Locus 2962

Sequence ID 2R_DroMel_CAF1
Location 10,221,767 – 10,221,896
Length 129
Max. P 0.851375
window4899 window4900 window4901

overview

Window 9

Location 10,221,767 – 10,221,857
Length 90
Sequences 6
Columns 92
Reading direction reverse
Mean pairwise identity 87.24
Mean single sequence MFE -19.20
Consensus MFE -15.01
Energy contribution -14.73
Covariance contribution -0.27
Combinations/Pair 1.26
Mean z-score -2.15
Structure conservation index 0.78
SVM decision value 0.04
SVM RNA-class probability 0.554108
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10221767 90 - 20766785
CCCUGCCAAACGCAAUAUUUGUGCAGUUUAUUUAUUUUAUUGUGGCUGCAUUUUU--UUUUUGUAUUUGUCAGCACAAAUGACUAGCUUUUG
..(((.((((..(((.....((((((((...............))))))))....--...)))..)))).)))................... ( -16.96)
>DroSec_CAF1 50965 90 - 1
CCCUGCCAAAUGCAAUAUUUGUGCAGUUUAUUUAUUUUAUUGUGGCAGCAUUUUU--UUUUUGCAUUUGUCAGCAGAAAUGACUGCCUUUUG
..((((((((((...)))))).)))).................(((((((((((.--....(((........))))))))).)))))..... ( -22.20)
>DroSim_CAF1 51245 92 - 1
CCCUGCCAAAUGCAAUAUUUGUGCAGUUUAUUUAUUUUAUUGUGGCUGUAUUUUUUUUUUUUGCAUUUGUCAGCACAAAUGACUGCCUUUUG
..(((.(((((((((.....((((((((...............)))))))).........))))))))).)))................... ( -19.10)
>DroEre_CAF1 55456 86 - 1
CCCUGCCAAACGCAAUAUUUGUGCAGCUUAUUUAUUUUAUUGUGGCUGCAUUU------UUUGCAUUUGUCAGCACAACUGACUGCCUUUUG
....((.....((((.....((((((((...............))))))))..------.))))....(((((.....))))).))...... ( -21.46)
>DroYak_CAF1 50822 86 - 1
CCCUGCCAAACGCAAUAUUUGUGCAGUUUAUUUAUCUUAUUGUGGCUGCAUUU------UUUGCAUUUGUCAGCUCAAAUGACUGCCUUUUG
..(((.((((.((((.....((((((((...............))))))))..------.)))).)))).)))................... ( -18.36)
>DroAna_CAF1 53733 85 - 1
CCCUGCCAAAGGCAAUAUUUAUGUCGCAUAUUUAUUUUAUUGGAGCUGCAUA-------CUUGCAUUUGUCAGCAUAACUGACUGCAAUUUG
...((((...)))).....(((((.((...((((......)))))).)))))-------.(((((...(((((.....)))))))))).... ( -17.10)
>consensus
CCCUGCCAAACGCAAUAUUUGUGCAGUUUAUUUAUUUUAUUGUGGCUGCAUUU______UUUGCAUUUGUCAGCACAAAUGACUGCCUUUUG
..(((.((((.((((.....((((((((...............)))))))).........)))).)))).)))................... (-15.01 = -14.73 +  -0.27)

alignment

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secondary structure

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Window 0

Location 10,221,784 – 10,221,896
Length 112
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 85.04
Mean single sequence MFE -23.70
Consensus MFE -16.49
Energy contribution -16.77
Covariance contribution 0.28
Combinations/Pair 1.21
Mean z-score -2.91
Structure conservation index 0.70
SVM decision value 0.25
SVM RNA-class probability 0.651213
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10221784 112 + 20766785
UGCUGACAAAUACAAAAA--AAAAAUGCAGCCACAAUAAAAUAAAUAAACUGCACAAAUAUUGCGUUUGGCAGGGCAAACUACGUACAUAUAUGUAAAUGAGUAA-ACGGUCAGC
.((((((...(((.....--.........(((....((.......))..((((.(((((.....))))))))))))....((((((....)))))).....))).-...)))))) ( -24.10)
>DroSec_CAF1 50982 108 + 1
UGCUGACAAAUGCAAAAA--AAAAAUGCUGCCACAAUAAAAUAAAUAAACUGCACAAAUAUUGCAUUUGGCAGGGCAAACUGCGU----AUAUGUAAAUGAGUAA-ACGGUCAGC
.((((((....(((....--.....)))((((....((.......))..((((.(((((.....))))))))))))).....(((----.(((........))).-))))))))) ( -23.00)
>DroSim_CAF1 51262 110 + 1
UGCUGACAAAUGCAAAAAAAAAAAAUACAGCCACAAUAAAAUAAAUAAACUGCACAAAUAUUGCAUUUGGCAGGGCAAACUACGU----AUAUGUAAAUGAGUAA-ACGGUCAGC
.((((((......................(((....((.......))..((((.(((((.....))))))))))))......(((----.(((........))).-))))))))) ( -22.50)
>DroEre_CAF1 55473 101 + 1
UGCUGACAAAUGCAAA------AAAUGCAGCCACAAUAAAAUAAAUAAGCUGCACAAAUAUUGCGUUUGGCAGGGCAAACU--------AUAUGUAAAUGAGUAAAACGGUCAGC
.((((((((((((((.------...((((((.................))))))......)))))))).(((.((....))--------...)))..............)))))) ( -23.83)
>DroYak_CAF1 50839 101 + 1
AGCUGACAAAUGCAAA------AAAUGCAGCCACAAUAAGAUAAAUAAACUGCACAAAUAUUGCGUUUGGCAGGGCAAACU--------AUAUGUAAAUGAGUGAAGCGGUCGGC
.((((((...((((..------...))))(((((...............((((.(((((.....))))))))).(((....--------...)))......)))..)).)))))) ( -24.30)
>DroAna_CAF1 53750 100 + 1
UGCUGACAAAUGCAAG-------UAUGCAGCUCCAAUAAAAUAAAUAUGCGACAUAAAUAUUGCCUUUGGCAGGGCAAGCU--------GUAUGUAAAUGAGAGAAAUGGUCAGU
.((((((...((((..-------..)))).((((((((.......)))...(((((....((((((......))))))...--------.)))))...)).))).....)))))) ( -24.50)
>consensus
UGCUGACAAAUGCAAA______AAAUGCAGCCACAAUAAAAUAAAUAAACUGCACAAAUAUUGCGUUUGGCAGGGCAAACU________AUAUGUAAAUGAGUAA_ACGGUCAGC
.((((((...((((...........))))(((....((.......))..((((.(((((.....)))))))))))).................................)))))) (-16.49 = -16.77 +   0.28)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,221,784 – 10,221,896
Length 112
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 85.04
Mean single sequence MFE -24.24
Consensus MFE -18.94
Energy contribution -19.17
Covariance contribution 0.22
Combinations/Pair 1.26
Mean z-score -2.78
Structure conservation index 0.78
SVM decision value 0.79
SVM RNA-class probability 0.851375
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10221784 112 - 20766785
GCUGACCGU-UUACUCAUUUACAUAUAUGUACGUAGUUUGCCCUGCCAAACGCAAUAUUUGUGCAGUUUAUUUAUUUUAUUGUGGCUGCAUUUUU--UUUUUGUAUUUGUCAGCA
((((((.((-..(((.((.((((....)))).)))))..))......(((..(((.....((((((((...............))))))))....--...)))..))))))))). ( -25.26)
>DroSec_CAF1 50982 108 - 1
GCUGACCGU-UUACUCAUUUACAUAU----ACGCAGUUUGCCCUGCCAAAUGCAAUAUUUGUGCAGUUUAUUUAUUUUAUUGUGGCAGCAUUUUU--UUUUUGCAUUUGUCAGCA
((((((...-................----..((((......)))).((((((((.....((((.(((...............))).))))....--...)))))))))))))). ( -25.26)
>DroSim_CAF1 51262 110 - 1
GCUGACCGU-UUACUCAUUUACAUAU----ACGUAGUUUGCCCUGCCAAAUGCAAUAUUUGUGCAGUUUAUUUAUUUUAUUGUGGCUGUAUUUUUUUUUUUUGCAUUUGUCAGCA
((((((...-................----..((((......)))).((((((((.....((((((((...............)))))))).........)))))))))))))). ( -25.40)
>DroEre_CAF1 55473 101 - 1
GCUGACCGUUUUACUCAUUUACAUAU--------AGUUUGCCCUGCCAAACGCAAUAUUUGUGCAGCUUAUUUAUUUUAUUGUGGCUGCAUUU------UUUGCAUUUGUCAGCA
((((((....................--------.(((((......)))))((((.....((((((((...............))))))))..------.))))....)))))). ( -28.96)
>DroYak_CAF1 50839 101 - 1
GCCGACCGCUUCACUCAUUUACAUAU--------AGUUUGCCCUGCCAAACGCAAUAUUUGUGCAGUUUAUUUAUCUUAUUGUGGCUGCAUUU------UUUGCAUUUGUCAGCU
((.(((....................--------.(((((......)))))((((.....((((((((...............))))))))..------.))))....))).)). ( -21.36)
>DroAna_CAF1 53750 100 - 1
ACUGACCAUUUCUCUCAUUUACAUAC--------AGCUUGCCCUGCCAAAGGCAAUAUUUAUGUCGCAUAUUUAUUUUAUUGGAGCUGCAUA-------CUUGCAUUUGUCAGCA
.(((((....................--------((((((((........)))((((..((((...))))..))))......)))))(((..-------..)))....))))).. ( -19.20)
>consensus
GCUGACCGU_UUACUCAUUUACAUAU________AGUUUGCCCUGCCAAACGCAAUAUUUGUGCAGUUUAUUUAUUUUAUUGUGGCUGCAUUU______UUUGCAUUUGUCAGCA
((((((.............................(((((......)))))((((.....((((((((...............)))))))).........))))....)))))). (-18.94 = -19.17 +   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 10:44:06 2006