Locus 3081

Sequence ID 2L_DroMel_CAF1
Location 8,786,304 – 8,786,433
Length 129
Max. P 0.997028
window4904 window4905 window4906

overview

Window 4

Location 8,786,304 – 8,786,407
Length 103
Sequences 3
Columns 103
Reading direction reverse
Mean pairwise identity 99.35
Mean single sequence MFE -16.40
Consensus MFE -16.40
Energy contribution -16.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.24
Structure conservation index 1.00
SVM decision value 1.39
SVM RNA-class probability 0.949224
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8786304 103 - 22407834
GAAUUUUGCCUCACAGGCAAAAAUAACCAAAAAUAAAAGAAAAUAAUGCAGACUGACGGGGGAAAAUGGCAACAAAAAAUCGUCAUAAUAAAAUCCCAAAGCU
...(((((((.....)))))))...............................((((((.......((....)).....)))))).................. ( -16.40)
>DroSec_CAF1 89014 103 - 1
GAAUUUUGCCUGACAGGCAAAAAUAACCAAAAAUAAAAGAAAAUAAUGCAGACUGACGGGGGAAAAUGGCAACAAAAAAUCGUCAUAAUAAAAUCCCAAAGCU
...(((((((.....)))))))...............................((((((.......((....)).....)))))).................. ( -16.40)
>DroSim_CAF1 92538 103 - 1
GAAUUUUGCCUCACAGGCAAAAAUAACCAAAAAUAAAAGAAAAUAAUGCAGACUGACGGGGGAAAAUGGCAACAAAAAAUCGUCAUAAUAAAAUCCCAAAGCU
...(((((((.....)))))))...............................((((((.......((....)).....)))))).................. ( -16.40)
>consensus
GAAUUUUGCCUCACAGGCAAAAAUAACCAAAAAUAAAAGAAAAUAAUGCAGACUGACGGGGGAAAAUGGCAACAAAAAAUCGUCAUAAUAAAAUCCCAAAGCU
...(((((((.....)))))))...............................((((((.......((....)).....)))))).................. (-16.40 = -16.40 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,786,343 – 8,786,433
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 94.89
Mean single sequence MFE -17.42
Consensus MFE -15.10
Energy contribution -15.70
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.39
Structure conservation index 0.87
SVM decision value 0.51
SVM RNA-class probability 0.763649
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8786343 90 + 22407834
UUCCCCCGUCAGUCUGCAUUAUUUUCUUUUAUUUUUGGUUAUUUUUGCCUGUGAGGCAAAAUUCACUGCUAGGUACAGUGAAAUUGUCAC
.......(.((((.............................(((((((.....)))))))(((((((.......))))))))))).).. ( -17.60)
>DroSec_CAF1 89053 90 + 1
UUCCCCCGUCAGUCUGCAUUAUUUUCUUUUAUUUUUGGUUAUUUUUGCCUGUCAGGCAAAAUUCACUGCUAGGUACAGUGAAAUUGUCAC
.......(.((((.............................(((((((.....)))))))(((((((.......))))))))))).).. ( -17.60)
>DroSim_CAF1 92577 90 + 1
UUCCCCCGUCAGUCUGCAUUAUUUUCUUUUAUUUUUGGUUAUUUUUGCCUGUGAGGCAAAAUUCACUGCUAGGUACAGUGAAAUUGUCAC
.......(.((((.............................(((((((.....)))))))(((((((.......))))))))))).).. ( -17.60)
>DroEre_CAF1 95603 87 + 1
UUUCCCCGUCAUUCUGCAUUAUUUUCUUUUAUUUUCGGUUAUUUUUGCCUGUGAGGCAAAAUUCACU---ACGUACAGUGAAAUUGUGAC
.......(((((..............................(((((((.....)))))))((((((---......))))))...))))) ( -16.70)
>DroYak_CAF1 94264 90 + 1
UUUUCCCGUCAGUCUGCAUUAUUUUCCUUUAUUUUUGGUUAUUUUUGCCUGUGAGGCAAAAUUCACUGCUAGGUACAGUGAAAUUGUCAC
.......(.((((.............................(((((((.....)))))))(((((((.......))))))))))).).. ( -17.60)
>consensus
UUCCCCCGUCAGUCUGCAUUAUUUUCUUUUAUUUUUGGUUAUUUUUGCCUGUGAGGCAAAAUUCACUGCUAGGUACAGUGAAAUUGUCAC
.......(.((((.............................(((((((.....)))))))(((((((.......))))))))))).).. (-15.10 = -15.70 +   0.60)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,786,343 – 8,786,433
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 94.89
Mean single sequence MFE -18.30
Consensus MFE -16.28
Energy contribution -16.68
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.11
Structure conservation index 0.89
SVM decision value 2.79
SVM RNA-class probability 0.997028
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8786343 90 - 22407834
GUGACAAUUUCACUGUACCUAGCAGUGAAUUUUGCCUCACAGGCAAAAAUAACCAAAAAUAAAAGAAAAUAAUGCAGACUGACGGGGGAA
.((.((..((((((((.....))))))))(((((((.....)))))))........................)))).............. ( -18.00)
>DroSec_CAF1 89053 90 - 1
GUGACAAUUUCACUGUACCUAGCAGUGAAUUUUGCCUGACAGGCAAAAAUAACCAAAAAUAAAAGAAAAUAAUGCAGACUGACGGGGGAA
.((.((..((((((((.....))))))))(((((((.....)))))))........................)))).............. ( -18.00)
>DroSim_CAF1 92577 90 - 1
GUGACAAUUUCACUGUACCUAGCAGUGAAUUUUGCCUCACAGGCAAAAAUAACCAAAAAUAAAAGAAAAUAAUGCAGACUGACGGGGGAA
.((.((..((((((((.....))))))))(((((((.....)))))))........................)))).............. ( -18.00)
>DroEre_CAF1 95603 87 - 1
GUCACAAUUUCACUGUACGU---AGUGAAUUUUGCCUCACAGGCAAAAAUAACCGAAAAUAAAAGAAAAUAAUGCAGAAUGACGGGGAAA
((((....(((((((....)---))))))(((((((.....)))))))...............................))))....... ( -18.10)
>DroYak_CAF1 94264 90 - 1
GUGACAAUUUCACUGUACCUAGCAGUGAAUUUUGCCUCACAGGCAAAAAUAACCAAAAAUAAAGGAAAAUAAUGCAGACUGACGGGAAAA
((((.....))))....(((..((((...(((((((.....)))))))....((.........))............))))..))).... ( -19.40)
>consensus
GUGACAAUUUCACUGUACCUAGCAGUGAAUUUUGCCUCACAGGCAAAAAUAACCAAAAAUAAAAGAAAAUAAUGCAGACUGACGGGGGAA
........((((((((.....))))))))(((((((.....))))))).......................................... (-16.28 = -16.68 +   0.40)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:55 2006