Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003236.1 Kokia drynarioides strain JFW-HI SEQ_115882, 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, 636
Length: 1061
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.27
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:639 original size:216 final size:214
Alignment explanation
Indices: 63--1061 Score: 887
Period size: 216 Copynumber: 4.6 Consensus size: 214
53 TTTTAATGAT
* * * * * * *
63 CAAAACTCGTTTACAAAATTA-ATACCTATTTAGACTAAATGATGCGATTTCCCGA-AAATGGAA
1 CAAAACTTGTTTACAAAATGACA-AACTATTTAGACCAAATGAAGCGATTTTCCGAGCAA--GAA
* * * * *
126 TGTTCAAAAATTCCTCAAAGGAATGGAACGTCTTGAATACTTTAAGGGACCGAAGTTATAAAAGA
63 TGTTCAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAATTATAAAAGA
* * * *
191 ACTCGTAAAAGTTTGACAAGTTCGGAAGTTCAT-CAATGAACAAAGAGAGAGAAACAATTCTCAC
128 ACTCGTAAAAGTTTGACTAGTTCGAAAGTTCGTCCAA-GAAC-CA-AGAGAGAAACAATTCTCAC
* * *
255 GTAAATAAGTTTTAAATTTAAAGAC
190 GTAAATAAGTTTTTAATTCAAAGAA
* * * * * *
280 CAAAACTTGTTTACAAAATGACAAACAATTTAGA-AAAATGATGAGATTTTTCTAGCATAGAATG
1 CAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGAAGCGATTTTCCGAGCA-AGAATG
* * *
344 TT-AAGAAAGTTGCTAGAAGGAATGTATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGA
65 TTCAA-AAA-TTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAATTATAAAAGA
* * *
408 ACTTGTAAAAGTTTGACTAGTTCGAAAGTTTGTCCAAGAACCAAGAGAGAAATAATTCTCACGTA
128 ACTCGTAAAAGTTTGACTAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTA
473 AATAAGTTTTTAATTC-AAGAAA
193 AATAAGTTTTTAATTCAAAG-AA
495 CAAAACCTT-TTTACAAAATGACAAACTATTTAGACCAAATGAAGCGATTTTCCGAGCAAGGAAT
1 CAAAA-CTTGTTTACAAAATGACAAACTATTTAGACCAAATGAAGCGATTTTCCGAGCAA-GAAT
* * * *
559 GTTCGAAAAATTGCTTGAAGGAATGGATCGTCTTGAATACTTTATGGAACTGAAATTACAAAAGA
64 GTTC-AAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAATTATAAAAGA
* * * *
624 ACTCGTAAAAGTTTGA-TAAGTTCGGAAGTTTGACCAAGAACC-A-AGCGAAACAATTCTCACGT
128 ACTCGTAAAAGTTTGACT-AGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGT
* *
686 AAATAAGTTTTTGATTCAAAGAC
192 AAATAAGTTTTTAATTCAAAGAA
******************************** * *
709 CAAAACTTGTTTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCA-TTTCTCAAG-AATTGAA
1 CAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGAAGCGATTTTC-CGAGCAA--GAA
* *
772 TGTTTAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGA-TATGAAA
63 TGTTCA-AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAA-ATTATAAAA
* * *
836 GAACTTGTAAAAGTTTGACTAGTTCAAAAGTTCGTCCAAGAACCAAGAGAGAAGCAATTCTCACG
126 GAACTCGTAAAAGTTTGACTAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACG
* *
901 TAAATAAGTTTATAATTCAAACAA
191 TAAATAAGTTTTTAATTCAAAGAA
* *
925 CAAAACCTT-TTAACAAAATGACAAATTATTTAGACCAAATGATA-CGA-TTTCCAGAGCATAGA
1 CAAAA-CTTGTTTACAAAATGACAAACTATTTAGACCAAATGA-AGCGATTTTCC-GAGCA-AGA
* * *
987 ATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTAGAATACTTTATGGAACTGAAATTATAAAA
62 ATGTTC-AAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAATTATAAAA
1052 GAACTCGTAA
126 GAACTCGTAA
Statistics
Matches: 616, Mismatches: 137, Indels: 59
0.76 0.17 0.07
Matches are distributed among these distances:
213 10 0.02
214 144 0.23
215 78 0.13
216 258 0.42
217 118 0.19
218 8 0.01
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.27
Consensus pattern (214 bp):
CAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGAAGCGATTTTCCGAGCAAGAATGT
TCAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAATTATAAAAGAACT
CGTAAAAGTTTGACTAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAT
AAGTTTTTAATTCAAAGAA
Done.