Locus 3497

Sequence ID	2L_DroMel_CAF1
Location	10,209,652 – 10,209,781
Length	129
Max. P	0.999963

overview

Window 2

Location	10,209,652 – 10,209,743
Length	91
Sequences	5
Columns	91
Reading direction	forward
Mean pairwise identity	92.42
Mean single sequence MFE	-24.26
Consensus MFE	-22.64
Energy contribution	-22.88
Covariance contribution	0.24
Combinations/Pair	1.08
Mean z-score	-2.84
Structure conservation index	0.93
SVM decision value	4.93
SVM RNA-class probability	0.999963
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10209652 91 + 22407834
GACGCAUCAAUGCCAUUUUAGCCACUUAGAUGGAACUCGAAAAGUAAAUAUUAUGUGGCGGUGGCAAAUGGAGACAUUAAGAACUAAGGCA
...((.....((((((....(((((...((((..(((.....)))...))))..))))).))))))((((....))))..........)). ( -25.30)
>DroSec_CAF1 2796 91 + 1
AACGCUUCAAUGCCAUUUUAGCCACUUAGAUGGAACUCCAAAAGUAAAUAUUAUGUGGCGGUGGCAAAUGGAGACAUUAAGAACUAAAGCA
...((((...((((((....(((((...((((..(((.....)))...))))..))))).))))))((((....))))........)))). ( -26.50)
>DroSim_CAF1 2530 91 + 1
AACGCUUCAAUGCCAUUUUAGCCACUUAGAUGGAACUCCAAAAGUAAAUAUUAUGUGGCGGUGGCAAAUGGAGACAUUAAGAACUAAGGCA
...((((...((((((....(((((...((((..(((.....)))...))))..))))).))))))((((....))))........)))). ( -26.20)
>DroEre_CAF1 2708 91 + 1
GGCGCUGUAAUGCCAUUUUAGCCAGUUAGAUAAAACUCCAAAAGUAAAUAUUAUAUGGCGGUGGCAAAUGAAGACAUUAAGAACUAAGGCA
...(((....((((((....((((....((((..(((.....)))...))))...)))).))))))((((....)))).........))). ( -18.20)
>DroYak_CAF1 2564 91 + 1
GCAGCUGUAAGGCCAUUUUAGCCACUUAGAUAAAACUCCAAAAGUAAAUAUUAUGUGGCGGUGGCAAAUGGAGACAUUAAGAACUAAGGCA
...(((...(((((((....(((((...((((..(((.....)))...))))..))))).))))).((((....)))).....))..))). ( -25.10)
>consensus
GACGCUUCAAUGCCAUUUUAGCCACUUAGAUGGAACUCCAAAAGUAAAUAUUAUGUGGCGGUGGCAAAUGGAGACAUUAAGAACUAAGGCA
...(((....((((((....(((((...((((..(((.....)))...))))..))))).))))))((((....)))).........))). (-22.64 = -22.88 +   0.24)

alignment

secondary structure

dotplot

Window 3

Location	10,209,682 – 10,209,781
Length	99
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	96.39
Mean single sequence MFE	-19.00
Consensus MFE	-16.68
Energy contribution	-17.08
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.38
Structure conservation index	0.88
SVM decision value	2.84
SVM RNA-class probability	0.997344
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10209682 99 + 22407834
UGGAACUCGAAAAGUAAAUAUUAUGUGGCGGUGGCAAAUGGAGACAUUAAGAACUAAGGCACAUAAAUACGUAUGCAAAUGUAUAU--AUAUACACAAAAC
.............(((....(((((((.((((....((((....))))....)))..).)))))))....((((((....))))))--...)))....... ( -20.10)
>DroSec_CAF1 2826 99 + 1
UGGAACUCCAAAAGUAAAUAUUAUGUGGCGGUGGCAAAUGGAGACAUUAAGAACUAAAGCACAUAAAUACGUAUGCAAAUGUAUAU--AUAUACACAAAAC
(((....)))...(((....(((((((.(..(((..((((....)))).....)))..))))))))....((((((....))))))--...)))....... ( -20.30)
>DroSim_CAF1 2560 99 + 1
UGGAACUCCAAAAGUAAAUAUUAUGUGGCGGUGGCAAAUGGAGACAUUAAGAACUAAGGCACAUAAAUACGUAUGCAAAUGUAUAU--AUAUACACAAAAC
(((....)))...(((....(((((((.((((....((((....))))....)))..).)))))))....((((((....))))))--...)))....... ( -22.30)
>DroEre_CAF1 2738 99 + 1
UAAAACUCCAAAAGUAAAUAUUAUAUGGCGGUGGCAAAUGAAGACAUUAAGAACUAAGGCACAUAAAUACGUAUGCAAAUGUAUAU--AUAUACACAAAAC
.............(((..((((.((((((..(((..((((....)))).....)))..)).)))))))).((((((....))))))--...)))....... ( -11.30)
>DroYak_CAF1 2594 101 + 1
UAAAACUCCAAAAGUAAAUAUUAUGUGGCGGUGGCAAAUGGAGACAUUAAGAACUAAGGCACAUAAAUACGUAUGCAAAUGUAUAUAUAUAUACACAAAAC
.............(((....(((((((.((((....((((....))))....)))..).)))))))(((..(((((....)))))..))).)))....... ( -21.00)
>consensus
UGGAACUCCAAAAGUAAAUAUUAUGUGGCGGUGGCAAAUGGAGACAUUAAGAACUAAGGCACAUAAAUACGUAUGCAAAUGUAUAU__AUAUACACAAAAC
.............(((....(((((((.((((....((((....))))....)))..).)))))))....((((((....)))))).....)))....... (-16.68 = -17.08 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:52 2006