Locus 6258

Sequence ID	3L_DroMel_CAF1
Location	16,670,708 – 16,670,828
Length	120
Max. P	0.999346

overview

Window 1

Location	16,670,708 – 16,670,828
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.08
Mean single sequence MFE	-40.72
Consensus MFE	-34.22
Energy contribution	-34.78
Covariance contribution	0.56
Combinations/Pair	1.10
Mean z-score	-3.07
Structure conservation index	0.84
SVM decision value	3.53
SVM RNA-class probability	0.999346
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16670708 120 + 23771897
UGCGGCGUAAGCCCCUCAGUGAUUACAUGAUGCUGGAGGAACAGCCAUCUACCUCCAGUCGUCCAACCACAUCCUCUUCCUAUUUAUCGGACCAGGAUCGUCCGAUGAGUUAUGCCGCUG
.(((((((((........(((.......(((((((((((............))))))).))))....)))............((((((((((.......))))))))))))))))))).. ( -43.30)
>DroSec_CAF1 38324 120 + 1
UGCGGCGUAAGCCACUCAGUGAUUACAUGAUGCUGGAGGAACAUCCAUCUACCUCCAGUCGUCCAACCACAUCCUCUUCCUAUUUAUCGGACCAGGAUCCUCCGAUGAGUUAUGCCGCUG
.((((((((....((((((((.......(((((((((((............))))))).))))....)))(((((..(((........)))..))))).......))))))))))))).. ( -42.40)
>DroSim_CAF1 38402 120 + 1
UGCGGCGUAAGCCACUCAGUGAUUACAUGAUGCUGGAGGAACAUCCAUCUACCUCCAGUCGUCCAACCACAUCCUCUUCCUAUUUAUCGGACCAGGAUCCUCCGAUGAGUUAUGCCGCUG
.((((((((....((((((((.......(((((((((((............))))))).))))....)))(((((..(((........)))..))))).......))))))))))))).. ( -42.40)
>DroEre_CAF1 38430 120 + 1
UGCGGCGUAAGCCACUAAGCGAUUACAUGAUGCUGGAGGAGCAACCAUUUGCAUCCAGUCGUCCAACCACAUCCUCCUCCCAUCUAUCGGACCAGGAUCCUCCGAUGAGUUACGCAGCUG
.(((((....))).....(((...((..((((..((((((((((....)))).....((.(.....).)).))))))...))))(((((((.........))))))).))..))).)).. ( -37.80)
>DroYak_CAF1 39617 120 + 1
UGCGGCAUAAGCCCCUAAGCGACUACAUGAUGCUGGAGGAGCAACCUUCUGCAGCCAGUCGUCCAACCACAUCCUCUUCCUAUUUAUCGGACCAAGAUCCUCCGAUGAGUUAUGCUGCUG
.(((((((((........((((((.......((((.(((((....))))).)))).))))))....................(((((((((.........)))))))))))))))))).. ( -37.70)
>consensus
UGCGGCGUAAGCCACUCAGUGAUUACAUGAUGCUGGAGGAACAACCAUCUACCUCCAGUCGUCCAACCACAUCCUCUUCCUAUUUAUCGGACCAGGAUCCUCCGAUGAGUUAUGCCGCUG
.(((((((((..................(((((((((((............))))))).))))...................(((((((((.........)))))))))))))))))).. (-34.22 = -34.78 +   0.56)

alignment

secondary structure

dotplot

Window 2

Location	16,670,708 – 16,670,828
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.08
Mean single sequence MFE	-43.96
Consensus MFE	-34.92
Energy contribution	-35.36
Covariance contribution	0.44
Combinations/Pair	1.09
Mean z-score	-2.00
Structure conservation index	0.79
SVM decision value	1.15
SVM RNA-class probability	0.923238
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16670708 120 - 23771897
CAGCGGCAUAACUCAUCGGACGAUCCUGGUCCGAUAAAUAGGAAGAGGAUGUGGUUGGACGACUGGAGGUAGAUGGCUGUUCCUCCAGCAUCAUGUAAUCACUGAGGGGCUUACGCCGCA
..(((((.((((((.((((...(((((..(((........)))..))))).((((((.(.((((((((((((....)))..)))))))..)).).)))))))))).))).))).))))). ( -46.50)
>DroSec_CAF1 38324 120 - 1
CAGCGGCAUAACUCAUCGGAGGAUCCUGGUCCGAUAAAUAGGAAGAGGAUGUGGUUGGACGACUGGAGGUAGAUGGAUGUUCCUCCAGCAUCAUGUAAUCACUGAGUGGCUUACGCCGCA
..(((((...(((((.......(((((..(((........)))..)))))(((((((.(.(((((((((............)))))))..)).).))))))))))))(.....)))))). ( -44.90)
>DroSim_CAF1 38402 120 - 1
CAGCGGCAUAACUCAUCGGAGGAUCCUGGUCCGAUAAAUAGGAAGAGGAUGUGGUUGGACGACUGGAGGUAGAUGGAUGUUCCUCCAGCAUCAUGUAAUCACUGAGUGGCUUACGCCGCA
..(((((...(((((.......(((((..(((........)))..)))))(((((((.(.(((((((((............)))))))..)).).))))))))))))(.....)))))). ( -44.90)
>DroEre_CAF1 38430 120 - 1
CAGCUGCGUAACUCAUCGGAGGAUCCUGGUCCGAUAGAUGGGAGGAGGAUGUGGUUGGACGACUGGAUGCAAAUGGUUGCUCCUCCAGCAUCAUGUAAUCGCUUAGUGGCUUACGCCGCA
..((.((((((((((((...((((....))))....))))))..((..(((((((((((.....(((.((((....)))))))))))))..)))))..))(((....))))))))).)). ( -42.80)
>DroYak_CAF1 39617 120 - 1
CAGCAGCAUAACUCAUCGGAGGAUCUUGGUCCGAUAAAUAGGAAGAGGAUGUGGUUGGACGACUGGCUGCAGAAGGUUGCUCCUCCAGCAUCAUGUAGUCGCUUAGGGGCUUAUGCCGCA
..((.(((((((((...((((((((((..(((........)))..))))((..((..(....)..))..)).........))))))(((..(.....)..)))...))).)))))).)). ( -40.70)
>consensus
CAGCGGCAUAACUCAUCGGAGGAUCCUGGUCCGAUAAAUAGGAAGAGGAUGUGGUUGGACGACUGGAGGUAGAUGGAUGUUCCUCCAGCAUCAUGUAAUCACUGAGUGGCUUACGCCGCA
..(((((.(((..(........(((((..(((........)))..)))))(((((((.(.(((((((((............)))))))..)).).))))))).....)..))).))))). (-34.92 = -35.36 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:04 2006