Locus 5240

Sequence ID 3L_DroMel_CAF1
Location 14,467,432 – 14,467,528
Length 96
Max. P 0.815690
window8288 window8289

overview

Window 8

Location 14,467,432 – 14,467,528
Length 96
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.49
Mean single sequence MFE -28.74
Consensus MFE -22.62
Energy contribution -22.94
Covariance contribution 0.32
Combinations/Pair 1.07
Mean z-score -1.48
Structure conservation index 0.79
SVM decision value 0.00
SVM RNA-class probability 0.535451
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14467432 96 + 23771897
UUUGGAAAUGUGAUAAUUGCAGGCAGCGCAGGCUGCACAGCAAACUGUCAGGCUUUCGAGAUGCAGUUAGAGAAAAUGUUGAAUA-----GCGGA-AAUUUC------------------
....(((((.(((((.((((..(((((....)))))...))))..))))).((((((((.((.............)).))))).)-----))...-.)))))------------------ ( -23.52)
>DroSec_CAF1 64349 96 + 1
UUUGGAAAUGUGAUAAUUGCAGGCAGCGCAGGCUGCACAGCAAACUGUCAGGCUUUCGAGAUACAGUUAGAGAAAUUGUUGUAUA-----GCGGA-CAUUUC------------------
....(((((((((((.((((..(((((....)))))...))))..)))))....((((..((((((...((....)).)))))).-----.))))-))))))------------------ ( -28.60)
>DroSim_CAF1 79579 96 + 1
UUUGGAAAUGUGAUAAUUGCAGGCAGCGCAGGCUGCACAGCAAACUGUCAGGCUUUCGAGAUGCAGUUAGCGAAAUUGUUGGGUA-----GCAAG-AAUUUC------------------
(((((((.(.(((((.((((..(((((....)))))...))))..))))).).)))))))..((.....))((((((.(((....-----.))).-))))))------------------ ( -28.10)
>DroEre_CAF1 80185 98 + 1
UUUGGAAAUGUGAUAAUUGCAGGCAGCGCAGGCUGCACAGCAAGCUGCCAGGCUUUCGAGAUGCAGUUAGAGAAACUGUUGGCAA-----GCGCCUAAUUUUU-----------------
(((((((.((..(...)..))((((((....(((....)))..))))))....)))))))..((((((.....)))))).(((..-----..)))........----------------- ( -28.30)
>DroYak_CAF1 71345 120 + 1
UUUGGAAAUGUGAUAAUUGCAGGCAGCGCAGGCUGCACAGCAAGCUGUCAGGCUUUCGAGAUGCAGUUAGAGAAAUGGUUGGAUAUGUUAGCUAACCAUCUUUAAAACCUAUUAGCAAGU
(((((((.(.(((((.((((..(((((....)))))...))))..))))).).))))))).(((..(((((((..(((((((.........)))))))))))))).........)))... ( -35.20)
>consensus
UUUGGAAAUGUGAUAAUUGCAGGCAGCGCAGGCUGCACAGCAAACUGUCAGGCUUUCGAGAUGCAGUUAGAGAAAUUGUUGGAUA_____GCGAA_AAUUUC__________________
(((((((.(.(((((.((((..(((((....)))))...))))..))))).).)))))))..((((((.....))))))......................................... (-22.62 = -22.94 +   0.32)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,467,432 – 14,467,528
Length 96
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.49
Mean single sequence MFE -24.20
Consensus MFE -15.48
Energy contribution -15.32
Covariance contribution -0.16
Combinations/Pair 1.05
Mean z-score -2.13
Structure conservation index 0.64
SVM decision value 0.66
SVM RNA-class probability 0.815690
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14467432 96 - 23771897
------------------GAAAUU-UCCGC-----UAUUCAACAUUUUCUCUAACUGCAUCUCGAAAGCCUGACAGUUUGCUGUGCAGCCUGCGCUGCCUGCAAUUAUCACAUUUCCAAA
------------------(((((.-.....-----.................(((((((...(....)..)).)))))(((.(.(((((....)))))).)))........))))).... ( -18.20)
>DroSec_CAF1 64349 96 - 1
------------------GAAAUG-UCCGC-----UAUACAACAAUUUCUCUAACUGUAUCUCGAAAGCCUGACAGUUUGCUGUGCAGCCUGCGCUGCCUGCAAUUAUCACAUUUCCAAA
------------------((((((-(....-----.................((((((....(....)....))))))(((.(.(((((....)))))).)))......))))))).... ( -24.10)
>DroSim_CAF1 79579 96 - 1
------------------GAAAUU-CUUGC-----UACCCAACAAUUUCGCUAACUGCAUCUCGAAAGCCUGACAGUUUGCUGUGCAGCCUGCGCUGCCUGCAAUUAUCACAUUUCCAAA
------------------((((((-.(((.-----....))).))))))((.(((((((...(....)..)).))))).))((((((((....)))))..)))................. ( -21.70)
>DroEre_CAF1 80185 98 - 1
-----------------AAAAAUUAGGCGC-----UUGCCAACAGUUUCUCUAACUGCAUCUCGAAAGCCUGGCAGCUUGCUGUGCAGCCUGCGCUGCCUGCAAUUAUCACAUUUCCAAA
-----------------........((.((-----(.((((.(((((.....))))).....(....)..)))))))((((.(.(((((....)))))).))))...........))... ( -26.50)
>DroYak_CAF1 71345 120 - 1
ACUUGCUAAUAGGUUUUAAAGAUGGUUAGCUAACAUAUCCAACCAUUUCUCUAACUGCAUCUCGAAAGCCUGACAGCUUGCUGUGCAGCCUGCGCUGCCUGCAAUUAUCACAUUUCCAAA
....(((..((((((((..((((((((((.....................)))))..)))))..))))))))..)))((((.(.(((((....)))))).))))................ ( -30.50)
>consensus
__________________GAAAUU_UCCGC_____UAUCCAACAAUUUCUCUAACUGCAUCUCGAAAGCCUGACAGUUUGCUGUGCAGCCUGCGCUGCCUGCAAUUAUCACAUUUCCAAA
...............................................................((((...(((.((.((((.(.(((((....)))))).)))))).)))..)))).... (-15.48 = -15.32 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:18 2006