Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402639.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5709.0, 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: 3280
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.32
Warning! 579 characters in sequence are not A, C, G, or T
Found at i:1473 original size:43 final size:43
Alignment explanation
Indices: 1424--1510 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
1414 GAAAATTGAT
* *
1424 TTTATGTTCGATTTTTATTTACATTTTTTATTAAAACCAACTA
1 TTTATGTTCAATTTTTATTTACATTTTTTATTAAAACAAACTA
*
1467 TTTATGTTCAATTTTTGTTTACATTTTTTATTAAAACAAACTA
1 TTTATGTTCAATTTTTATTTACATTTTTTATTAAAACAAACTA
1510 T
1 T
1511 AATTGAATGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.54
Consensus pattern (43 bp):
TTTATGTTCAATTTTTATTTACATTTTTTATTAAAACAAACTA
Found at i:2187 original size:171 final size:169
Alignment explanation
Indices: 1648--2197 Score: 448
Period size: 171 Copynumber: 3.2 Consensus size: 169
1638 NNNNNNNAGC
* * *** *
1648 CTTATTACTCACTTTAAATGGTTTTATAATCTCAAAATTCATTTTAAGTTCTTTTTTTTTTTACT
1 CTTATTACTCACTTTAAATAGTTTTATAATCTCATAATT-ATTTTAAGTTAAATTTTTTTATA--
* * * *
1713 TTTTTGGTTAAAATAGATTATAATTAAATA-TTTACCTTAGGAAACATGAGGAAAAAGGCATTCA
63 TTTTTGGTTAAAATAGATTATAATTAAA-AGTCTACCTTAGGAAACGTGAAGAAAAAAGCATTCA
* * ***
1777 TTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTTAANNNNN
127 TTGGCAAGAAAAGTCCATTTATAGTCTCCCATTCCTTTAA--AAG
******** * * * *
1822 NNNNNNNNT-GCTTTAAATATTTTTATAATCTCATAATTACTTTAAGTTCAAA--TTTTTATAGT
1 CTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTATTTTAAGTT-AAATTTTTTTATATT
** * * * * * * * *
1884 TTTCATTAAAACAGACTATAATTGAATGTCT-GCTTGTGGAAACGTGTAG-AAAAAGCCATTAAT
65 TTTGGTTAAAATAGATTATAATTAAAAGTCTACCTT-AGGAAACGTGAAGAAAAAAG-CATTCAT
* * **
1947 TGAG-AACAAAAGTCCAGTTATAGTCTTGCATTCCTTTAAAAG
128 TG-GCAAGAAAAGTCCATTTATAGTCTCCCATTCCTTTAAAAG
* * * * *
1989 CTTTGTTACTCACGTTCAATGGTTTTATAATCTCATAATTGATTTTAAGATAAATTTTTTTATAT
1 C-TTATTACTCACTTTAAATAGTTTTATAATCTCATAATT-ATTTTAAGTTAAATTTTTTTATAT
* * **
2054 TTTTGGTTAAAATAGATTATAATTAAAAGTCTACCATAAGAAACGTGAAGAAAAAAGTTTTCATT
64 TTTTGGTTAAAATAGATTATAATTAAAAGTCTACCTTAGGAAACGTGAAGAAAAAAGCATTCATT
* * *
2119 GGCAAGAAAAGTCCATTTATGGTCTCCCATTTCTTCAAAAG
129 GGCAAGAAAAGTCCATTTATAGTCTCCCATTCCTTTAAAAG
*
2160 ACTTATTACTCGCTTTAAATAGTTTTATAATCTCATAA
1 -CTTATTACTCACTTTAAATAGTTTTATAATCTCATAA
2198 NNNNNNNNNN
Statistics
Matches: 279, Mismatches: 83, Indels: 31
0.71 0.21 0.08
Matches are distributed among these distances:
168 9 0.03
169 97 0.35
170 10 0.04
171 119 0.43
172 18 0.06
173 25 0.09
174 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.39
Consensus pattern (169 bp):
CTTATTACTCACTTTAAATAGTTTTATAATCTCATAATTATTTTAAGTTAAATTTTTTTATATTT
TTGGTTAAAATAGATTATAATTAAAAGTCTACCTTAGGAAACGTGAAGAAAAAAGCATTCATTGG
CAAGAAAAGTCCATTTATAGTCTCCCATTCCTTTAAAAG
Found at i:2680 original size:171 final size:171
Alignment explanation
Indices: 2359--2683 Score: 374
Period size: 171 Copynumber: 1.9 Consensus size: 171
2349 NNNNNTCGCT
* *
2359 TTAAATTGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTAAATTTTTCATTAAAACAG
1 TTAAATGGTTTTATAATCTCATAATTGATTTGAAGTTAAATTTTTTAAATTTTTCATTAAAACAG
* * * * * *
2424 ACTCTAATTGATTGGCTGCCTCAGGAAACGAGTAGAAAAACCCATTTATTTGAAAAAAAAAGTCC
66 ACTCCAATTAAATGACTGCCTCAGGAAACGAGTAGAAAAACCCATTCATTTGAAAAAAAAAGCCC
**
2489 ATTTATAGTCTTTCATTCCTTCAAAAGCCTTATTACTATCC
131 ATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTATCC
* ** * *
2530 TTAAATGGTTTTATAATGTTGTAATTG-TATTGAAGTTGAATTTTTTTACATTTTTCATTAAAAC
1 TTAAATGGTTTTATAATCTCATAATTGAT-TTGAAGTT-AAATTTTTTAAATTTTTCATTAAAAC
* ** * *
2594 AGACTCCAATTAAAT-ACTTGCCT-TGGAAAAC-ATGTAGAAAAAGTCATTCA-TTGACAAGAAA
64 AGACTCCAATTAAATGAC-TGCCTCAGG-AAACGA-GTAGAAAAACCCATTCATTTGAAAAAAAA
2655 AGCCCATTTATAGT-TACCCATTCCTTCAA
126 AGCCCATTTATAGTCT-CCCATTCCTTCAA
2684 NNNNNNNNNN
Statistics
Matches: 128, Mismatches: 20, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
170 2 0.02
171 67 0.52
172 59 0.46
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (171 bp):
TTAAATGGTTTTATAATCTCATAATTGATTTGAAGTTAAATTTTTTAAATTTTTCATTAAAACAG
ACTCCAATTAAATGACTGCCTCAGGAAACGAGTAGAAAAACCCATTCATTTGAAAAAAAAAGCCC
ATTTATAGTCTCCCATTCCTTCAAAAGCCTTATTACTATCC
Found at i:3244 original size:171 final size:171
Alignment explanation
Indices: 2931--3278 Score: 431
Period size: 171 Copynumber: 2.0 Consensus size: 171
2921 NNNNNNNNNN
* *
2931 AAGCCTTATTACTTACTTTAAATGTTTTTATAATCTCATAATTGATTTTAAGTTAATTCTTTTTA
1 AAGCCTCATTACTTACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAATTCTTTTTA
* * *
2996 CATTTGTCATTAAAATAGACTATAATTGAATGTCTACCTAAAGAAACATATAAAGAAAGCCATTT
66 CATTTGTCATTAAAACAGACTATAACTGAATGTCTACCTAAAGAAACATATAAAGAAAGCCATTC
*
3061 ATTTGGAAGAAAAGTCCATGTATAGTCTCCCATACCTTCAA
131 ATTTGCAAGAAAAGTCCATGTATAGTCTCCCATACCTTCAA
* *
3102 AAGCCTCATTAC-TAGTCTTAAATGGTTTTATAATCTGATAATT-ATATTTAAGTTAATT-TTTT
1 AAGCCTCATTACTTACT-TTAAATGGTTTTATAATCTCATAATTGAT-TTTAAGTTAATTCTTTT
* * * * *
3164 TAATATTTTTCATTAAAACAGACTATAACTGAATG-CTTGCCT-TAGAAAACATGTAGAA-AAAG
64 T-ACATTTGTCATTAAAACAGACTATAACTGAATGTC-TACCTAAAG-AAACATATA-AAGAAAG
* * * *
3226 TCATTCA-TTGACAAGAAAAGTCCATTTATAGTCTCTCATTCCTTCAA
125 CCATTCATTTG-CAAGAAAAGTCCATGTATAGTCTCCCATACCTTCAA
3273 AAGCCT
1 AAGCCT
3279 TA
Statistics
Matches: 153, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
170 16 0.10
171 135 0.88
172 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (171 bp):
AAGCCTCATTACTTACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAATTCTTTTTA
CATTTGTCATTAAAACAGACTATAACTGAATGTCTACCTAAAGAAACATATAAAGAAAGCCATTC
ATTTGCAAGAAAAGTCCATGTATAGTCTCCCATACCTTCAA
Done.