Locus 7547

Sequence ID 3R_DroMel_CAF1
Location 20,221,880 – 20,222,024
Length 144
Max. P 0.792687
window12179 window12180

overview

Window 9

Location 20,221,880 – 20,221,996
Length 116
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 95.52
Mean single sequence MFE -28.43
Consensus MFE -24.04
Energy contribution -24.04
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.88
Structure conservation index 0.85
SVM decision value 0.51
SVM RNA-class probability 0.765149
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20221880 116 + 27905053
AGCA-AUACGCAGACUUUGAUUCUU-GUUGUGUUUGCUACAAAAGACGACCUUUGAUUGGAAGACAUACGAUUUUAUGUUUUUUGAAUCUCAGGGUCAAGCCGCAUAU--UUAUCAAAUA
.((.-....((((((..((((....-)))).))))))..........((((((.(((..(((((((((......)))))))))..).))..)))))).....))....--.......... ( -27.70)
>DroVir_CAF1 42887 117 + 1
AGCA-AUACGCAGACUUUGAUUCUU-GUUGUGUUUGCUACAAAAGACGACCUUUGAUUGGAAGACAUCCGAUUUUAUGUUU-UUGAAUCUCAGGGUCAAGCCGCAUAUAUAUAUCAAAUA
.((.-....((((((..((((....-)))).))))))..........((((((.((((.((((((((........))))))-)).))))..)))))).....))................ ( -28.20)
>DroGri_CAF1 46579 115 + 1
AGCA-AUACGCAGACUUUGAUUCUU-GUUGUGUUUGCUACAAAAGACGACCUUUGAUUGGAAGACAUCCGAUUUUAUGUUU-UUGAAUCUCAGGGUCAAGCCGCAUAU--AUAUCAAAUA
.((.-....((((((..((((....-)))).))))))..........((((((.((((.((((((((........))))))-)).))))..)))))).....))....--.......... ( -28.20)
>DroWil_CAF1 34124 116 + 1
AGCA-AUACGCAGACU-UGAUUCUUUUUUGUGUUUGCUACAAAAGACGACCUUUGAUUGGAAGACAUACGAUUUUAUGUUUUUUGAAUCUCAGGGUCAAGCCGCAUAU--AUAUCAGAUU
....-....((.(.((-(((((((((((((((.....))))))))).))(((..(((..(((((((((......)))))))))..).))..)))))))))).))....--.......... ( -28.60)
>DroMoj_CAF1 40562 118 + 1
AGCAAAUACGCAGACUUUGUUUCUU-GUUGUGUUUGCUACAAUAGACGACCUUUGAUUGGAAGACAUCCGAUUUUAUGUUU-UUGAAUCUCAGGGUCAAGCCGCAUAUAUAUAUCAAAUA
((((((((((((((.......)).)-).)))))))))).........((((((.((((.((((((((........))))))-)).))))..))))))....................... ( -30.20)
>DroPer_CAF1 37388 116 + 1
AGCA-AUACGCAGACUUUGAUUCUU-GUUGUGUUUGCUACAAAAGACGACCUUUGAUUGGAAGACAUACGAUUUUAUGUUUUUUGAAUCUCAGGGUCAAGCCGCAUAU--AUAUCAAAUA
.((.-....((((((..((((....-)))).))))))..........((((((.(((..(((((((((......)))))))))..).))..)))))).....))....--.......... ( -27.70)
>consensus
AGCA_AUACGCAGACUUUGAUUCUU_GUUGUGUUUGCUACAAAAGACGACCUUUGAUUGGAAGACAUACGAUUUUAUGUUU_UUGAAUCUCAGGGUCAAGCCGCAUAU__AUAUCAAAUA
.((......((((((................))))))..........((((((.((((.((((((((........)))))).)).))))..)))))).....))................ (-24.04 = -24.04 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,221,918 – 20,222,024
Length 106
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 78.09
Mean single sequence MFE -19.60
Consensus MFE -16.40
Energy contribution -17.07
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.18
Structure conservation index 0.84
SVM decision value 0.59
SVM RNA-class probability 0.792687
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20221918 106 + 27905053
AAAAGACGACCUUUGAUUGGAAGACAUACGAUUUUAUGUUUUUUGAAUCUCAGGGUCAAGCCGCAUAU--UUAUCAAAUACCUCA-AU--------UUCCUGUUUACAUCGUAAUUA
.......((((((.(((..(((((((((......)))))))))..).))..))))))...........--...............-..--------..................... ( -18.30)
>DroVir_CAF1 42925 85 + 1
AAAAGACGACCUUUGAUUGGAAGACAUCCGAUUUUAUGUUU-UUGAAUCUCAGGGUCAAGCCGCAUAUAUAUAUCAAAUACUUAUU-------------------------------
.......((((((.((((.((((((((........))))))-)).))))..)))))).............................------------------------------- ( -18.80)
>DroPse_CAF1 38850 106 + 1
AAAAGACGACCUUUGAUUGGAAGACAUACGAUUUUAUGUUUUUUGAAUCUCAGGGUCAAGCCGCAUAU--AUAUCAAAUACGUCA-AU--------UUCUUGAUUACACCAUAAGUU
....(((((((((.(((..(((((((((......)))))))))..).))..))))))...........--...........((((-(.--------...)))))..........))) ( -20.30)
>DroGri_CAF1 46617 83 + 1
AAAAGACGACCUUUGAUUGGAAGACAUCCGAUUUUAUGUUU-UUGAAUCUCAGGGUCAAGCCGCAUAU--AUAUCAAAUACUUAGU-------------------------------
.......((((((.((((.((((((((........))))))-)).))))..))))))...........--................------------------------------- ( -18.80)
>DroWil_CAF1 34162 114 + 1
AAAAGACGACCUUUGAUUGGAAGACAUACGAUUUUAUGUUUUUUGAAUCUCAGGGUCAAGCCGCAUAU--AUAUCAGAUUACUUA-GUUUUUCAGUUUUGUUUUUGUUUAAUAACUA
.((((((((.....(((((((((((....(((..(((((..(((((.((....)))))))..))))).--..)))((....))..-)))))))))))))))))))............ ( -21.10)
>DroPer_CAF1 37426 106 + 1
AAAAGACGACCUUUGAUUGGAAGACAUACGAUUUUAUGUUUUUUGAAUCUCAGGGUCAAGCCGCAUAU--AUAUCAAAUACGUCA-AU--------UUCUUGAUUACACCAUAAGUU
....(((((((((.(((..(((((((((......)))))))))..).))..))))))...........--...........((((-(.--------...)))))..........))) ( -20.30)
>consensus
AAAAGACGACCUUUGAUUGGAAGACAUACGAUUUUAUGUUUUUUGAAUCUCAGGGUCAAGCCGCAUAU__AUAUCAAAUACCUCA_AU________UUC_UG_UUACA_CAUAA_U_
.......((((((.(((..(((((((((......)))))))))..).))..))))))............................................................ (-16.40 = -17.07 +   0.67)

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 12:48:32 2006