Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402938.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_599.0, 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: 4933
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.27
Warning! 1345 characters in sequence are not A, C, G, or T
Found at i:1044 original size:171 final size:172
Alignment explanation
Indices: 594--1247 Score: 483
Period size: 171 Copynumber: 3.8 Consensus size: 172
584 NNNNNTTTTG
* * * * * *
594 TTAAAACAGACTATAATTGAATGTCTACCTTGAGACACGTGCA-AAACAATTCATTCATTGAGAA
1 TTAAAACAGACTATAATTGAATGCCTATCTTGAGAAAAGTGTAGAAA-AAGTCATTCATTGAGAA
* * * *
658 AAAAAGTTCATTTATAGTC-ACTTATTCCTTTAAAAGCCTTATTA-TCCGCTATAAATGGTTTTA
65 AAAAAGTCCATTTATAGTCAAC-CATTCCTTTAAAAGGCTTATTACTCCGCTATAAATGATTTTA
* * * *
721 TAATTTCATAATTGATTTTAAGTTGAAATTTTTTATATTTTTCT
129 TAATCTCATAATTGATTGTAAGTTGAAATTTTCTACATTTTTCT
* * * * * *
765 TTAAAACAGACTATAATTGAATGCCTAGGTC-AG-GAAATGTATTGAAAAAGTCCTTCATTGATA
1 TTAAAACAGACTATAATTGAATGCCTA--TCTTGAGAAAAGTGTAGAAAAAGTCATTCATTGAGA
* * * * * * * *
828 AGAAAAA-TCTATTTTTAGTCATCCATTCTTTTGAAA-GCTTTATTACT-TGGTTTAAATGATTT
64 A-AAAAAGTCCATTTATAGTCAACCATTCCTTTAAAAGGC-TTATTACTCCGCTATAAATGATTT
*
890 TATAATCTCATAATTGATTGTAAGTTGAACTTTTCTACATTTTTCT
127 TATAATCTCATAATTGATTGTAAGTTGAAATTTTCTACATTTTTCT
* *
936 TTAAAATAGA-TAATAATTGAATGCCTATCTTGAGAAAAGTGTAGAAAAAGTCATTGATTGAGAA
1 TTAAAACAGACT-ATAATTGAATGCCTATCTTGAGAAAAGTGTAGAAAAAGTCATTCATTGAGAA
* * * * * * *
1000 AAAAAGTCCGTTTATAGTCAACCACTCCTTCAAAAGGCTTATTACT-CACTTTGAAT-AGTTTTN
65 AAAAAGTCCATTTATAGTCAACCATTCCTTTAAAAGGCTTATTACTCCGCTATAAATGA-TTTTA
********* * * **
1063 NNNNNNNNNAATTGATTTTAAGTT-AAATTTTTTTACATTTTTGA
129 TAATCTCATAATTGATTGTAAGTTGAAA-TTTTCTACATTTTTCT
* * * ** * * * * * *
1107 TTACAATATACTATAATTGAATGTTTACCTTGAGACACGTGAAGAAACAAG-CATTCATTGATAG
1 TTAAAACAGACTATAATTGAATGCCTATCTTGAGAAAAGTGTAGAAA-AAGTCATTCATTGAGAA
* * * * * * *
1171 AAAAAGTCTATTTAGAGTC-ACCTATTCCTTCAAAAAGCTTATTACT-CTCTTTAAATGGTTTTA
65 AAAAAGTCCATTTATAGTCAACC-ATTCCTTTAAAAGGCTTATTACTCCGCTATAAATGATTTTA
1234 TAATCTCATAATTG
129 TAATCTCATAATTG
1248 NNNNNNNNNN
Statistics
Matches: 373, Mismatches: 92, Indels: 36
0.74 0.18 0.07
Matches are distributed among these distances:
169 2 0.01
170 14 0.04
171 339 0.91
172 17 0.05
173 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.39
Consensus pattern (172 bp):
TTAAAACAGACTATAATTGAATGCCTATCTTGAGAAAAGTGTAGAAAAAGTCATTCATTGAGAAA
AAAAGTCCATTTATAGTCAACCATTCCTTTAAAAGGCTTATTACTCCGCTATAAATGATTTTATA
ATCTCATAATTGATTGTAAGTTGAAATTTTCTACATTTTTCT
Found at i:1695 original size:171 final size:171
Alignment explanation
Indices: 1385--1751 Score: 463
Period size: 171 Copynumber: 2.1 Consensus size: 171
1375 TCTATTTAGA
* *
1385 GTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTAATATAGTTTTATAATCTCAAAATTGATTA
1 GTCACCCATTCCTTCAAAAGGCTTATTACCCGCTTAATATAGTTTAATAATCTCAAAATTGATTA
* * * * *
1450 TAAGTTGAATTTTTTTATATTTTTTGTTAAAACAGACTATAATTAATTGTCTGCCTCAGGAAACA
66 TAAGTAGAATTTTTTTAAATTTTTTGTTAAAACAGACTATAATTAATTGCCTACCTCAGGAAAAA
**
1515 TCCAGAAAAAGCCATTCATTGAGAAGAAAGGTCCATTTATG
131 TCCAGAAAAAGCCATTCATTGAGAAGAAAAATCCATTTATG
* * * *
1556 GTCACTCATTTCTTCAAAAGTCTTATTACCCGCTTTAA-ATGGTTTAATAATCTCATAAA-TGAT
1 GTCACCCATTCCTTCAAAAGGCTTATTACCCGC-TTAATATAGTTTAATAATCTCA-AAATTGAT
* *
1619 TTTAAGTAGAATTTTTTTAAATTTTTTTTTAAAACAGACTATAATTGAA-TGCCTACCTCA-GAA
64 TATAAGTAGAATTTTTTTAAATTTTTTGTTAAAACAGACTATAATT-AATTGCCTACCTCAGGAA
** * *
1682 AAAGTGTAGAAAAAGCCATTCATTGAGAAGAAAAATCCATTTTTA
128 AAA-TCCAGAAAAAGCCATTCATTGAGAAGAAAAATCCATTTATG
* * * *
1727 CTCACCCATTCTTTCGAAAGACTTA
1 GTCACCCATTCCTTCAAAAGGCTTA
1752 NNNNNNNNNN
Statistics
Matches: 167, Mismatches: 25, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
170 5 0.03
171 153 0.92
172 9 0.05
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (171 bp):
GTCACCCATTCCTTCAAAAGGCTTATTACCCGCTTAATATAGTTTAATAATCTCAAAATTGATTA
TAAGTAGAATTTTTTTAAATTTTTTGTTAAAACAGACTATAATTAATTGCCTACCTCAGGAAAAA
TCCAGAAAAAGCCATTCATTGAGAAGAAAAATCCATTTATG
Found at i:1779 original size:171 final size:171
Alignment explanation
Indices: 1386--1872 Score: 459
Period size: 171 Copynumber: 2.8 Consensus size: 171
1376 CTATTTAGAG
* * *
1386 TCACCCATTCCTTCAAAAGGCTTATTACTCGC-TTAATAT-AGTTTTATAATCTCA-AAATTGAT
1 TCACCCATTTCTTCAAAAGACTTATTACCCGCTTTAA-ATGA-TTTTATAATCTCATAAA-TGAT
* * * * *
1448 TATAAGTTGAATTTTTTTATATTTTTTGTTAAAACAGACTATAATT-AATTGTCTGCCTCAGGAA
63 TTTAAGTAGAATTTTTTTAAATTTTTTTTTAAAACAGACTATAATTGAA-TGTCTACCTCA-GAA
* ** ** **
1512 ACA-TCCAGAAAAAGCCATTCATTGAGAAGAAAGGTCCATTTATGG
126 AAAGTATAGAAAAAGCCATTCATTGAGAAGAAAAATCCATTTATAC
* * * *
1557 TCACTCATTTCTTCAAAAGTCTTATTACCCGCTTTAAATGGTTTAATAATCTCATAAATGATTTT
1 TCACCCATTTCTTCAAAAGACTTATTACCCGCTTTAAATGATTTTATAATCTCATAAATGATTTT
*
1622 AAGTAGAATTTTTTTAAATTTTTTTTTAAAACAGACTATAATTGAATGCCTACCTCAGAAAAAGT
66 AAGTAGAATTTTTTTAAATTTTTTTTTAAAACAGACTATAATTGAATGTCTACCTCAGAAAAAGT
* *
1687 GTAGAAAAAGCCATTCATTGAGAAGAAAAATCCATTTTTAC
131 ATAGAAAAAGCCATTCATTGAGAAGAAAAATCCATTTATAC
* ********** * *
1728 TCACCCA-TTCTTTCGAAAGACTTANNNNNNNNNNTAAATGATTTTATAATCTCATAATTAATTT
1 TCACCCATTTC-TTCAAAAGACTTATTACCCGCTTTAAATGATTTTATAATCTCATAAATGATTT
* * * * * * *
1792 TAAGTTA-AACTTTTTTACATTTTTCTTTAACACAGACAATAATTGAATGTCTAACT-TGAGAAA
65 TAAG-TAGAATTTTTTTAAATTTTTTTTTAAAACAGACTATAATTGAATGTCTACCTCAGA-AAA
*
1855 CGTATAGAAAAAGCCATT
128 AGTATAGAAAAAGCCATT
1873 GATTCAAAAG
Statistics
Matches: 261, Mismatches: 47, Indels: 16
0.81 0.15 0.05
Matches are distributed among these distances:
170 10 0.04
171 240 0.92
172 11 0.04
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (171 bp):
TCACCCATTTCTTCAAAAGACTTATTACCCGCTTTAAATGATTTTATAATCTCATAAATGATTTT
AAGTAGAATTTTTTTAAATTTTTTTTTAAAACAGACTATAATTGAATGTCTACCTCAGAAAAAGT
ATAGAAAAAGCCATTCATTGAGAAGAAAAATCCATTTATAC
Found at i:3120 original size:171 final size:170
Alignment explanation
Indices: 2688--3421 Score: 652
Period size: 171 Copynumber: 4.3 Consensus size: 170
2678 CTGAGGCAGG
* ** * * * * * *
2688 CATTCAATTATAGTCTGTTTTAAAGAAAAATTTAAAATAATTCTATTTCAAATCATTTATGAGAT
1 CATTCAATTATAGTATG-TTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * * * * *
2753 TATAAAACCATTTAAAGTGGGTAATAAGACTTTTAAAGGAAT-GAGTGACTATAAATGGACCTTT
65 TATAAAACCATTTAAAGAGAGTAATAAGCCTTTTGAAGGAATAG-GTGACTCTAAATAGA-CTTT
* ** * * * * *
2817 CTTC--TCAATAAATGGCTT-TTTCTGGATGTTTCCTGAGGCAGA
128 -TTCTGTCAATGAAT-GCTTGTTTCTTCACGTGTCTTAAGGTAGA
* * * * *
2859 CAATCAATTATAGTCTGTTTTAA-CAAAGAATATAAAAAAAATTCAACTTAGAATCAATTTTGAG
1 CATTCAATTATAGTATG-TTTAATCAAA-AATGT-AAAAAAATTCAACTTAAAATCAATTATGAG
* * * * * *
2923 ATTATAAAACTATATCAAGCGAGTAATAAGCCTTTTGAAAGAATAGGTGCCTCTAAATAGACTTT
63 ATTATAAAACCATTTAAAGAGAGTAATAAGCCTTTTGAAGGAATAGGTGACTCTAAATAGACTTT
* * * * *
2988 TTTTGTCAATGAATGCTTGTTTCTTCGCGTTTCTTGAGGTAAA
128 TTCTGTCAATGAATGCTTGTTTCTTCACGTGTCTTAAGGTAGA
* **********
3031 CATTCAATTATAGTATGTTTCACTCAAAAATGTAAAAAAATTCAACTTAAAATCNNNNNNNNNNT
1 CATTCAATTATAGTATGTTT-AATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
3096 TATAAAACCATTTAAAGAGAGTAATAAG-CTTTTCGAAGGAATAGGTGACTCTAAATAGACTTTT
65 TATAAAACCATTTAAAGAGAGTAATAAGCCTTTT-GAAGGAATAGGTGACTCTAAATAGACTTTT
* *
3160 TCTGTCAATGAATGCTTATTTCTTCACGTGTCTCAAGGTAGA
129 TCTGTCAATGAATGCTTGTTTCTTCACGTGTCTTAAGGTAGA
* ****************
3202 CGTTCAATTATAGTATGTTTTAATNNNNNNNNNNNNNNNNTTCAACTTAAAATCAATTATGAGAT
1 CATTCAATTATAGTATG-TTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGAT
* * * *
3267 TATAAAATCATTTAAAGAGAGTAATAAGCTTTTTGAAGGAATAGGTGACTCTAAATGGACTGTTT
65 TATAAAACCATTTAAAGAGAGTAATAAGCCTTTTGAAGGAATAGGTGACTCTAAATAGACTTTTT
*
3332 CTGTCAATGAATGCTTGTTTCTTCACGTGTCTTAAAGTAGA
130 CTGTCAATGAATGCTTGTTTCTTCACGTGTCTTAAGGTAGA
3373 CATTCAATTATAGTATGTTGTAATCAAAAATGTAAAAAAATTCAACTTA
1 CATTCAATTATAGTATGTT-TAATCAAAAATGTAAAAAAATTCAACTTA
3422 NNNNNNNNNN
Statistics
Matches: 441, Mismatches: 110, Indels: 24
0.77 0.19 0.04
Matches are distributed among these distances:
170 12 0.03
171 301 0.68
172 123 0.28
173 5 0.01
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (170 bp):
CATTCAATTATAGTATGTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATT
ATAAAACCATTTAAAGAGAGTAATAAGCCTTTTGAAGGAATAGGTGACTCTAAATAGACTTTTTC
TGTCAATGAATGCTTGTTTCTTCACGTGTCTTAAGGTAGA
Done.