Locus 2947

Sequence ID 2L_DroMel_CAF1
Location 8,470,413 – 8,470,527
Length 114
Max. P 0.999922
window4676 window4677 window4678 window4679

overview

Window 6

Location 8,470,413 – 8,470,503
Length 90
Sequences 4
Columns 90
Reading direction forward
Mean pairwise identity 75.00
Mean single sequence MFE -21.75
Consensus MFE -10.24
Energy contribution -9.80
Covariance contribution -0.44
Combinations/Pair 1.20
Mean z-score -2.96
Structure conservation index 0.47
SVM decision value 2.03
SVM RNA-class probability 0.986130
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8470413 90 + 22407834
AUCCACAUUCACAUCCACAUCCAUGGACAUAGCCAUGGCCAUAGCCGUAGCUCUUUGGCCAUGGCAAUUGCGAUUGCAUUUUCUUUAUCG
.....((.((.((((((......))))....((((((((((.(((....)))...))))))))))...)).)).)).............. ( -28.70)
>DroGri_CAF1 9885 69 + 1
AGCAGCA--AACAACCACA--CAUGGACA----------CAUAGAAAUAUCU-----GAGAUUGCAA--GCGAUUUGACUUUUCUUAUCG
.((.(((--(.(..(((..--..))).((----------.(((....))).)-----).).))))..--))(((..((....))..))). ( -11.10)
>DroSec_CAF1 11029 78 + 1
AUCCAC------AUCCACAUCCAUGGACA------UGGCCAUAGCCGUAGCUCUUUGGCCAUGGCAAUUGCGAUUGCAUUUUCUUUAUCG
......------.((((......))))((------((((((.(((....)))...))))))))(((((....)))))............. ( -23.60)
>DroSim_CAF1 11129 78 + 1
AUCCAC------AUCCACAUCCAUGGACA------UGGCCAUAGCCGUAGCUCUUUGGCCAUGGCAAUUGCGAUUGCAUUUUCUUUAUCG
......------.((((......))))((------((((((.(((....)))...))))))))(((((....)))))............. ( -23.60)
>consensus
AUCCAC______AUCCACAUCCAUGGACA______UGGCCAUAGCCGUAGCUCUUUGGCCAUGGCAAUUGCGAUUGCAUUUUCUUUAUCG
.............((((......))))................(((((.((......)).))))).....((((............)))) (-10.24 =  -9.80 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,470,413 – 8,470,503
Length 90
Sequences 4
Columns 90
Reading direction reverse
Mean pairwise identity 75.00
Mean single sequence MFE -27.30
Consensus MFE -16.42
Energy contribution -17.43
Covariance contribution 1.00
Combinations/Pair 1.09
Mean z-score -3.48
Structure conservation index 0.60
SVM decision value 4.57
SVM RNA-class probability 0.999922
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8470413 90 - 22407834
CGAUAAAGAAAAUGCAAUCGCAAUUGCCAUGGCCAAAGAGCUACGGCUAUGGCCAUGGCUAUGUCCAUGGAUGUGGAUGUGAAUGUGGAU
.............(((.((((....((((((((((...(((....))).))))))))))...((((((....)))))))))).))).... ( -39.30)
>DroGri_CAF1 9885 69 - 1
CGAUAAGAAAAGUCAAAUCGC--UUGCAAUCUC-----AGAUAUUUCUAUG----------UGUCCAUG--UGUGGUUGUU--UGCUGCU
.(((..((....))..)))((--..((((((.(-----((((((......)----------))))....--)).)))))).--.)).... ( -13.50)
>DroSec_CAF1 11029 78 - 1
CGAUAAAGAAAAUGCAAUCGCAAUUGCCAUGGCCAAAGAGCUACGGCUAUGGCCA------UGUCCAUGGAUGUGGAU------GUGGAU
.................(((((.....((((((((...(((....))).))))))------))(((((....))))))------)))).. ( -28.20)
>DroSim_CAF1 11129 78 - 1
CGAUAAAGAAAAUGCAAUCGCAAUUGCCAUGGCCAAAGAGCUACGGCUAUGGCCA------UGUCCAUGGAUGUGGAU------GUGGAU
.................(((((.....((((((((...(((....))).))))))------))(((((....))))))------)))).. ( -28.20)
>consensus
CGAUAAAGAAAAUGCAAUCGCAAUUGCCAUGGCCAAAGAGCUACGGCUAUGGCCA______UGUCCAUGGAUGUGGAU______GUGGAU
((((............))))......(((((((((...(((....))).)))))........((((((....))))))......)))).. (-16.42 = -17.43 +   1.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,470,435 – 8,470,527
Length 92
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 77.71
Mean single sequence MFE -24.68
Consensus MFE -15.49
Energy contribution -15.93
Covariance contribution 0.44
Combinations/Pair 1.20
Mean z-score -3.14
Structure conservation index 0.63
SVM decision value 2.25
SVM RNA-class probability 0.991103
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8470435 92 + 22407834
AUGGACA------UAGCCA------UGGCCAUAGCCGUAGCUCUUUGGCCAUGGCAAUUGCGAUUGCAUUUUCUUUAUCGCAUCCUGCACAAAUUACGAAAAUA
..(((..------..((((------((((((.(((....)))...))))))))))...((((((............)))))))))................... ( -31.90)
>DroSec_CAF1 11045 86 + 1
AUGGACA------------------UGGCCAUAGCCGUAGCUCUUUGGCCAUGGCAAUUGCGAUUGCAUUUUCUUUAUCGCAUCCUGCACAAAUUACGAAAAUA
.....((------------------((((((.(((....)))...))))))))(((..((((((............))))))...)))................ ( -26.40)
>DroSim_CAF1 11145 86 + 1
AUGGACA------------------UGGCCAUAGCCGUAGCUCUUUGGCCAUGGCAAUUGCGAUUGCAUUUUCUUUAUCGCAUCCUGCACAAAUUACGAAAAUA
.....((------------------((((((.(((....)))...))))))))(((..((((((............))))))...)))................ ( -26.40)
>DroEre_CAF1 11448 104 + 1
ACAUCCAUGGCCAUAGCCAUAGCCAUUGCCAUUGCCGUAGCUCUUGGGCCAUGGCAAUUGCGAUUGCAUUUUCUUUAUCGCAUCCUGCACAAAUUACGAAAAUA
......(((((....))))).((.(((((.((((((((.(((....))).)))))))).))))).))((((((......((.....)).........)))))). ( -32.06)
>DroAna_CAF1 11104 79 + 1
-------------------------AUGCUAUGGCCAUAGCUCUCUGGCUACGGCAAUUGCGAUUGCAUUUUCUUUAUCGCAUCCUGCACAAAUUACAAAAAUA
-------------------------.(((..((((((........))))))..)))..((((((............))))))...................... ( -19.40)
>DroPer_CAF1 12354 72 + 1
AUGGUCA------------------UGGCAAU------------UU--CCAUUGCGAUUGCUAUUGCAUUUUCUUUAUCGCAGCCUGCACAAAUUACAAAAAUA
..(((.(------------------(((....------------..--))))(((((((((....)))........)))))))))................... ( -11.90)
>consensus
AUGGACA__________________UGGCCAUAGCCGUAGCUCUUUGGCCAUGGCAAUUGCGAUUGCAUUUUCUUUAUCGCAUCCUGCACAAAUUACGAAAAUA
...........................(((((.((((........)))).)))))...((((((............))))))...................... (-15.49 = -15.93 +   0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,470,435 – 8,470,527
Length 92
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 77.71
Mean single sequence MFE -27.32
Consensus MFE -14.27
Energy contribution -14.10
Covariance contribution -0.17
Combinations/Pair 1.16
Mean z-score -2.99
Structure conservation index 0.52
SVM decision value 2.08
SVM RNA-class probability 0.987580
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8470435 92 - 22407834
UAUUUUCGUAAUUUGUGCAGGAUGCGAUAAAGAAAAUGCAAUCGCAAUUGCCAUGGCCAAAGAGCUACGGCUAUGGCCA------UGGCUA------UGUCCAU
.......(((.....))).(((((((((............)))))....((((((((((...(((....))).))))))------))))..------.)))).. ( -36.30)
>DroSec_CAF1 11045 86 - 1
UAUUUUCGUAAUUUGUGCAGGAUGCGAUAAAGAAAAUGCAAUCGCAAUUGCCAUGGCCAAAGAGCUACGGCUAUGGCCA------------------UGUCCAU
................((((..((((((............)))))).))))((((((((...(((....))).))))))------------------))..... ( -29.10)
>DroSim_CAF1 11145 86 - 1
UAUUUUCGUAAUUUGUGCAGGAUGCGAUAAAGAAAAUGCAAUCGCAAUUGCCAUGGCCAAAGAGCUACGGCUAUGGCCA------------------UGUCCAU
................((((..((((((............)))))).))))((((((((...(((....))).))))))------------------))..... ( -29.10)
>DroEre_CAF1 11448 104 - 1
UAUUUUCGUAAUUUGUGCAGGAUGCGAUAAAGAAAAUGCAAUCGCAAUUGCCAUGGCCCAAGAGCUACGGCAAUGGCAAUGGCUAUGGCUAUGGCCAUGGAUGU
..........(((..((.....((((((............))))))...(((((((((....(((((..((....))..)))))..)))))))))))..))).. ( -34.30)
>DroAna_CAF1 11104 79 - 1
UAUUUUUGUAAUUUGUGCAGGAUGCGAUAAAGAAAAUGCAAUCGCAAUUGCCGUAGCCAGAGAGCUAUGGCCAUAGCAU-------------------------
..............((((....((((((............))))))...((((((((......))))))))....))))------------------------- ( -22.40)
>DroPer_CAF1 12354 72 - 1
UAUUUUUGUAAUUUGUGCAGGCUGCGAUAAAGAAAAUGCAAUAGCAAUCGCAAUGG--AA------------AUUGCCA------------------UGACCAU
......((((.....))))((.((((((........(((....)))))))))((((--..------------....)))------------------)..)).. ( -12.70)
>consensus
UAUUUUCGUAAUUUGUGCAGGAUGCGAUAAAGAAAAUGCAAUCGCAAUUGCCAUGGCCAAAGAGCUACGGCUAUGGCCA__________________UGUCCAU
.((((((........(((.....))).....))))))((....))....(((((.(((..........))).)))))........................... (-14.27 = -14.10 +  -0.17)

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 10:40:16 2006