Locus 2362

Sequence ID	3L_DroMel_CAF1
Location	6,623,692 – 6,623,985
Length	293
Max. P	0.994257

overview

Window 1

Location	6,623,692 – 6,623,801
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.48
Mean single sequence MFE	-26.42
Consensus MFE	-21.04
Energy contribution	-21.00
Covariance contribution	-0.04
Combinations/Pair	1.16
Mean z-score	-1.49
Structure conservation index	0.80
SVM decision value	0.22
SVM RNA-class probability	0.639746
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6623692 109 + 23771897
CCACUAAAU-UCUUU----------GUUAAUGUGCCAUUUAACGGCGCGGACCAGAGAGUCAAAGUCAAGUCGAGUAAUUUCCUUUAAUGGCUUUUCAUUUCAUCGAUAGUGACACUUUC
.(((((.((-(((((----------(....((((((.......))))))...)))))))).(((((((((..((....))..))....)))))))............)))))........ ( -25.60)
>DroSec_CAF1 731 109 + 1
CCACUAAAU-UCUUU----------GUUAAUGUGCCAUUUAACGGUGCGGACCAGAGAGUCAAAGUCAAGUCGGGUAAUUUCCUUUAAUGGCUUUUCAUUUCAUCGAUAGUGACACUUUC
.(((((.((-(((((----------(....((..((.......))..))...)))))))).(((((((....(((......)))....)))))))............)))))........ ( -26.10)
>DroSim_CAF1 8866 109 + 1
CCACUAAAU-UCUUU----------GUUAAUGUGCCAUUUAACGGCGCGGACCAGAGAGUCAAAGUCAAGUCGGGUAAUUUCCUUUAAUGGCUUUUCAUUUCAUCGAUAGUGACACUUUC
.(((((.((-(((((----------(....((((((.......))))))...)))))))).(((((((....(((......)))....)))))))............)))))........ ( -28.50)
>DroYak_CAF1 2704 110 + 1
CCACUAAAUUUCUUU----------GCUAAUGUGCCAUUUAACGGCGCGGACCAGAGACUCAAAGUCAAGUCGGGUAAUUUCCUUUAAUGGCUUUUCAUUUCAUCGAUAGUGACACUUUC
.(((((....(((((----------(....((((((.......))))))...))))))...(((((((....(((......)))....)))))))............)))))........ ( -26.80)
>DroAna_CAF1 839 119 + 1
CUACUAAAU-UUUUUCCUCUAUGUCGUUAAUGUGCCAUUUAACGGCGGAGCGAGCAAAGUCAAAGUCAAGUUGGGUAAUUUCCUCUAAUGGCUUUUCAUUUCAUCGAUAGUGACACUUUC
.(((((...-......((((..((((((((........))))))))))))(((..(((...(((((((....(((......)))....)))))))...)))..))).)))))........ ( -25.10)
>consensus
CCACUAAAU_UCUUU__________GUUAAUGUGCCAUUUAACGGCGCGGACCAGAGAGUCAAAGUCAAGUCGGGUAAUUUCCUUUAAUGGCUUUUCAUUUCAUCGAUAGUGACACUUUC
.(((((........................((((((.......)))))).....((((...(((((((....(((......)))....)))))))...)))).....)))))........ (-21.04 = -21.00 +  -0.04)

alignment

secondary structure

dotplot

Window 2

Location	6,623,801 – 6,623,894
Length	93
Sequences	4
Columns	95
Reading direction	reverse
Mean pairwise identity	95.04
Mean single sequence MFE	-30.18
Consensus MFE	-24.79
Energy contribution	-24.48
Covariance contribution	-0.31
Combinations/Pair	1.10
Mean z-score	-1.81
Structure conservation index	0.82
SVM decision value	0.08
SVM RNA-class probability	0.575528
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6623801 93 - 23771897
UUAGCACUUCUUUUUCGGAAGGGUGCGGGG--GCUUAGUAAUUGACCACGCCCCCGUUGUGUAGUUGUCUUUUUUACGGCAUCACGAUGGCCAUU
...(((((.((((....)))))))))((((--((...((.....))...))))))((((((....((((........)))).))))))....... ( -30.70)
>DroSec_CAF1 840 93 - 1
UUAGCACUUCUUUUUCGGAAGGGUGCUGGG--GCUUAGUAAUUGACCACGCCCCCGUUGUGUAGUUGUCUUUUUUACGGCAUCACGAUGGCCAUU
.(((((((.((((....)))))))))))((--((...((.....))...))))((((((((....((((........)))).))))))))..... ( -29.50)
>DroSim_CAF1 8975 93 - 1
UUAGCACUUAUUUUUCGGAAGGGUGCGGGG--GCUUAGUAAUUGACCACGCCCCCGUUGUGUAGUUGUCUUUUUUACGGCAUCACGAUGGCCAUU
...(((((..((.....))..)))))((((--((...((.....))...))))))((((((....((((........)))).))))))....... ( -29.00)
>DroYak_CAF1 2814 95 - 1
UUAGCACUUAUUUUUCGGAAGGGUGCGGGGCGGUGUAGUAAUUGACCACGCCCCCGUCUUGUAGUUGUCUUUUUUACGGCAUCAGGAUGGCCAUU
...(((((..((.....))..)))))((((((..((........))..))))))(((((((....((((........)))).)))))))...... ( -31.50)
>consensus
UUAGCACUUAUUUUUCGGAAGGGUGCGGGG__GCUUAGUAAUUGACCACGCCCCCGUUGUGUAGUUGUCUUUUUUACGGCAUCACGAUGGCCAUU
................((..(((((.((.................)).)))))((((((((....((((........)))).))))))))))... (-24.79 = -24.48 +  -0.31)

alignment

secondary structure

dotplot

Window 3

Location	6,623,894 – 6,623,985
Length	91
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.19
Mean single sequence MFE	-24.10
Consensus MFE	-22.88
Energy contribution	-22.56
Covariance contribution	-0.32
Combinations/Pair	1.07
Mean z-score	-2.07
Structure conservation index	0.95
SVM decision value	2.46
SVM RNA-class probability	0.994257
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6623894 91 + 23771897
ACAGGAAAUGAUUUCCUGGCCACU-----------------------------CUCAACCCUCUGGUAAUGAAAUCAUGAAUUAGAUUUUGAGCUUGAAAAUUGUUAUUGUUUUCGGCCA
..(((((.....)))))((((...-----------------------------(((((...((((((.(((....)))..))))))..)))))...((((((.......)))))))))). ( -25.00)
>DroSec_CAF1 933 91 + 1
ACAGGAAAUGAUUUUCUGGCCACU-----------------------------CUCAACCCUCUGGUAAUGAAAUCAUGAAUUAGAUUUUGAGCUUGAAAAUUGUUAUUGUUUUCGGCCA
...(((((....)))))((((...-----------------------------(((((...((((((.(((....)))..))))))..)))))...((((((.......)))))))))). ( -23.40)
>DroSim_CAF1 9068 91 + 1
ACAGGAAAUGAUUUUCUGGCCACU-----------------------------CUCAACCCUCUGGUAAUGAAAUCAUGAAUUAGAUUUUGAGCUUGAAAAUUGUUAUUGUUUUCGGCCA
...(((((....)))))((((...-----------------------------(((((...((((((.(((....)))..))))))..)))))...((((((.......)))))))))). ( -23.40)
>DroYak_CAF1 2909 95 + 1
ACAGGAAAUGAUUUUCUGGCCACUCU-------------------------CUCUCAACCCUCUGGUAAUGAAAUCAUGAAUUAGAUUUUGAGCUUGAAAAUUGUUAUUGUUUUCGGCCA
...(((((....)))))((((.....-------------------------..(((((...((((((.(((....)))..))))))..)))))...((((((.......)))))))))). ( -23.40)
>DroAna_CAF1 1058 120 + 1
ACAGGAAAUGAUUUUCUGGCCACUCCUUAGCCUCCAGCCCUCAGCCCUUAGCUCUCAGCCCUCUGGUAAUGAAAUCAUGAAUUAGAUUUUGAGCUUGAAAAUUGUUAUUGUUUUCGGCCA
...(((((....)))))((((............................(((((...(((....)))...((((((........))))))))))).((((((.......)))))))))). ( -25.30)
>consensus
ACAGGAAAUGAUUUUCUGGCCACU_____________________________CUCAACCCUCUGGUAAUGAAAUCAUGAAUUAGAUUUUGAGCUUGAAAAUUGUUAUUGUUUUCGGCCA
..(((((.....)))))((((................................(((((...((((((.(((....)))..))))))..)))))...((((((.......)))))))))). (-22.88 = -22.56 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:26 2006