Locus 6537

Sequence ID	X_DroMel_CAF1
Location	16,365,023 – 16,365,156
Length	133
Max. P	0.996593

overview

Window 1

Location	16,365,023 – 16,365,123
Length	100
Sequences	4
Columns	102
Reading direction	reverse
Mean pairwise identity	84.74
Mean single sequence MFE	-26.10
Consensus MFE	-20.81
Energy contribution	-21.38
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-3.34
Structure conservation index	0.80
SVM decision value	2.72
SVM RNA-class probability	0.996593
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16365023 100 - 22224390
AAAGCGACGAUGUGAGCGAGAUUGGCGUAAAAGGGACAAGGGUGUCUCAAAUUGCCUUGGCUUAGCUCACAAAAAAUUGAACCAAAAA--AAAAAAAAAAUG
..........((((((((((...((((.....((((((....))))))....))))....))).))))))).................--............ ( -25.20)
>DroSec_CAF1 37830 99 - 1
AAAGCGACUAUGUGAGCGAGAUUGGCGUAAAAGGGACAAGGGUGUCUCAAAUUGCCUUGGUUUAGCUCACAAAAAAUUGAAUCUAAAA--AA-AAAAAAAUU
..........(((((((.((((..(.((((..((((((....))))))...)))).)..)))).))))))).................--..-......... ( -25.30)
>DroSim_CAF1 26186 99 - 1
AAAGCGACUGUGUGAGCGAGAUUGGCGAAAAAGGGACAAGGGUGUCUCAAAUUGCCUUGGCUUAGCUCACACAAAAUUGAAUCUAAAA--AA-AAAAAAAUG
........((((((((((((...(((((....((((((....))))))...)))))....))).)))))))))...............--..-......... ( -30.10)
>DroEre_CAF1 23501 90 - 1
-AAGCGGCGAUGAGAGCGCGAUUGGCGUAAGAGGGACAAGGGUUUCUCAAAUUGCCUUGGCUUAGCUCACAAAAAACU----------GAAC-AUCAAAAUG
-.......((((.((((((.(..((((...(((..((....))..)))....)))).).))...)))).((......)----------)..)-)))...... ( -23.80)
>consensus
AAAGCGACGAUGUGAGCGAGAUUGGCGUAAAAGGGACAAGGGUGUCUCAAAUUGCCUUGGCUUAGCUCACAAAAAAUUGAAUCUAAAA__AA_AAAAAAAUG
..........((((((((((...((((.....((((((....))))))....))))....))).)))))))............................... (-20.81 = -21.38 +   0.56)

alignment

secondary structure

dotplot

Window 2

Location	16,365,048 – 16,365,156
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.46
Mean single sequence MFE	-30.46
Consensus MFE	-20.34
Energy contribution	-21.18
Covariance contribution	0.84
Combinations/Pair	1.05
Mean z-score	-1.89
Structure conservation index	0.67
SVM decision value	0.15
SVM RNA-class probability	0.605364
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16365048 108 - 22224390
UCCGAA------GAGAGCA-GGAUAUGCAAGAGAGCGCAGA-----AAGCGACGAUGUGAGCGAGAUUGGCGUAAAAGGGACAAGGGUGUCUCAAAUUGCCUUGGCUUAGCUCACAAAAA
..((..------....(((-.....))).......(((...-----..))).)).((((((((((...((((.....((((((....))))))....))))....))).))))))).... ( -31.90)
>DroSec_CAF1 37854 108 - 1
UCCAAA------GAGAGCA-GGAUAUUCAAGAGAGCGCUGA-----AAGCGACUAUGUGAGCGAGAUUGGCGUAAAAGGGACAAGGGUGUCUCAAAUUGCCUUGGUUUAGCUCACAAAAA
(((...------.......-)))..........(((((...-----..))).)).(((((((.((((..(.((((..((((((....))))))...)))).)..)))).))))))).... ( -30.30)
>DroSim_CAF1 26210 108 - 1
UCCAAA------GAGAGCA-GGAUAUUCAAGAGAGCGCUGA-----AAGCGACUGUGUGAGCGAGAUUGGCGAAAAAGGGACAAGGGUGUCUCAAAUUGCCUUGGCUUAGCUCACACAAA
(((...------.......-)))..........(((((...-----..))).))(((((((((((...(((((....((((((....))))))...)))))....))).))))))))... ( -34.30)
>DroEre_CAF1 23517 105 - 1
UCCACG------GAGAGCA-GCGAAUUGCAGAGAGCGA--------AAGCGGCGAUGAGAGCGCGAUUGGCGUAAGAGGGACAAGGGUUUCUCAAAUUGCCUUGGCUUAGCUCACAAAAA
......------..(((((-((.((.........((..--------..))((((((....((((.....))))..(((..((....))..)))..)))))))).)))..))))....... ( -35.00)
>DroYak_CAF1 22544 120 - 1
UCCAAAAAGAGAGAGAGCAAAUAAAUUCAAGAGAGCGACGAAAUUCAAGCGACGAUGAGAGCGAGAUUGGCGUAAAAGGGACAAGGGUGUCUCAAAUUGCCUUGGCUUAGCGCACAAAAA
................((.......((((.....((............)).....)))).(((((...((((.....((((((....))))))....))))....))).))))....... ( -20.80)
>consensus
UCCAAA______GAGAGCA_GGAUAUUCAAGAGAGCGCUGA_____AAGCGACGAUGUGAGCGAGAUUGGCGUAAAAGGGACAAGGGUGUCUCAAAUUGCCUUGGCUUAGCUCACAAAAA
..................................((............)).....((((((((((...((((.....((((((....))))))....))))....))).))))))).... (-20.34 = -21.18 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:16:14 2006