Locus 858

Sequence ID	X_DroMel_CAF1
Location	2,436,157 – 2,436,280
Length	123
Max. P	0.777191

overview

Window 3

Location	2,436,157 – 2,436,269
Length	112
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	82.86
Mean single sequence MFE	-38.63
Consensus MFE	-26.96
Energy contribution	-27.88
Covariance contribution	0.92
Combinations/Pair	1.27
Mean z-score	-1.76
Structure conservation index	0.70
SVM decision value	0.14
SVM RNA-class probability	0.603553
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2436157 112 - 22224390
GGCCCAAACGCUGAUGAAGUCGCGUUUGGCGGGCGCCACCAAGGGACAUGGUCUGCUAAAGAAAAAGGCGGAUGCCCUGCAGAUGCGCUUUCGUCUGAUUCUGGGCAAGAUC
.(((((....(.(((((((.((((((((..(((((((......)).)...(((((((.........)))))))))))..)))))))).))))))).)....)))))...... ( -45.90)
>DroVir_CAF1 171054 112 - 1
GGCACAAACUUUGAUGAAAUCGCGUCUGGCGGGCGCCACAAAGGGCCAUGGCCUGCUUAAGAAGAAGGCCGAUGCGCUGCAGAUGCGUUUUCGCCUGAUUCUGGGCAAGAUC
...............((((.((((((((((((((.((.....))))).((((((.((.....)).))))))...)))..)))))))).))))((((......))))...... ( -43.00)
>DroGri_CAF1 126453 112 - 1
CGCACAAAUUUUGAUGAAAUCGCGCCUGGCGGGCGCCACCAAGGGUCAUGGCCUGCUUAAAAAGAAGGCAGAUGCUCUCCAAAUGCGUUUUCGCCUAAUUCUGGGCAAGAUC
...............((((.((((..(((.((((((((((...)))...)))((((((.......))))))..)))).)))..)))).))))(((((....)))))...... ( -36.10)
>DroWil_CAF1 111701 112 - 1
GGCCCAAACUUUGAUGAAAUCUCGAUUGGCUGGUGCCACCAAGGGCCAUGGUCUGUUAAAAAAGAAGGCCGAUGCCUUGCAAAUGCGUUUCCGUUUGAUUUUGGGCAAAAUU
(((((.....((((.(....))))).((((....))))....))))).((((((...........)))))).(((((..((((((......)))))).....)))))..... ( -35.00)
>DroMoj_CAF1 164605 112 - 1
AGCACAAACGUUGAUGAAAUCGCGUCUGGCGGGCGCCACGAAAGGCCAUGGCCUACUUAAGAAGAAGGCUGACGCUUUGCAGAUGCGUUUCCGUUUGAUUCUGGGCAAGAUC
....((((((.....((((.((((((((..(((((((......)))...(((((.((.....)).)))))...))))..))))))))))))))))))..(((.....))).. ( -36.40)
>DroAna_CAF1 94135 112 - 1
AGCUCAGACAUUGAUGAAAUCCCGUCUGGCUGGUGCCACAAAGGGACAUGGCCUCCUCAAGAAAAAGGCCGAUGCUCUACAAAUGCGUUUUCGUUUAAUUUUGGGCAAAAUA
.(((((((....((((((.((((...((((....))))....))))...(((((...........)))))(((((.........)))))))))))....)))))))...... ( -35.40)
>consensus
GGCACAAACUUUGAUGAAAUCGCGUCUGGCGGGCGCCACCAAGGGCCAUGGCCUGCUUAAGAAGAAGGCCGAUGCUCUGCAAAUGCGUUUUCGUCUGAUUCUGGGCAAGAUC
.((.((......(((((((.((((((((((....)))....((((.((((((((...........))))).)))))))..))))))).)))))))......)).))...... (-26.96 = -27.88 +   0.92)

alignment

secondary structure

dotplot

Window 4

Location	2,436,189 – 2,436,280
Length	91
Sequences	6
Columns	91
Reading direction	reverse
Mean pairwise identity	78.05
Mean single sequence MFE	-30.20
Consensus MFE	-20.38
Energy contribution	-20.68
Covariance contribution	0.31
Combinations/Pair	1.36
Mean z-score	-1.45
Structure conservation index	0.67
SVM decision value	0.55
SVM RNA-class probability	0.777191
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2436189 91 - 22224390
CCAUGUUGUAGGGCCCAAACGCUGAUGAAGUCGCGUUUGGCGGGCGCCACCAAGGGACAUGGUCUGCUAAAGAAAAAGGCGGAUGCCCUGC
.......(((((((((((((((.(((...)))))))))))....((((.(((.......)))(((.....)))....))))...))))))) ( -33.50)
>DroEre_CAF1 84079 84 - 1
-------GUAGUGCCCAAACGCUGAUGAAGUCGCGUUUGGCGGGCGCCACCAAGGGGCAUGGCCUGCUGAAGAAGAAGGCAGACGCCCUGC
-------((.((((((((((((.(((...)))))))))...)))))).))...(((((...((((.((.....)).))))....))))).. ( -34.70)
>DroWil_CAF1 111733 87 - 1
CA----UUUAGGGCCCAAACUUUGAUGAAAUCUCGAUUGGCUGGUGCCACCAAGGGCCAUGGUCUGUUAAAAAAGAAGGCCGAUGCCUUGC
..----.....(((((.....((((.(....))))).((((....))))....))))).((((((...........))))))......... ( -24.10)
>DroYak_CAF1 79321 89 - 1
CC--AUUGUAGGGCACAAACGCUGAUGAAGUCGCGUUUGGCCGGCGCCACCAAGGGACAUGGUUUGCUCAAGAAGAAGGCCGAUGCCCUGC
..--...(((((((((((((((.(((...))))))))))..((((((.((((.......))))..))((.....))..)))).)))))))) ( -33.50)
>DroMoj_CAF1 164637 85 - 1
------CGCAGAGCACAAACGUUGAUGAAAUCGCGUCUGGCGGGCGCCACGAAAGGCCAUGGCCUACUUAAGAAGAAGGCUGACGCUUUGC
------.(((((((.....((((((((......)))).))))(((....(....))))..(((((.((.....)).)))))...))))))) ( -27.50)
>DroAna_CAF1 94167 82 - 1
---------AGAGCUCAGACAUUGAUGAAAUCCCGUCUGGCUGGUGCCACAAAGGGACAUGGCCUCCUCAAGAAAAAGGCCGAUGCUCUAC
---------(((((((..............((((...((((....))))....))))...(((((...........))))))).))))).. ( -27.90)
>consensus
______UGUAGGGCCCAAACGCUGAUGAAAUCGCGUUUGGCGGGCGCCACCAAGGGACAUGGCCUGCUAAAGAAGAAGGCCGAUGCCCUGC
.......(((((((..((((((.(((...)))))))))(((....)))...........((((((...........))))))..))))))) (-20.38 = -20.68 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:27 2006