Locus 1896

Sequence ID 2R_DroMel_CAF1
Location 7,148,958 – 7,149,091
Length 133
Max. P 0.997663
window3144 window3145

overview

Window 4

Location 7,148,958 – 7,149,066
Length 108
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 84.90
Mean single sequence MFE -17.28
Consensus MFE -16.14
Energy contribution -16.14
Covariance contribution 0.00
Combinations/Pair 1.09
Mean z-score -1.41
Structure conservation index 0.93
SVM decision value 0.12
SVM RNA-class probability 0.595115
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7148958 108 - 20766785
UAUCGCAACAAAAUUUGCUCUUGCCCCACUAAAUUGAA--AAGGGUUUCACAAAAGCAAACCAAAUAAUGGUAAA--AGGUUUCGUAACAAUCCAAUAACAUUGUGAUUAAA
.(((((((.....((((((.(((.(((...........--..))).....))).))))))........(((....--..(((....)))...)))......))))))).... ( -16.42)
>DroSec_CAF1 12391 109 - 1
UAUCGCAACAACAUUUGCUCUUGCCCCACUAAAUUAAAA-AAGGGUUUCACAAAAGCAAGCCAAAUAAUGGUAGA--AGGUUUCGUAACAAUCAAAUAACAUUGUGAUUAAA
.(((((((......(((((.(((.(((............-..))).....))).)))))((((.....)))).((--..(((....)))..))........))))))).... ( -17.74)
>DroSim_CAF1 12780 109 - 1
UAUCGCAACAACAUUUGCUCUUGCCCCACUAAAUUAAAA-AAGGGUUUCACAAAAGCAAGCCAAAUAAUGGUAGA--AGGUUUCGUAACAAUCAAAUAACAUUGUGAUUAAC
.(((((((......(((((.(((.(((............-..))).....))).)))))((((.....)))).((--..(((....)))..))........))))))).... ( -17.74)
>DroEre_CAF1 14156 102 - 1
UAUCGCAACAACAUUUGCUCUUGCCCCACUAAAAUGUAA-AAGGGUUUCGCAAAAGCAAGCCA-----UGGCACAUUCCAUUUCAUAACAAUCAACUAACAUUGUGAU----
.(((((((......(((((.(((((((((......))..-..)))....)))).)))))((..-----..)).............................)))))))---- ( -19.80)
>DroYak_CAF1 12635 103 - 1
UAUCGCAACAACAUUUGCUCUUGCCCCACUAAAAUACAAAAAGGGUUUCACCAAAGCAAGCCA-----CGGCGUAUUCCAUUUCAUAACAAUCAAAUAACAUUGUGAU----
.(((((((....(((((...............(((((.....((......)).......((..-----..)))))))...............)))))....)))))))---- ( -14.71)
>consensus
UAUCGCAACAACAUUUGCUCUUGCCCCACUAAAUUAAAA_AAGGGUUUCACAAAAGCAAGCCAAAUAAUGGUAGA__AGGUUUCGUAACAAUCAAAUAACAUUGUGAUUAA_
.(((((((......(((((.(((.(((...............))).....))).)))))((((.....)))).............................))))))).... (-16.14 = -16.14 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,148,996 – 7,149,091
Length 95
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 90.93
Mean single sequence MFE -25.23
Consensus MFE -23.26
Energy contribution -23.54
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -2.03
Structure conservation index 0.92
SVM decision value 2.90
SVM RNA-class probability 0.997663
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7148996 95 + 20766785
ACCAUUAUUUGGUUUGCUUUUGUGAAACCCUU--UUCAAUUUAGUGGGGCAAGAGCAAAUUUUGUUGCGAUAGCGAUUCAAUAACAAAAGCCACUCA
.........((((((((((((((....(((..--...........)))))))))))..(((..(((((....)))))..))).....)))))).... ( -22.52)
>DroSec_CAF1 12429 96 + 1
ACCAUUAUUUGGCUUGCUUUUGUGAAACCCUU-UUUUAAUUUAGUGGGGCAAGAGCAAAUGUUGUUGCGAUAGCGAUUCAAUAACAAAAGCCACUCA
.........((((((((((((((....(((..-............)))))))))))...((((((((.(((....))))))))))).)))))).... ( -26.44)
>DroSim_CAF1 12818 96 + 1
ACCAUUAUUUGGCUUGCUUUUGUGAAACCCUU-UUUUAAUUUAGUGGGGCAAGAGCAAAUGUUGUUGCGAUAGCGAUUCAAUAACAAAAGCCACUCA
.........((((((((((((((....(((..-............)))))))))))...((((((((.(((....))))))))))).)))))).... ( -26.44)
>DroEre_CAF1 14192 91 + 1
GCCA-----UGGCUUGCUUUUGCGAAACCCUU-UUACAUUUUAGUGGGGCAAGAGCAAAUGUUGUUGCGAUAGCGAUUCAAUAACAAAAGCGACUCA
....-----..((((((((((((....(((..-............)))))))))))...((((((((.(((....))))))))))).))))...... ( -23.94)
>DroYak_CAF1 12671 92 + 1
GCCG-----UGGCUUGCUUUGGUGAAACCCUUUUUGUAUUUUAGUGGGGCAAGAGCAAAUGUUGUUGCGAUAGCGAUUCAAUAACAAAAGCCACUCA
...(-----(((((((((..(.(((((..(.....)..))))).)..))).........((((((((.(((....))))))))))).)))))))... ( -26.80)
>consensus
ACCAUUAUUUGGCUUGCUUUUGUGAAACCCUU_UUUUAAUUUAGUGGGGCAAGAGCAAAUGUUGUUGCGAUAGCGAUUCAAUAACAAAAGCCACUCA
.........((((((((((((((....(((...............)))))))))))...((((((((.(((....))))))))))).)))))).... (-23.26 = -23.54 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:52 2006