Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400716.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3897.0, 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: 3301
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.27
Warning! 866 characters in sequence are not A, C, G, or T
Found at i:703 original size:33 final size:33
Alignment explanation
Indices: 655--724 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
645 AAAATTATAA
* *
655 AAAAATTTAACTTAAAACCAATTATGAGTTTAC
1 AAAAATTCAACTTAAAACCAATTATGAGATTAC
* * *
688 AAAAATTCAATTTAAAATCAATTATGAGATTAT
1 AAAAATTCAACTTAAAACCAATTATGAGATTAC
721 AAAA
1 AAAA
725 CCATTTNNNN
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.33
Consensus pattern (33 bp):
AAAAATTCAACTTAAAACCAATTATGAGATTAC
Found at i:986 original size:170 final size:169
Alignment explanation
Indices: 741--2190 Score: 1311
Period size: 171 Copynumber: 8.5 Consensus size: 169
731 NNNNNNNNNN
** * * *
741 ATAAGGCTTTCGAAGACATGGGTGACTATAAATAGACTTTTCTTACCAATTG-ATATCTTTTCCT
1 ATAAGGCTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTT-TCAA-TGAATATCTTTTTCT
* * * * *
805 TCACATTTCTCTAGGCAGATATTCAATTATAATCTATTTTAATAAAAAATATAAAAAACTCAACC
64 TCACGTTTCTCTAGGCAGACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAATTCAACT
* * ** *
870 TAAAATCAATTATGAGGTTATAAAAACATTTGTAGCGAGAA
129 TAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTA
*
911 ATAAGGCTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTCATCAATGAATATCTTTTTCTT
1 ATAAGGCTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCT-TTCAATGAATATCTTTTTCTT
* * *
976 CACGTTTCTCTAGGCAAATATTCAATTATAATCT-TTTTAA-ATAAAAATGTAAAAAAATTCAAC
65 CACGTTTCTCTAGGCAGACATTCAATTATAATCTGTTTTAATA-AAAAATAT-AAAAAATTCAAC
* * * * * * *
1039 TTTAAATCAATTAGGAGGTTCTGAAATCATTTAATGCAAGTA
128 TTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTA
* * * * *
1081 ATAAGGCTTCCGAAGGCATGGGTAACGATTAATGGACTTTTCTTGTCAAT-AGATATCTTTTTTT
1 ATAAGGCTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTT-TCAATGA-ATATC--TTTTT
* * * * * *
1145 TTTCACGTTTCT-TGAGGTAAACATTCAATTATAATATGTTTGAATAAAAAATATAAAAAAATTT
62 CTTCACGTTTCTCT-AGGCAGACATTCAATTATAATCTGTTTTAATAAAAAATAT-AAAAAATTC
* * * * * *
1209 AACTTAAAACCAATTATAAGGTTATAAAAACAATTAAGGCGAGTA
125 AACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTA
* * * *
1254 ATAAGGCTTTCGAAGGTATAGGTGACTATAAATGAACTTTTCTTACCAATGGATATCTTTTTCTT
1 ATAAGGCTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTT-TCAATGAATATCTTTTTCTT
* ** * *
1319 TATATTT-T-TAGAGACAGACATTCAATTATAATATGTTTTAATAAAAAATATAAAAAAATTTAA
65 CACGTTTCTCTAG-G-CAGACATTCAATTATAATCTGTTTTAATAAAAAATAT-AAAAAATTCAA
* * * *
1382 CTTAGAACCAATTATGAGATTACAAAACCATTTAAAGCGAGTA
127 CTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTA
* * * * * * * * * *
1425 ATAACGCTTCCGAAAGCATAGGTGAGTATCAATTGACTTTTCTTGTCAATGGATATCTTTCTCTT
1 ATAAGGCTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTT-TCAATGAATATCTTTTTCTT
* * * *
1490 TACGTTTCT-TGAGGTAGACATTCAATTGTAATATGTTTTAATAAAAAATATAAAATAATTCAAC
65 CACGTTTCTCT-AGGCAGACATTCAATTATAATCTGTTTTAATAAAAAATATAAAA-AATTCAAC
* * *
1554 TTAAAATCAATTATGAGATTATAAACTCATTTCAACCGAGTA
128 TTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTA
* * * * * **
1596 ATAAGGCTTTCAAATGTATAGGTGACTATAAATGGACCTTTCTTGCAAATGAATGGCTTTTTCTT
1 ATAAGGCTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTTTC-AATGAATATCTTTTTCTT
** * * * ** * * *** * *
1661 CGTGTTTTTC-ATGACAAACATTCAATTATTTTTTCTTTTACCCAAAAATGTAAAAAAATCCAAC
65 CACGTTTCTCTA-GGCAGACATTCAATTATAATCTGTTTTAATAAAAAATAT-AAAAAATTCAAC
* * * * *
1725 GTAAAATCATTTATGAGATTACAAAATTATTTAAAGTGAGTA
128 TTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTA
** * * * * * * *
1767 ATAAGGCTTTTAAAGGTATGGGTAATTATAAGTAGAGTTTTCTTGCAATGAACATCTTTTTCTTC
1 ATAAGGCTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTTTCAATGAATATCTTTTTCTTC
* ** * * * * * * * *
1832 ACGTTTCTCGAGAAAGGCATTCAATTTTTACCTATTTTAATATAAAATATATAAAATTCTACTTA
66 ACGTTTCTCTAGGCAGACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAATTCAACTTA
* * *
1897 AAGTCAATTATGAGATTATAAAAACATTTAAAGCTAGTA
131 AAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTA
* * * * *
1936 ATAAGGCTTTCGAAGGCATGTGTGACTATAAATGAACTTTTCTTGCGAATGGATATAC-TTTTCT
1 ATAAGGCTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTTTC-AATGAATAT-CTTTTTCT
* * * * *
2000 TCAAGTTTATCGAGGCAGACATTCAATTACAATCTGTTTTAATAAAAAATATAGAAAAATTTAAC
64 TCACGTTTCTCTAGGCAGACATTCAATTATAATCTGTTTTAATAAAAAATATA-AAAAATTCAAC
* *
2065 TTAAAATCAATTATGATG-TTATAATATCATTTAAAGCGATTA
128 TTAAAATCAATTATGA-GATTATAAAATCATTTAAAGCGAGTA
* * * * *
2107 ATAAGGCTTTCAAAGGTATGGGTGACTATGAATGAACTTTTCTTGCCAATGGATATCTTTTTCTT
1 ATAAGGCTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTT-TCAATGAATATCTTTTTCTT
* * *
2172 CATGTTTCTCAAGGTAGAC
65 CACGTTTCTCTAGGCAGAC
2191 NNNNNNNNNN
Statistics
Matches: 1043, Mismatches: 209, Indels: 55
0.80 0.16 0.04
Matches are distributed among these distances:
168 1 0.00
169 97 0.09
170 290 0.28
171 505 0.48
172 45 0.04
173 104 0.10
174 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (169 bp):
ATAAGGCTTTCGAAGGTATGGGTGACTATAAATGGACTTTTCTTTCAATGAATATCTTTTTCTTC
ACGTTTCTCTAGGCAGACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAATTCAACTTA
AAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTA
Found at i:2022 original size:511 final size:502
Alignment explanation
Indices: 741--2180 Score: 1397
Period size: 511 Copynumber: 2.8 Consensus size: 502
731 NNNNNNNNNN
* ** * * * *
741 ATAAGGCTTTCGAAGACATGGGTGACTATAAAT-AGACTTTTCTTACCAATTG-ATATCTTTTCC
1 ATAAGGCTTTCAAAGGTATAGGTAACTATAAATGA-ACTTTTCTTACCAA-TGAACATCTTTTTC
** ** * * * *
804 TTCACATTTCTCTAGGCAGATATTCAATTATAATCTATTTTAATAAAAAATATAAAAAACTCAAC
64 TTCACATTTCTAGAGAAAGACATTCAATTATAACCTATTTTAATAAAAAATATAAAAAATTCTA-
* * ** * *
869 CTAAAATCAATTATGAGGTTATAAAAACATTTGTAGCGAGAAATAAGGCTTTCGAAGGTATGGGT
128 CTTAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAGGCAT-GGT
* * * *
934 GACTATAAATGGACTTTTCTCAT-CAATGAATATCTTTTTCTTCACGTTTCTCTAGGCAAATATT
192 GACTATAAAT-GACTTTTCT--TGCAATGGATATC-TTTTCTTCACGTTTCTCGAGGCAGACATT
* * * *
998 CAATTATAATCT-TTTTAA-ATAAAAATGTAAAAAAATTCAACTTTAAATCAATTAGGAGGTTCT
253 CAATTATAATCTGTTTTAATA-AAAAATAT-AAAAAATTCAACTTAAAATCAATTATGA-GTTAT
* * * * * * *
1061 GAAATCATTTAATGCAAGTAATAAGGCTTCCGAAGGCATGGGTAACGATTAATGGACTTTTCTTG
315 -AAATCATTTAA-GCGAGTAATAAGGCTTTCAAAGGTATGGGTGACTATAAATGGACTTTTCTTG
* * * ** * *
1126 TCAAT-AGATATCTTTTTTTTTTCACGTTTCTTGAGGTAAACATTCAATTATAATATGTTTGAAT
378 -CAATGA-ATATC--TTTTTCTTCATGTTTCTTCAGACAAACATTCAATTATAATATCTTTGAAC
** * * * *
1190 AAAAAATATAAAAAAATTTAACTTAAAACCAATTATAAGGTTATAAAAACAATTAAGGCGAGTA
439 AAAAAATATAAAAAAATCCAACGTAAAACCAATTATAAGATTACAAAAACAATTAAAGCGAGTA
* * * *
1254 ATAAGGCTTTCGAAGGTATAGGTGACTATAAATGAACTTTTCTTACCAATGGATATCTTTTTCTT
1 ATAAGGCTTTCAAAGGTATAGGTAACTATAAATGAACTTTTCTTACCAATGAACATCTTTTTCTT
* * * * ** *
1319 TATATTTTTAGAGACAGACATTCAATTATAATATGTTTTAATAAAAAATATAAAAAAATT-TAAC
66 CACATTTCTAGAGAAAGACATTCAATTATAACCTATTTTAATAAAAAATAT-AAAAAATTCT-AC
* * * * * *
1383 TTAGAACCAATTATGAGATTACAAAACCATTTAAAGCGAGTAATAACGCTTCCGAAAGCATAGGT
129 TTA-AATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAGGCAT-GGT
* * * * *
1448 GAGTATCAATTGACTTTTCTTGTCAATGGATATCTTTCTCTTTACGTTTCTTGAGGTAGACATTC
192 GACTAT-AAATGACTTTTCTTG-CAATGGATATCTTT-TCTTCACGTTTCTCGAGGCAGACATTC
* *
1513 AATTGTAATATGTTTTAATAAAAAATATAAAATAATTCAACTTAAAATCAATTATGAGATTATAA
254 AATTATAATCTGTTTTAATAAAAAATATAAAA-AATTCAACTTAAAATCAATTATGAG-TTATAA
* * * *
1578 ACTCATTTCAACCGAGTAATAAGGCTTTCAAATGTATAGGTGACTATAAATGGACCTTTCTTGCA
317 A-TCATTT-AAGCGAGTAATAAGGCTTTCAAAGGTATGGGTGACTATAAATGGACTTTTCTTGC-
** * ** * * * *
1643 AATGAATGGCTTTTTCTTCGTGTTT-TTCATGACAAACATTCAATTATTTTTTCTTTTACCCAAA
379 AATGAATATCTTTTTCTTCATGTTTCTTCA-GACAAACATTCAATTATAATATCTTTGAACAAAA
* * * * ** * *
1707 AATGTAAAAAAATCCAACGTAAAATCATTTATGAGATTACAAAATTATTTAAAGTGAGTA
443 AATATAAAAAAATCCAACGTAAAACCAATTATAAGATTACAAAAACAATTAAAGCGAGTA
* * * * * *
1767 ATAAGGCTTTTAAAGGTATGGGTAATTATAAGT-AGAGTTTTCTT-GCAATGAACATCTTTTTCT
1 ATAAGGCTTTCAAAGGTATAGGTAACTATAAATGA-ACTTTTCTTACCAATGAACATCTTTTTCT
* * * * * * *
1830 TCACGTTTCTCGAGAAAGGCATTCAATTTTTACCTATTTTAATATAAAATATATAAAATTCTACT
65 TCACATTTCTAGAGAAAGACATTCAATTATAACCTATTTTAATAAAAAATATAAAAAATTCTACT
*
1895 TAAAGTCAATTATGAGATTATAAAAACATTTAAAGCTAGTAATAAGGCTTTCGAAGGCATGTGTG
130 TAAA-TCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATG-GTG
* *
1960 ACTATAAATGAACTTTTCTTGCGAATGGATATACTTTTCTTCAAGTTTATCGAGGCAGACATTCA
193 ACTATAAATG-ACTTTTCTTGC-AATGGATAT-CTTTTCTTCACGTTTCTCGAGGCAGACATTCA
* *
2025 ATTACAATCTGTTTTAATAAAAAATATAGAAAAATTTAACTTAAAATCAATTATGATGTTATAAT
255 ATTATAATCTGTTTTAATAAAAAATATA-AAAAATTCAACTTAAAATCAATTATGA-GTTATAA-
* * *
2090 ATCATTTAAAGCGATTAATAAGGCTTTCAAAGGTATGGGTGACTATGAATGAACTTTTCTTGCCA
317 ATCATTT-AAGCGAGTAATAAGGCTTTCAAAGGTATGGGTGACTATAAATGGACTTTTCTTG-CA
*
2155 ATGGATATCTTTTTCTTCATGTTTCT
380 ATGAATATCTTTTTCTTCATGTTTCT
2181 CAAGGTAGAC
Statistics
Matches: 759, Mismatches: 138, Indels: 61
0.79 0.14 0.06
Matches are distributed among these distances:
510 8 0.01
511 237 0.31
512 74 0.10
513 221 0.29
514 121 0.16
515 94 0.12
516 4 0.01
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (502 bp):
ATAAGGCTTTCAAAGGTATAGGTAACTATAAATGAACTTTTCTTACCAATGAACATCTTTTTCTT
CACATTTCTAGAGAAAGACATTCAATTATAACCTATTTTAATAAAAAATATAAAAAATTCTACTT
AAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATAAGGCTTTCGAAGGCATGGTGACT
ATAAATGACTTTTCTTGCAATGGATATCTTTTCTTCACGTTTCTCGAGGCAGACATTCAATTATA
ATCTGTTTTAATAAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGTTATAAATCATTTAA
GCGAGTAATAAGGCTTTCAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCAATGAATATCTT
TTTCTTCATGTTTCTTCAGACAAACATTCAATTATAATATCTTTGAACAAAAAATATAAAAAAAT
CCAACGTAAAACCAATTATAAGATTACAAAAACAATTAAAGCGAGTA
Done.