Locus 759

Sequence ID 3R_DroMel_CAF1
Location 2,664,838 – 2,664,977
Length 139
Max. P 0.756584
window1211 window1212 window1213

overview

Window 1

Location 2,664,838 – 2,664,945
Length 107
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 81.99
Mean single sequence MFE -28.09
Consensus MFE -17.65
Energy contribution -18.73
Covariance contribution 1.08
Combinations/Pair 1.05
Mean z-score -1.96
Structure conservation index 0.63
SVM decision value 0.40
SVM RNA-class probability 0.723156
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2664838 107 + 27905053
AAAGAGGCUAGCCUAAUUGUCCAGCAGGCUGUUGACUUUUGUGUUCCUAAA-UAAUAGGGCAAUUAAGUGCAGGGUUACCAAAAGCUAUAACUGCACAUGGUUCUAUA
..((((.(((...((((((((((((.....)))).((.((((........)-))).)))))))))).((((((((((......))))....)))))).)))))))... ( -24.60)
>DroSec_CAF1 24335 107 + 1
AAAGAGCCUAGCCUAAUUGUCCACCUGGCUGUUUACUUUUGUGUUCCUAAA-GAAGAGGGCAAUUAAAUGCAGGGCUACCAAAAGGAAUAACUGCACAUGGUUCUAUA
..((((((.....(((((((((..((....(..(((....)))..)....)-)....)))))))))..(((((.....((....)).....)))))...))))))... ( -26.60)
>DroSim_CAF1 17429 107 + 1
AAAGAGCCUAGCCUAAUUGUCCACCAGGCUGUUGACUUUUGUGUUCCUAAA-GAAGAGGGCAAUUAAGUGCAGGGUUACCGAAAGGUAUAACUGCACAUAGUUCUAUA
..(((((......(((((((((..(((....))).(((((..........)-)))).))))))))).((((((...((((....))))...))))))...)))))... ( -35.30)
>DroEre_CAF1 17376 107 + 1
AAAGUGGCUAGCCUAAUUGUCCACCAGGCUGUUGACUUUUGUGUUCGUAAAAAAAGAGGUCAAUUAAGUGCAGCGUUACCAA-AGGUAUAGCUGCACAUAGUUCUUUA
((((.(((((((((...........)))).((((((((((..............))))))))))...(((((((..((((..-.))))..))))))).))))))))). ( -32.14)
>DroYak_CAF1 24581 86 + 1
AAAGUGGCUAGGCUAAUUGUCCACCAGGCUG------------UUCCUAAAAAAAGAGGUCAAUU-AGUGCAGGGUUGCCAAAAGGUACAACUGCACAA---------
..((..(((.((...........)).)))..------------))(((........)))......-.((((((...((((....))))...))))))..--------- ( -21.80)
>consensus
AAAGAGGCUAGCCUAAUUGUCCACCAGGCUGUUGACUUUUGUGUUCCUAAA_AAAGAGGGCAAUUAAGUGCAGGGUUACCAAAAGGUAUAACUGCACAUAGUUCUAUA
.............(((((((((...................................))))))))).((((((...((((....))))...))))))........... (-17.65 = -18.73 +   1.08)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,664,878 – 2,664,977
Length 99
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 85.43
Mean single sequence MFE -23.07
Consensus MFE -13.88
Energy contribution -15.00
Covariance contribution 1.12
Combinations/Pair 1.11
Mean z-score -2.55
Structure conservation index 0.60
SVM decision value 0.49
SVM RNA-class probability 0.756584
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2664878 99 + 27905053
GUGUUCCUAAA-UAAUAGGGCAAUUAAGUGCAGGGUUACCAAAAGCUAUAACUGCACAUGGUUCUAUAUUCCAUAGAGAAACACCUAGAAUUGAAAUUAA
(((((((((..-.((((.((.(((((.((((((((((......))))....)))))).))))))).))))...))).).)))))................ ( -19.40)
>DroSec_CAF1 24375 99 + 1
GUGUUCCUAAA-GAAGAGGGCAAUUAAAUGCAGGGCUACCAAAAGGAAUAACUGCACAUGGUUCUAUAUUCCAUAGAGAAACAACUAGAAUUAAAAUUUA
((.((((((..-(((.(((((.......(((((.....((....)).....)))))....)))))...)))..))).)))...))............... ( -17.60)
>DroSim_CAF1 17469 99 + 1
GUGUUCCUAAA-GAAGAGGGCAAUUAAGUGCAGGGUUACCGAAAGGUAUAACUGCACAUAGUUCUAUAUUCCAUAGAGAAACAACUAGAAUUAAAUUUAA
((.((((((..-(((...((.(((((.((((((...((((....))))...)))))).)))))))...)))..))).)))...))............... ( -29.10)
>DroEre_CAF1 17416 99 + 1
GUGUUCGUAAAAAAAGAGGUCAAUUAAGUGCAGCGUUACCAA-AGGUAUAGCUGCACAUAGUUCUUUACUCCAUAAAGAUACCCCUGGCCAUUAAAUUAA
.................(((((((((.(((((((..((((..-.))))..))))))).))))((((((.....))))))......))))).......... ( -26.20)
>consensus
GUGUUCCUAAA_GAAGAGGGCAAUUAAGUGCAGGGUUACCAAAAGGUAUAACUGCACAUAGUUCUAUAUUCCAUAGAGAAACAACUAGAAUUAAAAUUAA
..............(((((((...((.((((((...((((....))))...)))))).)))))))))................................. (-13.88 = -15.00 +   1.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,664,878 – 2,664,977
Length 99
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 85.43
Mean single sequence MFE -20.10
Consensus MFE -14.26
Energy contribution -14.83
Covariance contribution 0.56
Combinations/Pair 1.10
Mean z-score -1.47
Structure conservation index 0.71
SVM decision value 0.02
SVM RNA-class probability 0.544619
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2664878 99 - 27905053
UUAAUUUCAAUUCUAGGUGUUUCUCUAUGGAAUAUAGAACCAUGUGCAGUUAUAGCUUUUGGUAACCCUGCACUUAAUUGCCCUAUUA-UUUAGGAACAC
..........((((..(((((((.....)))))))))))....((((((...((.(....).))...))))))........((((...-..))))..... ( -18.50)
>DroSec_CAF1 24375 99 - 1
UAAAUUUUAAUUCUAGUUGUUUCUCUAUGGAAUAUAGAACCAUGUGCAGUUAUUCCUUUUGGUAGCCCUGCAUUUAAUUGCCCUCUUC-UUUAGGAACAC
.................(((((((....((((...........((((((.....((....)).....))))))............)))-)..))))))). ( -16.40)
>DroSim_CAF1 17469 99 - 1
UUAAAUUUAAUUCUAGUUGUUUCUCUAUGGAAUAUAGAACUAUGUGCAGUUAUACCUUUCGGUAACCCUGCACUUAAUUGCCCUCUUC-UUUAGGAACAC
.................((((((((((((...)))))).....((((((...((((....))))...))))))...............-....)))))). ( -20.10)
>DroEre_CAF1 17416 99 - 1
UUAAUUUAAUGGCCAGGGGUAUCUUUAUGGAGUAAAGAACUAUGUGCAGCUAUACCU-UUGGUAACGCUGCACUUAAUUGACCUCUUUUUUUACGAACAC
..............((((((.(((((((...))))))).....(((((((..((((.-..))))..))))))).......)))))).............. ( -25.40)
>consensus
UUAAUUUUAAUUCUAGGUGUUUCUCUAUGGAAUAUAGAACCAUGUGCAGUUAUACCUUUUGGUAACCCUGCACUUAAUUGCCCUCUUC_UUUAGGAACAC
..................((((((..((((.........))))((((((...((((....))))...))))))...................)))))).. (-14.26 = -14.83 +   0.56)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:26 2006