Locus 2875

Sequence ID 2R_DroMel_CAF1
Location 9,935,514 – 9,935,609
Length 95
Max. P 0.973824
window4751 window4752

overview

Window 1

Location 9,935,514 – 9,935,609
Length 95
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 81.26
Mean single sequence MFE -23.50
Consensus MFE -13.42
Energy contribution -13.74
Covariance contribution 0.32
Combinations/Pair 1.12
Mean z-score -2.79
Structure conservation index 0.57
SVM decision value 1.72
SVM RNA-class probability 0.973824
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9935514 95 + 20766785
CGACGGUAUAAAAA--A--ACACCAGCAACUGCUGCAACU--AACUACACC---AGCAACACCAACAUU-ACCA--------ACCAGCAACAGCUGACGUUCAAUGAACGCUU
....(((.......--.--....((((....)))).....--......)))---(((............-....--------..((((....))))..((((...))))))). ( -16.20)
>DroSec_CAF1 70977 107 + 1
CGGCGGUAUAAAACACA--CCAGCAGCAACUGCUGCAACUACAACUAAACC---AGCAACACCAACAUU-ACGAACAUUGCCACCAGCAACAGCUGACGUUCAAUGAACGCUU
.((((((.........)--)).(((((....)))))...............---...............-.........)))..((((....)))).(((((...)))))... ( -24.30)
>DroSim_CAF1 56834 107 + 1
CGGCGGUAUAAAACACA--CCAGCAGCAACUGCUGCAACUACAACUAAAGC---AGCAACACCAACAUU-ACGAACAUUGCCACCAGCAACAGCUGACGUUCAAUGAACGCUU
.((((((.........)--)).(((((....)))))...............---...............-.........)))..((((....)))).(((((...)))))... ( -24.30)
>DroEre_CAF1 58868 107 + 1
CGGCGCUAUAAAACACA--CCAGCCACUGCUGCUGCAACUACAACAGCAAC---AGCAACAUCAGCAAC-AGCAACAUUGCCACCAGCAACAGCUGACGUUCGAUGAGCGUUU
.((((((..........--........(((((.(((..........))).)---)))).(((((((..(-(((....((((.....))))..))))..))).)))))))))). ( -30.00)
>DroYak_CAF1 54274 111 + 1
CGGCGCUAUAAAACACACUCCAGCAACUGCUGCUGCAACUACAACUACAACUAAAGCAAC--UAGCAACUAGCAACAUUGCCAACAGCAACAGCUGACGUUCGAUGAGCGUUU
.(((((((............(((((.....)))))....................((...--..))...))))......)))..((((....))))((((((...)))))).. ( -22.70)
>consensus
CGGCGGUAUAAAACACA__CCAGCAGCAACUGCUGCAACUACAACUACAAC___AGCAACACCAACAUU_ACCAACAUUGCCACCAGCAACAGCUGACGUUCAAUGAACGCUU
......................(((((....)))))..................(((...........................((((....))))..((((...))))))). (-13.42 = -13.74 +   0.32)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 2

Location 9,935,514 – 9,935,609
Length 95
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 81.26
Mean single sequence MFE -36.34
Consensus MFE -19.39
Energy contribution -20.17
Covariance contribution 0.78
Combinations/Pair 1.13
Mean z-score -2.64
Structure conservation index 0.53
SVM decision value 1.29
SVM RNA-class probability 0.940575
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9935514 95 - 20766785
AAGCGUUCAUUGAACGUCAGCUGUUGCUGGU--------UGGU-AAUGUUGGUGUUGCU---GGUGUAGUU--AGUUGCAGCAGUUGCUGGUGU--U--UUUUUAUACCGUCG
..((((((...))))))((((((((((...(--------(((.-.(..(..(.....).---.)..)..))--))..))))))))))..(((((--.--.....))))).... ( -28.80)
>DroSec_CAF1 70977 107 - 1
AAGCGUUCAUUGAACGUCAGCUGUUGCUGGUGGCAAUGUUCGU-AAUGUUGGUGUUGCU---GGUUUAGUUGUAGUUGCAGCAGUUGCUGCUGG--UGUGUUUUAUACCGCCG
..((((((...))))))((((((..((..(..(((....(((.-.....))))))..).---.)).)))))).....(((((....))))).((--((.((.....)))))). ( -34.30)
>DroSim_CAF1 56834 107 - 1
AAGCGUUCAUUGAACGUCAGCUGUUGCUGGUGGCAAUGUUCGU-AAUGUUGGUGUUGCU---GCUUUAGUUGUAGUUGCAGCAGUUGCUGCUGG--UGUGUUUUAUACCGCCG
..(((..(((((..(..((((....))))..).)))))..)))-......(((...(((---((.......))))).(((((....))))).((--((((...))))))))). ( -36.60)
>DroEre_CAF1 58868 107 - 1
AAACGCUCAUCGAACGUCAGCUGUUGCUGGUGGCAAUGUUGCU-GUUGCUGAUGUUGCU---GUUGCUGUUGUAGUUGCAGCAGCAGUGGCUGG--UGUGUUUUAUAGCGCCG
............(((((((((....((.((..((...))..))-)).)))))))))((.---.((((((((((....))))))))))..)).((--(((........))))). ( -44.00)
>DroYak_CAF1 54274 111 - 1
AAACGCUCAUCGAACGUCAGCUGUUGCUGUUGGCAAUGUUGCUAGUUGCUA--GUUGCUUUAGUUGUAGUUGUAGUUGCAGCAGCAGUUGCUGGAGUGUGUUUUAUAGCGCCG
..((((((......((.(((((((((((((..(((((...(((((..((..--...)).)))))....)))))....))))))))))))).)))))))).............. ( -38.00)
>consensus
AAGCGUUCAUUGAACGUCAGCUGUUGCUGGUGGCAAUGUUGGU_AAUGUUGGUGUUGCU___GGUGUAGUUGUAGUUGCAGCAGUUGCUGCUGG__UGUGUUUUAUACCGCCG
..((((((...))))))((((((((((.....(((((..........((.......))..........)))))....)))))))))).......................... (-19.39 = -20.17 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:43 2006