Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003567.1 Kokia drynarioides strain JFW-HI SEQ_116431, 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: 13548
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Found at i:6947 original size:277 final size:277
Alignment explanation
Indices: 6453--7001 Score: 949
Period size: 277 Copynumber: 2.0 Consensus size: 277
6443 TCTCTAAAGA
* * *
6453 GCTATTCTAAGAATCATATTTATGTTTTGGTTAAGGATAATAGTGATGATAGGGAATGGAGATTT
1 GCTATTCTAAGAATCATATTTATGTTTTGGTTAAGGAAAATAGTAATGATAAGGAATGGAGATTT
6518 ATAGAGTTTTATGGAGCGCCTTTTGCTAGTGATAGGAATACCACTTGGAACTTACTGCGTAGGTT
66 ATAGAGTTTTATGGAGCGCCTTTTGCTAGTGATAGGAATACCACTTGGAACTTACTGCGTAGGTT
*
6583 AGGTTAGAATCAAAATTATCCTTGGCTGGTGTATGGAGACTTTAATGAAATCATGTATTCTTTTG
131 AGGTTAGAATCAAAATTATCCTTGGCTAGTGTATGGAGACTTTAATGAAATCATGTATTCTTTTG
6648 AGAAGGTTGAGGGTGCCAAGAGAGGAAAGAAGGATAGTGGCTTTCCGGAAAGTACTTGAAGATTG
196 AGAAGGTTGAGGGTGCCAAGAGAGGAAAGAAGGATAGTGGCTTTCCGGAAAGTACTTGAAGATTG
*
6713 TAGACTTCTAGAAATAG
261 TAAACTTCTAGAAATAG
6730 GCTATTCTAAGAATCATATTTATGTTTTGGTTAAGGAAAATAGTAATGATAAGGAATGGAGATTT
1 GCTATTCTAAGAATCATATTTATGTTTTGGTTAAGGAAAATAGTAATGATAAGGAATGGAGATTT
* * * *
6795 ATCGGGTTTTATGGAGTGCCTTTTGCTAGTGATAGGAATACCACTTGGAACTTATTGCAG-AGGT
66 ATAGAGTTTTATGGAGCGCCTTTTGCTAGTGATAGGAATACCACTTGGAACTTACTGC-GTAGGT
*
6859 TAGGTTAGAATCAAAATTATCCTTGGCTAGTGTGTGGAGACTTTAATGAAATCATGTATTCTTTT
130 TAGGTTAGAATCAAAATTATCCTTGGCTAGTGTATGGAGACTTTAATGAAATCATGTATTCTTTT
* * *
6924 GAGAAGGTTG-GGAGTGCCAAGAGAGGAGAGAAGGATGGTGGCTTTCTGGAAAGTACTTGAAGAT
195 GAGAAGGTTGAGG-GTGCCAAGAGAGGAAAGAAGGATAGTGGCTTTCCGGAAAGTACTTGAAGAT
6988 TGTAAACTTCTAGA
259 TGTAAACTTCTAGA
7002 TGTAGGTTAT
Statistics
Matches: 257, Mismatches: 13, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
276 2 0.01
277 254 0.99
278 1 0.00
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.33
Consensus pattern (277 bp):
GCTATTCTAAGAATCATATTTATGTTTTGGTTAAGGAAAATAGTAATGATAAGGAATGGAGATTT
ATAGAGTTTTATGGAGCGCCTTTTGCTAGTGATAGGAATACCACTTGGAACTTACTGCGTAGGTT
AGGTTAGAATCAAAATTATCCTTGGCTAGTGTATGGAGACTTTAATGAAATCATGTATTCTTTTG
AGAAGGTTGAGGGTGCCAAGAGAGGAAAGAAGGATAGTGGCTTTCCGGAAAGTACTTGAAGATTG
TAAACTTCTAGAAATAG
Done.