Locus 7709

Sequence ID X_DroMel_CAF1
Location 19,208,589 – 19,208,722
Length 133
Max. P 0.997069
window12641 window12642 window12643

overview

Window 1

Location 19,208,589 – 19,208,684
Length 95
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.07
Mean single sequence MFE -19.52
Consensus MFE -16.67
Energy contribution -16.91
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.06
Structure conservation index 0.85
SVM decision value 0.03
SVM RNA-class probability 0.547048
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19208589 95 - 22224390
AAGCGCCCUUUGUGCCGAAAUCAAACUGCAAAUACAUGGCCUAAAAGCAUUGGCAAACAAGCAAACAUGGCCAUGCAUC------CUCACUCCUUUAACGC-------------------
..((((..((((.........))))..)).....(((((((.....((.(((.....)))))......)))))))....------..............))------------------- ( -18.90)
>DroSec_CAF1 29950 106 - 1
AAGCGCCCUUUGUGCCGAAAUCAAACUGCAAAUACAUGGCCUAAAAGCAUUGGCAAACAAGCAAACAUGGCCAUGC---------CACACCCCCUU----CCCGCC-CGCCCUUCCUUCC
..((((..((((.........))))..)).....(((((((.....((.(((.....)))))......))))))).---------...........----...)).-............. ( -19.70)
>DroSim_CAF1 5216 110 - 1
AAGCGCCCUUUGUGCCGAAAUCAAACUGCAAAUACAUGGCCUAAAAGCAUUGGCAAACAAGCAAACAUGGCCAUGC---------CACACCCCCUUACCGCCCGCC-CGCCCUUCAUUCC
..((((.....)))).(((...............(((((((.....((.(((.....)))))......))))))).---------..............((.....-.))..)))..... ( -19.90)
>DroYak_CAF1 27720 108 - 1
AAGCGCCCUUUGUGCCGGAAUCAAACUGCAAAUACAUGGCCUAAAAGCAUUGGCAAACA----AACUCGGCCAUGUACUCUACUCCCCGCCCCCUUUCC--CUGCCACGCCCCU------
..(((.......(((.(........).)))..(((((((((....((..(((.....))----).)).)))))))))......................--......)))....------ ( -19.60)
>consensus
AAGCGCCCUUUGUGCCGAAAUCAAACUGCAAAUACAUGGCCUAAAAGCAUUGGCAAACAAGCAAACAUGGCCAUGC_________CACACCCCCUUACC_CCCGCC_CGCCCUU______
..((((.....))))...................(((((((........(((.....)))........)))))))............................................. (-16.67 = -16.91 +   0.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,208,605 – 19,208,722
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.73
Mean single sequence MFE -36.86
Consensus MFE -26.39
Energy contribution -26.87
Covariance contribution 0.48
Combinations/Pair 1.03
Mean z-score -2.57
Structure conservation index 0.72
SVM decision value 0.86
SVM RNA-class probability 0.868354
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19208605 117 + 22224390
-GAUGCAUGGCCAUGUUUGCUUGUUUGCCAAUGCUUUUAGGCCAUGUAUUUGCAGUUUGAUUUCGGCACAAAGGGCGCUUUGAACUGCUGUCG--UAUUUGCAUUUGCUCAAUCAAACAG
-(((((((((((.((...(((((.....))).))...)))))))))))))....((((((((..(((((((((....)))))...(((.....--.....)))..)))).)))))))).. ( -35.70)
>DroSec_CAF1 29980 114 + 1
----GCAUGGCCAUGUUUGCUUGUUUGCCAAUGCUUUUAGGCCAUGUAUUUGCAGUUUGAUUUCGGCACAAAGGGCGCUUUGAACUGCUGUCC--UAUUUGCAUUGGCUCAAUCAAACAG
----.........((((((.(((...((((((((...((((.((.......((((((..(...((.(......).))..)..)))))))).))--))...)))))))).))).)))))). ( -39.51)
>DroSim_CAF1 5250 114 + 1
----GCAUGGCCAUGUUUGCUUGUUUGCCAAUGCUUUUAGGCCAUGUAUUUGCAGUUUGAUUUCGGCACAAAGGGCGCUUUGAACUGCUGUCC--UAUUUGCAUUGGCUCAAUCAAACAG
----.........((((((.(((...((((((((...((((.((.......((((((..(...((.(......).))..)..)))))))).))--))...)))))))).))).)))))). ( -39.51)
>DroEre_CAF1 27218 109 + 1
-------UGGCCGAGUU----UGUUUGCCAAUGCUUUUAGGCCAUGUAUUUGCAGUUUGAUUACGGCACAAAGGGCGCUUUGAACUGCAGUCGUGUAUUUGCAUGUGCUCAAUCAAACAU
-------((((((((((----((.....))).))))...)))))(((....)))((((((((..(((((....(((((........)).)))((((....))))))))).)))))))).. ( -30.80)
>DroYak_CAF1 27752 114 + 1
GAGUACAUGGCCGAGUU----UGUUUGCCAAUGCUUUUAGGCCAUGUAUUUGCAGUUUGAUUCCGGCACAAAGGGCGCUUUGAACUGCAGUCG--UAUUUGCAUUUGCUCAAUCAAACGG
(((((((((((((((((----((.....))).))))...))))))))))))...((((((((..(((((((((....)))))...(((((...--...)))))..)))).)))))))).. ( -38.80)
>consensus
____GCAUGGCCAUGUUUGCUUGUUUGCCAAUGCUUUUAGGCCAUGUAUUUGCAGUUUGAUUUCGGCACAAAGGGCGCUUUGAACUGCUGUCG__UAUUUGCAUUUGCUCAAUCAAACAG
....((((((((.........((.....)).........)))))))).......((((((((..(((.(((((....)))))...(((............)))...))).)))))))).. (-26.39 = -26.87 +   0.48)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,208,605 – 19,208,722
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.73
Mean single sequence MFE -30.26
Consensus MFE -26.33
Energy contribution -27.13
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.33
Structure conservation index 0.87
SVM decision value 2.79
SVM RNA-class probability 0.997069
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19208605 117 - 22224390
CUGUUUGAUUGAGCAAAUGCAAAUA--CGACAGCAGUUCAAAGCGCCCUUUGUGCCGAAAUCAAACUGCAAAUACAUGGCCUAAAAGCAUUGGCAAACAAGCAAACAUGGCCAUGCAUC-
..((((((((((((...(((.....--.....)))))))...((((.....))))...))))))))........(((((((.....((.(((.....)))))......)))))))....- ( -30.40)
>DroSec_CAF1 29980 114 - 1
CUGUUUGAUUGAGCCAAUGCAAAUA--GGACAGCAGUUCAAAGCGCCCUUUGUGCCGAAAUCAAACUGCAAAUACAUGGCCUAAAAGCAUUGGCAAACAAGCAAACAUGGCCAUGC----
.((((((.(((.((((((((...((--((.((((((((....((((.....)))).(....).)))))).......)).))))...))))))))...))).)))))).........---- ( -32.51)
>DroSim_CAF1 5250 114 - 1
CUGUUUGAUUGAGCCAAUGCAAAUA--GGACAGCAGUUCAAAGCGCCCUUUGUGCCGAAAUCAAACUGCAAAUACAUGGCCUAAAAGCAUUGGCAAACAAGCAAACAUGGCCAUGC----
.((((((.(((.((((((((...((--((.((((((((....((((.....)))).(....).)))))).......)).))))...))))))))...))).)))))).........---- ( -32.51)
>DroEre_CAF1 27218 109 - 1
AUGUUUGAUUGAGCACAUGCAAAUACACGACUGCAGUUCAAAGCGCCCUUUGUGCCGUAAUCAAACUGCAAAUACAUGGCCUAAAAGCAUUGGCAAACA----AACUCGGCCA-------
..(((((((((.(((((((((..........))))((.....))......)))))..)))))))))..........(((((....((..(((.....))----).)).)))))------- ( -24.30)
>DroYak_CAF1 27752 114 - 1
CCGUUUGAUUGAGCAAAUGCAAAUA--CGACUGCAGUUCAAAGCGCCCUUUGUGCCGGAAUCAAACUGCAAAUACAUGGCCUAAAAGCAUUGGCAAACA----AACUCGGCCAUGUACUC
..((((((((((((...((((....--....))))))))...((((.....))))...))))))))......(((((((((....((..(((.....))----).)).)))))))))... ( -31.60)
>consensus
CUGUUUGAUUGAGCAAAUGCAAAUA__CGACAGCAGUUCAAAGCGCCCUUUGUGCCGAAAUCAAACUGCAAAUACAUGGCCUAAAAGCAUUGGCAAACAAGCAAACAUGGCCAUGC____
..((((((((((((...(((............)))))))...((((.....))))...))))))))........(((((((........(((.....)))........)))))))..... (-26.33 = -27.13 +   0.80)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:45:35 2006