Locus 4273

Sequence ID 3R_DroMel_CAF1
Location 11,400,588 – 11,400,707
Length 119
Max. P 0.825496
window6938 window6939

overview

Window 8

Location 11,400,588 – 11,400,707
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.70
Mean single sequence MFE -22.95
Consensus MFE -18.42
Energy contribution -19.18
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.38
Structure conservation index 0.80
SVM decision value 0.55
SVM RNA-class probability 0.778855
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11400588 119 + 27905053
ACAUGCCGCACAAAUCACGUAUUUGUCAAA-AAACAAACUGCAAUAAAGGCAAACAAAUUGCCAAAAAAUGGGAAAAACAUGCCCAAAUAAUAAGCCAAUGCCUGGGGGCUAAGUCCCAA
..................((((((((....-..))))).)))......(((((.....)))))......(((((.......((((..........(((.....)))))))....))))). ( -24.10)
>DroSec_CAF1 148253 120 + 1
ACAUGCCGCACAAAUCACGUAUUUGUCAAAAAAACAAAUUGCAAUGGAGGCAAACAAAUUGCCAAAAAAUGGGAAAAACAUGCCCAAAUAAUAAGCCAAUGCCUGGGGGCUAAGUCCCAA
.......(.((((((.....))))))).............(((.(((.(((((.....)))))......((((.........)))).........))).)))...(((((...))))).. ( -26.00)
>DroSim_CAF1 139337 119 + 1
ACAUGCCGCACAAAUCACGUAUUUGUCAAA-AAACAAAUUGCAAUGGAGGCAAACAAAUUGCCAAAAAAUGGGAAAAACAUGCCCAAAUAAUAAGCCAAUGCCUGGGGGCUAAGUCCCAA
....(((.(.((........((((((....-..)))))).(((.(((.(((((.....)))))......((((.........)))).........))).))).))).))).......... ( -26.00)
>DroYak_CAF1 139320 118 + 1
ACAUGCCGCACAAAUCACGUAUUUGUCAAA-AAACAAACUGCAAACUAGGAAAACAAAUUGCCAAAAAAUGUGAAAAACACGCCCAAAUAAUAAGCCAAUGCCUGG-GGCCAAAUCCCAA
....(((...........((((((((....-..))))).)))...(((((....................(((.....)))((...........)).....)))))-))).......... ( -15.70)
>consensus
ACAUGCCGCACAAAUCACGUAUUUGUCAAA_AAACAAACUGCAAUGGAGGCAAACAAAUUGCCAAAAAAUGGGAAAAACAUGCCCAAAUAAUAAGCCAAUGCCUGGGGGCUAAGUCCCAA
..................((((((((.......))))).)))......(((((.....)))))......(((((.......((((..........(((.....)))))))....))))). (-18.42 = -19.18 +   0.75)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,400,588 – 11,400,707
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.70
Mean single sequence MFE -29.38
Consensus MFE -26.80
Energy contribution -27.05
Covariance contribution 0.25
Combinations/Pair 1.03
Mean z-score -1.75
Structure conservation index 0.91
SVM decision value 0.70
SVM RNA-class probability 0.825496
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11400588 119 - 27905053
UUGGGACUUAGCCCCCAGGCAUUGGCUUAUUAUUUGGGCAUGUUUUUCCCAUUUUUUGGCAAUUUGUUUGCCUUUAUUGCAGUUUGUUU-UUUGACAAAUACGUGAUUUGUGCGGCAUGU
.(((((....(((....)))....(((((.....))))).......)))))......(((((.....))))).....(((.(((((((.-...))))))).(((.......))))))... ( -30.50)
>DroSec_CAF1 148253 120 - 1
UUGGGACUUAGCCCCCAGGCAUUGGCUUAUUAUUUGGGCAUGUUUUUCCCAUUUUUUGGCAAUUUGUUUGCCUCCAUUGCAAUUUGUUUUUUUGACAAAUACGUGAUUUGUGCGGCAUGU
.(((((....(((....)))....(((((.....))))).......)))))......(((((.....))))).....(((.(((((((.....))))))).(((.......))))))... ( -30.20)
>DroSim_CAF1 139337 119 - 1
UUGGGACUUAGCCCCCAGGCAUUGGCUUAUUAUUUGGGCAUGUUUUUCCCAUUUUUUGGCAAUUUGUUUGCCUCCAUUGCAAUUUGUUU-UUUGACAAAUACGUGAUUUGUGCGGCAUGU
.(((((....(((....)))....(((((.....))))).......)))))......(((((.....))))).....(((.(((((((.-...))))))).(((.......))))))... ( -30.20)
>DroYak_CAF1 139320 118 - 1
UUGGGAUUUGGCC-CCAGGCAUUGGCUUAUUAUUUGGGCGUGUUUUUCACAUUUUUUGGCAAUUUGUUUUCCUAGUUUGCAGUUUGUUU-UUUGACAAAUACGUGAUUUGUGCGGCAUGU
(((((.......)-))))((....(((((.....)))))(..(...((((........((((.(((......))).)))).(((((((.-...)))))))..))))...)..).)).... ( -26.60)
>consensus
UUGGGACUUAGCCCCCAGGCAUUGGCUUAUUAUUUGGGCAUGUUUUUCCCAUUUUUUGGCAAUUUGUUUGCCUCCAUUGCAAUUUGUUU_UUUGACAAAUACGUGAUUUGUGCGGCAUGU
.(((((....(((....)))....(((((.....))))).......)))))......(((((.....))))).....(((.(((((((.....))))))).(((.......))))))... (-26.80 = -27.05 +   0.25)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:11 2006