Locus 4382

Sequence ID 3R_DroMel_CAF1
Location 11,578,065 – 11,578,190
Length 125
Max. P 0.999129
window7159 window7160 window7161

overview

Window 9

Location 11,578,065 – 11,578,162
Length 97
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 85.16
Mean single sequence MFE -28.40
Consensus MFE -24.80
Energy contribution -25.20
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -3.08
Structure conservation index 0.87
SVM decision value 3.39
SVM RNA-class probability 0.999129
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11578065 97 + 27905053
AGUUUUCCCAUUUUUU--U-GUUUUUGUUAUUUUACUUGGCAAACGUGGCGCAUUUUUAAAUGGUCACGUUUGGCAGUUUAAGCGCCUCGGUGGGGCAAC
.(((.((((((.....--.-...(((((((.......)))))))((.(((((....((((((.((((....)))).))))))))))).)))))))).))) ( -29.80)
>DroSec_CAF1 107041 94 + 1
AGUUUUCCCAUAUUU------UUUUUGUUAUUUUACUUGGCAAACGUGGCGCAUUUUUAAAUGGUCACGUUUGGCAGUUUAAGCGCCUCGGUGGGGCAAC
.(((.((((((....------..(((((((.......)))))))((.(((((....((((((.((((....)))).))))))))))).)))))))).))) ( -30.40)
>DroSim_CAF1 111008 98 + 1
AGUUUUCCCAUUUUUU--UUUUUUUUGUUAUUUUACUUGGCAAACGUGGCGCAUUUUUAAAUGGUCACGUUUGGCAGUUUAAGCGCCUCGGUGGGGCAAC
.(((.((((((.....--.....(((((((.......)))))))((.(((((....((((((.((((....)))).))))))))))).)))))))).))) ( -29.80)
>DroYak_CAF1 108119 100 + 1
AGUUUUUCGUUUCGUUUCUUUUUUUUGUUAUUUUGCUUGGCAAACGUGGCGCAUUUUUAAAUGGUCACGUUUGGCAGUUUAAGCGCCUCGGUGGGGCAAC
..................................(((((.((((((((((.((((....)))))))))))))).)).....)))((((.....))))... ( -28.40)
>DroAna_CAF1 194233 86 + 1
UGUUUCUCCGUUUUUU--U------------UUUCUUUGCCAAACGUGGCGCAUUUUUAAAUGGUCACGUUUCGCAGUUUAAGCGCCACGCCAAGGCAAC
................--.------------.....(((((...((((((((....((((((.((........)).))))))))))))))....))))). ( -23.60)
>consensus
AGUUUUCCCAUUUUUU__U__UUUUUGUUAUUUUACUUGGCAAACGUGGCGCAUUUUUAAAUGGUCACGUUUGGCAGUUUAAGCGCCUCGGUGGGGCAAC
....................................(((.((((((((((.((((....)))))))))))))).))).......((((.....))))... (-24.80 = -25.20 +   0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,578,065 – 11,578,162
Length 97
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 85.16
Mean single sequence MFE -22.26
Consensus MFE -16.04
Energy contribution -16.24
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.90
Structure conservation index 0.72
SVM decision value 1.87
SVM RNA-class probability 0.980810
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11578065 97 - 27905053
GUUGCCCCACCGAGGCGCUUAAACUGCCAAACGUGACCAUUUAAAAAUGCGCCACGUUUGCCAAGUAAAAUAACAAAAAC-A--AAAAAAUGGGAAAACU
(((..((((....(((((.......)).(((((((.(((((....)))).).))))))))))..((......))......-.--......))))..))). ( -22.50)
>DroSec_CAF1 107041 94 - 1
GUUGCCCCACCGAGGCGCUUAAACUGCCAAACGUGACCAUUUAAAAAUGCGCCACGUUUGCCAAGUAAAAUAACAAAAA------AAAUAUGGGAAAACU
(((..((((....(((((.......)).(((((((.(((((....)))).).))))))))))..((......)).....------.....))))..))). ( -22.50)
>DroSim_CAF1 111008 98 - 1
GUUGCCCCACCGAGGCGCUUAAACUGCCAAACGUGACCAUUUAAAAAUGCGCCACGUUUGCCAAGUAAAAUAACAAAAAAAA--AAAAAAUGGGAAAACU
(((..((((....(((((.......)).(((((((.(((((....)))).).))))))))))..((......))........--......))))..))). ( -22.50)
>DroYak_CAF1 108119 100 - 1
GUUGCCCCACCGAGGCGCUUAAACUGCCAAACGUGACCAUUUAAAAAUGCGCCACGUUUGCCAAGCAAAAUAACAAAAAAAAGAAACGAAACGAAAAACU
((((((.......)))(((.....((.((((((((.(((((....)))).).)))))))).)))))..................)))............. ( -19.10)
>DroAna_CAF1 194233 86 - 1
GUUGCCUUGGCGUGGCGCUUAAACUGCGAAACGUGACCAUUUAAAAAUGCGCCACGUUUGGCAAAGAAA------------A--AAAAAACGGAGAAACA
.(((((..((((((((((..............................)))))))))).))))).....------------.--................ ( -24.71)
>consensus
GUUGCCCCACCGAGGCGCUUAAACUGCCAAACGUGACCAUUUAAAAAUGCGCCACGUUUGCCAAGUAAAAUAACAAAAA__A__AAAAAAUGGGAAAACU
((((((.......)))........((.((((((((.(((((....)))).).)))))))).)).................................))). (-16.04 = -16.24 +   0.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,578,097 – 11,578,190
Length 93
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 80.12
Mean single sequence MFE -28.15
Consensus MFE -15.73
Energy contribution -16.40
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.11
Structure conservation index 0.56
SVM decision value 0.42
SVM RNA-class probability 0.731018
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11578097 93 + 27905053
CUUGGCAAACGUGGCGCAUUUUUAAAUGGUCACGUUUGGCAGUUUAAGCGCCUCGGUGGGGCAACGAAAAUACAUCAAAGCGGCG---------CGAAAAGU
.(((.((((((((((.((((....)))))))))))))).))).....(((((.(..((((....)(......).)))..).))))---------)....... ( -33.00)
>DroVir_CAF1 109935 95 + 1
--UGGCAAACGUGGCGCAUUUUUAAAUGGUCACGUUUUGCAGUUUAAGCGCCAGGC--AGGCA--GCAAAUACAUCAAAGCGGCGAAAGCGACGCG-AAAGU
--..(((((((((((.((((....)))))))))).))))).......(((((....--.))).--))............(((((....))..))).-..... ( -30.80)
>DroGri_CAF1 256144 95 + 1
--UGGCAAACGGGGCGCAUUUUUAAAUGGUCACGUUUUGCAGUUUAAGCGCCAGGC--AGGCA--GCAAAUACAUCAAAGCGGCGAAGGCGACGCG-AAACU
--..(((((((.(((.((((....))))))).)).)))))(((((..(((((....--.))).--))............(((((....))..))).-))))) ( -26.90)
>DroWil_CAF1 189557 90 + 1
-UUGGCAAACGUGGCGCAUUUUUAAAUGGUCACGUUUUUCAGUUUAAGCGCCAAAUAAAGGGAAAAGAACAACAUCAAAGCGU-----------UGAAAAGU
-((((((((((((((.((((....)))))))))))))....((....)))))))...............((((........))-----------))...... ( -22.40)
>DroMoj_CAF1 106309 84 + 1
--UGGCAAACGUGGCGCAUUUUUAAAUGGUCACGUUCUGCAGUUUAAGCGCCUGGC--AGCCA--GCAAAUACAUCAAAGCGGCGA------------AAGU
--..(((((((((((.((((....)))))))))))).)))........(((((((.--..)))--((............)))))).------------.... ( -23.90)
>DroAna_CAF1 194254 92 + 1
UUUGCCAAACGUGGCGCAUUUUUAAAUGGUCACGUUUCGCAGUUUAAGCGCCACGCCAAGGCAACGAAAAUACAUCAAAGCGGCG---------CGA-AAGU
.((((.(((((((((.((((....))))))))))))).)))).....(((((.(((....))...((.......))...).))))---------)..-.... ( -31.90)
>consensus
__UGGCAAACGUGGCGCAUUUUUAAAUGGUCACGUUUUGCAGUUUAAGCGCCAGGC__AGGCA__GCAAAUACAUCAAAGCGGCG_________CG_AAAGU
...((((((((((((.((((....))))))))))))).((.......))))).................................................. (-15.73 = -16.40 +   0.67)

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 11:27:45 2006