Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402212.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_53.0, 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: 23656
ACGTcount: A:0.24, C:0.07, G:0.08, T:0.23
Warning! 9031 characters in sequence are not A, C, G, or T
Found at i:2664 original size:41 final size:41
Alignment explanation
Indices: 2610--2687 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
2600 AAACATATTA
* **
2610 TAATTAAATGCTTAGCTTGAGACTCATAAAGAAAAAGGTAT
1 TAATTAAATGCTTACCTTGAGAAACATAAAGAAAAAGGTAT
*
2651 TAATTAAATGCTTACCTTGAGAAACATGAAGAAAAAG
1 TAATTAAATGCTTACCTTGAGAAACATAAAGAAAAAG
2688 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (41 bp):
TAATTAAATGCTTACCTTGAGAAACATAAAGAAAAAGGTAT
Found at i:5205 original size:172 final size:171
Alignment explanation
Indices: 4726--5291 Score: 590
Period size: 173 Copynumber: 3.3 Consensus size: 171
4716 NNNNNNNNNN
* * * * * *
4726 TTCTTACCAATGAATACTTTTTTCTTTATGTTTCTCAAGGTAGACATTCAATTACACTCTATTTT
1 TTCTTACCAATGAATTCTTTTTTCTTCATGTTTCTCAACGTAGACATTCAATTATAATCTGTTTT
* * * * * * *
4791 AACCAAAAATGTAAAAAAATT-AAGCTTAAAATCAATTATGGGACTATAAAATCATTTAAA-ACG
66 AACAAAAAAGGAAAAAAAATTGAA-CTTAAAATCAATTTTGAGATTATAAAACCATTTAAATA-G
**
4854 ATTAATAAGGCTTTTGAAGAAATAGGTGACAATAAATAGACTT
129 AGCAATAAGGCTTTTGAAGAAATAGGTGACAATAAATAGACTT
* * ** * * *
4897 TTCTTGCCACTGAATGTC-TTTTTCTTCACATTTCTCGACGTAGAGATTCAATTATAATCTGCTT
1 TTCTTACCAATGAAT-TCTTTTTTCTTCATGTTTCTCAACGTAGACATTCAATTATAATCTGTTT
* * *
4961 TAACTAAAAAAGTCAAAAAAAATTGAACTTAAAATCAATTTCGAGATTATTAAACCATTTAAAGT
65 TAAC-AAAAAAG-GAAAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAA-T
* * * *
5026 -GAGCAATAAAGCTTTTGAAGAGATGGGTGATAATAAATAGACCTT
127 AGAGCAATAAGGCTTTTGAAGAAATAGGTGACAATAAATAGA-CTT
* * * * * *
5071 TT-TTATCAATGAATTCTTTTTTCTTGATGTATCTCAATGTAGACATTTAATTATAATATGTTTT
1 TTCTTACCAATGAATTCTTTTTTCTTCATGTTTCTCAACGTAGACATTCAATTATAATCTGTTTT
*
5135 AACAAAAAAAGGAAAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAATATA
66 AAC-AAAAAAGGAAAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAATAGA
* * * *
5200 GCAATAAGGCTTTTGAAGGAAT-GGAAGACTATAAAT-GAATTT
130 GCAATAAGGCTTTTGAAGAAATAGG-TGACAATAAATAG-ACTT
* * *
5242 TTCTTGCCAATAAATGCTTTTTTCTTCATGTTTCTCAA-GATAGACATTCA
1 TTCTTACCAATGAATTCTTTTTTCTTCATGTTTCTCAACG-TAGACATTCA
5292 NNNNNNNNNN
Statistics
Matches: 321, Mismatches: 61, Indels: 25
0.79 0.15 0.06
Matches are distributed among these distances:
171 62 0.19
172 122 0.38
173 130 0.40
174 7 0.02
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (171 bp):
TTCTTACCAATGAATTCTTTTTTCTTCATGTTTCTCAACGTAGACATTCAATTATAATCTGTTTT
AACAAAAAAGGAAAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAATAGAG
CAATAAGGCTTTTGAAGAAATAGGTGACAATAAATAGACTT
Found at i:6367 original size:171 final size:171
Alignment explanation
Indices: 6004--6600 Score: 452
Period size: 171 Copynumber: 3.5 Consensus size: 171
5994 TTCGTCATGT
* * * * *
6004 TTCTCATGGTAGACATTCAATTATAATCTGTTTTGACCAA-AAATATGAAAAAAATTGAACTTAA
1 TTCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAACAAATGT-AAAAAAATTAAACTTAA
* * ********** * *
6068 AATCAATTTTGAGAATNNNNNNNNNNTTAAAGTGAGTAATAAGGCTTTTGAAGAAATGAGAGATT
65 AATCAATTTCGAGACTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATG-GAGATA
* * * * ****
6133 ATAAATGGACTTTTCTTACCAATGAATATTTTTTTCTTCGTGT
129 ATAAATAGACTTTTCTTGCCAATGAATGTCTTTTTCTTCACAC
* * *
6176 TTCTCAAGGTAGACATTCAATTGTACTCTATTTTAA-CTACAAATGTAAAAAAATTAAACTTAAA
1 TTCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAACAAATGTAAAAAAATTAAACTTAAA
* * * * * *
6240 ATCAATTAT-GGGACTATAAAATCATTTAAAGCGATTAATAAGGCTTTGGAAGAAATAGGCGACA
66 ATCAATT-TCGAGACTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAAT-GGAGATA
*
6304 ATAAATAAACTTTTCTTGCCAATGAATGTCTTTTTCTTCACAC
129 ATAAATAGACTTTTCTTGCCAATGAATGTCTTTTTCTTCACAC
** * * * ********** *
6347 TTCTTGATGTAGAGATTCAATTATAATCTGTTTTAACCANNNNNNNNNNAAAAATTGAACTTAAA
1 TTCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAACAAATGTAAAAAAATTAAACTTAAA
* * *
6412 ATCAATTTCGAGATTATAAAACCATTTAAA-CGAGTAATAAGGCTTTTGAAGAGATGGGTGATAA
66 ATCAATTTCGAGACTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAAT-GGAGATAA
* * * **
6476 TAAATAGACTTTTTTTGTCAATGAATGCCTTTTTCTTCA-TG
130 TAAATAGACTTTTCTTGCCAATGAATGTCTTTTTCTTCACAC
* * * * * * * *
6517 TATCTTAATGTAGACATTCAATTATAATATGTTTTAACCAA-AAAAG-GAAACAATTGAACTTAA
1 T-TCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAACAAATGTAAAAAAATTAAACTTAA
* *
6580 AATCAATTTTGAGATTATAAA
65 AATCAATTTCGAGACTATAAA
6601 NNNNNNNNNN
Statistics
Matches: 337, Mismatches: 82, Indels: 15
0.78 0.19 0.03
Matches are distributed among these distances:
169 34 0.10
170 1 0.00
171 223 0.66
172 79 0.23
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35
Consensus pattern (171 bp):
TTCTCAAGGTAGACATTCAATTATAATCTATTTTAACCAACAAATGTAAAAAAATTAAACTTAAA
ATCAATTTCGAGACTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGGAGATAAT
AAATAGACTTTTCTTGCCAATGAATGTCTTTTTCTTCACAC
Found at i:10695 original size:168 final size:170
Alignment explanation
Indices: 10405--10836 Score: 512
Period size: 168 Copynumber: 2.5 Consensus size: 170
10395 NNNNNNNNNN
* * * * *
10405 ATTATACTCTGTTTTAACTAAAAATGTAAAAAAATTTAACTTAAAATCAATTATCG-GACTATAA
1 ATTATAATCTGTTTTAACCAAAAA-GTAAAAAAAATTAACTTAAAATCAATT-TTGAGATTATAA
* * * *
10469 AACTATTTAAAGCGAGTAATAAGACTTTTGAAGGAATGAGAGACAATAAATTGACTTTTCTTGCC
64 AACTATTTAAAGCGAGTAATAAGACTTTTAAAGGAAGGAGAGACAATAAATGGACTTTTCTTACC
* *
10534 AATGATTACC-TTTT-TTCACGTTTCTCAATGTTGAGATTCA
129 AATGAATACCTTTTTCTTCACGTTTCTCAATGTAGAGATTCA
* * *
10574 ATTATAGTCTGTTTTAGCCAAAAAGTAAAAAAAATTAACTTAAAATCAATTTTGATATTATAAAA
1 ATTATAATCTGTTTTAACCAAAAAGTAAAAAAAATTAACTTAAAATCAATTTTGAGATTATAAAA
* * * * * *
10639 CCATTTAAAGTGAGTAGTAA-AGCTTTTAAAGGAAGGGGTGATAATAAATGGACTTTTCTTACCA
66 CTATTTAAAGCGAGTAATAAGA-CTTTTAAAGGAAGGAGAGACAATAAATGGACTTTTCTTACCA
* * *
10703 ATGAATACCTTTTTCTTCATGTTTCTTAATGTAGATATTCA
130 ATGAATACCTTTTTCTTCACGTTTCTCAATGTAGAGATTCA
* * * * *
10744 ATTATAATATGTTTTATCCAAAAAGTGAAAAAAATTGAGCTTAAAATTAATTTTGAGATTATAAA
1 ATTATAATCTGTTTTAACCAAAAAGTAAAAAAAATT-AACTTAAAATCAATTTTGAGATTATAAA
*** *
10809 ACTATTTAAATATAGTAATAAGGCTTTT
65 ACTATTTAAAGCGAGTAATAAGACTTTT
10837 GNNNNNNNNN
Statistics
Matches: 222, Mismatches: 35, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
167 3 0.01
168 94 0.42
169 25 0.11
170 54 0.24
171 46 0.21
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (170 bp):
ATTATAATCTGTTTTAACCAAAAAGTAAAAAAAATTAACTTAAAATCAATTTTGAGATTATAAAA
CTATTTAAAGCGAGTAATAAGACTTTTAAAGGAAGGAGAGACAATAAATGGACTTTTCTTACCAA
TGAATACCTTTTTCTTCACGTTTCTCAATGTAGAGATTCA
Found at i:18645 original size:173 final size:169
Alignment explanation
Indices: 18333--18751 Score: 464
Period size: 173 Copynumber: 2.4 Consensus size: 169
18323 NNNNNNNNTC
*
18333 AAAAAAATTAAACTTAAAATTAATTTTGAGAATATAAAATAATTTAAAGTGAGTAATAAGGCTTT
1 AAAAAAATTAAACTTAAAATTAATTTTGAGAATATAAAATCATTTAAAGTGAGTAATAA-GCTTT
* * *
18398 TAAAGGAATAGAAGATTATAAATGGACTTTTCTTACCAATGAACACTTTTTTCTTCACGTTTCTT
65 TAAAGGAATGGAAGACTATAAATGGACTTCTCTTACCAATGAACACTTTTTTCTTCACGTTTCTT
*
18463 AATGTAGACATTCAATCATACTCTGTTTTAACAAAAAATGTAA
130 -ATGTAGACATTCAATCATACTCTATTTTAACAAAAAA--TAA
* * *
18506 AAAAAAATTAAACTTAACATCAATTTTGAGAATATAAAATCATTTAAAGTGAGTAATAAGTCCTT
1 AAAAAAATTAAACTTAAAATTAATTTTGAGAATATAAAATCATTTAAAGTGAGTAATAAG-CTTT
* * * ********** *
18571 TAAAGGAATGGGAGACTATAAATGGACTTCTCTTGCCAATGAATACNNNNNNNNNNATGTTTCTC
65 TAAAGGAATGGAAGACTATAAATGGACTTCTCTTACCAATGAACACTTTTTTCTTCACGTTTCT-
* * *
18636 T-TGGTAGACATTCAATTATACTCTATTTTAACCAAAAATAT
129 TAT-GTAGACATTCAATCATACTCTATTTTAACAAAAAATAA
* * * * **
18677 AAAAAAATTAAACTTAAAATTAATTATGGGACTATCAAA-CTATTTAAAGCAAGTAATAAAGCTT
1 AAAAAAATTAAACTTAAAATTAATTTTGAGAATATAAAATC-ATTTAAAGTGAGTAAT-AAGCTT
18741 TTAAAGGAATG
64 TTAAAGGAATG
18752 AGTGACAATA
Statistics
Matches: 207, Mismatches: 34, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
170 1 0.00
171 62 0.30
172 5 0.02
173 138 0.67
174 1 0.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.33
Consensus pattern (169 bp):
AAAAAAATTAAACTTAAAATTAATTTTGAGAATATAAAATCATTTAAAGTGAGTAATAAGCTTTT
AAAGGAATGGAAGACTATAAATGGACTTCTCTTACCAATGAACACTTTTTTCTTCACGTTTCTTA
TGTAGACATTCAATCATACTCTATTTTAACAAAAAATAA
Found at i:20393 original size:170 final size:162
Alignment explanation
Indices: 20179--20512 Score: 304
Period size: 173 Copynumber: 2.0 Consensus size: 162
20169 ATTTAAAGTG
* * *
20179 AGTAATAAGGCTTTTGAAGGAATGTGAGACCATAAATAGACTTTTCTTGGC-AAT-AA-ATGC-A
1 AGTAAAAAGGCTTTTGAAAGAATGGGAGACCATAAATAGACTTTTCTT-GCAAATAAACAT-CTA
* * *
20240 TTTTGTTCATGTTCCTCGAGGTAAAT-ATTCAATTATAGTCTACTTTAACTTAAAGTGTA-CAAA
64 TTTTGTTCATGTTCCTCAAGGT-AATCATTCAATTATAGTCTACTTTAA-TTAAAAT-TATAAAA
20303 -AATTCAACTTAAAATCAATTATGAGATTATAAAACT
126 GAATTCAACTTAAAATCAATTATGAGATTATAAAACT
* * *
20339 ANNNNNNNNNNGTAAAAAGGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTTCTTGCAAATA
1 A----------GTAAAAAGGCTTTTGAAAGAATGGGAGACCATAAATAGACTTTTCTTGCAAATA
* * * * * **
20404 AACATCTTTTTTTTTTCATGTTTCTCAAGGTAGTCATTTAATTATAGTCTGTTTTAATTAAAATT
56 AACATC-TATTTTGTTCATGTTCCTCAAGGTAATCATTCAATTATAGTCTACTTTAATTAAAATT
* * *
20469 ATAAAAGAATTTAACTTAAAATTATTTATGAGATTATAAAACT
120 ATAAAAGAATTCAACTTAAAATCAATTATGAGATTATAAAACT
20512 A
1 A
20513 TTTAAAGCGA
Statistics
Matches: 137, Mismatches: 19, Indels: 23
0.77 0.11 0.13
Matches are distributed among these distances:
160 1 0.01
169 2 0.01
170 44 0.32
171 5 0.04
172 13 0.09
173 72 0.53
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.37
Consensus pattern (162 bp):
AGTAAAAAGGCTTTTGAAAGAATGGGAGACCATAAATAGACTTTTCTTGCAAATAAACATCTATT
TTGTTCATGTTCCTCAAGGTAATCATTCAATTATAGTCTACTTTAATTAAAATTATAAAAGAATT
CAACTTAAAATCAATTATGAGATTATAAAACT
Done.