Locus 4436

Sequence ID 3R_DroMel_CAF1
Location 11,708,235 – 11,708,383
Length 148
Max. P 0.925725
window7250 window7251 window7252

overview

Window 0

Location 11,708,235 – 11,708,350
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.72
Mean single sequence MFE -31.77
Consensus MFE -18.97
Energy contribution -18.25
Covariance contribution -0.72
Combinations/Pair 1.30
Mean z-score -1.98
Structure conservation index 0.60
SVM decision value 1.17
SVM RNA-class probability 0.925725
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11708235 115 + 27905053
GAGUAAUGCCCAAACAAGGGAGGGAUUCAGGGAAGUGGCCACCGAAAUAAUAAAUUACAUUGAACGCAAUUUUAUUGCAUACUUGCAGGGGCAUUGCAAGAUUUCCCCAUUG-----UGU
((((....(((......)))....)))).(((((((.............................(((((...)))))...(((((((.....)))))))))))))).....-----... ( -28.30)
>DroPse_CAF1 50289 96 + 1
GUGG-------AAAAUAGGGGGGAAUUC----------CGCCCGAAAUAAUAAAUUAUGUUCAACGCAAUUUUAUUGCAUACUUGCAGGGGCAUUGUGGGAUUUCCCCUC-------UGU
....-------...(((((((((((.((----------(....(((((((....)))).)))..((((((.(..(((((....)))))..).))))))))).))))))))-------))) ( -34.40)
>DroSim_CAF1 47191 115 + 1
GAGUAAUGCCCAAACAAGGGAGGGAUUCAAGGAAGUGGCCACCGAAAUAAUAAAUUACAUUGAACGCAAUUUUAUUGCAUACUUGCAGGGGCACUGCAAGAUUUCCCCAUUG-----UGU
((((....(((......)))....))))..((((((.............................(((((...)))))...(((((((.....)))))))))))))......-----... ( -28.00)
>DroEre_CAF1 45508 115 + 1
GAGUAAUGCCCAAACAAGGGUGGGAUUCAAGGAAGUGGCCACCGAAAUAAUAAAUUACAUUGAACGCAAUUUUAUUGCAUACUUGCAGGGGCACUGCAAGAUUUCCCCAUAG-----GGU
..(((.(((((...(((((((((..(((...)))....)))))......................(((((...)))))...))))...))))).))).......(((....)-----)). ( -30.80)
>DroAna_CAF1 45372 120 + 1
GACUAAUGGGCAAACAAAGGAGGGAUUCGGAAAAGUGGCCCCCGAAAUAAUAAAUUACUGGGAGGGCAAUUUUAUUGCAUACUUGCAGGGGCAAGGCGAGAUUCCCCCGUUUGCAUGUGG
..(((....((((((...((.((((.((...(((((.((((((.(.............).)).)))).))))).((((...(((((....))))))))))).))))))))))))...))) ( -37.52)
>DroPer_CAF1 46181 96 + 1
GUGG-------AAAAUAGGGGGGAAUUC----------CACCCGAAAUAAUAAAUUAUGUUCAACGCAAUUUUAUUGCAUACUUGCAGGGGCACUGUGGGAUUUCCCCUC-------UGU
....-------...(((((((((((.((----------(....(((((((....)))).)))..((((......(((((....)))))......))))))).))))))))-------))) ( -31.60)
>consensus
GAGUAAUGCCCAAACAAGGGAGGGAUUCA_GGAAGUGGCCACCGAAAUAAUAAAUUACAUUGAACGCAAUUUUAUUGCAUACUUGCAGGGGCACUGCAAGAUUUCCCCAUUG_____UGU
.................(((.(((((.......................................(((((...)))))...(((((((.....)))))))))))))))............ (-18.97 = -18.25 +  -0.72)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,708,235 – 11,708,350
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.72
Mean single sequence MFE -28.35
Consensus MFE -13.28
Energy contribution -13.92
Covariance contribution 0.64
Combinations/Pair 1.18
Mean z-score -2.16
Structure conservation index 0.47
SVM decision value 0.64
SVM RNA-class probability 0.807804
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11708235 115 - 27905053
ACA-----CAAUGGGGAAAUCUUGCAAUGCCCCUGCAAGUAUGCAAUAAAAUUGCGUUCAAUGUAAUUUAUUAUUUCGGUGGCCACUUCCCUGAAUCCCUCCCUUGUUUGGGCAUUACUC
...-----.................(((((((..(((((.........(((((((((...))))))))).....(((((.((......))))))).......)))))..))))))).... ( -26.70)
>DroPse_CAF1 50289 96 - 1
ACA-------GAGGGGAAAUCCCACAAUGCCCCUGCAAGUAUGCAAUAAAAUUGCGUUGAACAUAAUUUAUUAUUUCGGGCG----------GAAUUCCCCCCUAUUUU-------CCAC
..(-------(.((((((.(((......((((........(((((((...))))))).(((.((((....))))))))))))----------)).)))))).)).....-------.... ( -25.60)
>DroSim_CAF1 47191 115 - 1
ACA-----CAAUGGGGAAAUCUUGCAGUGCCCCUGCAAGUAUGCAAUAAAAUUGCGUUCAAUGUAAUUUAUUAUUUCGGUGGCCACUUCCUUGAAUCCCUCCCUUGUUUGGGCAUUACUC
...-----.((((((((..((..(.((((((((((((....))))...(((((((((...)))))))))........)).)).))))..)..)).)))).(((......))))))).... ( -27.70)
>DroEre_CAF1 45508 115 - 1
ACC-----CUAUGGGGAAAUCUUGCAGUGCCCCUGCAAGUAUGCAAUAAAAUUGCGUUCAAUGUAAUUUAUUAUUUCGGUGGCCACUUCCUUGAAUCCCACCCUUGUUUGGGCAUUACUC
.((-----(....))).........(((((((..(((((.........(((((((((...)))))))))........(((((...(......)....))))))))))..))))))).... ( -32.00)
>DroAna_CAF1 45372 120 - 1
CCACAUGCAAACGGGGGAAUCUCGCCUUGCCCCUGCAAGUAUGCAAUAAAAUUGCCCUCCCAGUAAUUUAUUAUUUCGGGGGCCACUUUUCCGAAUCCCUCCUUUGUUUGCCCAUUAGUC
......((((((((((((.((..(((((((....)))))...)).........((((((..(((((....)))))..)))))).........)).))))))....))))))......... ( -33.90)
>DroPer_CAF1 46181 96 - 1
ACA-------GAGGGGAAAUCCCACAGUGCCCCUGCAAGUAUGCAAUAAAAUUGCGUUGAACAUAAUUUAUUAUUUCGGGUG----------GAAUUCCCCCCUAUUUU-------CCAC
..(-------(.((((((.(((......((((........(((((((...))))))).(((.((((....))))))))))))----------)).)))))).)).....-------.... ( -24.20)
>consensus
ACA_____CAAUGGGGAAAUCUCGCAGUGCCCCUGCAAGUAUGCAAUAAAAUUGCGUUCAAUGUAAUUUAUUAUUUCGGGGGCCACUUCC_UGAAUCCCUCCCUUGUUUGGGCAUUACUC
............(((((...........(((((((((....))))...((((((((.....))))))))........)).)))............))))).................... (-13.28 = -13.92 +   0.64)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,708,275 – 11,708,383
Length 108
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 79.15
Mean single sequence MFE -23.47
Consensus MFE -15.45
Energy contribution -14.57
Covariance contribution -0.89
Combinations/Pair 1.24
Mean z-score -1.34
Structure conservation index 0.66
SVM decision value 0.15
SVM RNA-class probability 0.607911
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11708275 108 + 27905053
ACCGAAAUAAUAAAUUACAUUGAACGCAAUUUUAUUGCAUACUUGCAGGGGCAUUGCAAGAUUUCCCCAUUGUGU--AUACAGUUGUGUAUAAGAUAAUAGAAUACGGGU
.(((...........((((.((...(((((...)))))...(((((((.....))))))).......)).))))(--(((((....)))))).............))).. ( -22.30)
>DroPse_CAF1 50312 85 + 1
CCCGAAAUAAUAAAUUAUGUUCAACGCAAUUUUAUUGCAUACUUGCAGGGGCAUUGUGGGAUUUCCCCUC--UGU--CUGCAGGAGUGU---------------------
........((((((...(((.....)))..))))))((((.(((((((..(((..(.(((....))))..--)))--))))))).))))--------------------- ( -21.60)
>DroSim_CAF1 47231 108 + 1
ACCGAAAUAAUAAAUUACAUUGAACGCAAUUUUAUUGCAUACUUGCAGGGGCACUGCAAGAUUUCCCCAUUGUGU--CUACAGUUGUGUAUAAAAUAAUAGGAUAUGGGU
...(((((.................(((((...)))))...(((((((.....))))))))))))(((((....(--(((..(((........)))..))))..))))). ( -25.40)
>DroEre_CAF1 45548 108 + 1
ACCGAAAUAAUAAAUUACAUUGAACGCAAUUUUAUUGCAUACUUGCAGGGGCACUGCAAGAUUUCCCCAUAGGGU--CUACAGUGGUGUACAAAAUAAUAGGAUAUGGCU
...(((((.................(((((...)))))...(((((((.....)))))))))))).(((((...(--(((...((.....))......)))).))))).. ( -23.00)
>DroYak_CAF1 45880 110 + 1
ACCGAAAUAAUAAAUUACAUUGAACGCAAUUUUAUUGCAUACUUGCAGGGGCACUGCAAGAUUUCCCCAUUGUGUCUCUACAGUUGUGUACAAACUAAUAGGAUACGGCU
.(((((((.................(((((...)))))...(((((((.....))))))))))))......(((((.(((.((((.......))))..)))))))))).. ( -26.90)
>DroPer_CAF1 46204 85 + 1
CCCGAAAUAAUAAAUUAUGUUCAACGCAAUUUUAUUGCAUACUUGCAGGGGCACUGUGGGAUUUCCCCUC--UGU--CUGCAGGAGUGU---------------------
........((((((...(((.....)))..))))))((((.(((((((..(((..(.(((....))))..--)))--))))))).))))--------------------- ( -21.60)
>consensus
ACCGAAAUAAUAAAUUACAUUGAACGCAAUUUUAUUGCAUACUUGCAGGGGCACUGCAAGAUUUCCCCAUUGUGU__CUACAGUUGUGUA_AAAAUAAUAGGAUA_GG_U
...(((((.................(((((...)))))...(((((((.....))))))))))))............................................. (-15.45 = -14.57 +  -0.89)

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 11:29:13 2006