Locus 1948

Sequence ID	2R_DroMel_CAF1
Location	7,359,887 – 7,360,034
Length	147
Max. P	0.841006

overview

Window 8

Location	7,359,887 – 7,359,995
Length	108
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	88.27
Mean single sequence MFE	-34.92
Consensus MFE	-26.86
Energy contribution	-27.54
Covariance contribution	0.68
Combinations/Pair	1.07
Mean z-score	-1.93
Structure conservation index	0.77
SVM decision value	0.75
SVM RNA-class probability	0.841006
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7359887 108 - 20766785
CGGGAAGGAAUCCCGUCCGGUAG-GGACUACUAGCAUUCGCAAGUGACGUCCAGCAACCGGAGGACCCCCAACUGUAGAAUCCGCAUCACCAUCCUAAUCC-CAACAAAC
.((((((((...((.((((((..-((((((((.((....)).))))..))))....)))))))).........(((.......)))......))))..)))-)....... ( -32.30)
>DroSec_CAF1 6845 108 - 1
CGGGAAGGAUUCCCGGCCGGAAG-GGACUACUAGCAUCCGCAAGUGGCGUCCAACAACCGGAGGACUCCCUACCGUAGAAUCCGCAUCACCAUCCUAAUCC-AAAGCAAC
.((((.((((((...((.((.((-((((((((.((....)).))))).((((..(....)..))))))))).)))).))))))...)).))..........-........ ( -34.70)
>DroSim_CAF1 13292 108 - 1
CGGGAAGGAUUCCCGGCCGGAAG-GGACUACUAGCAUCCGCAAGUGGCGUCCAACAACCGGAGGACUCCCUACCGUAGAAUCCGCAUCACCAUCCUAAUCC-CAACCAAC
.((((.((((((...((.((.((-((((((((.((....)).))))).((((..(....)..))))))))).)))).))))))(......).......)))-)....... ( -36.00)
>DroEre_CAF1 6862 109 - 1
CGGGAAGGAUUCCCGUCCGGAAGGGGACUACUAGCAUCCGCAAGUGGCGUCCAAUAACCGGAGGUUUCCCUACCGAGGAAUCCGCAUCACCAUUGUAGAAC-CAAUCAAC
.((((.(((((((....(((.(((((((((((.((....)).)))))(.(((.......))).).)))))).))).)))))))...)).))..........-........ ( -36.30)
>DroYak_CAF1 6231 110 - 1
CGGGAAGGAUUCCCGGCCGGAAGGGGACUACUAGCAUCCGCAAGUGGCGUCCAGCAACCGGAGGUCUCCCUUCCGAAGAUUCCGCAUUACCAUCCUAUAACCCAACCAAC
.(((.(((((.....(((((((((((...(((.((....)).)))(((.(((.......))).))))))))))))..(....)))......)))))....)))....... ( -35.30)
>consensus
CGGGAAGGAUUCCCGGCCGGAAG_GGACUACUAGCAUCCGCAAGUGGCGUCCAACAACCGGAGGACUCCCUACCGUAGAAUCCGCAUCACCAUCCUAAUCC_CAACCAAC
.((((.((((((.(((((((....((((((((.((....)).))))..)))).....))))(((....))).)))..))))))...)).))................... (-26.86 = -27.54 +   0.68)

alignment

secondary structure

dotplot

Window 9

Location	7,359,916 – 7,360,034
Length	118
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	84.92
Mean single sequence MFE	-38.90
Consensus MFE	-29.42
Energy contribution	-29.54
Covariance contribution	0.12
Combinations/Pair	1.15
Mean z-score	-1.71
Structure conservation index	0.76
SVM decision value	0.29
SVM RNA-class probability	0.672181
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7359916 118 + 20766785
UUCUACAGUUGGGGGUCCUCCGGUUGCUGGACGUCACUUGCGAAUGCUAGUAGUCC-CUACCGGACGGGAUUCCUUCCCGAAAUCUUACUCCUCUGGUCCCGACUCCUUAUACCAGCAA
.......((((((((.((((((((....((((...(((.((....)).))).))))-..))))))(((((.....)))))...............)).)))(....).....))))).. ( -40.80)
>DroSec_CAF1 6874 118 + 1
UUCUACGGUAGGGAGUCCUCCGGUUGUUGGACGCCACUUGCGGAUGCUAGUAGUCC-CUUCCGGCCGGGAAUCCUUCCCGAAAUCGUACUCCUCCGGUCCCGACUACUUAUACUAGCAA
.....(((.(((....)))))).(((((((.(((.....)))......(((((((.-...((((.(((((.....))))).....(....)..))))....)))))))....))))))) ( -35.70)
>DroSim_CAF1 13321 118 + 1
UUCUACGGUAGGGAGUCCUCCGGUUGUUGGACGCCACUUGCGGAUGCUAGUAGUCC-CUUCCGGCCGGGAAUCCUUCCCGAAAUCGUACUCCUUCGGUCCCGACUCCUUAUACUAGCAA
..(((..((((((((((.((((((((..((((...(((.((....)).))).))))-....))))))))........(((((..........)))))....))))))))))..)))... ( -39.70)
>DroEre_CAF1 6891 107 + 1
UUCCUCGGUAGGGAAACCUCCGGUUAUUGGACGCCACUUGCGGAUGCUAGUAGUCCCCUUCCGGACGGGAAUCCUUCCCGAAAUCGUACUCCU------------CCUAGUACUAGCAA
.(((((((.(((....))))))).....)))(((.....)))..((((((((((((......))))((((.....))))..............------------.....)))))))). ( -37.20)
>DroYak_CAF1 6261 119 + 1
AUCUUCGGAAGGGAGACCUCCGGUUGCUGGACGCCACUUGCGGAUGCUAGUAGUCCCCUUCCGGCCGGGAAUCCUUCCCGAUCUCGUACUUCUCCGGUUCCGACUCCAAGUACUAGCUA
.....((((((((.(((.......((((((.(((.....)))....)))))))))))))))))(((((((.....))))).....((((((...((....)).....))))))..)).. ( -41.11)
>consensus
UUCUACGGUAGGGAGUCCUCCGGUUGUUGGACGCCACUUGCGGAUGCUAGUAGUCC_CUUCCGGCCGGGAAUCCUUCCCGAAAUCGUACUCCUCCGGUCCCGACUCCUUAUACUAGCAA
.....(((..(((((....((((.....((((...(((.((....)).))).))))....)))).(((((.....)))))........))))))))....................... (-29.42 = -29.54 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:03 2006