Locus 6332

Sequence ID	2L_DroMel_CAF1
Location	17,672,427 – 17,672,541
Length	114
Max. P	0.965505

overview

Window 1

Location	17,672,427 – 17,672,541
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	94.64
Mean single sequence MFE	-20.49
Consensus MFE	-18.30
Energy contribution	-18.54
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.50
Structure conservation index	0.89
SVM decision value	1.17
SVM RNA-class probability	0.925979
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17672427 114 + 22407834
CAAAAGUGACAAUGAAAAGCAGGAAAGCGGGAAAUUCCACUGCCAGGAUAAGACAGGAUGGAAAAAAGUGCUGCGUAAUCAGAUUAAAAGUGCGAAAAAGGAAAAGAGCUUUGG
.......................(((((......(((((...((.(.......).)).)))))....(..((...((((...))))..))..)..............))))).. ( -15.40)
>DroSec_CAF1 67940 114 + 1
CAAAAGUGACAAUGAAAAGCAGGAAAGCGGGAAAUUCCACUGCCAGGAUAAGGCAGGAUGGAAAAAAGUGUUGCGUAAUCAGAUUAAAAGUGCGAAAAAGGAAAAGAGCUUUGG
.....(..(((.......((......))......((((((((((.......)))))..))))).....)))..)............(((((.(............).))))).. ( -21.20)
>DroSim_CAF1 50457 114 + 1
CAAAAGUGACAAUGAAAAGCAGGAAAGCGGGAAAUUCCACUGCCAGGAUAAGGCAGGAUGGAAAAAAGUGCUGCGUAAUCAGAUUAAAAGUGCGAAAAAGGAAGAGAGCUUUGG
.......................(((((......((((.(((((.......)))))...........(..((...((((...))))..))..)......))))....))))).. ( -22.60)
>DroEre_CAF1 55298 111 + 1
CAAAAGUGACAAUGAAAAGCAGGAAAGCGGGAAAUUCCACUGCCAGAAUAAGGCAGCAUGGAA--AACUGCUACGUAAUCAGAUUAAAAGUGCGAAAAAG-AAAAGAGCUUUGG
...............(((((.....(((((....((((((((((.......)))))..)))))--..))))).((((.............))))......-......))))).. ( -24.92)
>DroYak_CAF1 71709 112 + 1
CAAAAGUGACAAUGAAAAGCAGGAAAGCGGGAAAUUCCACUGCCAGGAUAGGGGAGGAUGGAAA-AAUUGCUACGUAAUCAGAUUAAAAGUGCGAAAAAG-AAAAAAGCUUUGG
...............(((((.....(((((....(((((((.((.......)).))..))))).-..))))).((((.............))))......-......))))).. ( -18.32)
>consensus
CAAAAGUGACAAUGAAAAGCAGGAAAGCGGGAAAUUCCACUGCCAGGAUAAGGCAGGAUGGAAAAAAGUGCUGCGUAAUCAGAUUAAAAGUGCGAAAAAGGAAAAGAGCUUUGG
...............(((((.....((((.....((((((((((.......)))))..))))).....)))).((((.............)))).............))))).. (-18.30 = -18.54 +   0.24)

alignment

secondary structure

dotplot

Window 2

Location	17,672,427 – 17,672,541
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	94.64
Mean single sequence MFE	-16.68
Consensus MFE	-14.75
Energy contribution	-14.75
Covariance contribution	0.00
Combinations/Pair	1.10
Mean z-score	-1.67
Structure conservation index	0.88
SVM decision value	1.58
SVM RNA-class probability	0.965505
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17672427 114 - 22407834
CCAAAGCUCUUUUCCUUUUUCGCACUUUUAAUCUGAUUACGCAGCACUUUUUUCCAUCCUGUCUUAUCCUGGCAGUGGAAUUUCCCGCUUUCCUGCUUUUCAUUGUCACUUUUG
..(((((..............((.................))(((......(((((..(((((.......))))))))))......))).....)))))............... ( -16.03)
>DroSec_CAF1 67940 114 - 1
CCAAAGCUCUUUUCCUUUUUCGCACUUUUAAUCUGAUUACGCAACACUUUUUUCCAUCCUGCCUUAUCCUGGCAGUGGAAUUUCCCGCUUUCCUGCUUUUCAUUGUCACUUUUG
..(((((..............((.................)).........(((((..(((((.......))))))))))......)))))....................... ( -16.63)
>DroSim_CAF1 50457 114 - 1
CCAAAGCUCUCUUCCUUUUUCGCACUUUUAAUCUGAUUACGCAGCACUUUUUUCCAUCCUGCCUUAUCCUGGCAGUGGAAUUUCCCGCUUUCCUGCUUUUCAUUGUCACUUUUG
..(((((..............((.................))(((......(((((..(((((.......))))))))))......))).....)))))............... ( -18.73)
>DroEre_CAF1 55298 111 - 1
CCAAAGCUCUUUU-CUUUUUCGCACUUUUAAUCUGAUUACGUAGCAGUU--UUCCAUGCUGCCUUAUUCUGGCAGUGGAAUUUCCCGCUUUCCUGCUUUUCAUUGUCACUUUUG
.(((((.......-..........................((((((...--.....)))))).......(((((((((((......((......)).))))))))))).))))) ( -19.40)
>DroYak_CAF1 71709 112 - 1
CCAAAGCUUUUUU-CUUUUUCGCACUUUUAAUCUGAUUACGUAGCAAUU-UUUCCAUCCUCCCCUAUCCUGGCAGUGGAAUUUCCCGCUUUCCUGCUUUUCAUUGUCACUUUUG
.(((((((....(-(...................))......)))....-...................(((((((((((......((......)).)))))))))))..)))) ( -12.61)
>consensus
CCAAAGCUCUUUUCCUUUUUCGCACUUUUAAUCUGAUUACGCAGCACUUUUUUCCAUCCUGCCUUAUCCUGGCAGUGGAAUUUCCCGCUUUCCUGCUUUUCAUUGUCACUUUUG
..(((((..............((.................))(((......(((((..(((((.......))))))))))......))).....)))))............... (-14.75 = -14.75 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:32 2006