Locus 4054

Sequence ID 2R_DroMel_CAF1
Location 13,373,430 – 13,373,547
Length 117
Max. P 0.614281
window6530 window6531

overview

Window 0

Location 13,373,430 – 13,373,547
Length 117
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 82.13
Mean single sequence MFE -29.75
Consensus MFE -19.60
Energy contribution -19.96
Covariance contribution 0.36
Combinations/Pair 1.27
Mean z-score -1.59
Structure conservation index 0.66
SVM decision value 0.02
SVM RNA-class probability 0.541492
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13373430 117 + 20766785
UGCCGGCAGCAAGAAAUUGAGGGCCAACGAAAUAGAUUUCGUUUUAUUCCCACUAUCGUUUUCUUGGCCAAACAAGUCUGUUAGCUGUUUGCCGUGCAUAUACUCGUAUGUAUUUCU-
((((((((((((((((.((((((..(((((((....))))))).....)))....))).)))))))((..((((....)))).))...)))))).))).((((......))))....- ( -30.70)
>DroSec_CAF1 72173 117 + 1
UGCCGGCAGCAACAAAUUGAGGGCCAACGAAAUAGAUUUCGUUUUAUUGCCACUAUCGUUGUGUUGGCCAAACAAGUCUGUUAGCUGUUUGCCGUGCAUAUACUCGUAUAUAAUUCU-
.(((((((((((((..(((..((((((((.....(((...((......))....)))....))))))))...)))...)))).))....))))).))(((((....)))))......- ( -32.90)
>DroSim_CAF1 75503 117 + 1
UGCCGGCAGCAACAAAUUGAGGGCCAACGAAAUAGAUUUCGUUUUAUUGCCACUAUCGUUGUCUUGGCCAAACAAGUCUGUUAGCUGUUUGCCGUGCAUAUACUCGUAUAUAUUUCU-
.(((((((((((((..(((..((((((.((....(((...((......))....)))....))))))))...)))...)))).))....))))).))(((((....)))))......- ( -30.60)
>DroEre_CAF1 73493 110 + 1
UGCCGGCAGCAACAAAUUGAGGGCCAACGAAAUAGAUU----UUUAUUCCCACUAUCGUUGUCUUGGCCAAACAAGUCUGUUAGCUGUUUGCUGUGCAUAUAUG--UGUGUA-UUUU-
.((..(((((((((..(((..((((((.((....(((.----............)))....))))))))...)))...)))).)))))..)).(((((((....--))))))-)...- ( -31.72)
>DroYak_CAF1 74506 112 + 1
UGCCGGCAGCAACAAAUUGAGGGCCAACGAAAUAGAUAUCAGUUUAUUCCCACUAUCGUUGUCUUGGCCAAACAAGUCUGUUAGCUGUUUGCUCUGCAUAUAUG--UAUU---UGUU-
.((..(((((((((..(((..((((((.((....((((...............))))....))))))))...)))...)))).)))))..))..((((....))--))..---....- ( -28.66)
>DroAna_CAF1 71372 113 + 1
UGCGAACUGUGGCAAAUUGAGGGCCAACAAAAUUUGU-UCAAUUUAUUGCCACCAGCUUUGUCUUGCUCAAAUUAUUUUGUUAGCUGUUUGCAAA--AUAA--GUGUGUGUUAUUUUC
.((((((((((((((((((((...(((......))))-)))))...)))))).))).)))))...((.((..(((((((((.........)))))--))))--...)).))....... ( -23.90)
>consensus
UGCCGGCAGCAACAAAUUGAGGGCCAACGAAAUAGAUUUCGUUUUAUUCCCACUAUCGUUGUCUUGGCCAAACAAGUCUGUUAGCUGUUUGCCGUGCAUAUACGCGUAUGUA_UUCU_
.((.((((((((((..(((..((((((.((....(((.................)))....))))))))...)))...)))).)))))).)).......................... (-19.60 = -19.96 +   0.36)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,373,430 – 13,373,547
Length 117
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 82.13
Mean single sequence MFE -29.37
Consensus MFE -17.20
Energy contribution -18.96
Covariance contribution 1.75
Combinations/Pair 1.10
Mean z-score -2.22
Structure conservation index 0.59
SVM decision value 0.16
SVM RNA-class probability 0.614281
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13373430 117 - 20766785
-AGAAAUACAUACGAGUAUAUGCACGGCAAACAGCUAACAGACUUGUUUGGCCAAGAAAACGAUAGUGGGAAUAAAACGAAAUCUAUUUCGUUGGCCCUCAAUUUCUUGCUGCCGGCA
-....((((......)))).(((.(((((....((((((......).)))))(((((((((....))(((.....(((((((....)))))))..)))....))))))).)))))))) ( -31.50)
>DroSec_CAF1 72173 117 - 1
-AGAAUUAUAUACGAGUAUAUGCACGGCAAACAGCUAACAGACUUGUUUGGCCAACACAACGAUAGUGGCAAUAAAACGAAAUCUAUUUCGUUGGCCCUCAAUUUGUUGCUGCCGGCA
-......(((((....)))))((.(((((....((.((((((.(((...((((..(((.......))).......(((((((....)))))))))))..)))))))))))))))))). ( -34.00)
>DroSim_CAF1 75503 117 - 1
-AGAAAUAUAUACGAGUAUAUGCACGGCAAACAGCUAACAGACUUGUUUGGCCAAGACAACGAUAGUGGCAAUAAAACGAAAUCUAUUUCGUUGGCCCUCAAUUUGUUGCUGCCGGCA
-....((((((....))))))((.(((((....((.((((((.(((...((((..(...((....))..).....(((((((....)))))))))))..)))))))))))))))))). ( -32.70)
>DroEre_CAF1 73493 110 - 1
-AAAA-UACACA--CAUAUAUGCACAGCAAACAGCUAACAGACUUGUUUGGCCAAGACAACGAUAGUGGGAAUAAA----AAUCUAUUUCGUUGGCCCUCAAUUUGUUGCUGCCGGCA
-....-......--............((...((((.((((((.(((...(((((.....((((.((((((......----..)))))))))))))))..)))))))))))))...)). ( -28.10)
>DroYak_CAF1 74506 112 - 1
-AACA---AAUA--CAUAUAUGCAGAGCAAACAGCUAACAGACUUGUUUGGCCAAGACAACGAUAGUGGGAAUAAACUGAUAUCUAUUUCGUUGGCCCUCAAUUUGUUGCUGCCGGCA
-....---....--............((...((((.((((((.(((...(((((.....((((.((((((.((......)).)))))))))))))))..)))))))))))))...)). ( -28.50)
>DroAna_CAF1 71372 113 - 1
GAAAAUAACACACAC--UUAU--UUUGCAAACAGCUAACAAAAUAAUUUGAGCAAGACAAAGCUGGUGGCAAUAAAUUGA-ACAAAUUUUGUUGGCCCUCAAUUUGCCACAGUUCGCA
.(((((((.......--))))--)))((...(((((..((((....)))).(.....)..)))))(((((((...(((((-.(((......)))....)))))))))))).....)). ( -21.40)
>consensus
_AAAA_UACAUACGAGUAUAUGCACGGCAAACAGCUAACAGACUUGUUUGGCCAAGACAACGAUAGUGGCAAUAAAACGAAAUCUAUUUCGUUGGCCCUCAAUUUGUUGCUGCCGGCA
..........................((...((((.((((((.(((...(((((.....((((.(((((..............))))))))))))))..)))))))))))))...)). (-17.20 = -18.96 +   1.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:37 2006