTAATAAGGCTTTTC-AAAGCATGGGTGACTATAAATGGACTTTTCTTGTCA
* * *
1577 ATGAATAGCTTTTTCTTCATGTTTCTAGAGGTAGACATTGAATTATAATATGTTTTAACCAAAAA
129 ATGAATAGCTTTTTCTTCATGTTTCTAGAGGTAGACATTGAATTATAATATCTTTCAACAAAAAA
* * * * *
1642 TGTAAAATAATTTAACCTAAAATCAATTATGAGATTATTAAACGATAAAAAGAAAGTAATAACGC
194 TATAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAACAATAAAAAGAAAGTAATAACGC
** * *
1707 CTTTAAAAGAATGGGTAACTATAAATGCACTTCTCTTGCATATGAATGCCTTTTCCTTCAAGTTT
259 CTTTAAAAGAATACGTAACTATAAATGCACTTCTCATGCATATGAATGACTTTTCCTTCAAGTTT
1772 CCTGAAGCAAACATTCAA
324 CCTGAAGCAAACATTCAA
* * * * *
1790 TTATAATCTGTTTTAACCAGAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATACAAC
1 TTATAATCTGTTTTAACAAAAAATATAAAAAATTCAACCTAAAATCAATTATGAGATAATAAAAC
** * * *
1855 CATTTAACGCAAGTAATAAGGCTTTTCAAGGCTTGGGTGACTATAAATGTACTTT
66 CATTTAAAACAAGTAATAAGGCTTTTCAAAGCATGGGTGACTATAAATGGACTTT
1910 CCTTACCAAT
Statistics
Matches: 375, Mismatches: 75, Indels: 25
0.79 0.16 0.05
Matches are distributed among these distances:
341 77 0.21
342 279 0.74
343 17 0.05
344 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (341 bp):
TTATAATCTGTTTTAACAAAAAATATAAAAAATTCAACCTAAAATCAATTATGAGATAATAAAAC
CATTTAAAACAAGTAATAAGGCTTTTCAAAGCATGGGTGACTATAAATGGACTTTTCTTGTCAAT
GAATAGCTTTTTCTTCATGTTTCTAGAGGTAGACATTGAATTATAATATCTTTCAACAAAAAATA
TAAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAACAATAAAAAGAAAGTAATAACGCCT
TTAAAAGAATACGTAACTATAAATGCACTTCTCATGCATATGAATGACTTTTCCTTCAAGTTTCC
TGAAGCAAACATTCAA
Found at i:1900 original size:170 final size:169
Alignment explanation
Indices: 1295--1909 Score: 623
Period size: 171 Copynumber: 3.6 Consensus size: 169
1285 TCTTTCAATA
* * **
1295 AAAAATATAAAAAAATTCAACTTAAAATCAATTATCG-GATTATAAAACAATTAAAAGTGAGTAA
1 AAAAATATAAAACAATTCAACCTAAAATCAATTAT-GAGATTATAAAACAATTAAAAGCAAGTAA
* * ** * *
1359 TAAGGCTTTCAAAGGCTTACGTGACTATAAATAGACTTTTCATGTCAATGAATGACTTTTTGTTC
65 TAAGGCTTTCAAAAGCATGGGTGACTATAAAT-GACTTTTCTTGTCAATGAATG-CTTTTTCTTC
* * * * ***
1424 ACGTTTCTTGAGGCCAGCATTCAATTATAATCTGTTTTAGTA
128 AAGTTTCCTGAGGCAAACATTCAATTATAATCTGTTTTAACC
* * * **
1466 AAAAATGTAAAACAATTCAACCTAAAATCAATTATGTGATAATAAAACTTTTTAAAA-CAAGTAA
1 AAAAATATAAAACAATTCAACCTAAAATCAATTATGAGATTATAAAAC-AATTAAAAGCAAGTAA
*
1530 TAAGGCTTTCAAAAGCATGGGTGGCTATAAATGGACTTTTCTTGTCAATGAATAGCTTTTTCTTC
65 TAAGGCTTTCAAAAGCATGGGTGACTATAAAT-GACTTTTCTTGTCAATGAAT-GCTTTTTCTTC
* * * * *
1595 ATGTTT-CTAGAGGTAGACATTGAATTATAATATGTTTTAACC
128 AAGTTTCCT-GAGGCAAACATTCAATTATAATCTGTTTTAACC
* * * * * * *
1637 AAAAATGTAAAATAATTTAACCTAAAATCAATTATGAGATTATTAAACGATAAAAAGAAAGTAAT
1 AAAAATATAAAACAATTCAACCTAAAATCAATTATGAGATTATAAAACAATTAAAAGCAAGTAAT
* * * * *
1702 AACGCCTTT-AAAAGAATGGGTAACTATAAATGCACTTCTCTTG-CATATGAATGCCTTTTCCTT
66 AA-GGCTTTCAAAAGCATGGGTGACTATAAATG-ACTTTTCTTGTCA-ATGAATG-CTTTTTCTT
*
1765 CAAGTTTCCTGAAGCAAACATTCAATTATAATCTGTTTTAACC
127 CAAGTTTCCTGAGGCAAACATTCAATTATAATCTGTTTTAACC
* * * * * *
1808 AGAAATATAAAA-AATTCAACTTAAAATCAATTATGAGATTATACAACCATTTAACGCAAGTAAT
1 AAAAATATAAAACAATTCAACCTAAAATCAATTATGAGATTATAAAACAATTAAAAGCAAGTAAT
* *
1872 AAGGCTTTTC-AAGGCTTGGGTGACTATAAATGTACTTT
66 AAGGC-TTTCAAAAGCATGGGTGACTATAAATG-ACTTT
1910 CCTTACCAAT
Statistics
Matches: 366, Mismatches: 66, Indels: 25
0.80 0.14 0.05
Matches are distributed among these distances:
169 2 0.01
170 81 0.22
171 269 0.73
172 14 0.04
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (169 bp):
AAAAATATAAAACAATTCAACCTAAAATCAATTATGAGATTATAAAACAATTAAAAGCAAGTAAT
AAGGCTTTCAAAAGCATGGGTGACTATAAATGACTTTTCTTGTCAATGAATGCTTTTTCTTCAAG
TTTCCTGAGGCAAACATTCAATTATAATCTGTTTTAACC
Done.