Locus 6025

Sequence ID	3L_DroMel_CAF1
Location	16,067,618 – 16,067,853
Length	235
Max. P	0.987044

overview

Window 3

Location	16,067,618 – 16,067,733
Length	115
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	84.51
Mean single sequence MFE	-27.13
Consensus MFE	-19.78
Energy contribution	-19.90
Covariance contribution	0.12
Combinations/Pair	1.14
Mean z-score	-2.18
Structure conservation index	0.73
SVM decision value	0.53
SVM RNA-class probability	0.771770
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16067618 115 + 23771897
AAUGAAAAACCUAUUCA-----AUAUUAAUAUCCAAUAGGGCCCUCUUCGUUCACGGAUUUACCGUGGAUGAGAAAGGAUACAAGAUGUCGAAAUCUUUGGGAAAUGUAAUUUCCCCAAA
.........((((((..-----(((....)))..))))))..(((.(((((((((((.....)))))))))))..)))....(((((......))))).(((((((...))))))).... ( -31.30)
>DroSim_CAF1 2659 115 + 1
AAUAAGAAACCUCUUCA-----AUAUUAAUAUCCAAUAGAGCCCUCUUUGUUCACGGAUUUACCGUGGAUGAAAAAGGAUACAAGAUGUCAAAAUCGUUGGGAAACGUAAUUUCUCCAAA
....(((((......((-----((.....(((((....((....))((..(((((((.....)))))))..))...)))))...(((......)))))))(....)....)))))..... ( -23.70)
>DroYak_CAF1 2720 117 + 1
---AAAAAACCUUUUUAUCCCCAUCUUUACCUCCAAUAGAGCCCUCUUUGUUCACGGAUUCACAGUGGAUGAGAAGGGAUACAAGAUGUCGAAAUCGUUGGGUAACGUAAUUUCCCCAAA
---..............((..((((((...(((.....)))((((..(..(((((.........)))))..)..))))....))))))..)).....(((((.((......)).))))). ( -26.40)
>consensus
AAUAAAAAACCUAUUCA_____AUAUUAAUAUCCAAUAGAGCCCUCUUUGUUCACGGAUUUACCGUGGAUGAGAAAGGAUACAAGAUGUCGAAAUCGUUGGGAAACGUAAUUUCCCCAAA
.............................(((((....((....))(((((((((((.....)))))))))))...)))))...(((......))).(((((.((......)).))))). (-19.78 = -19.90 +   0.12)

alignment

secondary structure

dotplot

Window 4

Location	16,067,693 – 16,067,813
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	91.67
Mean single sequence MFE	-36.70
Consensus MFE	-31.79
Energy contribution	-32.57
Covariance contribution	0.78
Combinations/Pair	1.03
Mean z-score	-2.30
Structure conservation index	0.87
SVM decision value	0.70
SVM RNA-class probability	0.827049
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16067693 120 - 23771897
CUGUAAUGGACAUGUGCUGCGUUCCAUGGGAGGCAACCCACCAACGCAGUGCAUCCGUACCAUAUUUCUUGGUUAUCUGCUUUGGGGAAAUUACAUUUCCCAAAGAUUUCGACAUCUUGU
.(((.(((((..((..(((((((...((((......))))..)))))))..)))))))((((.......))))......((((((((((......))))))))))......)))...... ( -41.20)
>DroSim_CAF1 2734 120 - 1
CUGUAAUGGACAUGUGCUGCGUUCCAUGGGAGGCAACCCACCAACGCAGUGCAUCUGUACCAUAUUUCUUGGUUAUCUGCUUUGGAGAAAUUACGUUUCCCAACGAUUUUGACAUCUUGU
.....(((((((((..(((((((...((((......))))..)))))))..))..))).))))........((((....(.((((.(((((...))))))))).)....))))....... ( -36.00)
>DroYak_CAF1 2797 120 - 1
CCGUUAUGGACAUGUGUUGCGUUCCAUGGGAAGCCACCCACCAACGCAGUGCAUCCGUCCCAUACUUUUUGGUAAUCUGCUUUGGGGAAAUUACGUUACCCAACGAUUUCGACAUCUUGU
..((...(((((((..(((((((...((((......))))..)))))))..)))..))))...))...((((.((((....(((((............))))).))))))))........ ( -32.90)
>consensus
CUGUAAUGGACAUGUGCUGCGUUCCAUGGGAGGCAACCCACCAACGCAGUGCAUCCGUACCAUAUUUCUUGGUUAUCUGCUUUGGGGAAAUUACGUUUCCCAACGAUUUCGACAUCUUGU
.....(((((((((..(((((((...((((......))))..)))))))..)))..)).))))........(((.....(.((((((((......)))))))).).....)))....... (-31.79 = -32.57 +   0.78)

alignment

secondary structure

dotplot

Window 5

Location	16,067,733 – 16,067,853
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	92.22
Mean single sequence MFE	-41.03
Consensus MFE	-38.44
Energy contribution	-38.67
Covariance contribution	0.23
Combinations/Pair	1.05
Mean z-score	-3.06
Structure conservation index	0.94
SVM decision value	2.06
SVM RNA-class probability	0.987044
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16067733 120 - 23771897
CAUAGAUUUUCUGCCGCUUGCUGCAGUAGCUUAUCGCUCACUGUAAUGGACAUGUGCUGCGUUCCAUGGGAGGCAACCCACCAACGCAGUGCAUCCGUACCAUAUUUCUUGGUUAUCUGC
..(((((.....(((......(((((((((.....))).))))))(((((((((..(((((((...((((......))))..)))))))..)))..)).)))).......))).))))). ( -41.30)
>DroSim_CAF1 2774 120 - 1
CUCAGAUUUUCUGCCGCUUGCUGCAGUAGCUUAUCGCUCACUGUAAUGGACAUGUGCUGCGUUCCAUGGGAGGCAACCCACCAACGCAGUGCAUCUGUACCAUAUUUCUUGGUUAUCUGC
..(((((.....(((......(((((((((.....))).))))))(((((((((..(((((((...((((......))))..)))))))..))..))).)))).......))).))))). ( -43.10)
>DroYak_CAF1 2837 120 - 1
CUCAGAUUUUCUGCCGCCUGCUGCAGUAGCUUAUCGCUAACCGUUAUGGACAUGUGUUGCGUUCCAUGGGAAGCCACCCACCAACGCAGUGCAUCCGUCCCAUACUUUUUGGUAAUCUGC
..((((((..((((.(....).))))((((.....))))((((.((((((((((..(((((((...((((......))))..)))))))..)))..)).))))).....)))))))))). ( -38.70)
>consensus
CUCAGAUUUUCUGCCGCUUGCUGCAGUAGCUUAUCGCUCACUGUAAUGGACAUGUGCUGCGUUCCAUGGGAGGCAACCCACCAACGCAGUGCAUCCGUACCAUAUUUCUUGGUUAUCUGC
..(((((.....(((......(((((((((.....))).))))))(((((((((..(((((((...((((......))))..)))))))..)))..)).)))).......))).))))). (-38.44 = -38.67 +   0.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:14 2006