Locus 4974

Sequence ID	2R_DroMel_CAF1
Location	16,219,938 – 16,220,038
Length	100
Max. P	0.991303

overview

Window 1

Location	16,219,938 – 16,220,038
Length	100
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	77.53
Mean single sequence MFE	-38.18
Consensus MFE	-23.12
Energy contribution	-23.76
Covariance contribution	0.64
Combinations/Pair	1.21
Mean z-score	-2.53
Structure conservation index	0.61
SVM decision value	2.26
SVM RNA-class probability	0.991303
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16219938 100 + 20766785
----GUGGGUGGGUGAGUGGCGCUUCCGCUACGAAUUGAUUUGCUCCACUUG-AGGAGCACCAU-----CACAGCUCCUGGCAAAAUCCAGCCCACUUAAUUAAACCAGC
----((((((((((((((((((....)))))).........((((((.....-.))))))...)-----))).((.....)).....))).))))).............. ( -36.30)
>DroSec_CAF1 975 93 + 1
GU--------GGGUGAGUGGGGCUUCCGCUUCGAAUUGAUUUGCUCCACUCG-AGGAGCUG--------UGCUGGUGCUGCGAAAAUCCAACCCACUUAAUUAAACCAGC
((--------(((((((((((((.....(........)....))))))))).-.(((....--------(((.......)))....))).)))))).............. ( -33.30)
>DroSim_CAF1 998 101 + 1
GUGUGUGAGUGGGUGAGUGGGGCUUCCGCUUCGAAUUGAUUUGCUCCACUCG-AGGAGCUG--------UGCUGGUGCUGCGAAAAUCCUGCCCACUUAAUUAAACCAGC
.....((((((((((((((((((.....(........)....))))))))).-((((....--------(((.......)))....)))))))))))))........... ( -38.00)
>DroEre_CAF1 5749 103 + 1
------GAGUGGGUGAGUGGGGCAUCCGCCUCGAAUUGAUUUGCUCCACUCG-AGGAGCUGGUGGGGAAGUAGGGCGGUGGGAAAGUACAGCCCACUUAAUUAAACCAGC
------(((((((..((((((((....)))))......)))..).)))))).-....((((((....((((.((((.(((......))).))))))))......)))))) ( -42.30)
>DroYak_CAF1 12097 99 + 1
------GAGUGGGUGUGUGGGGCAUCCGCUUUGAAUUGAUUUGCUCCACUUGGUGGAGCGGGCG-----UUUUGGGGGUGGGCGAAUACAGCCCACUUAAUUAAACCAGC
------((((((((((.....))))))))))......(.((((((((((...)))))))))))(-----(((...((((((((.......))))))))....)))).... ( -41.00)
>consensus
______GAGUGGGUGAGUGGGGCUUCCGCUUCGAAUUGAUUUGCUCCACUCG_AGGAGCUG________UGCUGGUGCUGGGAAAAUCCAGCCCACUUAAUUAAACCAGC
......((((((((...((((((....)))))).........(((((.......)))))...............................))))))))............ (-23.12 = -23.76 +   0.64)

alignment

secondary structure

dotplot

Window 2

Location	16,219,938 – 16,220,038
Length	100
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	77.53
Mean single sequence MFE	-31.29
Consensus MFE	-19.08
Energy contribution	-19.28
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.18
Structure conservation index	0.61
SVM decision value	1.46
SVM RNA-class probability	0.955857
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16219938 100 - 20766785
GCUGGUUUAAUUAAGUGGGCUGGAUUUUGCCAGGAGCUGUG-----AUGGUGCUCCU-CAAGUGGAGCAAAUCAAUUCGUAGCGGAAGCGCCACUCACCCACCCAC----
..............(((((((((......)))).....(((-----((((((((((.-.....))))).............((....)))))).))))...)))))---- ( -35.30)
>DroSec_CAF1 975 93 - 1
GCUGGUUUAAUUAAGUGGGUUGGAUUUUCGCAGCACCAGCA--------CAGCUCCU-CGAGUGGAGCAAAUCAAUUCGAAGCGGAAGCCCCACUCACCC--------AC
..............((((((.((..((((((.((....)).--------..(((((.-.....))))).............))))))..)).))))))..--------.. ( -30.60)
>DroSim_CAF1 998 101 - 1
GCUGGUUUAAUUAAGUGGGCAGGAUUUUCGCAGCACCAGCA--------CAGCUCCU-CGAGUGGAGCAAAUCAAUUCGAAGCGGAAGCCCCACUCACCCACUCACACAC
.............((((((..((..((((((.((....)).--------..(((((.-.....))))).............))))))..))......))))))....... ( -29.20)
>DroEre_CAF1 5749 103 - 1
GCUGGUUUAAUUAAGUGGGCUGUACUUUCCCACCGCCCUACUUCCCCACCAGCUCCU-CGAGUGGAGCAAAUCAAUUCGAGGCGGAUGCCCCACUCACCCACUC------
((((((......((((((((.((........)).)))).))))....))))))....-.((((((.(((......((((...))))))).))))))........------ ( -32.80)
>DroYak_CAF1 12097 99 - 1
GCUGGUUUAAUUAAGUGGGCUGUAUUCGCCCACCCCCAAAA-----CGCCCGCUCCACCAAGUGGAGCAAAUCAAUUCAAAGCGGAUGCCCCACACACCCACUC------
((((((........((((((.......))))))........-----.))).(((((((...)))))))............)))((.((.......)).))....------ ( -28.53)
>consensus
GCUGGUUUAAUUAAGUGGGCUGGAUUUUCCCAGCACCAGAA________CAGCUCCU_CGAGUGGAGCAAAUCAAUUCGAAGCGGAAGCCCCACUCACCCACUC______
..............(((((................................(((((.......))))).............((....)))))))................ (-19.08 = -19.28 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:30 2006