Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399383.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2649.0, 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: 2870
ACGTcount: A:0.24, C:0.08, G:0.09, T:0.23
Warning! 1023 characters in sequence are not A, C, G, or T
Found at i:2667 original size:171 final size:171
Alignment explanation
Indices: 2337--2724 Score: 451
Period size: 171 Copynumber: 2.3 Consensus size: 171
2327 NNNNNNNNNN
* * * *
2337 TTTAACCAAAAATCTAAAAACATTCAACTTAAAACCAATTATGAGATTACAAAACTATTTAAAGC
1 TTTAACCAAAAATCTAAAAAAATTCAACTTAAAATCAATTATGAGACTACAAAACAATTTAAAGC
* * * * * *
2402 GAGTAATAAGTCTTTTGAAGGAATGGGTAACTAAAAACGGACTTTTTTTACTAGTCAATGTCTTT
66 GAGTAATAAGTCTTCTGAAGGAATAGGTAACTAAAAACGGACTTTTGTTACCAATCAATGGCTTT
* * * ***
2467 TTCTTCATATTTCTCGACGTTGACATTCAATTATAGTCTAT
131 TTCTTCACACTTCTCGAAGGCAACATTCAATTATAGTCTAT
* * * *
2508 TTTAACCAAATATCTAAAAAAATTCAACTTAAGATCAATTATGAGGCTATAAAACAATTTAAAGC
1 TTTAACCAAAAATCTAAAAAAATTCAACTTAAAATCAATTATGAGACTACAAAACAATTTAAAGC
* * * * *
2573 GAGTAGT-AGTGCTTCTGAAGGAATAGGTAACTACAAATGGACTTTTGTTCCCAATGAATGGCTT
66 GAGTAATAAGT-CTTCTGAAGGAATAGGTAACTAAAAACGGACTTTTGTTACCAATCAATGGCTT
* *
2637 TTT-TTACACGCTTC-CTAAGGCAAGCATTCAATTATAGTCTAT
130 TTTCTT-CACACTTCTCGAAGGCAA-CATTCAATTATAGTCTAT
* *
2679 TTTAACTAAAAAT-GAAAAAAATTTCAACTTAAAATCAATTATGAGA
1 TTTAACCAAAAATCTAAAAAAA-TTCAACTTAAAATCAATTATGAGA
2725 TTATNNNNNN
Statistics
Matches: 181, Mismatches: 32, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
170 16 0.09
171 165 0.91
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.34
Consensus pattern (171 bp):
TTTAACCAAAAATCTAAAAAAATTCAACTTAAAATCAATTATGAGACTACAAAACAATTTAAAGC
GAGTAATAAGTCTTCTGAAGGAATAGGTAACTAAAAACGGACTTTTGTTACCAATCAATGGCTTT
TTCTTCACACTTCTCGAAGGCAACATTCAATTATAGTCTAT
Found at i:2838 original size:171 final size:169
Alignment explanation
Indices: 2337--2870 Score: 448
Period size: 171 Copynumber: 3.1 Consensus size: 169
2327 NNNNNNNNNN
* * * * * *
2337 TTTAACCAAAAATCTAAAAACATTCAACTTAAAACCAATTATGAGATTACAAAACTATTTAAAGC
1 TTTAA-CAAAAAT-GAAAAAAATTCAACTTAAAATCAATTATGAGACTATAAAACAATTTAAAGC
* * * * * * *
2402 GAGTAATAAGTCTTTTGAAGGAATGGGTAACTAAAAACGGACTTTTTTTACTAGTCAATGTCTTT
64 GAGTAATAAGGCTTTTGAAGGAATGAGTAACTAAAAATGGACTTTTCTTACCAATGAATGTCTTT
* * *
2467 TTCTTCATATTTCTCGA-CGTTGACATTCAATTATAGTCTAT
129 TTCTTCAAATTTCTTGAGC-TAGACATTCAATTATAGTCTAT
* * * *
2508 TTTAACCAAATATCTAAAAAAATTCAACTTAAGATCAATTATGAGGCTATAAAACAATTTAAAGC
1 TTTAA-CAAAAAT-GAAAAAAATTCAACTTAAAATCAATTATGAGACTATAAAACAATTTAAAGC
* * * * * *
2573 GAGTAGT-AGTGCTTCTGAAGGAAT-AGGTAACTACAAATGGACTTTTGTTCCCAATGAATGGCT
64 GAGTAATAAG-GCTTTTGAAGGAATGA-GTAACTAAAAATGGACTTTTCTTACCAATGAATGTCT
*** * * *
2636 TTTT-TTACACGCTTCCTAAGGCAAG-CATTCAATTATAGTCTAT
127 TTTTCTT-CAAATTTCTTGA-GCTAGACATTCAATTATAGTCTAT
* **********
2679 TTTAACTAAAAATGAAAAAAATTTCAACTTAAAATCAATTATGAGATTATNNNNNNNNNNAAAGC
1 TTTAAC-AAAAATGAAAAAAA-TTCAACTTAAAATCAATTATGAGACTATAAAACAATTTAAAGC
* * * * * *
2744 AAGTAATAAGGCTTTTGAAGGAATGAGTTACCATAAATAGACTTTTCTTGCCAATGAATGTCTTT
64 GAGTAATAAGGCTTTTGAAGGAATGAGTAACTAAAAATGGACTTTTCTTACCAATGAATGTCTTT
* * *
2809 TTCTTCAAATTTCTTGAGCTAGACATTCAATTATAATATGT
129 TTCTTCAAATTTCTTGAGCTAGACATTCAATTATAGTCTAT
*
2850 TTTAACAAATAATGTAAAAAA
1 TTTAACAAA-AATGAAAAAAA
Statistics
Matches: 288, Mismatches: 63, Indels: 24
0.77 0.17 0.06
Matches are distributed among these distances:
170 19 0.07
171 262 0.91
172 6 0.02
173 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.34
Consensus pattern (169 bp):
TTTAACAAAAATGAAAAAAATTCAACTTAAAATCAATTATGAGACTATAAAACAATTTAAAGCGA
GTAATAAGGCTTTTGAAGGAATGAGTAACTAAAAATGGACTTTTCTTACCAATGAATGTCTTTTT
CTTCAAATTTCTTGAGCTAGACATTCAATTATAGTCTAT
Done.