Locus 1914

Sequence ID 3R_DroMel_CAF1
Location 5,438,590 – 5,438,722
Length 132
Max. P 0.999055
window3145 window3146

overview

Window 5

Location 5,438,590 – 5,438,709
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 75.74
Mean single sequence MFE -26.02
Consensus MFE -20.71
Energy contribution -20.78
Covariance contribution 0.06
Combinations/Pair 1.06
Mean z-score -2.54
Structure conservation index 0.80
SVM decision value 3.35
SVM RNA-class probability 0.999055
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5438590 119 - 27905053
CCGGCAAAAACCGCAUGGUUAGCCCAUGUGACCGGGCUAAGAAGAAACCUUGGCUCACAAAAAAAA-AAGGGUUCGCUUGAAUACGAAAACAAACUGAAUACAAAAGUACAUUUUUUUUG
...........(((((((.....)))))))...((((((((.......)))))))).(((((((((-..(..((((........))))..)..(((.........)))...))))))))) ( -28.90)
>DroSim_CAF1 20340 111 - 1
CCGGCAAAAACCGCAUGGUGA--CCAUGUGACCGGGCUAAGAAGAAACCUUGGCUCAAA----AAA-AAGGGAUCACUUUAAUACAAAUACAAAUUAAAUUCAAAAGUUUAUU--UUUUG
((.........(((((((...--)))))))...((((((((.......))))))))...----...-..))...................((((.(((((......)))))..--.)))) ( -22.20)
>DroEre_CAF1 25784 94 - 1
CCGGCAAAAACCGCAUGGUGA--CCAUGUGACCGGGCUAAGAAGAAACCUUGGCUCAAA----AAA-AACGGUUCACUUGAAUACAA-----------------AAUGAUCCG--UUUUU
...........(((((((...--)))))))...((((((((.......))))))))...----(((-(((((.(((.((.......)-----------------).))).)))--))))) ( -28.40)
>DroYak_CAF1 26210 94 - 1
CCGGCAAAAACCGCAUGGUGA--CCAUGCAA-CGGGCUAAGAAGAAACCUUGGCUCAAA----AAAAAAGGGUUCUCUUGAAUAAAA-----------------AAUGAUUCU--UUUUU
..((......))((((((...--))))))..-.((((((((.......))))))))...----(((((((((((.(.((......))-----------------.).))))))--))))) ( -24.60)
>consensus
CCGGCAAAAACCGCAUGGUGA__CCAUGUGACCGGGCUAAGAAGAAACCUUGGCUCAAA____AAA_AAGGGUUCACUUGAAUACAA_________________AAGGAUACU__UUUUG
........((((((((((.....))))))....((((((((.......))))))))..............)))).............................................. (-20.71 = -20.78 +   0.06)

alignment

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secondary structure

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dotplot

Postscript

Window 6

Location 5,438,630 – 5,438,722
Length 92
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 90.13
Mean single sequence MFE -23.73
Consensus MFE -21.81
Energy contribution -21.88
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -2.24
Structure conservation index 0.92
SVM decision value 1.93
SVM RNA-class probability 0.982923
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5438630 92 - 27905053
UAAAUGCAUUCAUCCGGCAAAAACCGCAUGGUUAGCCCAUGUGACCGGGCUAAGAAGAAACCUUGGCUCACAAAAAAAA-AAGGGUUCGCUUG
.....((....((((.........(((((((.....)))))))...((((((((.......))))))))..........-..))))..))... ( -24.40)
>DroSim_CAF1 20378 86 - 1
UAAAUGCAUUCCUCCGGCAAAAACCGCAUGGUGA--CCAUGUGACCGGGCUAAGAAGAAACCUUGGCUCAAA----AAA-AAGGGAUCACUUU
....((.((((((...........(((((((...--)))))))...((((((((.......))))))))...----...-.)))))))).... ( -24.50)
>DroEre_CAF1 25805 86 - 1
UAAAUGCAUUCCUCCGGCAAAAACCGCAUGGUGA--CCAUGUGACCGGGCUAAGAAGAAACCUUGGCUCAAA----AAA-AACGGUUCACUUG
.............(((........(((((((...--)))))))...((((((((.......))))))))...----...-..)))........ ( -22.50)
>DroYak_CAF1 26231 86 - 1
UAAAUGCAUUCCUCCGGCAAAAACCGCAUGGUGA--CCAUGCAA-CGGGCUAAGAAGAAACCUUGGCUCAAA----AAAAAAGGGUUCUCUUG
....(((.........)))..((((((((((...--))))))..-.((((((((.......))))))))...----.......))))...... ( -23.50)
>consensus
UAAAUGCAUUCCUCCGGCAAAAACCGCAUGGUGA__CCAUGUGACCGGGCUAAGAAGAAACCUUGGCUCAAA____AAA_AAGGGUUCACUUG
....(((.........)))..((((((((((.....))))))....((((((((.......))))))))..............))))...... (-21.81 = -21.88 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:42 2006