Locus 4208

Sequence ID 3L_DroMel_CAF1
Location 12,305,512 – 12,305,655
Length 143
Max. P 0.979489
window6520 window6521 window6522

overview

Window 0

Location 12,305,512 – 12,305,623
Length 111
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 79.95
Mean single sequence MFE -27.80
Consensus MFE -16.06
Energy contribution -17.28
Covariance contribution 1.23
Combinations/Pair 1.13
Mean z-score -2.17
Structure conservation index 0.58
SVM decision value 0.66
SVM RNA-class probability 0.815898
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12305512 111 - 23771897
CGAGCGGAAACGGAAACUAUUUGCUGCCAUU-UGG-GCAAUGGCAAAUGGCAAAUAGCAAAUGGCAGAAUGCGAGCAUUAAUAGAAAUUUCAUAGGCAAAUGCAAAGUUGGCC
....((....))(((((((((((((((((((-((.-.......))))))))....)))))))))...((((....))))........))))...(((.(((.....))).))) ( -30.10)
>DroSim_CAF1 40525 107 - 1
----CGGAAACGGAAACUAUUUGCUGCCAUU-UGG-GCAAUGGCAAAUGGCAAAUAGCAAAUGGCAGAAUGCGAGCAUUAAUAGAAAUUUCAUAGGCAAACGCAAAGUUGGCC
----((....))(((((((((((((((((((-((.-.......))))))))....)))))))))...((((....))))........))))...(((.(((.....))).))) ( -32.10)
>DroEre_CAF1 41232 106 - 1
----CGGAAACGGAAACUAUUUGCUGCCAUU-UGG-GCAAUGGCAAACGGCAA-UGGCAAGUGGCAGAAUGCGAGCAUUAAUAGAAAUUUCAUAGGCAAAUGCUGAGUUGGCC
----((....))(((((((((..((((((((-(.(-.((.((.(....).)).-)).))))))))))((((....)))))))))...))))...(((.(((.....))).))) ( -29.20)
>DroWil_CAF1 60105 94 - 1
----CGGAAACGGAAACUAUUUGCUGGCAUU-UCA-G-------------CAAAUGGCAAAUGGCAAAAGCCAAACAUUAAUAGAAAUUUCAUAUGCAAAUAUAAAGUUUAGC
----((....))....(((((((((((....-)))-)-------------)))))))....((((....))))...........((((((.((((....)))).))))))... ( -24.40)
>DroYak_CAF1 43384 104 - 1
----CGGAAACGGAAACUAUUUGCUGCCAUUUUGG-GCAAUGGCAAGUGGCAAGUGGCAAAUGGCAGAAUGCGAGCAUUAAUAGAAAUUUCAUAGGCAAAUGCAAAGUU----
----((....))(((((((((..((((((((...(-.((...((.....))...)).).))))))))((((....)))))))))...))))....((....))......---- ( -26.00)
>DroAna_CAF1 37510 104 - 1
----CGGAAGCGGAAACUAUUUGCUGCCAUU-UGGAUCAAUGGCGGA--GCAAAUGGUAAAUGGCAAGCGGCAAGUAUUAAUAGAAAUUUCAUUGGAAGCCCCAGAUCUAG--
----.((..((.(..((((((((((((((((-......))))))..)--)))))))))...).))....(((.....(((((.((....)))))))..)))))........-- ( -25.00)
>consensus
____CGGAAACGGAAACUAUUUGCUGCCAUU_UGG_GCAAUGGCAAAUGGCAAAUGGCAAAUGGCAGAAUGCGAGCAUUAAUAGAAAUUUCAUAGGCAAAUGCAAAGUUGGCC
....((....))(((((((((((((((((((.......)))))))....))))))))......((.....))...............))))...................... (-16.06 = -17.28 +   1.23)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,305,546 – 12,305,655
Length 109
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 81.94
Mean single sequence MFE -19.53
Consensus MFE -15.52
Energy contribution -16.32
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.09
Structure conservation index 0.79
SVM decision value 1.24
SVM RNA-class probability 0.935352
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12305546 109 + 23771897
AAUGCUCGCAUUCUGCCAUUUGCUAUUUGCCAUUUGCCAUUGCCCA-AAUGGCAGCAAAUAGUUUCCGUUUCCGCUCGUUCCGUGCCACUACCCCAAUCCACACACCACU
...((.((......((.....(((((((((....(((((((.....-))))))))))))))))..........))......)).))........................ ( -21.76)
>DroSec_CAF1 40739 90 + 1
AAUGCUCGCAUUCUGCCAUUUGCUAUUUGCCAUUUGCCAUUGCCCA-AAUGGCAGCAAAUAGUUUCCGUUUCCG-------------------CCAAUCCACACACCCCU
...((..((.....)).....(((((((((....(((((((.....-))))))))))))))))..........)-------------------)................ ( -20.50)
>DroSim_CAF1 40559 90 + 1
AAUGCUCGCAUUCUGCCAUUUGCUAUUUGCCAUUUGCCAUUGCCCA-AAUGGCAGCAAAUAGUUUCCGUUUCCG-------------------CCAAUCCACACACCCCU
...((..((.....)).....(((((((((....(((((((.....-))))))))))))))))..........)-------------------)................ ( -20.50)
>DroEre_CAF1 41266 88 + 1
AAUGCUCGCAUUCUGCCACUUGCCA-UUGCCGUUUGCCAUUGCCCA-AAUGGCAGCAAAUAGUUUCCGUUUCCG-------------------CUGCGCCGUGCCACAA-
.......((((..(((...((((..-.(((((((((........))-)))))))))))..(((..........)-------------------)))))..)))).....- ( -18.80)
>DroYak_CAF1 43414 91 + 1
AAUGCUCGCAUUCUGCCAUUUGCCACUUGCCACUUGCCAUUGCCCAAAAUGGCAGCAAAUAGUUUCCGUUUCCG-------------------CUUCUCCCUGCCGCCCC
..(((..(((....((.....))....)))....(((((((......))))))))))................(-------------------(........))...... ( -16.10)
>consensus
AAUGCUCGCAUUCUGCCAUUUGCUAUUUGCCAUUUGCCAUUGCCCA_AAUGGCAGCAAAUAGUUUCCGUUUCCG___________________CCAAUCCACACACCCCU
.......((.....)).....(((((((((....(((((((......))))))))))))))))............................................... (-15.52 = -16.32 +   0.80)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,305,546 – 12,305,655
Length 109
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 81.94
Mean single sequence MFE -28.80
Consensus MFE -22.96
Energy contribution -22.52
Covariance contribution -0.44
Combinations/Pair 1.22
Mean z-score -2.41
Structure conservation index 0.80
SVM decision value 1.84
SVM RNA-class probability 0.979489
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12305546 109 - 23771897
AGUGGUGUGUGGAUUGGGGUAGUGGCACGGAACGAGCGGAAACGGAAACUAUUUGCUGCCAUU-UGGGCAAUGGCAAAUGGCAAAUAGCAAAUGGCAGAAUGCGAGCAUU
.((..(((((.(..........).)))))..))...((....))....(((((((((((((((-((........))))))))....)))))))))...((((....)))) ( -30.00)
>DroSec_CAF1 40739 90 - 1
AGGGGUGUGUGGAUUGG-------------------CGGAAACGGAAACUAUUUGCUGCCAUU-UGGGCAAUGGCAAAUGGCAAAUAGCAAAUGGCAGAAUGCGAGCAUU
...(((((.((.(((..-------------------((....))....(((((((((((((((-((........))))))))....)))))))))...))).)).))))) ( -28.80)
>DroSim_CAF1 40559 90 - 1
AGGGGUGUGUGGAUUGG-------------------CGGAAACGGAAACUAUUUGCUGCCAUU-UGGGCAAUGGCAAAUGGCAAAUAGCAAAUGGCAGAAUGCGAGCAUU
...(((((.((.(((..-------------------((....))....(((((((((((((((-((........))))))))....)))))))))...))).)).))))) ( -28.80)
>DroEre_CAF1 41266 88 - 1
-UUGUGGCACGGCGCAG-------------------CGGAAACGGAAACUAUUUGCUGCCAUU-UGGGCAAUGGCAAACGGCAA-UGGCAAGUGGCAGAAUGCGAGCAUU
-.....((....((((.-------------------((....))...........((((((((-(.(.((.((.(....).)).-)).))))))))))..)))).))... ( -28.60)
>DroYak_CAF1 43414 91 - 1
GGGGCGGCAGGGAGAAG-------------------CGGAAACGGAAACUAUUUGCUGCCAUUUUGGGCAAUGGCAAGUGGCAAGUGGCAAAUGGCAGAAUGCGAGCAUU
..(((((((((.((...-------------------((....))....)).))))))))).......(((.((.((..((.(....).))..)).))...)))....... ( -27.80)
>consensus
AGGGGUGUGUGGAUUGG___________________CGGAAACGGAAACUAUUUGCUGCCAUU_UGGGCAAUGGCAAAUGGCAAAUAGCAAAUGGCAGAAUGCGAGCAUU
......((((..........................((....))....(((((((((((((((....((....)).))))))....)))))))))....))))....... (-22.96 = -22.52 +  -0.44)

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 11:16:49 2006