Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009733.1 Kokia drynarioides strain JFW-HI SEQ_124452, 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: 13356
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Found at i:450 original size:37 final size:37
Alignment explanation
Indices: 400--509 Score: 130
Period size: 37 Copynumber: 3.0 Consensus size: 37
390 CATATCACTT
* *
400 GTTTTGATCCACTTCTCTGTGTTTCATCAGGAAGATG
1 GTTTTGATCCACTTCTCAGTATTTCATCAGGAAGATG
* * * *
437 GTTTTGATTCACTTCCCCGTATTTCATCAGGAAGACG
1 GTTTTGATCCACTTCTCAGTATTTCATCAGGAAGATG
** * *
474 AATTTGGTCCACTTCTCAGTATCTCATCAGGAAGAT
1 GTTTTGATCCACTTCTCAGTATTTCATCAGGAAGAT
510 AACCTTTTAT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (37 bp):
GTTTTGATCCACTTCTCAGTATTTCATCAGGAAGATG
Found at i:812 original size:205 final size:205
Alignment explanation
Indices: 455--1256 Score: 1388
Period size: 205 Copynumber: 3.9 Consensus size: 205
445 TCACTTCCCC
* * *
455 GTATTTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATAACCTTTTAT
1 GTATCTCATCAGGAAGACGAATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTAT
* * *
520 TGCTTCGACCTGCTTCTTAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCACATCGAGT
66 TGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGC
* *
585 GTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGTGTCGTTTGTTTCAAT
131 GTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAAT
650 TCGCTTCTCT
196 TCGCTTCTCT
660 GTATCTCATCAGGAAGACGAATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTAT
1 GTATCTCATCAGGAAGACGAATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTAT
*
725 TGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGT
66 TGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGC
* *
790 GTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAAATGACCGCGTCATTTGTTTCAAT
131 GTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAAT
* *
855 TCGATTCTTT
196 TCGCTTCTCT
* *
865 GTATCTCATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTAT
1 GTATCTCATCAGGAAGACGAATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTAT
* * *
930 TGCTTCGACCTACTTCTCAGTGTCTCATTAGGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGC
66 TGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGC
995 GTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAAT
131 GTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAAT
1060 TCGCTTCTCT
196 TCGCTTCTCT
* *
1070 GTATCTCACCAGGAAGACGAGTTTGGTACACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTAT
1 GTATCTCATCAGGAAGACGAATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTAT
* *
1135 TGCTTCGACCTGCTTCTCAATGTCTCATCAGGGAGCTGGGGTTCGAAGATTTGCTCACATCGAGC
66 TGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGC
* *
1200 ATGGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACCGCGTCGTTT
131 GTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTT
1257 ATGGATAATC
Statistics
Matches: 565, Mismatches: 32, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
205 565 1.00
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (205 bp):
GTATCTCATCAGGAAGACGAATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTAT
TGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGC
GTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAAT
TCGCTTCTCT
Done.