Locus 1425

Sequence ID	3L_DroMel_CAF1
Location	4,134,657 – 4,134,823
Length	166
Max. P	0.893351

overview

Window 3

Location	4,134,657 – 4,134,752
Length	95
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	78.36
Mean single sequence MFE	-26.11
Consensus MFE	-21.42
Energy contribution	-21.37
Covariance contribution	-0.05
Combinations/Pair	1.35
Mean z-score	-1.52
Structure conservation index	0.82
SVM decision value	0.98
SVM RNA-class probability	0.893351
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4134657 95 + 23771897
UGUAUAUUUAC-------UUAUCCCAUUUAGAAAUCAAGGAGUGUGCCUCACUGCUGAAUGAGCUUAGGUCAAGGUCGCAGGACGCGACCUUUGCCAAUUUC
.(((....)))-------......(((((((......(((......))).....)))))))......(((.((((((((.....)))))))).)))...... ( -27.30)
>DroVir_CAF1 14619 98 + 1
U--ACA--GAGCUCAUACUAAUCCCUUGCAGAAAUCAAGAGCUGUGCGCCGGUGCUAAGCGAACUCCAGUUGAAGCGUAACGACCCCGACUUUGCCAAGCAA
.--.((--.(((((........................))))).))......((((..(((((.((..((((........))))...)).)))))..)))). ( -19.46)
>DroSec_CAF1 10921 95 + 1
AAUAUAUUUAC-------AUAUCCCAUUUAGAAAUCAAGGAGUGUGCCUCACUGCUGAAUGAGCUAAGGUCAAGGUCGCAGGACGCGACCUUUGCAAAUUUC
...........-------........(((((...(((((.((((.....)))).))...))).)))))((.((((((((.....)))))))).))....... ( -25.10)
>DroSim_CAF1 11983 95 + 1
AAUGUAUUUAC-------AUAUCCCAUUUAGAAAUCAAGGAGUGUGCCUCACUGCUGAAUGAGCUAAGGUCAAGGUCGCAGGACGCGACCUUUGCCAAUUUC
.((((....))-------)).......((((...(((((.((((.....)))).))...))).))))(((.((((((((.....)))))))).)))...... ( -28.70)
>DroEre_CAF1 12860 94 + 1
UGAAUAUUUAC-------CUAUCCCAU-UAGAAAUCAAGGAGUGUGCCUCGCUGCUGAAUGAGCUAAGGUCAAGGUCGCAGGACGCGACCUUUGCCAAUUUC
...........-------........(-(((...(((((.((((.....)))).))...))).))))(((.((((((((.....)))))))).)))...... ( -27.60)
>DroYak_CAF1 11144 95 + 1
UGAAUAUUAAC-------CUAUUCCAUUUAGAAAUCAAGGAGUGCGCCACGCUGCUGAAUGAGCUAAGGUCAAGGUCGCAGGACGCGACCUUUGCCAACUUC
.(((((.....-------.)))))...((((...(((((.((((.....)))).))...))).))))(((.((((((((.....)))))))).)))...... ( -28.50)
>consensus
UGUAUAUUUAC_______AUAUCCCAUUUAGAAAUCAAGGAGUGUGCCUCACUGCUGAAUGAGCUAAGGUCAAGGUCGCAGGACGCGACCUUUGCCAAUUUC
...........................((((..((..((.((((.....)))).))..))...))))(((.((((((((.....)))))))).)))...... (-21.42 = -21.37 +  -0.05)

alignment

secondary structure

dotplot

Window 4

Location	4,134,657 – 4,134,752
Length	95
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	78.36
Mean single sequence MFE	-26.72
Consensus MFE	-17.83
Energy contribution	-17.83
Covariance contribution	0.01
Combinations/Pair	1.38
Mean z-score	-1.35
Structure conservation index	0.67
SVM decision value	0.31
SVM RNA-class probability	0.684728
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4134657 95 - 23771897
GAAAUUGGCAAAGGUCGCGUCCUGCGACCUUGACCUAAGCUCAUUCAGCAGUGAGGCACACUCCUUGAUUUCUAAAUGGGAUAA-------GUAAAUAUACA
......((..((((((((.....))))))))..))....((((((.((.(((((((......)))).))).)).))))))....-------(((....))). ( -25.30)
>DroVir_CAF1 14619 98 - 1
UUGCUUGGCAAAGUCGGGGUCGUUACGCUUCAACUGGAGUUCGCUUAGCACCGGCGCACAGCUCUUGAUUUCUGCAAGGGAUUAGUAUGAGCUC--UGU--A
((((...)))).(((((.((.((...(((((....)))))..))...)).)))))(((.((((((((((..(.....)..)))))...))))).--)))--. ( -27.00)
>DroSec_CAF1 10921 95 - 1
GAAAUUUGCAAAGGUCGCGUCCUGCGACCUUGACCUUAGCUCAUUCAGCAGUGAGGCACACUCCUUGAUUUCUAAAUGGGAUAU-------GUAAAUAUAUU
...(((((((((((((((.....))))))))........((((((.((.(((((((......)))).))).)).))))))...)-------))))))..... ( -27.00)
>DroSim_CAF1 11983 95 - 1
GAAAUUGGCAAAGGUCGCGUCCUGCGACCUUGACCUUAGCUCAUUCAGCAGUGAGGCACACUCCUUGAUUUCUAAAUGGGAUAU-------GUAAAUACAUU
......((..((((((((.....))))))))..))....((((((.((.(((((((......)))).))).)).))))))..((-------((....)))). ( -25.30)
>DroEre_CAF1 12860 94 - 1
GAAAUUGGCAAAGGUCGCGUCCUGCGACCUUGACCUUAGCUCAUUCAGCAGCGAGGCACACUCCUUGAUUUCUA-AUGGGAUAG-------GUAAAUAUUCA
(((.......((((((((.....)))))))).((((...((((((.((...(((((......)))))....)))-)))))..))-------)).....))). ( -29.60)
>DroYak_CAF1 11144 95 - 1
GAAGUUGGCAAAGGUCGCGUCCUGCGACCUUGACCUUAGCUCAUUCAGCAGCGUGGCGCACUCCUUGAUUUCUAAAUGGAAUAG-------GUUAAUAUUCA
((((((((..((((((((.....))))))))..))...(((.....))).(((...))).......))))))......(((((.-------.....))))). ( -26.10)
>consensus
GAAAUUGGCAAAGGUCGCGUCCUGCGACCUUGACCUUAGCUCAUUCAGCAGCGAGGCACACUCCUUGAUUUCUAAAUGGGAUAA_______GUAAAUAUACA
......((..((((((((.....))))))))..))....((((((.(((((.(((.....))).)))....)).))))))...................... (-17.83 = -17.83 +   0.01)

alignment

secondary structure

dotplot

Window 5

Location	4,134,712 – 4,134,823
Length	111
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	71.61
Mean single sequence MFE	-43.17
Consensus MFE	-22.46
Energy contribution	-24.61
Covariance contribution	2.15
Combinations/Pair	1.36
Mean z-score	-1.52
Structure conservation index	0.52
SVM decision value	0.12
SVM RNA-class probability	0.593488
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4134712 111 + 23771897
GCUUAGGUCAAGGUCGCAGGACGCGACCUUUGCCAAUUUCCUGCGUGCCUCGAACGCGGUUUGCCAAAACAAGGGCACCCAGGUGUGCUGCCCCACUGGCCAGGG---CAUUAC
.....(((.((((((((.....)))))))).))).....((((.((((((.......((....)).......)))))).))))(((.(((((.....)).))).)---)).... ( -43.94)
>DroVir_CAF1 14677 111 + 1
ACUCCAGUUGAAGCGUAACGACCCCGACUUUGCCAAGCAAUUGCAGGCCUCCAAUUUGGUAUGCGGCAGGGUUGGCACCCAGGUCUGUUGUCCCACGGGCCAAAC---GGUGAC
......((((........)))).(((((((((((((....))(((.(((........))).))))))))))))))((((..(((((((......)))))))....---)))).. ( -39.40)
>DroSec_CAF1 10976 111 + 1
GCUAAGGUCAAGGUCGCAGGACGCGACCUUUGCAAAUUUCCUGCGUGCCUCGAACGCGGUUUGCCAGAACAAGGGCACCCAGGUGUGCUGUCCCACUGGCCAGGG---CAUCAC
(((..((((((((((((.....)))))))).(((.....((((.((((((.......((....)).......)))))).))))..))).........))))..))---)..... ( -43.64)
>DroSim_CAF1 12038 111 + 1
GCUAAGGUCAAGGUCGCAGGACGCGACCUUUGCCAAUUUCCUGCGUGCCUCGAACGCGGUCUGCCAGAACAAGGGCACCCAGGUGUGCUGUCCCACUGGCCAGGG---CAUCAC
(((..(((.((((((((.....)))))))).)))......((((((.......)))))).(((((((....((.((((....)))).))......)))).)))))---)..... ( -46.10)
>DroYak_CAF1 11199 114 + 1
GCUAAGGUCAAGGUCGCAGGACGCGACCUUUGCCAACUUCCUGCGUGCCUCCAACACCAUUUGCCAGAACAGGGGCACCCAGGUGUGCUGCCCCACCGCACAGGGCAACAACGC
((...(((.((((((((.....)))))))).))).((..((((.(((((((....................))))))).)))).))))(((((.........)))))....... ( -43.75)
>DroPer_CAF1 10033 111 + 1
ACUGAUUGCCAAGCAGAAGGAUUCCACCUUCGUGAGCUUCCUGCAGGCCUCGCAGCGCAUCUGCGGCAACGUAGGCUCCACGGUCUGCUGCCCCAAUGGCCAGAC---GGCGAC
.....(((((.....(((((......)))))((((((...((((.......)))).....(((((....)))))))).))).(((((..(((.....))))))))---))))). ( -42.20)
>consensus
GCUAAGGUCAAGGUCGCAGGACGCGACCUUUGCCAAUUUCCUGCGUGCCUCGAACGCGGUUUGCCAGAACAAGGGCACCCAGGUGUGCUGCCCCACUGGCCAGGG___CAUCAC
.....(((.((((((((.....)))))))).))).....((((.((((((.......((....)).......)))))).))))....(((.((....)).)))........... (-22.46 = -24.61 +   2.15)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:11 2006