Locus 3577

Sequence ID 3L_DroMel_CAF1
Location 10,524,949 – 10,525,094
Length 145
Max. P 0.542568
window5576 window5577

overview

Window 6

Location 10,524,949 – 10,525,059
Length 110
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 82.49
Mean single sequence MFE -29.37
Consensus MFE -21.12
Energy contribution -20.79
Covariance contribution -0.33
Combinations/Pair 1.18
Mean z-score -1.44
Structure conservation index 0.72
SVM decision value 0.02
SVM RNA-class probability 0.542568
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10524949 110 - 23771897
GCUGC---UGAUGCC-CAAGAAGACUGGGAAAUUAAGUGCCCUGUUUUUUGGGCUAUCAUUAAAGCCUGUAUCCUGCGGGCGCGCCUCAUAAAUAUCGCCAAAGCAUAUUGAUG
((.((---(((((((-(((((((...(((..........)))..)))))))))).)))).....((((((.....))))))))))..(((.(((((.((....))))))).))) ( -36.40)
>DroVir_CAF1 450821 103 - 1
-----AGCAGCUACCCAAAUGAAGCU--GAAAUUAAGUGCCCUCUUU--UAGGCUAUCAUUAAAGCCUGUAUCCUGCGGGCGCGUCUCAUAAAUAUCGCC--AGCAUACUGAUG
-----..(((((.(......).))))--).......((((((.(...--((((((........))))))......).))))))................(--((....)))... ( -25.80)
>DroGri_CAF1 414337 102 - 1
-----AGCAGCUCCU-CAAUGAAGCU--GAAAUUAAGUGCCCUAUUU--UAGGGUAUCAUUAAAGCCUGUAUCCUGCGGGCGCGCCUCAUAAAUAUCGCC--AGCAUAUUGAUG
-----..(((((.(.-....).))))--).......((((((((...--))))))))((((((.((((((.....))))))(((............))).--......)))))) ( -27.60)
>DroEre_CAF1 413464 108 - 1
-----UGCGGAUGCC-CGAAGAGACUGGGAAAUUAAGUGCCCUGUUUUUCGGGCUAUCAUUAAAGCCCGUAUCCUGCGGGCGCGCCUCAUAAAUAUCGCCAAAGCAUAUUGAUG
-----.(((((((((-(((((((...(((..........)))..)))))))))).)))......((((((.....)))))).)))..(((.(((((.((....))))))).))) ( -40.20)
>DroWil_CAF1 654512 94 - 1
-------------CU-CCC---AACUG-GAAAUUAAGUGCCCUGUUU--UGGGCUAUCAUUAAAGCCUGUAUCCUGCGGGCGCGCCUCAUAAAUAUCGCCAAAGUAUAUUGAUG
-------------.(-((.---....)-))........((((.....--.))))...((((((.((((((.....))))))(((............))).........)))))) ( -21.80)
>DroMoj_CAF1 518039 102 - 1
------GUAGCCGCCCAAAUGAAGCU--GAAAUUAAGUGCCCUGUUU--UAGGCUAUCAUUAAAGCCUGUAUCCUGCGGGCGCGCCUCAUAAAUAUCGCC--AGCAUAUUGAUG
------.................(((--(.......((((((.((..--((((((........))))))......))))))))((............)))--)))......... ( -24.40)
>consensus
______GCAGCUGCC_CAAUGAAACU__GAAAUUAAGUGCCCUGUUU__UAGGCUAUCAUUAAAGCCUGUAUCCUGCGGGCGCGCCUCAUAAAUAUCGCC__AGCAUAUUGAUG
....................................((((((.......((((((........))))))........))))))....(((.(((((.((....))))))).))) (-21.12 = -20.79 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,524,989 – 10,525,094
Length 105
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 79.47
Mean single sequence MFE -32.48
Consensus MFE -24.75
Energy contribution -25.20
Covariance contribution 0.45
Combinations/Pair 1.28
Mean z-score -1.31
Structure conservation index 0.76
SVM decision value -0.04
SVM RNA-class probability 0.515683
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10524989 105 - 23771897
GGUGGUU-CGGUGUAUGUGU---AUGAUAUGAUGGCGGUGC--UGC---UGAUGCCCAAGAAGACUGGGAAAUUAAGUGCCCUGUUUUUUGGGCUAUCAUUAAAGCCUGUAUCC
.......-............---.......((((.(((.((--(..---((((((((((((((...(((..........)))..)))))))))).))))....)))))))))). ( -29.70)
>DroSec_CAF1 404521 94 - 1
---------------UGUGU---AUGAUAUGGUGGUGGUGC--UGCUGCUGAUGCCCGAGAAGACUGCGAAAUUAAGUGCCCUGUUUUUUGGGCUAUCAUUAAAGCCCGUAUCC
---------------.....---..(((((((.((..(...--..)..))(((((((((((((...(((........)))....)))))))))).)))........))))))). ( -28.30)
>DroSim_CAF1 412910 94 - 1
---------------UAUGU---AUGAUAUGGUGGCGGUGC--UGCUGUUGAUGCCCGAGAAGACUGCGAAAUUAAGUGCCCUGUUUUUUGGGCUAUCAUUAAAGCCCGUAUCC
---------------.....---.......((..((((.((--(.....((((((((((((((...(((........)))....)))))))))).))))....)))))))..)) ( -29.30)
>DroEre_CAF1 413504 102 - 1
GGUGGUU-CGGUA--UGUGGGC-AUGAUAUGGUGGUGC--------UGCGGAUGCCCGAAGAGACUGGGAAAUUAAGUGCCCUGUUUUUCGGGCUAUCAUUAAAGCCCGUAUCC
....(((-((...--..)))))-..(((((((....((--------(...(((((((((((((...(((..........)))..)))))))))).))).....)))))))))). ( -34.30)
>DroYak_CAF1 413329 112 - 1
GGUGGCUCCGGUA--UGUGUAUGGUGAUAUGGUGGUGCUCCAGUACUGCUGAUGCCCGAAGAGACUGGGAAAUUAAGUGCCCUGUUUUUCGGGCUAUCAUUAAAGCCCGUAUCC
((.....))((((--((.((.((((((((.((..((((....))))..))...((((((((((...(((..........)))..))))))))))))))))))..)).)))))). ( -40.80)
>consensus
GGUGG_U_CGGU___UGUGU___AUGAUAUGGUGGUGGUGC__UGCUGCUGAUGCCCGAGAAGACUGGGAAAUUAAGUGCCCUGUUUUUUGGGCUAUCAUUAAAGCCCGUAUCC
.........................(((((((.((((((.....))))))(((((((((((((...(((..........)))..)))))))))).)))........))))))). (-24.75 = -25.20 +   0.45)

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 11:01:23 2006