Locus 4885

Sequence ID	X_DroMel_CAF1
Location	12,699,011 – 12,699,133
Length	122
Max. P	0.514823

overview

Window 2

Location	12,699,011 – 12,699,101
Length	90
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	84.31
Mean single sequence MFE	-20.68
Consensus MFE	-13.78
Energy contribution	-14.28
Covariance contribution	0.50
Combinations/Pair	1.15
Mean z-score	-2.23
Structure conservation index	0.67
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12699011 90 - 22224390
----UUCCCGGCCAACAAACAAAGGCAACUGCCAAUCAAAACUUUGGCAUUUGUUCCUAUUUUGCGGCUCACUUCGAUUAGGCCACC----UCAACUA
----.....((((..((((...((((((.((((((........)))))).)))..)))..))))(((......)))....))))...----....... ( -21.60)
>DroPse_CAF1 65361 89 - 1
----UUCCCGGCCACCAGACAAAGACAGCUGCCAAUCAAAAGUUUUGCAUUUGUUUCUAUGUUGCGGCUCACUUCGAU-ACGCCAUC----CAAGGCA
----.....((((....((((.((((((.(((.((........)).))).))))))...))))..)))).........-..(((...----...))). ( -18.30)
>DroSec_CAF1 51844 90 - 1
----UUCCUCGCCAACAAACAAAGGCAACUGCCAAUCAAAACUUUGGCAGUUGUUUCUAUUUUGCGGCUCUCUUCGAUUAGGCCACC----UCAACUA
----......(((..((((...(((((((((((((........)))))))))))))....))))(((......)))....)))....----....... ( -24.00)
>DroEre_CAF1 51255 94 - 1
----UUCCCGGCCAACAAACAAAGGCAACUGCCAAUCAAAACUUUGGCAUUUGUUUCUAUUUUGCGGCUCACUUCGAUUAGGCCACCUAUAUCAACUA
----.....((((..((((...((((((.((((((........)))))).))))))....))))(((......)))....)))).............. ( -22.20)
>DroAna_CAF1 57629 92 - 1
UUCCUUUCCGGCCUACAAACAAAGGCAACUGCCAAUCAAAAGUUUGCCAUUUGUUUCUAUUUUGUGGCUCACUUCGAUUC-GCCACC-----AAACUA
.........(((...........(((....)))((((..((((..(((((..((....))...)))))..)))).)))).-)))...-----...... ( -19.70)
>DroPer_CAF1 80427 89 - 1
----UUCCCGGCCACCAGACAAAGACAGCUGCCAAUCAAAAGUUUUGCAUUUGUUUCUAUGUUGCGGCUCACUUCGAU-ACGCCAUC----CAAGGCA
----.....((((....((((.((((((.(((.((........)).))).))))))...))))..)))).........-..(((...----...))). ( -18.30)
>consensus
____UUCCCGGCCAACAAACAAAGGCAACUGCCAAUCAAAACUUUGGCAUUUGUUUCUAUUUUGCGGCUCACUUCGAUUAGGCCACC____UAAACUA
.........((((..((((...((((((.((((((........)))))).))))))....)))).))))............................. (-13.78 = -14.28 +   0.50)

alignment

secondary structure

dotplot

Window 3

Location	12,699,033 – 12,699,133
Length	100
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	84.95
Mean single sequence MFE	-25.02
Consensus MFE	-17.83
Energy contribution	-17.94
Covariance contribution	0.11
Combinations/Pair	1.17
Mean z-score	-2.19
Structure conservation index	0.71
SVM decision value	-0.04
SVM RNA-class probability	0.514823
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12699033 100 - 22224390
U-AUAAAGUUGCGGCUUGCC---AAACUUUCUA---CAU----UUCCCGGCCAACAAACAAAGGCAACUGCCAAUCAAAACUUUGGCAUUUGUUCCUAUUUUGCGGCUCAC
.-..((((((..((....))---.))))))...---...----.....((((..((((...((((((.((((((........)))))).)))..)))..)))).))))... ( -23.30)
>DroPse_CAF1 65382 100 - 1
U-CUAAAGUUGCGGCUUGUC---AAAGUUUCCA---AAU----UUCCCGGCCACCAGACAAAGACAGCUGCCAAUCAAAAGUUUUGCAUUUGUUUCUAUGUUGCGGCUCAC
.-....((((((((((((((---...((..((.---...----.....))..))..)))))((((((.(((.((........)).))).))))))....)))))))))... ( -21.00)
>DroSec_CAF1 51866 100 - 1
U-AUAAAGUUGCGGCUUGCC---AAACUUUCUA---CAU----UUCCUCGCCAACAAACAAAGGCAACUGCCAAUCAAAACUUUGGCAGUUGUUUCUAUUUUGCGGCUCUC
.-..((((((..((....))---.))))))...---...----......(((..((((...(((((((((((((........)))))))))))))....)))).))).... ( -29.40)
>DroYak_CAF1 55429 100 - 1
U-AUAAAGUUGCGGCUUGGC---AAAGUUUCUA---CAU----UUCCCGGCCAACAAACAAAGGCAACUGCCAAUCAAAACUUUGGCAUUUGUUUCUAUUUUGCGGCUCAC
.-....((((((((((.((.---(((((....)---).)----)))).)))).........((((((.((((((........)))))).)))))).......))))))... ( -28.10)
>DroAna_CAF1 57649 111 - 1
CCCUGGAGUUGCGGUUUGCCGCAAAACUUUCCCAAAAACUUCCUUUCCGGCCUACAAACAAAGGCAACUGCCAAUCAAAAGUUUGCCAUUUGUUUCUAUUUUGUGGCUCAC
....((((((((((....))))))....))))................((((.((((((((((((((((..........)).))))).))))).......))))))))... ( -27.31)
>DroPer_CAF1 80448 100 - 1
U-CUAAAGUUGCGGCUUGUC---AAAGUUUCCA---AAU----UUCCCGGCCACCAGACAAAGACAGCUGCCAAUCAAAAGUUUUGCAUUUGUUUCUAUGUUGCGGCUCAC
.-....((((((((((((((---...((..((.---...----.....))..))..)))))((((((.(((.((........)).))).))))))....)))))))))... ( -21.00)
>consensus
U_AUAAAGUUGCGGCUUGCC___AAACUUUCCA___AAU____UUCCCGGCCAACAAACAAAGGCAACUGCCAAUCAAAACUUUGGCAUUUGUUUCUAUUUUGCGGCUCAC
......((((((((((.(............................).)))).........((((((.((((((........)))))).)))))).......))))))... (-17.83 = -17.94 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:20 2006