Locus 4665

Sequence ID 2R_DroMel_CAF1
Location 15,240,977 – 15,241,075
Length 98
Max. P 0.941736
window7501 window7502

overview

Window 1

Location 15,240,977 – 15,241,075
Length 98
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 77.48
Mean single sequence MFE -25.46
Consensus MFE -21.86
Energy contribution -22.06
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.60
Structure conservation index 0.86
SVM decision value 1.30
SVM RNA-class probability 0.939405
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15240977 98 + 20766785
GCAAA-AACUGCACA-------------AAAAGGAAAAAU--UUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGG
(((..-...)))...-------------............--...(((((((((((.......)))))....(((((.(....))))))....((((...))))....)))))) ( -25.20)
>DroSim_CAF1 60630 110 + 1
GCAAAAAACUACACACCUUUU--GAAGUCAAAGAAAAAAU--UUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGG
.............(((((...--((((.(...((((....--)))).....(((((.......)))))).)))).)))))....(((......((((...))))......))). ( -25.00)
>DroEre_CAF1 64682 98 + 1
ACAAA--AAGAAAAAA--------AGGAAAGAAAAG------AUUCCCAUACCGGGAAUCGAACCCGGGCUUCCUGGGUGAAAGCCAGACGUCCUAGCCACUAGACCAUAUGGG
.....--.........--------((((.......(------((((((.....)))))))..(((((((...)))))))............))))..........((....)). ( -27.10)
>DroWil_CAF1 161321 91 + 1
-------------AAG--------UGGAAAAAAAA--AAUUACUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGG
-------------.((--------(((........--......(((((.....)))))........(((...(((((.(....))))))...)))..)))))...((....)). ( -23.90)
>DroYak_CAF1 67939 110 + 1
AUAAA--AAUACACACCUUUCAUUUGGGUAAAAAAGAAGU--CUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGG
.....--.......((((.......))))...........--...(((((((((((.......)))))....(((((.(....))))))....((((...))))....)))))) ( -26.10)
>consensus
ACAAA__AAUACACAC________AGGAAAAAAAAAAAAU__CUUCCCAUACCGGGAAUCGAACCCGGGCCUUCUGGGUGAAAGCCAGAUAUCCUAGCCACUAGACCAUAUGGG
.............................................(((((((((((.......)))))....(((((.......)))))....((((...))))....)))))) (-21.86 = -22.06 +   0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,240,977 – 15,241,075
Length 98
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 77.48
Mean single sequence MFE -29.06
Consensus MFE -27.98
Energy contribution -27.66
Covariance contribution -0.32
Combinations/Pair 1.09
Mean z-score -1.30
Structure conservation index 0.96
SVM decision value 1.32
SVM RNA-class probability 0.941736
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15240977 98 - 20766785
CCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAA--AUUUUUCCUUUU-------------UGUGCAGUU-UUUGC
(((((((((((....)))).........(((((((.....)))))))((((.......)))))))))))...--............-------------.........-..... ( -27.70)
>DroSim_CAF1 60630 110 - 1
CCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAA--AUUUUUUCUUUGACUUC--AAAAGGUGUGUAGUUUUUUGC
(((((((((((....)))).........(((((((.....)))))))((((.......)))))))))))(((--(((...(((((......--.))))).....)))))).... ( -30.00)
>DroEre_CAF1 64682 98 - 1
CCCAUAUGGUCUAGUGGCUAGGACGUCUGGCUUUCACCCAGGAAGCCCGGGUUCGAUUCCCGGUAUGGGAAU------CUUUUCUUUCCU--------UUUUUUCUU--UUUGU
......(((((....)))))((((.((.(((((((.....))))))).))))))(((((((.....))))))------)...........--------.........--..... ( -29.20)
>DroWil_CAF1 161321 91 - 1
CCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAGUAAUU--UUUUUUUUCCA--------CUU-------------
(((((((((((....)))).........(((((((.....)))))))((((.......)))))))))))........--...........--------...------------- ( -27.70)
>DroYak_CAF1 67939 110 - 1
CCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAG--ACUUCUUUUUUACCCAAAUGAAAGGUGUGUAUU--UUUAU
(((((((((((....)))).........(((((((.....)))))))((((.......))))))))))).(.--((.((((((..........)))))).)).)...--..... ( -30.70)
>consensus
CCCAUAUGGUCUAGUGGCUAGGAUAUCUGGCUUUCACCCAGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAA__AUUUCUUUUUUUUCCA________GUGUGUAGU__UUUGC
(((((((((((....)))).........(((((((.....)))))))((((.......)))))))))))............................................. (-27.98 = -27.66 +  -0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:07 2006