Locus 4472

Sequence ID 2R_DroMel_CAF1
Location 14,698,152 – 14,698,279
Length 127
Max. P 0.985585
window7154 window7155 window7156

overview

Window 4

Location 14,698,152 – 14,698,244
Length 92
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 95.34
Mean single sequence MFE -23.78
Consensus MFE -20.90
Energy contribution -20.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.88
SVM decision value 1.58
SVM RNA-class probability 0.965102
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14698152 92 + 20766785
GACAGUAUGUGUUUAUGUUUGCUGAUUUGCUGCUUGUUUGGUUUCGGUUUUCACACAAAUUGCAAUU------GCAAUUGCAGUUGGCUCUGCUGCUA
..((((((((((....(...(((((...(((........))).)))))...)))))).....(((((------((....)))))))....)))))... ( -21.60)
>DroSec_CAF1 3664 92 + 1
GACAGUAUGUGUUUAUGUUUGCUGAUUUGCUGCUUGUUUGGUUUCGGUUCUCACACAAAUUGCAAUU------GCAAUUGCAGUUGGCUCGGCUGCUA
.......(((((....(...(((((...(((........))).))))).)..)))))((((((....------))))))(((((((...))))))).. ( -22.20)
>DroSim_CAF1 6008 92 + 1
GACAGUAUGUGUUUAUGUUUGCUGAUUUGCUGCUUGUUUGGUUUCGGUUUUCACACAAAUUGCAAUU------GCAAUUGCAGUUGGCUCUGCUGCUA
..((((((((((....(...(((((...(((........))).)))))...)))))).....(((((------((....)))))))....)))))... ( -21.60)
>DroEre_CAF1 3504 92 + 1
GACAGUGUGUGUUUAUGUUUGCUGAUUUGCUGCUUGUUUGGUUUCGGUUUUCACACAAAUUGCAAUU------GCAAUUGCAGUUUGCUCUGCUGCUA
.....((((((.........(((((...(((........))).)))))...))))))((((((....------))))))(((((.......))))).. ( -22.90)
>DroYak_CAF1 3621 98 + 1
GACAGUGUGUGUUUAUGUUUGCUGAUUUGCUGCUUGUUUGGUUUCGGUUUUCACACAAAUUGCAAUUGCAAUUGCAAUUGCAGUUUGCUCUGCUGCUA
..(((((((((.........(((((...(((........))).)))))...)))))(((((((((((((....))))))))))))).....))))... ( -30.60)
>consensus
GACAGUAUGUGUUUAUGUUUGCUGAUUUGCUGCUUGUUUGGUUUCGGUUUUCACACAAAUUGCAAUU______GCAAUUGCAGUUGGCUCUGCUGCUA
..((((.(((((....(...(((((...(((........))).)))))...))))))((((((((((........))))))))))......))))... (-20.90 = -20.90 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,698,152 – 14,698,244
Length 92
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 95.34
Mean single sequence MFE -17.06
Consensus MFE -14.80
Energy contribution -14.80
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.96
Structure conservation index 0.87
SVM decision value 2.01
SVM RNA-class probability 0.985585
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14698152 92 - 20766785
UAGCAGCAGAGCCAACUGCAAUUGC------AAUUGCAAUUUGUGUGAAAACCGAAACCAAACAAGCAGCAAAUCAGCAAACAUAAACACAUACUGUC
.....((.((.....((((..((((------....))))((((.((....)))))).........))))....)).)).................... ( -15.20)
>DroSec_CAF1 3664 92 - 1
UAGCAGCCGAGCCAACUGCAAUUGC------AAUUGCAAUUUGUGUGAGAACCGAAACCAAACAAGCAGCAAAUCAGCAAACAUAAACACAUACUGUC
.....((.((.....((((..((((------....))))((((.((....)))))).........))))....)).)).................... ( -14.40)
>DroSim_CAF1 6008 92 - 1
UAGCAGCAGAGCCAACUGCAAUUGC------AAUUGCAAUUUGUGUGAAAACCGAAACCAAACAAGCAGCAAAUCAGCAAACAUAAACACAUACUGUC
.....((.((.....((((..((((------....))))((((.((....)))))).........))))....)).)).................... ( -15.20)
>DroEre_CAF1 3504 92 - 1
UAGCAGCAGAGCAAACUGCAAUUGC------AAUUGCAAUUUGUGUGAAAACCGAAACCAAACAAGCAGCAAAUCAGCAAACAUAAACACACACUGUC
.....((((.((((..(((....))------).))))....((((((......(....).........((......)).........)))))))))). ( -17.10)
>DroYak_CAF1 3621 98 - 1
UAGCAGCAGAGCAAACUGCAAUUGCAAUUGCAAUUGCAAUUUGUGUGAAAACCGAAACCAAACAAGCAGCAAAUCAGCAAACAUAAACACACACUGUC
.....((((.......(((((((((....)))))))))...((((((......(....).........((......)).........)))))))))). ( -23.40)
>consensus
UAGCAGCAGAGCCAACUGCAAUUGC______AAUUGCAAUUUGUGUGAAAACCGAAACCAAACAAGCAGCAAAUCAGCAAACAUAAACACAUACUGUC
..((((....((....(((((((........))))))).((((.((....)))))).........)).((......))...............)))). (-14.80 = -14.80 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,698,182 – 14,698,279
Length 97
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 85.71
Mean single sequence MFE -24.38
Consensus MFE -18.54
Energy contribution -18.74
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.33
Structure conservation index 0.76
SVM decision value 1.33
SVM RNA-class probability 0.943413
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14698182 97 + 20766785
UGCUUGUUUGGUUUCGGUUUUCACACAAAUUGCAAUU------GCAAUUGCAGUUGGCUCUGCUGCUAAACAUAAAGCUCAGUUCCAUGACGCCGGCC-----CCCCU
.........((..(((((..(((....(((((((((.------...)))))))))((..(((..(((........))).)))..)).))).)))))..-----))... ( -25.20)
>DroSec_CAF1 3694 102 + 1
UGCUUGUUUGGUUUCGGUUCUCACACAAAUUGCAAUU------GCAAUUGCAGUUGGCUCGGCUGCUAAACAUAAAGCUGAGUUCCAUGCCUCACCACCCCCCACCCC
........((((...(((..............(((((------((....)))))))((((((((...........)))))))).....)))..))))........... ( -24.80)
>DroSim_CAF1 6038 101 + 1
UGCUUGUUUGGUUUCGGUUUUCACACAAAUUGCAAUU------GCAAUUGCAGUUGGCUCUGCUGCUAAACAUAAAGCUCAGUUCCAUGCCUCCCCCCCUUC-CCCCU
.(((((((((((..(((..(..((...((((((....------))))))...))..)..)))..))))))))...)))........................-..... ( -20.00)
>DroEre_CAF1 3534 93 + 1
UGCUUGUUUGGUUUCGGUUUUCACACAAAUUGCAAUU------GCAAUUGCAGUUUGCUCUGCUGCUAAACAUAAAGCUCAGUUCCAUAACCCC---------UCCCA
.(((((((((((..(((........(((((((((((.------...)))))))))))..)))..))))))))...)))................---------..... ( -22.00)
>DroYak_CAF1 3651 98 + 1
UGCUUGUUUGGUUUCGGUUUUCACACAAAUUGCAAUUGCAAUUGCAAUUGCAGUUUGCUCUGCUGCUAAACAUAAAGCUCAGUUCCAUAACCUC---------CCCC-
.(((((((((((..(((........((((((((((((((....))))))))))))))..)))..))))))))...)))................---------....- ( -29.90)
>consensus
UGCUUGUUUGGUUUCGGUUUUCACACAAAUUGCAAUU______GCAAUUGCAGUUGGCUCUGCUGCUAAACAUAAAGCUCAGUUCCAUGACCCC___C_____CCCCU
.(((((((((((..(((..........((((((((((........))))))))))....)))..))))))))...))).............................. (-18.54 = -18.74 +   0.20)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:37 2006