Locus 2072

Sequence ID	3R_DroMel_CAF1
Location	5,890,911 – 5,891,068
Length	157
Max. P	0.820383

overview

Window 2

Location	5,890,911 – 5,891,028
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.80
Mean single sequence MFE	-35.70
Consensus MFE	-29.19
Energy contribution	-29.70
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.71
Structure conservation index	0.82
SVM decision value	0.13
SVM RNA-class probability	0.599758
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5890911 117 + 27905053
CGUCAUGCGGUUUUCAUCGGGUAUUAUUUUCCAUGGACUUAUUUCUUUAUCAGGAAAGGGGUGGCCUGACAAGGGUCAC--ACCCUCCGAUGGGCA-AUGCCUUUCUUAACGCACAAUCA
.....((((.....(((((((......((((((((((........)))))..)))))((((((((((.....)))))))--.))))))))))(((.-..)))........))))...... ( -37.00)
>DroSim_CAF1 15623 117 + 1
CGUCAUGCGGUUUUCAUCGCGUAUUAUUUUCCAUGGAUUUAUUUCUUUAUCAGGAAAGGGGUGGCCUGACAAGGGUCAC--ACCCUCCUAUGGGCA-AUGCCUUUCUUAACGCACAAUCA
(((.(((((((....)))))))..((((.(((((((.....(((((......)))))((((((((((.....)))))))--.)))..))))))).)-))).........)))........ ( -34.70)
>DroEre_CAF1 14808 117 + 1
CGUCAUGCGGUUUUCAUCGCGUAUUAUUUUCCAUGGACUUAUUUC-UGAUCAGGAAAGGGGUGGCCUGUCAAGGGUCAC--ACCCUCCGAUGGGCAAAUGCCUUUCUUAACGCACAAUCA
.....((((.....(((((........(((((.(((.(.......-.).))))))))((((((((((.....)))))))--.)))..)))))(((....)))........))))...... ( -36.60)
>DroYak_CAF1 15091 118 + 1
CGUCCUGCGGUUUUCAGCGCGUAUUAUUUUCCAUGGACUUAUUUU-GGAUCAGGAAAGGGGUGGCCUGACAUGGGUCACACACCCUCCGAUGGGCA-AUGCCUUUCUUAACGCACAAUCA
......((........))((((.......((((...........)-)))..((((((((.(((((((.....)))))))...(((......)))..-...)))))))).))))....... ( -34.50)
>consensus
CGUCAUGCGGUUUUCAUCGCGUAUUAUUUUCCAUGGACUUAUUUC_UGAUCAGGAAAGGGGUGGCCUGACAAGGGUCAC__ACCCUCCGAUGGGCA_AUGCCUUUCUUAACGCACAAUCA
.....((((.....(((((........(((((.(((.............))))))))((((((((((.....)))))))...)))..)))))(((....)))........))))...... (-29.19 = -29.70 +   0.50)

alignment

secondary structure

dotplot

Window 3

Location	5,890,951 – 5,891,068
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.65
Mean single sequence MFE	-32.25
Consensus MFE	-27.50
Energy contribution	-28.00
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.00
Structure conservation index	0.85
SVM decision value	0.68
SVM RNA-class probability	0.820383
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5890951 117 + 27905053
AUUUCUUUAUCAGGAAAGGGGUGGCCUGACAAGGGUCAC--ACCCUCCGAUGGGCA-AUGCCUUUCUUAACGCACAAUCAAAUCACUUUGCGAAUUCAAUUUGGCAAAAAUAAUGUGAAU
............(((..((((((((((.....)))))))--.))))))((.((((.-..)))).))................(((((((((.((......)).)))))......)))).. ( -31.90)
>DroSim_CAF1 15663 117 + 1
AUUUCUUUAUCAGGAAAGGGGUGGCCUGACAAGGGUCAC--ACCCUCCUAUGGGCA-AUGCCUUUCUUAACGCACAAUCAAAUCACUUUGCGAAUUCAAUUUGGCAAAAAUAAUGUGAAU
...........((((((((.(((((((.....)))))))--.(((......)))..-...))))))))..............(((((((((.((......)).)))))......)))).. ( -31.70)
>DroEre_CAF1 14848 117 + 1
AUUUC-UGAUCAGGAAAGGGGUGGCCUGUCAAGGGUCAC--ACCCUCCGAUGGGCAAAUGCCUUUCUUAACGCACAAUCAAAUCACUUUGGGAAUUCAAUUUGGCAAAAAUAAUGUGAAU
.....-.....((((((((.((.(((((((.((((....--.))))..)))))))..)).))))))))..((((........(((..((((....))))..))).........))))... ( -31.23)
>DroYak_CAF1 15131 118 + 1
AUUUU-GGAUCAGGAAAGGGGUGGCCUGACAUGGGUCACACACCCUCCGAUGGGCA-AUGCCUUUCUUAACGCACAAUCAAAUCACUUUGCGAAUUCAAUUUGGCAAAAAUAAUGUGCAU
.....-.....((((((((.(((((((.....)))))))...(((......)))..-...))))))))...(((((..........(((((.((......)).))))).....))))).. ( -34.16)
>consensus
AUUUC_UGAUCAGGAAAGGGGUGGCCUGACAAGGGUCAC__ACCCUCCGAUGGGCA_AUGCCUUUCUUAACGCACAAUCAAAUCACUUUGCGAAUUCAAUUUGGCAAAAAUAAUGUGAAU
...........((((((((.(((((((.....)))))))...(((......)))......))))))))..............(((((((((.((......)).)))))......)))).. (-27.50 = -28.00 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:36 2006