Locus 446

Sequence ID	3L_DroMel_CAF1
Location	1,297,141 – 1,297,277
Length	136
Max. P	0.989997

overview

Window 0

Location	1,297,141 – 1,297,252
Length	111
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	87.65
Mean single sequence MFE	-36.81
Consensus MFE	-28.67
Energy contribution	-29.27
Covariance contribution	0.60
Combinations/Pair	1.19
Mean z-score	-2.46
Structure conservation index	0.78
SVM decision value	1.69
SVM RNA-class probability	0.972447
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1297141 111 + 23771897
UCAAAGCGGAUCUUAAAAGUCCGCAAGCGAUGCAGCCCUAGCUUAAGCCCAUUGUCAGGGCUGCCAACGUGGGCAAUGUGGCCCUAUCCCAACCAGUUGGCAUCGCCACCA
.....((((((.......))))))..(((((..((((((..(...........)..))))))((((((..((((......))))...........)))))))))))..... ( -42.02)
>DroSec_CAF1 926 111 + 1
UAGGAGCGGAUCUUAAAAAUCCGAAAGCGAUGCAGCCCUAGCUUAAGUUAAUUUCCAGAGCUGCCAACGUGGGCAAAGUGGCCCUAUGCCAACCAGUUGGCAUCGCCACCA
..((..(((((.......)))))...(((((((.....((((((.............)))))).((((.(((......((((.....)))).))))))))))))))..)). ( -34.92)
>DroSim_CAF1 4227 111 + 1
UAGAAGCGGAUCUUAAAAAUCCGCAAGCGAUGCAGCCCUAGCUUAAGUUCAUUUCCAGAGCUGCCAACGUGGGCAAAGUGGCCCUAUGCCAACCAGUUGGCAUCGCCACCA
.....((((((.......))))))..(((((((.((((.......(((((.......)))))........))))....((((.....))))........)))))))..... ( -38.96)
>DroEre_CAF1 902 110 + 1
UAGAAGUGGAGCUUUAAAAUUCGCAAGCGAUGCAGCCCUAGCUUGAAUCCAUUUACAGCGCUGCCAACGUGGGCAAAGUGGCUCU-UGCCAAUCAGUUGGCAUCGCCACCA
...(((((((.............(((((............)))))..)))))))...(((.(((((((...(((((........)-)))).....))))))).)))..... ( -34.06)
>DroYak_CAF1 4140 110 + 1
UAAGAGCAAAUCUUAAAAAUUCGCAAGCUAUGCAGCCCUAGCUUUAAUCCAUUUGCAGAGCUGCCAACGUGGACAAAGUGGCGUU-UGCCAAACAGUUGGCAUCGCCACCA
(((((.....)))))....(((((.......(((((.((.((............)))).)))))....)))))....((((((..-((((((....)))))).)))))).. ( -34.10)
>consensus
UAGAAGCGGAUCUUAAAAAUCCGCAAGCGAUGCAGCCCUAGCUUAAGUCCAUUUCCAGAGCUGCCAACGUGGGCAAAGUGGCCCUAUGCCAACCAGUUGGCAUCGCCACCA
.....((((((.......))))))..(((((((.((((((((((.............)))))).......))))....((((.....))))........)))))))..... (-28.67 = -29.27 +   0.60)

alignment

secondary structure

dotplot

Window 1

Location	1,297,141 – 1,297,252
Length	111
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	87.65
Mean single sequence MFE	-42.23
Consensus MFE	-33.44
Energy contribution	-34.72
Covariance contribution	1.28
Combinations/Pair	1.10
Mean z-score	-2.69
Structure conservation index	0.79
SVM decision value	2.19
SVM RNA-class probability	0.989997
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1297141 111 - 23771897
UGGUGGCGAUGCCAACUGGUUGGGAUAGGGCCACAUUGCCCACGUUGGCAGCCCUGACAAUGGGCUUAAGCUAGGGCUGCAUCGCUUGCGGACUUUUAAGAUCCGCUUUGA
....((((((.((((....))))....((((......))))......((((((((.......(((....))))))))))))))))).(((((((....)).)))))..... ( -43.01)
>DroSec_CAF1 926 111 - 1
UGGUGGCGAUGCCAACUGGUUGGCAUAGGGCCACUUUGCCCACGUUGGCAGCUCUGGAAAUUAACUUAAGCUAGGGCUGCAUCGCUUUCGGAUUUUUAAGAUCCGCUCCUA
.((.(((((((((((....)))))...((((......))))......((((((((((...(((...))).)))))))))))))))...((((((.....))))))).)).. ( -44.60)
>DroSim_CAF1 4227 111 - 1
UGGUGGCGAUGCCAACUGGUUGGCAUAGGGCCACUUUGCCCACGUUGGCAGCUCUGGAAAUGAACUUAAGCUAGGGCUGCAUCGCUUGCGGAUUUUUAAGAUCCGCUUCUA
....(((((((((((....)))))...((((......))))......((((((((((.............)))))))))))))))).(((((((.....)))))))..... ( -47.42)
>DroEre_CAF1 902 110 - 1
UGGUGGCGAUGCCAACUGAUUGGCA-AGAGCCACUUUGCCCACGUUGGCAGCGCUGUAAAUGGAUUCAAGCUAGGGCUGCAUCGCUUGCGAAUUUUAAAGCUCCACUUCUA
.(((((.(.(((((((((...((((-((......)))))))).))))))).)(((......((((((.(((....)))(((.....)))))))))...))).))))).... ( -34.90)
>DroYak_CAF1 4140 110 - 1
UGGUGGCGAUGCCAACUGUUUGGCA-AACGCCACUUUGUCCACGUUGGCAGCUCUGCAAAUGGAUUAAAGCUAGGGCUGCAUAGCUUGCGAAUUUUUAAGAUUUGCUCUUA
.(((((((.((((((....))))))-..)))))))........((((((((((((((............)).)))))))).))))..(((((((.....)))))))..... ( -41.20)
>consensus
UGGUGGCGAUGCCAACUGGUUGGCAUAGGGCCACUUUGCCCACGUUGGCAGCUCUGGAAAUGGACUUAAGCUAGGGCUGCAUCGCUUGCGGAUUUUUAAGAUCCGCUUCUA
..(((((.(((((((....)))))))...))))).........((..(((((((((...............)))))))))...))..(((((((.....)))))))..... (-33.44 = -34.72 +   1.28)

alignment

secondary structure

dotplot

Window 2

Location	1,297,181 – 1,297,277
Length	96
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	90.93
Mean single sequence MFE	-31.05
Consensus MFE	-25.10
Energy contribution	-25.98
Covariance contribution	0.88
Combinations/Pair	1.04
Mean z-score	-2.06
Structure conservation index	0.81
SVM decision value	1.49
SVM RNA-class probability	0.958338
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1297181 96 + 23771897
GCUUAAGCCCAUUGUCAGGGCUGCCAACGUGGGCAAUGUGGCCCUAUCCCAACCAGUUGGCAUCGCCACCAUUAUUUAUUGGUUUUUUGUUGCUGG
((...(((((.......)))))((((((..((((......))))...........))))))...)).((((........))))............. ( -27.92)
>DroSec_CAF1 966 96 + 1
GCUUAAGUUAAUUUCCAGAGCUGCCAACGUGGGCAAAGUGGCCCUAUGCCAACCAGUUGGCAUCGCCACCAUUAUUUGUUGGUUUUUUGUUGCUGG
..............(((((((.(((((((........(((((...(((((((....))))))).))))).......))))))).....))).)))) ( -31.36)
>DroSim_CAF1 4267 96 + 1
GCUUAAGUUCAUUUCCAGAGCUGCCAACGUGGGCAAAGUGGCCCUAUGCCAACCAGUUGGCAUCGCCACCAUUAUUUGUUGGUUUUUUGUUGCUGG
..............(((((((.(((((((........(((((...(((((((....))))))).))))).......))))))).....))).)))) ( -31.36)
>DroEre_CAF1 942 95 + 1
GCUUGAAUCCAUUUACAGCGCUGCCAACGUGGGCAAAGUGGCUCU-UGCCAAUCAGUUGGCAUCGCCACCAUUAUUUGUUGGUUUUUUGUUGCUGG
...............((((((.(((((((........(((((...-((((((....))))))..))))).......))))))).....).))))). ( -30.66)
>DroYak_CAF1 4180 95 + 1
GCUUUAAUCCAUUUGCAGAGCUGCCAACGUGGACAAAGUGGCGUU-UGCCAAACAGUUGGCAUCGCCACCAUUAUUUGUUGGUUUUUUGUUGCUGG
........(((...((((((..(((((((........((((((..-((((((....)))))).)))))).......))))))).))))))...))) ( -33.96)
>consensus
GCUUAAGUCCAUUUCCAGAGCUGCCAACGUGGGCAAAGUGGCCCUAUGCCAACCAGUUGGCAUCGCCACCAUUAUUUGUUGGUUUUUUGUUGCUGG
...............((((((.(((((((........(((((...(((((((....))))))).))))).......))))))).....))).))). (-25.10 = -25.98 +   0.88)

alignment

secondary structure

dotplot

Window 3

Location	1,297,181 – 1,297,277
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	90.93
Mean single sequence MFE	-29.20
Consensus MFE	-22.26
Energy contribution	-22.70
Covariance contribution	0.44
Combinations/Pair	1.06
Mean z-score	-2.55
Structure conservation index	0.76
SVM decision value	1.48
SVM RNA-class probability	0.957518
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1297181 96 - 23771897
CCAGCAACAAAAAACCAAUAAAUAAUGGUGGCGAUGCCAACUGGUUGGGAUAGGGCCACAUUGCCCACGUUGGCAGCCCUGACAAUGGGCUUAAGC
(((((.........(((((......((((......))))....)))))....((((......))))..))))).(((((.......)))))..... ( -30.60)
>DroSec_CAF1 966 96 - 1
CCAGCAACAAAAAACCAACAAAUAAUGGUGGCGAUGCCAACUGGUUGGCAUAGGGCCACUUUGCCCACGUUGGCAGCUCUGGAAAUUAACUUAAGC
((((......................((((((.(((((((....)))))))...))))))(((((......)))))..)))).............. ( -28.90)
>DroSim_CAF1 4267 96 - 1
CCAGCAACAAAAAACCAACAAAUAAUGGUGGCGAUGCCAACUGGUUGGCAUAGGGCCACUUUGCCCACGUUGGCAGCUCUGGAAAUGAACUUAAGC
((((......................((((((.(((((((....)))))))...))))))(((((......)))))..)))).............. ( -28.90)
>DroEre_CAF1 942 95 - 1
CCAGCAACAAAAAACCAACAAAUAAUGGUGGCGAUGCCAACUGAUUGGCA-AGAGCCACUUUGCCCACGUUGGCAGCGCUGUAAAUGGAUUCAAGC
(((...((.....((((........))))((((.(((((((((...((((-((......)))))))).))))))).))))))...)))........ ( -30.10)
>DroYak_CAF1 4180 95 - 1
CCAGCAACAAAAAACCAACAAAUAAUGGUGGCGAUGCCAACUGUUUGGCA-AACGCCACUUUGUCCACGUUGGCAGCUCUGCAAAUGGAUUAAAGC
((((((........(((((.......(((((((.((((((....))))))-..)))))))........)))))......)))...)))........ ( -27.50)
>consensus
CCAGCAACAAAAAACCAACAAAUAAUGGUGGCGAUGCCAACUGGUUGGCAUAGGGCCACUUUGCCCACGUUGGCAGCUCUGGAAAUGGACUUAAGC
...((......................(((((.(((((((....)))))))...)))))..((((......))))))................... (-22.26 = -22.70 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:03 2006