Locus 9935

Sequence ID 3R_DroMel_CAF1
Location 26,584,736 – 26,584,829
Length 93
Max. P 0.976548
window15838 window15839

overview

Window 8

Location 26,584,736 – 26,584,829
Length 93
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 77.98
Mean single sequence MFE -25.45
Consensus MFE -15.41
Energy contribution -15.91
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.59
Structure conservation index 0.61
SVM decision value 1.77
SVM RNA-class probability 0.976548
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26584736 93 + 27905053
UUUGCAACCCCAAAUUGCAUUCGCUACCCAUUCCCC-------G--CUGC--CUUCA---UCAUUGGCAACUUUUCAUUAUGCUAA-ACCGUAAAUGAAGAGGGUUGA
....((((((......((....))............-------.--.(((--(....---.....))))..((((((((.(((...-...))))))))))))))))). ( -20.70)
>DroVir_CAF1 213939 91 + 1
UUUGCAACCCUAAAUUGCAUUUUAUGCGCAUCUCGCUC--------GUGC-----CC---UGAUCAGC-ACUUUUCAUUAUGCUAAAACCGUAAAUGAAGAGGGUUGC
...((((((((.....((((...))))((.....))..--------((((-----..---......))-)).(((((((.(((.......)))))))))))))))))) ( -24.60)
>DroPse_CAF1 216489 88 + 1
UUUGCAACCCCAAAUUGCAUUCGC---CCUCUCCCU-----------GGG--CCUCA---UCAUCGGCAACUUUUCAUUAUGCUAA-ACCGUAAAUGAAGAGGGUUGC
...(((((((....((((....((---((.......-----------)))--)..(.---.....))))).((((((((.(((...-...)))))))))))))))))) ( -26.40)
>DroGri_CAF1 347561 98 + 1
GUUGCAACCCUAAAUUGCAUUUUAUGCGCCCGUCUCUC-----GCCGUGCGGCAUCA---UCAUCAGC-ACUUUUCAUUAUGCUAA-ACCGUAAAUGAAGAGGGUUGC
...((((((((.....((((...))))...........-----(((....)))....---........-...(((((((.(((...-...)))))))))))))))))) ( -25.20)
>DroWil_CAF1 200484 103 + 1
UUUGCAACCCUAAAUUGCAUUUUAUGCCCAUGGCCCAGAUGCGG--CGGC--CUUAACAGUCAUCAGCAACUUUUCAUUAUGCUAA-ACCGUAAAUGAAGAGGGUUGC
...((((((((...((((.......((((((.......))).))--)(((--.......)))....))))..(((((((.(((...-...)))))))))))))))))) ( -29.40)
>DroPer_CAF1 214723 88 + 1
UUUGCAACCCCAAAUUGCAUUCGC---CCUCUCCCU-----------GGG--CCUCA---UCAUCGGCAACUUUUCAUUAUGCUAA-ACCGUAAAUGAAGAGGGUUGC
...(((((((....((((....((---((.......-----------)))--)..(.---.....))))).((((((((.(((...-...)))))))))))))))))) ( -26.40)
>consensus
UUUGCAACCCCAAAUUGCAUUCGAUGCCCACUCCCC___________GGC__CCUCA___UCAUCAGCAACUUUUCAUUAUGCUAA_ACCGUAAAUGAAGAGGGUUGC
...(((((((....((((................................................)))).((((((((.(((.......)))))))))))))))))) (-15.41 = -15.91 +   0.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 26,584,736 – 26,584,829
Length 93
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 77.98
Mean single sequence MFE -29.48
Consensus MFE -17.93
Energy contribution -18.18
Covariance contribution 0.25
Combinations/Pair 1.04
Mean z-score -2.43
Structure conservation index 0.61
SVM decision value 1.61
SVM RNA-class probability 0.967101
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26584736 93 - 27905053
UCAACCCUCUUCAUUUACGGU-UUAGCAUAAUGAAAAGUUGCCAAUGA---UGAAG--GCAG--C-------GGGGAAUGGGUAGCGAAUGCAAUUUGGGGUUGCAAA
...(((((((((........(-(((......))))..((((((.....---....)--))))--)-------)))))..))))......((((((.....)))))).. ( -23.70)
>DroVir_CAF1 213939 91 - 1
GCAACCCUCUUCAUUUACGGUUUUAGCAUAAUGAAAAGU-GCUGAUCA---GG-----GCAC--------GAGCGAGAUGCGCAUAAAAUGCAAUUUAGGGUUGCAAA
((((((((.................((((..((....((-(((.....---.)-----))))--------...))..))))((((...)))).....))))))))... ( -29.00)
>DroPse_CAF1 216489 88 - 1
GCAACCCUCUUCAUUUACGGU-UUAGCAUAAUGAAAAGUUGCCGAUGA---UGAGG--CCC-----------AGGGAGAGG---GCGAAUGCAAUUUGGGGUUGCAAA
((((((((.((((((..((((-..(((..........)))))))..))---))))(--(((-----------.......))---))...........))))))))... ( -29.60)
>DroGri_CAF1 347561 98 - 1
GCAACCCUCUUCAUUUACGGU-UUAGCAUAAUGAAAAGU-GCUGAUGA---UGAUGCCGCACGGC-----GAGAGACGGGCGCAUAAAAUGCAAUUUAGGGUUGCAAC
((((((((.(((((((.((..-(((((((........))-)))))...---))((((.((.((.(-----....).)).)))))).))))).))...))))))))... ( -32.00)
>DroWil_CAF1 200484 103 - 1
GCAACCCUCUUCAUUUACGGU-UUAGCAUAAUGAAAAGUUGCUGAUGACUGUUAAG--GCCG--CCGCAUCUGGGCCAUGGGCAUAAAAUGCAAUUUAGGGUUGCAAA
((((((((..((((..(((((-((((((...(....)..)))))..))))))...(--(((.--.........))))))))((((...)))).....))))))))... ( -33.00)
>DroPer_CAF1 214723 88 - 1
GCAACCCUCUUCAUUUACGGU-UUAGCAUAAUGAAAAGUUGCCGAUGA---UGAGG--CCC-----------AGGGAGAGG---GCGAAUGCAAUUUGGGGUUGCAAA
((((((((.((((((..((((-..(((..........)))))))..))---))))(--(((-----------.......))---))...........))))))))... ( -29.60)
>consensus
GCAACCCUCUUCAUUUACGGU_UUAGCAUAAUGAAAAGUUGCCGAUGA___UGAAG__GCA___________GGGGAAUGGGCAGAAAAUGCAAUUUAGGGUUGCAAA
((((((((.((((((....((....))..))))))(((((((................................................)))))))))))))))... (-17.93 = -18.18 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:45:14 2006