Locus 1054

Sequence ID X_DroMel_CAF1
Location 3,067,312 – 3,067,456
Length 144
Max. P 0.941539
window1713 window1714

overview

Window 3

Location 3,067,312 – 3,067,416
Length 104
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 73.45
Mean single sequence MFE -22.62
Consensus MFE -14.65
Energy contribution -14.72
Covariance contribution 0.06
Combinations/Pair 1.11
Mean z-score -1.85
Structure conservation index 0.65
SVM decision value 1.32
SVM RNA-class probability 0.941539
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3067312 104 - 22224390
UUUUUCC----AGCUUGUCUAUUGAU----AUGUCUAAUGGGAAAUGUUGGUUAACCGUUAGACACAUGUAGCAAUGUGUAU----UUUCAUGUUCGAUUCCACGUUUUUUUUUUU
.......----.(((((((....)))----)((((((((((..(((....)))..)))))))))).....)))((((((...----..((......))...))))))......... ( -21.50)
>DroSec_CAF1 38781 97 - 1
UUUUUGUAUGUAUUUCGUCUAUUGAUACGUAUGUCUGAUGGGAAAUGUUGGUUAAGCGUUAGACACAUGUAGCAAUGUGUAU----UUUC-------------CGUUUUUUUUU--
.....(((((((((.........)))))))))....(((((((((((((.....))).....((((((......))))))))----))))-------------)))).......-- ( -21.80)
>DroEre_CAF1 39671 96 - 1
UUUUUCC----AGCUGGUCUAUUGAU----AUGUCUGAUGGGAGAUGUUGGUUAACCGUUAGACACAUGUAGCAAUGUGUUUUUUUUUUCAUGUUUGAUUCCG----------U--
....((.----(((.(((..((..((----((.(((....))).))))..))..)))...((((((((......))))))))..........))).)).....----------.-- ( -21.80)
>DroYak_CAF1 40456 91 - 1
U-UCUCC----AGCUGGUCUAUUGAU----GUGUCUGAUGGGAGAUGUUGGUUAACCGUUAGACAUAUGUAGCCAUGUGUAU----UUUCAUGUUCGAUUCCC----------U--
.-..((.----((((((.((((..((----(((((((((((..(((....)))..)))))))))))))))))))).(((...----...)))))).)).....----------.-- ( -25.40)
>consensus
UUUUUCC____AGCUGGUCUAUUGAU____AUGUCUGAUGGGAAAUGUUGGUUAACCGUUAGACACAUGUAGCAAUGUGUAU____UUUCAUGUUCGAUUCC___________U__
...................(((((.......((((((((((..(((....)))..)))))))))).......)))))....................................... (-14.65 = -14.72 +   0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,067,348 – 3,067,456
Length 108
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 82.96
Mean single sequence MFE -30.38
Consensus MFE -18.65
Energy contribution -18.53
Covariance contribution -0.12
Combinations/Pair 1.14
Mean z-score -2.27
Structure conservation index 0.61
SVM decision value 0.70
SVM RNA-class probability 0.827088
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3067348 108 - 22224390
AACGCUCAUAAGUCAAGCUAACCCACAGUGAAAGUGUAUUUUUUUCC----AGCUUGUCUAUUGAU----AUGUCUAAUGGGAAAUGUUGGUUAACCGUUAGACACAUGUAGCAAU
...((((((.((.((((((.((.....))(((((.......))))).----)))))).))......----.((((((((((..(((....)))..)))))))))).))).)))... ( -28.20)
>DroSec_CAF1 38802 116 - 1
CACGCUCAAAAGUCAAGCUAUCCCGCAGUGAAAGUGUAUUUUUUUGUAUGUAUUUCGUCUAUUGAUACGUAUGUCUGAUGGGAAAUGUUGGUUAAGCGUUAGACACAUGUAGCAAU
...(((((...(((......((((((((.(((((......)))))(((((((((.........)))))))))..))).)))))((((((.....)))))).)))...)).)))... ( -26.50)
>DroEre_CAF1 39699 105 - 1
---UCACUUAAGUGAAGCUAUACCACAGUGAAAGUGUAUUUUUUUCC----AGCUGGUCUAUUGAU----AUGUCUGAUGGGAGAUGUUGGUUAACCGUUAGACACAUGUAGCAAU
---((((....)))).((((((...(((((((((.......))))).----.))))(((....)))----.((((((((((..(((....)))..))))))))))..))))))... ( -30.30)
>DroYak_CAF1 40480 104 - 1
---UCACAAAAGUGAGGCUAUACCACAGCGAAAGUGUAUUU-UCUCC----AGCUGGUCUAUUGAU----GUGUCUGAUGGGAGAUGUUGGUUAACCGUUAGACAUAUGUAGCCAU
---((((....))))((((((....((((...((.......-.))..----.))))........((----(((((((((((..(((....)))..))))))))))))))))))).. ( -36.50)
>consensus
___GCACAAAAGUCAAGCUAUACCACAGUGAAAGUGUAUUUUUUUCC____AGCUGGUCUAUUGAU____AUGUCUGAUGGGAAAUGUUGGUUAACCGUUAGACACAUGUAGCAAU
................(((((..(((.......)))...................................((((((((((..(((....)))..))))))))))...)))))... (-18.65 = -18.53 +  -0.12)

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 10:00:30 2006