Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402971.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_633.0, 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: 17548
ACGTcount: A:0.25, C:0.07, G:0.08, T:0.23
Warning! 6479 characters in sequence are not A, C, G, or T
Found at i:6625 original size:172 final size:161
Alignment explanation
Indices: 6321--6786 Score: 344
Period size: 171 Copynumber: 2.8 Consensus size: 161
6311 NNNNNNNNNN
* * * * * * *
6321 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGATTATAAATGGACCTTTCTTACCAATGAATG
1 AAAGCGAGTAATAAGACTTTTGAAGGAATGAGAGATTATAAATAGACCTTTCTTACCAATAAATA
* * * *
6386 CCTTTCTCTTCACGTTTCATGAGGTAGATATTCAATTATAATCTGTTTTAACAAAAAATGTAAAA
66 CCTTTCTCTTCACGTTTCACGAGGTAGAAATTCAATTATAATATGTTTTAACAAAAAAAG-AAAA
6451 AAAATTGAATTTANNNNNNNNNNTGAGAATATAAAATCATTT
130 AAAATTGAATTTA----------TGAGAATATAAAATCATTT
* * *
6493 AAAGCGAGTAATAAGACTTTTGAAGGAATGAGAGATTATAAATAGACTTTTCTTGCCACTAAATA
1 AAAGCGAGTAATAAGACTTTTGAAGGAATGAGAGATTATAAATAGACCTTTCTTACCAATAAATA
* * * * * *
6558 CCTTT-TGGTTTATGTTTCCCGATGTAGAAATTCAATTATAATATGTTTTAATAAAAAAAGAAAA
66 CCTTTCT-CTTCACGTTTCACGAGGTAGAAATTCAATTATAATATGTTTTAACAAAAAAAGAAAA
* * *
6622 AAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCGTTT
130 AAAATTGAA-TT----T--A---TGAGAATATAAAATCATTT
* * * * * * * *
6664 AAAGTGACTAATAAGGCTTTTGAAGGAGTGGGTGATTATAAATAGA-CTTTTTTGACCAATGAAT
1 AAAGCGAGTAATAAGACTTTTGAAGGAATGAGAGATTATAAATAGACCTTTCTT-ACCAATAAAT
** * * ** * *
6728 GTCTTTCTGTTCACGTTTTATAAGGTAGACATTCAATTATAA-ACTGTTTTAACGAAAAA
65 ACCTTTCTCTTCACGTTTCACGAGGTAGAAATTCAATTATAATA-TGTTTTAACAAAAAA
6787 TATAAAACAA
Statistics
Matches: 234, Mismatches: 49, Indels: 23
0.76 0.16 0.08
Matches are distributed among these distances:
170 6 0.03
171 120 0.51
172 106 0.45
176 1 0.00
178 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.34
Consensus pattern (161 bp):
AAAGCGAGTAATAAGACTTTTGAAGGAATGAGAGATTATAAATAGACCTTTCTTACCAATAAATA
CCTTTCTCTTCACGTTTCACGAGGTAGAAATTCAATTATAATATGTTTTAACAAAAAAAGAAAAA
AAATTGAATTTATGAGAATATAAAATCATTT
Found at i:6703 original size:171 final size:171
Alignment explanation
Indices: 6321--6998 Score: 606
Period size: 172 Copynumber: 3.9 Consensus size: 171
6311 NNNNNNNNNN
* * *
6321 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGATTATAAATGGACCTTTCTTACCAATGAATG
1 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGATTATAAATAGACTTTTCTTGCCAATGAATG
* * * *
6386 CCTTTCTCTTCACGTTTCATGAGGTAGATATTCAATTATAATCTGTTTTAACAAAAAATGTAAAA
66 CCTTTCTGTTCACGTTTCATGAGGTAGAAATTCAATTATAATATGTTTTAACAAAAAAAG-AAAA
* ********** * *
6451 AAAATTGAATTTANNNNNNNNNNTGAGAATATAAAATCATTT
130 AAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTT
* * * * * * *
6493 AAAGCGAGTAATAAGACTTTTGAAGGAATGAGAGATTATAAATAGACTTTTCTTGCCACTAAATA
1 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGATTATAAATAGACTTTTCTTGCCAATGAATG
* * ** * *
6558 CCTTT-TGGTTTATGTTTCCCGATGTAGAAATTCAATTATAATATGTTTTAATAAAAAAAGAAAA
66 CCTTTCT-GTTCACGTTTCATGAGGTAGAAATTCAATTATAATATGTTTTAACAAAAAAAGAAAA
*
6622 AAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCGTTT
130 AAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTT
* *
6664 AAAGTGACTAATAAGGCTTTTGAAGGAGTGGGTGATTATAAATAGACTTTT-TTGACCAATGAAT
1 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGATTATAAATAGACTTTTCTTG-CCAATGAAT
* * * * * *
6728 GTCTTTCTGTTCACGTTTTATAAGGTAGACATTCAATTATAA-ACTGTTTTAACGAAAAATATAA
65 GCCTTTCTGTTCACGTTTCATGAGGTAGAAATTCAATTATAATA-TGTTTTAAC-AAAAAAAGAA
* * *
6792 AACAAATTAAACTTAAAATCGATTTTGAGATTATAAAACCATTT
128 AAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTT
*********** *** * * **
6836 AAAGCNNNNNNNNNNGCTTTTGAAGGAATGAAAGACTATAAATAGACTTTTTTTTATCAATGAAT
1 AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGATTATAAATAGAC-TTTTCTTGCCAATGAAT
* * ** * * * * *
6901 GCCTTTCTCTTCACGTTTCATAAAATAGACATTTAATTATAATCTGTTTTAATAAAAAATATAAA
65 GCCTTTCTGTTCACGTTTCATGAGGTAGAAATTCAATTATAATATGTTTTAACAAAAAA-AGAAA
* *
6966 AAAAATTAAACTTAAAATCGATTTTGAGATTAT
129 AAAAATTGAACTTAAAATCAATTTTGAGATTAT
6999 NNNNNNNNNN
Statistics
Matches: 410, Mismatches: 87, Indels: 17
0.80 0.17 0.03
Matches are distributed among these distances:
170 4 0.01
171 123 0.30
172 188 0.46
173 93 0.23
174 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.35
Consensus pattern (171 bp):
AAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGATTATAAATAGACTTTTCTTGCCAATGAATG
CCTTTCTGTTCACGTTTCATGAGGTAGAAATTCAATTATAATATGTTTTAACAAAAAAAGAAAAA
AAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTT
Found at i:9595 original size:173 final size:172
Alignment explanation
Indices: 9272--9640 Score: 492
Period size: 173 Copynumber: 2.1 Consensus size: 172
9262 NNNNNNNNNN
* * * **
9272 ACATTCAATTATAATTTGTTTTAACAAAAAATATAAAAACAATTAAACTTAAAATTGATTCTGAG
1 ACATTCAATTATAATCTGTTTCAACAAAAAATATAAAAAAAATTAAACTTAAAATCAATTCTGAG
* *
9337 ATTATAAAACTATTTAAAGCGAACAATAAGGCTTTGGAAGAAATGAGTGACTGTAAATGGACTAT
66 ATTATAAAACTATTTAAAGCGAACAATAAGGCTTTGGAAGAAATGAGTGACTATAAATAGACTAT
* * * * *
9402 TCTTGTCAATGAATGCCTTTCTCTTCACGTTTCATAAGGTAA
131 TCTTGCCAATAAAAGCCTTTCTCATCACGTTTCATAAGGCAA
*
9444 ACATTCAATTATAATCTGTTTCAACAAAAAATATTAAAAAAAATTAAACTTCAAATCAATT-TGG
1 ACATTCAATTATAATCTGTTTCAACAAAAAATA-TAAAAAAAATTAAACTTAAAATCAATTCT-G
* * * *
9508 AGATTATAAAACTATTTAAAATC-AGCAATAAGGCTTTTGAAGGAAT-AGGTGACTATAAATAGA
64 AGATTATAAAACTATTT-AAAGCGAACAATAAGGCTTTGGAAGAAATGA-GTGACTATAAATAGA
* * * *
9571 CTTTTCTTGCCAATAAAAGCCTTTCTCATCATGTTTCATGAGGCAG
127 CTATTCTTGCCAATAAAAGCCTTTCTCATCACGTTTCATAAGGCAA
9617 ACATTCAATTATAATCTGTTTCAA
1 ACATTCAATTATAATCTGTTTCAA
9641 NNNNNNNNNN
Statistics
Matches: 172, Mismatches: 21, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
172 33 0.19
173 135 0.78
174 4 0.02
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (172 bp):
ACATTCAATTATAATCTGTTTCAACAAAAAATATAAAAAAAATTAAACTTAAAATCAATTCTGAG
ATTATAAAACTATTTAAAGCGAACAATAAGGCTTTGGAAGAAATGAGTGACTATAAATAGACTAT
TCTTGCCAATAAAAGCCTTTCTCATCACGTTTCATAAGGCAA
Found at i:10390 original size:172 final size:170
Alignment explanation
Indices: 10030--10551 Score: 446
Period size: 171 Copynumber: 3.0 Consensus size: 170
10020 NNNNNNNNNN
* * * * *
10030 TTTCATGAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATTAAAAAAATT-GGACTTC
1 TTTCATGAAGTAGACATTCAATTATAATCTGTTTCAATAAAAAATA-TAAAAAAATTAAG-CTTA
* * * * *
10094 AAATCAATTTGGAGA-TATAAAACTATTTAAAGTGAGTAATAAGGTTTTTGAAGGAATAG-GTA-
64 AAATCAATTTTGAGATTATAAAACTATTTAAAGCGAGTAATAAGG-CTTTGAA-AAAAAGAG-AG
* ********** ** *
10156 ACTATAAATAGACTTTTCTTGCCNNNNNNNNNNTTTCTCATCATG
126 ACTATAAATAGACTTTTCTAGCCAATGAATGCCTTTCTTTTCACG
* *
10201 TTTCAT-AAGGCAGACATTCAATTATAATCTGTTTCAATAAAAAATATAAAAAAAGTTAAGTTTA
1 TTTCATGAA-GTAGACATTCAATTATAATCTGTTTCAATAAAAAATATAAAAAAA-TTAAGCTTA
10265 AAATCAATTTTGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTGAAAACAAAGAGAGAC
64 AAATCAATTTTGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTGAAAA-AAAGAGAGAC
*
10330 TATAAATAGACTTTTCTAGCCAATGAATGCCTTTCTTTTCACA
128 TATAAATAGACTTTTCTAGCCAATGAATGCCTTTCTTTTCACG
* ********** *
10373 TTTCATGAAGTAGACATTCAATTATAATATGTTTNNNNNNNNNNTATAAAAAAAATTAAACTTAA
1 TTTCATGAAGTAGACATTCAATTATAATCTGTTTCAATAAAAAATAT-AAAAAAATTAAGCTTAA
* * ** ** * *
10438 AATCAA-TTTGAGATTATAAAGCTATTTAAAGCTAACAATAAGGCTTTTGAAGGAATGAGAGACC
65 AATCAATTTTGAGATTATAAAACTATTTAAAGCGAGTAATAAGGC-TTTGAAAAAAAGAGAGACT
* * *
10502 ATAAATGGATTTTTCTTA-CCAATGAATGCCTTTTTTTTCACG
129 ATAAATAGACTTTTC-TAGCCAATGAATGCCTTTCTTTTCACG
10544 TTTCATGA
1 TTTCATGA
10552 GGTANNNNNN
Statistics
Matches: 287, Mismatches: 53, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
170 10 0.03
171 154 0.54
172 114 0.40
173 9 0.03
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.34
Consensus pattern (170 bp):
TTTCATGAAGTAGACATTCAATTATAATCTGTTTCAATAAAAAATATAAAAAAATTAAGCTTAAA
ATCAATTTTGAGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTGAAAAAAAGAGAGACTAT
AAATAGACTTTTCTAGCCAATGAATGCCTTTCTTTTCACG
Found at i:10957 original size:172 final size:162
Alignment explanation
Indices: 10663--10997 Score: 381
Period size: 172 Copynumber: 2.0 Consensus size: 162
10653 NNNCCTTATT
* * * *
10663 ACTCGCTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAATTCAAATTTTTTTATATTTTTTG
1 ACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTGAAATTCAAATTTTTTTATAATTTTTA
* * * * *
10728 TTGAAACAGATTATAATTGAATATCTGCCTCATGAAACATGATAAGAAAGGCATTCATTGGCAAG
66 TTAAAACAGATAATAATTGAATATCTACCTCATGAAACATGATAAGAAAGACATTCATTGGCAAA
*
10793 AAAAGTCTATTTATAGT-TAC-CTATTCCTTCAA
131 AAAAGTCCATTTATAGTCT-CTC-ATTCCTTCAA
* *
10825 ANNNNNNNNNNCTCACTTTAAATAGTTTTATAATCTCCAAATTGATTTGAAGTTC-AATTTTTTT
1 A----------CTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTGAAATTCAAATTTTTTT
* * *
10889 AATAATTTTTATTAAAACAGATAATAATTGAATGTTTACCTCATGAAACGTGA-AGAGAAAGACA
56 -ATAATTTTTATTAAAACAGATAATAATTGAATATCTACCTCATGAAACATGATA-AGAAAGACA
10953 TTCATTGGCAAAAAAAGTCCATTTATAGTCTCTCATTCCTTCAA
119 TTCATTGGCAAAAAAAGTCCATTTATAGTCTCTCATTCCTTCAA
10997 A
1 A
10998 AGCCTTATNN
Statistics
Matches: 144, Mismatches: 15, Indels: 18
0.81 0.08 0.10
Matches are distributed among these distances:
162 1 0.01
171 10 0.07
172 131 0.91
173 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.38
Consensus pattern (162 bp):
ACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTGAAATTCAAATTTTTTTATAATTTTTA
TTAAAACAGATAATAATTGAATATCTACCTCATGAAACATGATAAGAAAGACATTCATTGGCAAA
AAAAGTCCATTTATAGTCTCTCATTCCTTCAA
Found at i:12634 original size:172 final size:172
Alignment explanation
Indices: 12185--12845 Score: 453
Period size: 172 Copynumber: 3.8 Consensus size: 172
12175 NNGTTTTAAT
* * * * * *
12185 AAAAAATGTAAAAAAAATTAAACTTAAAATCGATTTTGAAATTATAGAACTATTTAAAGCGAACA
1 AAAAAATATAAAAAAAATTAAACTTAAAATCAATTTTGAGATTATAAAACAATTTAAAGCGAAGA
* ** * ********** *
12250 ATAAGGCTTTTGAAGGAATGAGAGACTATANNNNNNNNNNTCTTGCCAATGAATGTCTTTCTCTT
66 ATAAGGCTTTTAAAACAAAGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTCTCTT
* * * * * *
12315 CACGTTTTATCAGGTAAACATTCAATTATAATCTGTTTTAAT
131 CATGTTTCATGAGGCAAACATTCAATTATAATCTGTTTCAAC
* * * * * * *
12357 AAAAAATATTAAAACAGATTGAACTTCAAATCAATTTGGAGATTATAAAACTATTTAAAGTG-AG
1 AAAAAATA-TAAAAAAAATTAAACTTAAAATCAATTTTGAGATTATAAAACAATTTAAAGCGAAG
**********************
12421 TAATAAGNNNNNNNNNNNNNNNNNNNNNNATAAATAGACTTTTCTTGCCAATGAATGCCTTTCTC
65 -AATAAGGCTTTTAAAACAAAGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTCTC
* *
12486 ATCATGTTTCATGAGGCACACATTCAATTATAATCTGTTTCAAC
129 TTCATGTTTCATGAGGCAAACATTCAATTATAATCTGTTTCAAC
**********
12530 AAAAAATATAAAAAAANNNNNNNNNNAAATCAATTTTGAGATTATAAAACAATTTAAAGCG-AGT
1 AAAAAATATAAAAAAAATTAAACTTAAAATCAATTTTGAGATTATAAAACAATTTAAAGCGAAG-
* * *
12594 AATAGGGCTTTTAAAACAAAGAGAGACTATAAATAGACTTTTCTAGCCAATGAATACCTTTCTCT
65 AATAAGGCTTTTAAAACAAAGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTCTCT
* * * ** *
12659 TCATGTTTCATGATGTAAACATTTAATTATAATCTGTTTTGAT
130 TCATGTTTCATGAGGCAAACATTCAATTATAATCTGTTTCAAC
* * * * *
12702 AAAAAATGTAAAAAAAATTAAACTTAAAATCGATTTTGAGATTATAAACCTATTTAATGCGAAGA
1 AAAAAATATAAAAAAAATTAAACTTAAAATCAATTTTGAGATTATAAAACAATTTAAAGCGAAGA
* ** * * * * * *
12767 ATAAGGCTTTTGAAGGAATGAGAGACTATAAATGGATTTTTCTTACCAATGAATGCCTTTTTTTT
66 ATAAGGCTTTTAAAACAAAGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTCTCTT
*
12832 CACGTTTCATGAGG
131 CATGTTTCATGAGG
12846 TANNNNNNNN
Statistics
Matches: 357, Mismatches: 129, Indels: 6
0.73 0.26 0.01
Matches are distributed among these distances:
172 236 0.66
173 121 0.34
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.32
Consensus pattern (172 bp):
AAAAAATATAAAAAAAATTAAACTTAAAATCAATTTTGAGATTATAAAACAATTTAAAGCGAAGA
ATAAGGCTTTTAAAACAAAGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTCTCTT
CATGTTTCATGAGGCAAACATTCAATTATAATCTGTTTCAAC
Done.