Locus 1401

Sequence ID	2L_DroMel_CAF1
Location	3,734,794 – 3,734,887
Length	93
Max. P	0.844215

overview

Window 7

Location	3,734,794 – 3,734,887
Length	93
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	89.87
Mean single sequence MFE	-14.70
Consensus MFE	-11.44
Energy contribution	-11.92
Covariance contribution	0.48
Combinations/Pair	1.14
Mean z-score	-1.87
Structure conservation index	0.78
SVM decision value	0.76
SVM RNA-class probability	0.844215
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3734794 93 + 22407834
CAUUUAUAACCCGAAAACUUCUUAAUCAAGCCGCACAAACCACACAAGGG--UUUCCCUUGGUUUUCCCCGACUUCCAUUUCCCAUGGCUUUUCC
...........................((((((...........((((((--...))))))(((......)))............)))))).... ( -13.90)
>DroSec_CAF1 197015 93 + 1
CAUUUAUAACCCGAAAACUUCUUAAUCAAGCCGCACAAACCACACAAGGG--UUUCCCUUGGUUUUCCCCGACUUCCAUUUCCCAUGGCUUUUCC
...........................((((((...........((((((--...))))))(((......)))............)))))).... ( -13.90)
>DroSim_CAF1 204188 93 + 1
CAUUUAUAACCCGAAAACUUCUUAAUCAAGCCGCACAAACCACACAAGGG--UUUCCCUUGGUUUUCCCCGACUUCCAUUUCCCAUGGCUUUUCC
...........................((((((...........((((((--...))))))(((......)))............)))))).... ( -13.90)
>DroYak_CAF1 210609 93 + 1
CAUUUAUAACCCGAAAACUUCUUAAUCAAGCCGCACAAACCACACAAGGG--UUUCCCUUGGUUUUCCCCGACUUUCAUUUCCCAUGGCUUUCCC
...........................((((((...........((((((--...))))))(((......)))............)))))).... ( -13.90)
>DroAna_CAF1 222130 90 + 1
CAUUUAUAACCCGAAAACUUCUUAAUCAAGCCGCACAGACCGCAUUGGGGGUUUUCCCUCCGU----CCGGGCUUAUGUUUUCCC-AGCUUUUCC
............((((((.........(((((((.......))...(((((.....)))))..----...)))))..))))))..-......... ( -17.90)
>consensus
CAUUUAUAACCCGAAAACUUCUUAAUCAAGCCGCACAAACCACACAAGGG__UUUCCCUUGGUUUUCCCCGACUUCCAUUUCCCAUGGCUUUUCC
...........................(((((............((((((.....))))))(((......))).............))))).... (-11.44 = -11.92 +   0.48)

alignment

secondary structure

dotplot

Window 8

Location	3,734,794 – 3,734,887
Length	93
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	89.87
Mean single sequence MFE	-23.20
Consensus MFE	-19.28
Energy contribution	-19.32
Covariance contribution	0.04
Combinations/Pair	1.19
Mean z-score	-1.60
Structure conservation index	0.83
SVM decision value	0.70
SVM RNA-class probability	0.826364
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3734794 93 - 22407834
GGAAAAGCCAUGGGAAAUGGAAGUCGGGGAAAACCAAGGGAAA--CCCUUGUGUGGUUUGUGCGGCUUGAUUAAGAAGUUUUCGGGUUAUAAAUG
.(((((.((((.....))))((((((.(.(((((((((((...--)))))).))..))).).))))))..........)))))............ ( -23.40)
>DroSec_CAF1 197015 93 - 1
GGAAAAGCCAUGGGAAAUGGAAGUCGGGGAAAACCAAGGGAAA--CCCUUGUGUGGUUUGUGCGGCUUGAUUAAGAAGUUUUCGGGUUAUAAAUG
.(((((.((((.....))))((((((.(.(((((((((((...--)))))).))..))).).))))))..........)))))............ ( -23.40)
>DroSim_CAF1 204188 93 - 1
GGAAAAGCCAUGGGAAAUGGAAGUCGGGGAAAACCAAGGGAAA--CCCUUGUGUGGUUUGUGCGGCUUGAUUAAGAAGUUUUCGGGUUAUAAAUG
.(((((.((((.....))))((((((.(.(((((((((((...--)))))).))..))).).))))))..........)))))............ ( -23.40)
>DroYak_CAF1 210609 93 - 1
GGGAAAGCCAUGGGAAAUGAAAGUCGGGGAAAACCAAGGGAAA--CCCUUGUGUGGUUUGUGCGGCUUGAUUAAGAAGUUUUCGGGUUAUAAAUG
.....((((...((((((..((((((.(.(((((((((((...--)))))).))..))).).)))))).........)))))).))))....... ( -23.00)
>DroAna_CAF1 222130 90 - 1
GGAAAAGCU-GGGAAAACAUAAGCCCGG----ACGGAGGGAAAACCCCCAAUGCGGUCUGUGCGGCUUGAUUAAGAAGUUUUCGGGUUAUAAAUG
.....((((-.(((((...(((((((((----((.(.(((......)))....).)))))...)))))).........))))).))))....... ( -22.80)
>consensus
GGAAAAGCCAUGGGAAAUGGAAGUCGGGGAAAACCAAGGGAAA__CCCUUGUGUGGUUUGUGCGGCUUGAUUAAGAAGUUUUCGGGUUAUAAAUG
.....((((...((((((..((((((.(..((((((((((.....))))....)))))).).)))))).........)))))).))))....... (-19.28 = -19.32 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:46 2006