Locus 2384

Sequence ID X_DroMel_CAF1
Location 6,357,225 – 6,357,410
Length 185
Max. P 0.915127
window3878 window3879 window3880

overview

Window 8

Location 6,357,225 – 6,357,341
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 73.97
Mean single sequence MFE -27.45
Consensus MFE -13.21
Energy contribution -12.65
Covariance contribution -0.56
Combinations/Pair 1.50
Mean z-score -2.24
Structure conservation index 0.48
SVM decision value 0.68
SVM RNA-class probability 0.820635
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6357225 116 + 22224390
GUAGGGGAAUCGAGAG-AACACGA-AACGACAGGAUUUCGUGAAGAGAUAUUUCUGCCGAAAGGAGAAGAAGUAGGAGAAUGC-CCCA-UGACUAAGCCAAUAACCGAAAGGUUAUUUAA
...((((..((....)-).(((((-((........)))))))......(((((((.((....))...)))))))........)-))).-..........(((((((....)))))))... ( -36.90)
>DroPse_CAF1 36008 115 + 1
A-AACGGAAUGGAAUGAAACAAGGAAAUG--AGGAAUAUGCGACUGGCA--CUAUACUGAAGGGAUGGGAUGGGGAUGGAUGCGCUCACGGACUAAGGCAAUAACAGAAAGGUUAUUUAA
.-..(((.((((.......((......))--.......(((.....)))--)))).)))......(((..(((((.((....))))).))..)))....((((((......))))))... ( -13.10)
>DroSec_CAF1 41243 111 + 1
GUAGGGGAAUGG--CG-AAUACGG-AACGACAGGAUUUCGUGAGGGGAUAUUUCUGCCGAAAGGAGAAGAA---GGAUAAUGC-CCCA-UGACUAAGCCAAUAACCAAAAGGUUAUUUAA
.........(((--(.-..(((((-((........))))))).((((...(((((.((....))...))))---).......)-))).-.......))))((((((....)))))).... ( -32.20)
>DroEre_CAF1 39103 111 + 1
GUAGAGGAAUGG--AG-AACAUGG-AACGACAGGAUUUCGUGAAGAGAUAUUUCUGCCCAAAAGGGAAGAA---GUAGAAUAC-CUCA-UGACUAAGCCAAUAACCAAAAGGUUAUUUAA
...((((.....--..-..(((((-((........)))))))......(((((((.(((....))).))))---))).....)-))).-..........(((((((....)))))))... ( -27.60)
>consensus
GUAGGGGAAUGG__AG_AACACGG_AACGACAGGAUUUCGUGAAGAGAUAUUUCUGCCGAAAGGAGAAGAA___GGAGAAUGC_CCCA_UGACUAAGCCAAUAACCAAAAGGUUAUUUAA
...(((.............(((((...(....)....))))).........((((.((....))))))................)))............(((((((....)))))))... (-13.21 = -12.65 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,357,263 – 6,357,378
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 69.34
Mean single sequence MFE -26.90
Consensus MFE -12.05
Energy contribution -11.55
Covariance contribution -0.50
Combinations/Pair 1.26
Mean z-score -1.87
Structure conservation index 0.45
SVM decision value -0.02
SVM RNA-class probability 0.521473
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6357263 115 + 22224390
UGAAGAGAUAUUUCUGCCGAAAGGAGAAGAAGUAGGAGAAUGC-CCCA-UGACUAAGCCAAUAACCGAAAGGUUAUUUAAUAUUUGGC---AGUGGCGUGGCCUUAAAAAAAUACGAGCA
........(((((((.((....))...)))))))((...((((-(...-((.(((((..(((((((....))))))).....))))))---)..)))))..))................. ( -33.00)
>DroPse_CAF1 36045 97 + 1
CGACUGGCA--CUAUACUGAAGGGAUGGGAUGGGGAUGGAUGCGCUCACGGACUAAGGCAAUAACAGAAAGGUUAUUUAAUAUUUGACUACAGUUGGCU---------------------
((((((((.--((...((....)).(((..(((((.((....))))).))..)))))))((((((......)))))).............))))))...--------------------- ( -16.10)
>DroSec_CAF1 41279 112 + 1
UGAGGGGAUAUUUCUGCCGAAAGGAGAAGAA---GGAUAAUGC-CCCA-UGACUAAGCCAAUAACCAAAAGGUUAUUUAAUAUUUGGC---AGUGGCGUGGCCUUAAAAAAAUACGAGAA
(((((((...(((((.((....))...))))---).......)-)(((-((.(((.((((((((((....))))))........))))---..))))))))))))).............. ( -30.70)
>DroEre_CAF1 39139 108 + 1
UGAAGAGAUAUUUCUGCCCAAAAGGGAAGAA---GUAGAAUAC-CUCA-UGACUAAGCCAAUAACCAAAAGGUUAUUUAAUAUUUGGC---AGUGGCGUGGCCUUAAAAAAUAAG----G
........(((((((.(((....))).))))---)))......-.(((-((.(((.((((((((((....))))))........))))---..))))))))(((((.....))))----) ( -27.80)
>consensus
UGAAGAGAUAUUUCUGCCGAAAGGAGAAGAA___GGAGAAUGC_CCCA_UGACUAAGCCAAUAACCAAAAGGUUAUUUAAUAUUUGGC___AGUGGCGUGGCCUUAAAAAAAUAC____A
...........((((.((....)))))).......................(((..((((((((((....))))))........))))...))).......................... (-12.05 = -11.55 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,357,303 – 6,357,410
Length 107
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 82.49
Mean single sequence MFE -26.77
Consensus MFE -17.65
Energy contribution -17.43
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -2.57
Structure conservation index 0.66
SVM decision value 1.10
SVM RNA-class probability 0.915127
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6357303 107 + 22224390
UGCCCCAUGACUAAGCCAAUAACCGAAAGGUUAUUUAAUAUUUGGCAGUGGCGUGGCCUUAAAAAAAUACGAGCAAAAACACCCUUUCUUGGC--------UCCACUGCUCCACA
....(((((.(((.((((((((((....))))))........))))..))))))))..............(((((.......((......)).--------.....))))).... ( -27.72)
>DroSec_CAF1 41316 115 + 1
UGCCCCAUGACUAAGCCAAUAACCAAAAGGUUAUUUAAUAUUUGGCAGUGGCGUGGCCUUAAAAAAAUACGAGAAAAAACACCCUUUCUUGGCUCUACGGCUCCACUGGUCCACA
.(((...((.(((((..(((((((....))))))).....)))))))..)))((((((...........(((((((........)))))))(((....)))......)).)))). ( -29.30)
>DroEre_CAF1 39176 96 + 1
UACCUCAUGACUAAGCCAAUAACCAAAAGGUUAUUUAAUAUUUGGCAGUGGCGUGGCCUUAAAAAAUAAG----GAAAACACCCUUUUUUUG---------------GCUCCACA
..............((((((((((....))))))........)))).((((...((((....((((.(((----(.......)))).)))))---------------))))))). ( -23.30)
>consensus
UGCCCCAUGACUAAGCCAAUAACCAAAAGGUUAUUUAAUAUUUGGCAGUGGCGUGGCCUUAAAAAAAUACGAG_AAAAACACCCUUUCUUGGC________UCCACUGCUCCACA
....(((((.(((.((((((((((....))))))........))))..))))))))........................................................... (-17.65 = -17.43 +  -0.22)

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 10:33:14 2006