Locus 4297

Sequence ID 3L_DroMel_CAF1
Location 12,608,316 – 12,608,453
Length 137
Max. P 0.997991
window6648 window6649 window6650

overview

Window 8

Location 12,608,316 – 12,608,424
Length 108
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 80.94
Mean single sequence MFE -29.42
Consensus MFE -20.88
Energy contribution -21.12
Covariance contribution 0.24
Combinations/Pair 1.15
Mean z-score -1.55
Structure conservation index 0.71
SVM decision value 0.08
SVM RNA-class probability 0.574004
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12608316 108 + 23771897
AGAUGCUAUUCAAUUCAAAUGGCGUGGGUUGCAUGUGAAAUGGCACGCACAUGCGAAGGUGUGCCCUAUACCUAAAUAUAAUACC-CCUUAUUCCAUAUCCACAUC------CAG---
.(((((((((.......))))))((((((((((((((..........)))))))))(((((((...)))))))............-............))))))))------...--- ( -28.10)
>DroSec_CAF1 96193 98 + 1
AGAUGCUAUUCAAUUCAAAUGGCGUGGGUUGCAUGUGAAGUGGCACGCACAUGCUAAGGUGCGCCCCAUACCU----GUAAUACC-CCUUAUGCCAUAU------C------CAG---
..................(((((((((((((((.((...((((..(((((........)))))..)))))).)----)))..)))-)...)))))))..------.------...--- ( -28.70)
>DroSim_CAF1 99073 104 + 1
AGAUGCUAUUCAAUUCAAAUGGCGUGGGUUGCAUGUGAAAUGGCACGCACAUGCGAAGGUGCGCCCCAUACCU----GUAAUACC-CCUUAUUCCAUAUCCACAUC------CAG---
.(((((((((.......))))))((((((((((((((..........)))))))))(((((.......)))))----........-............))))))))------...--- ( -26.10)
>DroEre_CAF1 99394 104 + 1
AGAUGCCAUUCAAUUCAAAUGGCGUGGGAUGCACGUGGAAUGGCACGCACAUGCGAAGGUGUGCCGCACACCC----G---UACU-CCUUAUGCCACAUCCACAUC------CUGAUC
..((((((((.......))))))))(((((....(((((.((((((((....)))((((.((((.(.....).----)---))).-)))).)))))..))))))))------)).... ( -37.90)
>DroYak_CAF1 100124 108 + 1
AGAUGCUAUUCAAUUCAAAUGGCGUGGGAUGCACGUGAAGUGGCACGCACAUGCUAAGGUGUACC---CAUCC----A---UACCCCCCUAUGCCACAUCCACAUCUAGAUUCAGAUC
((((((((((.......))))))(((((((....))...((((((.((....))...(((((...---.....----)---))))......)))))).)))))))))........... ( -26.30)
>consensus
AGAUGCUAUUCAAUUCAAAUGGCGUGGGUUGCAUGUGAAAUGGCACGCACAUGCGAAGGUGUGCCCCAUACCU____GUAAUACC_CCUUAUGCCAUAUCCACAUC______CAG___
...................(((((((((..(((((((..........)))))))...((((.......))))...............)))))))))...................... (-20.88 = -21.12 +   0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,608,354 – 12,608,453
Length 99
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 78.61
Mean single sequence MFE -25.67
Consensus MFE -16.58
Energy contribution -16.70
Covariance contribution 0.12
Combinations/Pair 1.19
Mean z-score -2.98
Structure conservation index 0.65
SVM decision value 2.98
SVM RNA-class probability 0.997991
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12608354 99 + 23771897
AAUGGCACGCACAUGCGAAGGUGUGCCCUAUACCUAAAUAUAAUACC-CCUUAUUCCAUAUCCACAUC------CAG------AUCCCAAUCCAUAUCUAUGUGGAUACGCU
...(((.(((....))).(((((((...)))))))............-..........(((((((((.------.((------((..........))))))))))))).))) ( -22.30)
>DroSec_CAF1 96231 89 + 1
AGUGGCACGCACAUGCUAAGGUGCGCCCCAUACCU----GUAAUACC-CCUUAUGCCAUAU------C------CAG------AUCCAAAUCCAUAUCUAUGUGGAUACGGU
.((((..(((((........)))))..))))....----........-......(((.(((------(------((.------((..............)).)))))).))) ( -21.44)
>DroSim_CAF1 99111 95 + 1
AAUGGCACGCACAUGCGAAGGUGCGCCCCAUACCU----GUAAUACC-CCUUAUUCCAUAUCCACAUC------CAG------AUCCAAAUCCAUAUCUAUGUGGAUACGGU
.((((..(((((........)))))..))))....----........-.......((.(((((((((.------.((------((..........))))))))))))).)). ( -25.70)
>DroEre_CAF1 99432 98 + 1
AAUGGCACGCACAUGCGAAGGUGUGCCGCACACCC----G---UACU-CCUUAUGCCACAUCCACAUC------CUGAUCCGAAUCCGAAUCCAUAUCUAUGUGGAUACGGU
..((((((((....)))((((.((((.(.....).----)---))).-)))).)))))..........------...........(((.(((((((....))))))).))). ( -29.40)
>DroYak_CAF1 100162 102 + 1
AGUGGCACGCACAUGCUAAGGUGUACC---CAUCC----A---UACCCCCCUAUGCCACAUCCACAUCUAGAUUCAGAUCCAAAUCCGAAUCCAUAUCUAUGUGGAUACGGU
.((((((.((....))...(((((...---.....----)---))))......))))))((((((((...(((((.(((....))).))))).......))))))))..... ( -29.50)
>consensus
AAUGGCACGCACAUGCGAAGGUGUGCCCCAUACCU____GUAAUACC_CCUUAUGCCAUAUCCACAUC______CAG______AUCCAAAUCCAUAUCUAUGUGGAUACGGU
.((((((.((....))...((((.......))))...................))))))..........................((..(((((((....)))))))..)). (-16.58 = -16.70 +   0.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,608,354 – 12,608,453
Length 99
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 78.61
Mean single sequence MFE -34.30
Consensus MFE -18.13
Energy contribution -18.89
Covariance contribution 0.76
Combinations/Pair 1.16
Mean z-score -2.86
Structure conservation index 0.53
SVM decision value 2.49
SVM RNA-class probability 0.994594
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12608354 99 - 23771897
AGCGUAUCCACAUAGAUAUGGAUUGGGAU------CUG------GAUGUGGAUAUGGAAUAAGG-GGUAUUAUAUUUAGGUAUAGGGCACACCUUCGCAUGUGCGUGCCAUU
..(((((((((((.....(((((....))------)))------.)))))))))))........-((((((((((....)))))..(((((........))))))))))... ( -28.70)
>DroSec_CAF1 96231 89 - 1
ACCGUAUCCACAUAGAUAUGGAUUUGGAU------CUG------G------AUAUGGCAUAAGG-GGUAUUAC----AGGUAUGGGGCGCACCUUAGCAUGUGCGUGCCACU
.(((((((......)))))))......((------(((------.------..(((.(......-).)))..)----)))).(((.((((((........)))))).))).. ( -28.20)
>DroSim_CAF1 99111 95 - 1
ACCGUAUCCACAUAGAUAUGGAUUUGGAU------CUG------GAUGUGGAUAUGGAAUAAGG-GGUAUUAC----AGGUAUGGGGCGCACCUUCGCAUGUGCGUGCCAUU
.((((((((((((.....(((((....))------)))------.)))))))))))).......-........----....((((.((((((........)))))).)))). ( -35.40)
>DroEre_CAF1 99432 98 - 1
ACCGUAUCCACAUAGAUAUGGAUUCGGAUUCGGAUCAG------GAUGUGGAUGUGGCAUAAGG-AGUA---C----GGGUGUGCGGCACACCUUCGCAUGUGCGUGCCAUU
.((((((((((((.......((((((....))))))..------.))))))))))))......(-.(((---(----(.(..(((((.......)))))..).))))))... ( -37.00)
>DroYak_CAF1 100162 102 - 1
ACCGUAUCCACAUAGAUAUGGAUUCGGAUUUGGAUCUGAAUCUAGAUGUGGAUGUGGCAUAGGGGGGUA---U----GGAUG---GGUACACCUUAGCAUGUGCGUGCCACU
.....((((((((.....(((((((((((....))))))))))).))))))))(((((((..(((((((---(----.....---.)))).)))).((....))))))))). ( -42.20)
>consensus
ACCGUAUCCACAUAGAUAUGGAUUCGGAU______CUG______GAUGUGGAUAUGGCAUAAGG_GGUAUUAC____AGGUAUGGGGCACACCUUCGCAUGUGCGUGCCAUU
.((((((((((((................................))))))))))))............................(((((.((.......).).)))))... (-18.13 = -18.89 +   0.76)

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 11:18:56 2006