Locus 6292

Sequence ID	3R_DroMel_CAF1
Location	16,424,514 – 16,424,630
Length	116
Max. P	0.671828

overview

Window 3

Location	16,424,514 – 16,424,630
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	81.48
Mean single sequence MFE	-27.68
Consensus MFE	-17.64
Energy contribution	-19.56
Covariance contribution	1.92
Combinations/Pair	1.08
Mean z-score	-1.70
Structure conservation index	0.64
SVM decision value	0.04
SVM RNA-class probability	0.555238
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16424514 116 + 27905053
----ACGGCGAAACUAAUUAAGAUAAGACUAUCAUAGUGGUUUGGGUUAGCCAAUGCCAACCGUAGUCGGAACCAAAUAGCAACUAAUAAUGUUAUCAUCCGGCUUUCUCCCGCUUCGCU
----..((((((.........((((....))))...((((....((((.((....)).))))..(((((((.....((((((........))))))..))))))).....)))))))))) ( -30.10)
>DroSec_CAF1 20260 116 + 1
----ACGGCGAAACUAAUUAAGAUAAGACUAUCAUUGUGGUUUGGGUUAGCCAAUGCCAACCGUAGUCGAAACCAAAUAGCAACUCAUAAUGUUAUCAUCCGACUUUCGCCCGUUUAGCU
----..(((((((.............((((((.....((((...((....))...))))...))))))........((((((........))))))........)))))))......... ( -26.70)
>DroSim_CAF1 20871 115 + 1
----ACGGCGAAACUAAUUAAGAUAAGACUAUCAUAGUGGUUUG-GUUAGCCAAUGCCAACCGUAGUCGAAACCAAAUAGCAACUCAUAAUGUUAUCAUCCGACUUUCGCCCGUUUCGCU
----..((((((((............((((((.....(((((((-(....)))).))))...))))))((((....((((((........))))))........))))....)))))))) ( -28.70)
>DroEre_CAF1 20181 120 + 1
UUUAACUCCGAAACUAAUUAAGGUAAGACUAUCAUAAUGGUUUGGGUUAGCCAAUGCCAACCAUAGUCGGAACCAAAUAACAACUCAUAAUGGUAUCAUCCAACUUUCUUCCGUUUCGUU
........((((((..(..(((((..((((((.....((((...((....))...))))...))))))(((((((...............))))....))).)))))..)..)))))).. ( -25.66)
>DroYak_CAF1 22069 99 + 1
UUUAACGCCGAAACG-----CGGGAAAGCUA------UGGUUAGGGUUAGCCAAUGCCAACCGUAGUCGGAUCCAAAUAACAACUCAGAAUGGUAUCAUC----------CCGAUUCGCU
......((.(((...-----(((((..((((------((((...(((........))).))))))))..((((((...............))).))).))----------))).))))). ( -27.26)
>consensus
____ACGGCGAAACUAAUUAAGAUAAGACUAUCAUAGUGGUUUGGGUUAGCCAAUGCCAACCGUAGUCGGAACCAAAUAGCAACUCAUAAUGUUAUCAUCCGACUUUCGCCCGUUUCGCU
......((((((((............((((((.....((((...((....))...))))...))))))........((((((........))))))................)))))))) (-17.64 = -19.56 +   1.92)

alignment

secondary structure

dotplot

Window 4

Location	16,424,514 – 16,424,630
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.48
Mean single sequence MFE	-32.18
Consensus MFE	-20.90
Energy contribution	-22.62
Covariance contribution	1.72
Combinations/Pair	1.11
Mean z-score	-1.81
Structure conservation index	0.65
SVM decision value	0.29
SVM RNA-class probability	0.671828
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16424514 116 - 27905053
AGCGAAGCGGGAGAAAGCCGGAUGAUAACAUUAUUAGUUGCUAUUUGGUUCCGACUACGGUUGGCAUUGGCUAACCCAAACCACUAUGAUAGUCUUAUCUUAAUUAGUUUCGCCGU----
.(((((((..((((.(((((((((.((((.......)))).)))))))))..(((((.(((((((....)))))))((........)).)))))...)))).....)))))))...---- ( -35.60)
>DroSec_CAF1 20260 116 - 1
AGCUAAACGGGCGAAAGUCGGAUGAUAACAUUAUGAGUUGCUAUUUGGUUUCGACUACGGUUGGCAUUGGCUAACCCAAACCACAAUGAUAGUCUUAUCUUAAUUAGUUUCGCCGU----
.........(((((((.(.....(((((.(((((..((((.....((((((.(.....(((((((....)))))))))))))))))).))))).)))))......).)))))))..---- ( -30.70)
>DroSim_CAF1 20871 115 - 1
AGCGAAACGGGCGAAAGUCGGAUGAUAACAUUAUGAGUUGCUAUUUGGUUUCGACUACGGUUGGCAUUGGCUAAC-CAAACCACUAUGAUAGUCUUAUCUUAAUUAGUUUCGCCGU----
.(((((((.(((....)))((((((.(((.......)))((((((((((((.......(((((((....))))))-)))))))....)))))).))))))......)))))))...---- ( -34.81)
>DroEre_CAF1 20181 120 - 1
AACGAAACGGAAGAAAGUUGGAUGAUACCAUUAUGAGUUGUUAUUUGGUUCCGACUAUGGUUGGCAUUGGCUAACCCAAACCAUUAUGAUAGUCUUACCUUAAUUAGUUUCGGAGUUAAA
..((((((((((.....(..(((((((.(.......).)))))))..)))))(((((((((((((....)))))))((........))))))))............))))))........ ( -30.30)
>DroYak_CAF1 22069 99 - 1
AGCGAAUCGG----------GAUGAUACCAUUCUGAGUUGUUAUUUGGAUCCGACUACGGUUGGCAUUGGCUAACCCUAACCA------UAGCUUUCCCG-----CGUUUCGGCGUUAAA
(((((.((((----------((((....)))))))).))))).(((((..((((..(((((((((....))))))).......------..((......)-----))).))))..))))) ( -29.50)
>consensus
AGCGAAACGGGAGAAAGUCGGAUGAUAACAUUAUGAGUUGCUAUUUGGUUCCGACUACGGUUGGCAUUGGCUAACCCAAACCACUAUGAUAGUCUUAUCUUAAUUAGUUUCGCCGU____
.(((((((.......(((((((.((((.((........)).))))....)))))))..(((((((....)))))))..............................)))))))....... (-20.90 = -22.62 +   1.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:53 2006