Locus 6603

Sequence ID	3R_DroMel_CAF1
Location	17,370,089 – 17,370,215
Length	126
Max. P	0.628724

overview

Window 9

Location	17,370,089 – 17,370,190
Length	101
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	76.92
Mean single sequence MFE	-37.33
Consensus MFE	-16.95
Energy contribution	-17.45
Covariance contribution	0.50
Combinations/Pair	1.09
Mean z-score	-2.04
Structure conservation index	0.45
SVM decision value	0.20
SVM RNA-class probability	0.628724
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17370089 101 - 27905053
CAUUAGCCC-UGUGACCAGAAACCAGUUGCAUGCCAAUUGGUUUGCAAUUUGCCGCGCUUAGCAGGAGGAUGGGUGGGUGG-------UGCCUAGUGGCCGGGGUAAAU
..(((.(((-.((.((.((..((((((((((.(((....))).))))))).(((.((((((.........)))))))))))-------)..)).)).)).))).))).. ( -36.50)
>DroPse_CAF1 23503 89 - 1
CAUUAGCCCGCGCGACCA-AGACCAGUUGCAUGCCAAUUGGUUUGCAAUUUGGCGCGCUUAGAACGGAACG--GUGAUUGA-------UG-----AGGAAGGGG-----
......((((((((.(((-(.....((((((.(((....))).)))))))))))))))((((.((......--))..))))-------..-----.....))).----- ( -28.60)
>DroEre_CAF1 21411 99 - 1
CAUUAGCCC-UGUGACCAGAAACCAGUUGCAUGCCAAUUGGUUUGCAAUUUGCCGCGCUUAGCAGGGGGCGGGGUGGGCGG-------UGCCUGGUGGCCGGGG--AGU
......(((-.((.(((((..((((((((((.(((....))).))))))).(((.((((..((.....))..)))))))))-------)..))))).)).))).--... ( -46.20)
>DroYak_CAF1 28730 107 - 1
CAUUAGCCC-UGUGACCAGAAACCAGUUGCAUGCCAAUUGGUUUGCAAUUUGCCGCGCUUAGCAGGGGGCGGGGUGGGUGGUGCAUGGUGCCUGGUGGCCGGGGU-AGU
.((((.(((-.((.(((((..((((((((((.(((....))).))))(((..((.(((((......))))).))..)))...)).))))..))))).)).))).)-))) ( -49.00)
>DroAna_CAF1 15665 88 - 1
AAUUAUCCC-AGCGACC-GAAACCAGUUGCAUGCCAAUUGGUUUGCAAUUUGGUGCGCUUAGCCGAAG----GGUGGGAGG-------U----GGUGGGAGGGGU----
....(((((-..(.(((-...((((((((((.(((....))).))))).)))))((.(((.(((....----)))..))))-------)----))).)..)))))---- ( -35.10)
>DroPer_CAF1 16037 89 - 1
CAUUAGCCCGCGCGACCA-AGACCAGUUGCAUGCCAAUUGGUUUGCAAUUUGGCGCGCUUAGAACGGAACG--GUGAUUGA-------UG-----AGGAAGGGG-----
......((((((((.(((-(.....((((((.(((....))).)))))))))))))))((((.((......--))..))))-------..-----.....))).----- ( -28.60)
>consensus
CAUUAGCCC_UGCGACCAGAAACCAGUUGCAUGCCAAUUGGUUUGCAAUUUGCCGCGCUUAGCAGGGGGCG_GGUGGGUGG_______UG___GGUGGCAGGGG_____
......(((......((.....(.(((((((.(((....))).))))))).)...((((((.(.........).))))))................))..)))...... (-16.95 = -17.45 +   0.50)

alignment

secondary structure

dotplot

Window 0

Location	17,370,119 – 17,370,215
Length	96
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	80.54
Mean single sequence MFE	-31.05
Consensus MFE	-20.79
Energy contribution	-21.35
Covariance contribution	0.56
Combinations/Pair	1.15
Mean z-score	-1.44
Structure conservation index	0.67
SVM decision value	0.18
SVM RNA-class probability	0.619786
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17370119 96 - 27905053
--------CUCCUCCUGU------GCCUGCU-UCCUUGCCCAUUAGCCC-UGUGACCAGAAACCAGUUGCAUGCCAAUUGGUUUGCAAUUUGCCGCGCUUAGCAGGAGGAUG
--------.(((((((((------(((.((.-...((((.........(-((....)))((((((((((.....))))))))))))))...)).).))...))))))))).. ( -33.60)
>DroPse_CAF1 23522 96 - 1
--------UCCAUUCCGC------ACCCGUACCCCCAUCCCAUUAGCCCGCGCGACCA-AGACCAGUUGCAUGCCAAUUGGUUUGCAAUUUGGCGCGCUUAGAACGGAACG-
--------(((.(((.((------....))...................(((((.(((-(.....((((((.(((....))).)))))))))))))))...))).)))...- ( -27.70)
>DroSec_CAF1 18557 96 - 1
--------CUCCUCCUGC------GCCUGCU-UCCUUGCCCAUUAGCCC-UGUGACCAGAAACCAGUUGCAUGCCAAUUGGUUUGCAAUUUGCCGCGCUUAGCAGGGGGCGG
--------(.((((((((------(((.((.-...((((.........(-((....)))((((((((((.....))))))))))))))...)).).))...)))))))).). ( -32.80)
>DroSim_CAF1 27171 96 - 1
--------CUCCUCCUGC------GCCUGCU-UCCUUGCCCAUUAGCCC-UGUGACCAGAAACCAGUUGCAUGCCAAUUGGUUUGCAAUUUGCCGCGCUUAGCAGGGGGCGG
--------(.((((((((------(((.((.-...((((.........(-((....)))((((((((((.....))))))))))))))...)).).))...)))))))).). ( -32.80)
>DroEre_CAF1 21439 110 - 1
ACCUCCUCCUCGUCCUGCCUCUCAUCCUGCU-CCCUUGCCCAUUAGCCC-UGUGACCAGAAACCAGUUGCAUGCCAAUUGGUUUGCAAUUUGCCGCGCUUAGCAGGGGGCGG
..........................((((.-(((((((.....(((.(-.(..(...(((((((((((.....)))))))))).)...)..).).)))..))))))))))) ( -31.70)
>DroPer_CAF1 16056 96 - 1
--------UCCAUUCCGC------ACCCGUACCCCCAUCCCAUUAGCCCGCGCGACCA-AGACCAGUUGCAUGCCAAUUGGUUUGCAAUUUGGCGCGCUUAGAACGGAACG-
--------(((.(((.((------....))...................(((((.(((-(.....((((((.(((....))).)))))))))))))))...))).)))...- ( -27.70)
>consensus
________CUCCUCCUGC______GCCUGCU_CCCUUGCCCAUUAGCCC_UGUGACCAGAAACCAGUUGCAUGCCAAUUGGUUUGCAAUUUGCCGCGCUUAGCAGGGGGCGG
..........................(((((..((((((.....(((............((((((((((.....))))))))))((........)))))..))))))))))) (-20.79 = -21.35 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:37 2006