Locus 1817

Sequence ID 2R_DroMel_CAF1
Location 6,790,920 – 6,791,097
Length 177
Max. P 0.917753
window3015 window3016

overview

Window 5

Location 6,790,920 – 6,791,020
Length 100
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 88.36
Mean single sequence MFE -26.03
Consensus MFE -19.65
Energy contribution -20.15
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.59
Structure conservation index 0.75
SVM decision value 0.20
SVM RNA-class probability 0.631340
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6790920 100 - 20766785
GAAUUACAAACGAAGUAAUGUAUGGAAAUUCAUGGAA------------CUUUCUUCUCAGGACGAAGACCUGACCCCCGAGCAGAUUGCCGUUCUGCAGAAGGCAUUCAAC
((((.......(((((.(((.((....)).)))...)------------))))((((((((((((..((.(((.(......)))).))..))))))).)))))..))))... ( -23.20)
>DroSec_CAF1 41032 100 - 1
GAAUUACAAGCAAAGUAAUGUAUGGAAAUUCAUGGAA------------CUUUCUCCUCAGGACGAAGAUCUGACCCCCGAGCAGAUUGCCGUUCUGCAGAAGGCAUUCAAC
(((((.((.(((......))).))..))))).((((.------------((((((...(((((((..((((((.(......)))))))..))))))).))))))..)))).. ( -27.40)
>DroSim_CAF1 49974 100 - 1
GAAUUACAAACAAUGUAAUGUAUGGAAAUUCAUGGAA------------CUUUCUCCUCAGGACGAAGAUCUGACCCCCGAGCAGAUUGCCGUUCUGCAGAAGGCAUUCAAC
(((((.((.(((......))).))..))))).((((.------------((((((...(((((((..((((((.(......)))))))..))))))).))))))..)))).. ( -27.10)
>DroYak_CAF1 48921 112 - 1
AAAUUACAAACAAUGUAAUGUGUAAAAACUCACUGAACGCAUUUCUAUGCUUUCUCCUCAGGACGAAGACCUGACCCCCGAGCAGAUUGCCGUUCUGCAGAAGGCAUUCAAC
..((((((.....))))))((((.............))))......(((((((((..(((((.......))))).......(((((.......))))))))))))))..... ( -26.42)
>consensus
GAAUUACAAACAAAGUAAUGUAUGGAAAUUCAUGGAA____________CUUUCUCCUCAGGACGAAGACCUGACCCCCGAGCAGAUUGCCGUUCUGCAGAAGGCAUUCAAC
..(((((.......)))))..............................((((((...(((((((..((((((.(......)))))))..))))))).))))))........ (-19.65 = -20.15 +   0.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,790,983 – 6,791,097
Length 114
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 68.04
Mean single sequence MFE -22.70
Consensus MFE -11.73
Energy contribution -11.63
Covariance contribution -0.10
Combinations/Pair 1.20
Mean z-score -1.92
Structure conservation index 0.52
SVM decision value 1.12
SVM RNA-class probability 0.917753
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6790983 114 - 20766785
GGGGUAACACCUUGCACUUGAAAGCAGUGUUAAGGAAUAGAGAAAUGUCGUUUCUCAUCA---AUUUAAAGAUUUUUACCGAAUUACAAACGAAGUAAUGUAUGGAAAUUCAUGGAA
..(((((..((((((((((....).)))).)))))....(((((((...)))))))....---............)))))(((((.((.(((......))).))..)))))...... ( -23.40)
>DroSim_CAF1 50037 88 - 1
GGGGUAACUCCUUGCACUUGAAAGCAGUGUUAAGGA-----------------------------UUAAGGAUUUAUUCUGAAUUACAAACAAUGUAAUGUAUGGAAAUUCAUGGAA
(((((((.((((((..(((((........)))))..-----------------------------.)))))).)))))))(((((.((.(((......))).))..)))))...... ( -18.80)
>DroYak_CAF1 48996 109 - 1
GGGCAAACACCUUGCACUUGAAAA-AGUGUUAUGGAACAGAGAAAAUC-------CGUUUUUUUAUCACGGAUUUAUACCAAAUUACAAACAAUGUAAUGUGUAAAAACUCACUGAA
.........((..((((((....)-)))))...))..(((.(((((((-------(((.........)))))))).(((...((((((.....))))))..))).....)).))).. ( -25.90)
>consensus
GGGGUAACACCUUGCACUUGAAAGCAGUGUUAAGGAA_AGAGAAA__________C_U_______UUAAGGAUUUAUACCGAAUUACAAACAAUGUAAUGUAUGGAAAUUCAUGGAA
(((......((((((((((....).)))).))))).....................................(((((((...(((((.......))))))))))))..)))...... (-11.73 = -11.63 +  -0.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:51 2006