Locus 1790

Sequence ID 2L_DroMel_CAF1
Location 4,904,320 – 4,904,417
Length 97
Max. P 0.939915
window2885 window2886

overview

Window 5

Location 4,904,320 – 4,904,417
Length 97
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 83.06
Mean single sequence MFE -38.92
Consensus MFE -28.52
Energy contribution -29.55
Covariance contribution 1.03
Combinations/Pair 1.18
Mean z-score -2.67
Structure conservation index 0.73
SVM decision value 0.78
SVM RNA-class probability 0.848837
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4904320 97 + 22407834
UAAGAGCAGGAGGUGGCAGCUUAAAGCCACUUGGACCACCCAAAUUAAGGGAUCCUCCUGUAAAGACAGGAGGCACUGUUGUGGUGGU---UGUGGUGCU
....((((..(((((((........))))))).((((((((((....((....((((((((....))))))))..)).))).))))))---)....)))) ( -41.30)
>DroSec_CAF1 102 97 + 1
UCAGAGCAGGUGGUGGCAAUUUGAAGCCACUUGGACCACCCAAAUUAAGGGAUCCUCCUGUGAAGACAGGAGGCACUGUUGUGGUGGU---UGUGGUGCU
......((((((((..(.....)..))))))))((((((((((....((....((((((((....))))))))..)).))).))))))---)........ ( -40.70)
>DroSim_CAF1 102 97 + 1
UGAGAGCAGGUGGUGGCAGUUUGAAGCCACUUGGUCCACCCAAAUUAAGGGAUCCUCCUGUGAAGAUAGGAGGCACUGUUGUGGUGGU---UGUGGUGCU
...((.((((((((..(.....)..)))))))).))(((((((..........((((((((....))))))))((((.....)))).)---)).)))).. ( -36.70)
>DroEre_CAF1 101 97 + 1
UGAGAGCAGGUGGAGGCAGCCUAAAGCCACUUGGACCACCCAAUUUGAGGGAUCCUCCUGCGAAGGCAGGAGGCACUGUUGUGGUGGA---UGUGGUGCU
....(((((((.......))))...(((((.....(((((((((....((...((((((((....))))))))..)))))).))))).---.)))))))) ( -41.70)
>DroYak_CAF1 296 97 + 1
UGAGAGCAGGUGGUGGCAGCUUAAAACCACUUGGACCACCCAAUUUGAGGGAUCCUCCUGUGAAGACAGGAGACGCUGUUGUGGUGGA---UGUGGUGCU
......((((((((...........)))))))).((((((((...(((.((...(((((((....)))))))...)).)))...))).---.)))))... ( -34.20)
>DroPer_CAF1 105 100 + 1
CGAGGGCUGGCGGUGGCAGCUUGAACCCACUGGGGCCACCUAAAUUGAGAGGACCACCUGCAUAGGGCGGAGGAGCCGCAGUGGUGCUACUCGUACUGCU
....(((..(((((((((........((((((.((((.(((........))).((.(((.....))).))..).))).)))))))))))).)))...))) ( -38.90)
>consensus
UGAGAGCAGGUGGUGGCAGCUUAAAGCCACUUGGACCACCCAAAUUAAGGGAUCCUCCUGUGAAGACAGGAGGCACUGUUGUGGUGGU___UGUGGUGCU
....((((...((((((........))))))....((((((((.....((...((((((((....))))))))..)).))).))))).........)))) (-28.52 = -29.55 +   1.03)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,904,320 – 4,904,417
Length 97
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 83.06
Mean single sequence MFE -31.85
Consensus MFE -25.27
Energy contribution -25.80
Covariance contribution 0.53
Combinations/Pair 1.20
Mean z-score -3.13
Structure conservation index 0.79
SVM decision value 1.28
SVM RNA-class probability 0.939915
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4904320 97 - 22407834
AGCACCACA---ACCACCACAACAGUGCCUCCUGUCUUUACAGGAGGAUCCCUUAAUUUGGGUGGUCCAAGUGGCUUUAAGCUGCCACCUCCUGCUCUUA
((((.....---((((((.(((.((..((((((((....))))))))....))....)))))))))....(((((........)))))....)))).... ( -34.00)
>DroSec_CAF1 102 97 - 1
AGCACCACA---ACCACCACAACAGUGCCUCCUGUCUUCACAGGAGGAUCCCUUAAUUUGGGUGGUCCAAGUGGCUUCAAAUUGCCACCACCUGCUCUGA
((((.....---((((((.(((.((..((((((((....))))))))....))....)))))))))....(((((........)))))....)))).... ( -34.10)
>DroSim_CAF1 102 97 - 1
AGCACCACA---ACCACCACAACAGUGCCUCCUAUCUUCACAGGAGGAUCCCUUAAUUUGGGUGGACCAAGUGGCUUCAAACUGCCACCACCUGCUCUCA
((((.....---.(((((.(((.((..((((((........))))))....))....)))))))).....(((((........)))))....)))).... ( -29.50)
>DroEre_CAF1 101 97 - 1
AGCACCACA---UCCACCACAACAGUGCCUCCUGCCUUCGCAGGAGGAUCCCUCAAAUUGGGUGGUCCAAGUGGCUUUAGGCUGCCUCCACCUGCUCUCA
(((......---.....(((....)))((((((((....))))))))............((((((.....(..((.....))..)..))))))))).... ( -32.40)
>DroYak_CAF1 296 97 - 1
AGCACCACA---UCCACCACAACAGCGUCUCCUGUCUUCACAGGAGGAUCCCUCAAAUUGGGUGGUCCAAGUGGUUUUAAGCUGCCACCACCUGCUCUCA
((((.....---.(((((.(((.((..((((((((....))))))))....))....)))))))).....(((((........)))))....)))).... ( -28.10)
>DroPer_CAF1 105 100 - 1
AGCAGUACGAGUAGCACCACUGCGGCUCCUCCGCCCUAUGCAGGUGGUCCUCUCAAUUUAGGUGGCCCCAGUGGGUUCAAGCUGCCACCGCCAGCCCUCG
.((.....(((.((.(((((((((((......)))....))).))))).)))))......(((((((((...)))........))))))))......... ( -33.00)
>consensus
AGCACCACA___ACCACCACAACAGUGCCUCCUGUCUUCACAGGAGGAUCCCUCAAUUUGGGUGGUCCAAGUGGCUUCAAGCUGCCACCACCUGCUCUCA
.((..........(((((.(((.((..((((((((....))))))))....))....)))))))).....(((((........))))).....))..... (-25.27 = -25.80 +   0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:23 2006