Locus 3612

Sequence ID 3L_DroMel_CAF1
Location 10,643,212 – 10,643,306
Length 94
Max. P 0.996748
window5630 window5631

overview

Window 0

Location 10,643,212 – 10,643,306
Length 94
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 76.12
Mean single sequence MFE -14.52
Consensus MFE -8.06
Energy contribution -8.02
Covariance contribution -0.04
Combinations/Pair 1.08
Mean z-score -1.66
Structure conservation index 0.56
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10643212 94 + 23771897
UCAACCUUAGCCCAACCUUUGGCAAA---ACCGAAUUUUCCACACCUCCCAC----------------UUAUUUU-CGGGGAGUUGUUUUCCUGUCUCUUCGGUUGUGUU------UUUU
.(((((...(((........)))...---...((.......(((.(((((.(----------------.......-.)))))).))).......)).....)))))....------.... ( -20.24)
>DroSec_CAF1 5708 96 + 1
UCCACCUUAGCCCAACCUUUAUCCAA---ACCAAAUUUUCCACACCUCCCCC----------------UUAUUUU-CGGGGAGUUGUUUUCCUGUCUCUUCGGUUGUUUUU----UUUUU
............(((((.........---............(((.((((((.----------------.......-.)))))).)))......(......)))))).....----..... ( -16.10)
>DroSim_CAF1 5712 100 + 1
UCCACCUUAGCCCAACCUUUAGCCAA---AACGAAUUUUCCACACCUCCCCC----------------UUAUUUU-CGGGAAGUUGUUUUCCUGUCUCUUCGGUUGUUUUUUUUUUUUUU
............(((((...((.(((---(((.((((((((...........----------------.......-.))))))))))))...)).))....))))).............. ( -12.11)
>DroEre_CAF1 5820 97 + 1
UCCACCUCAGCCCAACCUUUAGCCA----ACCCGAUUUUCCCCAUCUACCCC----------CAGCCCACAUUUUCUGGGAAGUUGUUUUCCUGUCUCCUCGGUUGUU---------UUU
.......(((((.......(((.((----((..(((.......)))....((----------(((..........)))))..)))).....))).......)))))..---------... ( -12.44)
>DroYak_CAF1 5746 110 + 1
UCCACCUUAGCCCAACCUUUAGCCAACCAACCCGAUGUUCCGCACCUACCCCACCCCCCUACCAUCCCAU-UUUGCAGGGGAGUUGUUUUCCUGUCUCUUCAGUUGUU---------UUC
............((((.....((....((......))....))............(((((..((......-..)).))))).)))).....(((......))).....---------... ( -11.70)
>consensus
UCCACCUUAGCCCAACCUUUAGCCAA___ACCCAAUUUUCCACACCUCCCCC________________UUAUUUU_CGGGGAGUUGUUUUCCUGUCUCUUCGGUUGUUUU______UUUU
............(((((............................................................((((((....))))))(......)))))).............. ( -8.06 =  -8.02 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,643,212 – 10,643,306
Length 94
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 76.12
Mean single sequence MFE -23.94
Consensus MFE -11.89
Energy contribution -12.53
Covariance contribution 0.64
Combinations/Pair 1.22
Mean z-score -2.70
Structure conservation index 0.50
SVM decision value 2.74
SVM RNA-class probability 0.996748
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10643212 94 - 23771897
AAAA------AACACAACCGAAGAGACAGGAAAACAACUCCCCG-AAAAUAA----------------GUGGGAGGUGUGGAAAAUUCGGU---UUUGCCAAAGGUUGGGCUAAGGUUGA
....------....(((((...(((((.(((..(((.((((((.-.......----------------).))))).)))......))).))---)))(((........)))...))))). ( -25.20)
>DroSec_CAF1 5708 96 - 1
AAAAA----AAAAACAACCGAAGAGACAGGAAAACAACUCCCCG-AAAAUAA----------------GGGGGAGGUGUGGAAAAUUUGGU---UUGGAUAAAGGUUGGGCUAAGGUGGA
.....----.......(((..............(((.((((((.-.......----------------.)))))).))).......(((((---(..(.......)..)))))))))... ( -21.40)
>DroSim_CAF1 5712 100 - 1
AAAAAAAAAAAAAACAACCGAAGAGACAGGAAAACAACUUCCCG-AAAAUAA----------------GGGGGAGGUGUGGAAAAUUCGUU---UUGGCUAAAGGUUGGGCUAAGGUGGA
.................((.........))...(((.((((((.-.......----------------.)))))).)))......((((..---((((((........))))))..)))) ( -20.70)
>DroEre_CAF1 5820 97 - 1
AAA---------AACAACCGAGGAGACAGGAAAACAACUUCCCAGAAAAUGUGGGCUG----------GGGGUAGAUGGGGAAAAUCGGGU----UGGCUAAAGGUUGGGCUGAGGUGGA
...---------..(((((..(....).......(((((((((((..........)))----------)))...(((.......))).)))----))......)))))............ ( -22.30)
>DroYak_CAF1 5746 110 - 1
GAA---------AACAACUGAAGAGACAGGAAAACAACUCCCCUGCAAA-AUGGGAUGGUAGGGGGGUGGGGUAGGUGCGGAACAUCGGGUUGGUUGGCUAAAGGUUGGGCUAAGGUGGA
...---------..(((((..............((.((((((((((...-........))))))))))...)).((((.....)))).))))).((((((........))))))...... ( -30.10)
>consensus
AAAA______AAAACAACCGAAGAGACAGGAAAACAACUCCCCG_AAAAUAA________________GGGGGAGGUGUGGAAAAUUCGGU___UUGGCUAAAGGUUGGGCUAAGGUGGA
..............(.(((...............((.((((((..........................)))))).))................((((((........))))))))).). (-11.89 = -12.53 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:14 2006