Locus 2249

Sequence ID	2L_DroMel_CAF1
Location	6,133,381 – 6,133,603
Length	222
Max. P	0.998879

overview

Window 6

Location	6,133,381 – 6,133,486
Length	105
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	94.85
Mean single sequence MFE	-20.39
Consensus MFE	-19.74
Energy contribution	-19.74
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.42
Structure conservation index	0.97
SVM decision value	0.22
SVM RNA-class probability	0.638630
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6133381 105 + 22407834
UAAGCCUGCAAAGGAGCGAUUAAGAGUUUCGUUACAAAAAACACUCGUCCACUCGUCUUCUUCCUGUUUGUCUCGUCUCGUCUUUCGCUCCUACUAUCUUUCUCG
...........((((((((....(((...((..(((((.......((......))...........)))))..)).))).....))))))))............. ( -22.17)
>DroSec_CAF1 2067 100 + 1
UAAGCCUGCAAAGGAGCGAUUAAGAGUUUCGUUACAAAAAACACUCGUCCACU---CUUCUUCCUGUUUGU--CGUCUCGCCCUUCGCUCCUACUAUCUUUCUCG
...........((((((((....(((...((..(((((........(......---).........)))))--)).))).....))))))))............. ( -18.13)
>DroSim_CAF1 2065 102 + 1
UAAGCCUGCAAAGGAGCGAUUAAGAGUUUCGUUACAAAAAACACUCGUCCACU---CUUCUUCCUGUUUGUCUCGUCUCGUCCUUCGCUCCUACUAUCUUUCUCG
...........((((((((....(((...((..(((((........(......---).........)))))..)).))).....))))))))............. ( -20.63)
>DroEre_CAF1 2141 102 + 1
UAAGCCUGCAAAGGAGCGAUUAAGAGUUUCGUUACAAAAAACACUCGUCGACU---CUUCAUCCUGUUUGUCUCGUCUCGCCUUUCGCUCCUACCAUCUUUCUCG
...........((((((((....(((...((..(((((........(......---).........)))))..)).))).....))))))))............. ( -20.63)
>consensus
UAAGCCUGCAAAGGAGCGAUUAAGAGUUUCGUUACAAAAAACACUCGUCCACU___CUUCUUCCUGUUUGUCUCGUCUCGCCCUUCGCUCCUACUAUCUUUCUCG
...........((((((((....(((...((..(((((............................)))))..)).))).....))))))))............. (-19.74 = -19.74 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	6,133,486 – 6,133,603
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.26
Mean single sequence MFE	-28.06
Consensus MFE	-24.48
Energy contribution	-24.52
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.28
Structure conservation index	0.87
SVM decision value	0.21
SVM RNA-class probability	0.634644
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6133486 117 + 22407834
UUACAUUUAUUGGCGUGUUUGUGCAUAAUGAAGCAAAGUCCAUUUUUGUGGUUAGCUUCGGAUGCUCUCUCAUUUCUGUU---GCUCCCAACAUGCAAAUGAAAUGGCCAUUCAUUUGCG
..........((((......(.((((..((((((.....((((....))))...)))))).)))).)...((((((..((---((.........))))..)))))))))).......... ( -29.70)
>DroSec_CAF1 2167 117 + 1
UUACAUUUAUUGGCGUGUUUGUGCAUAAUGAAGCAAAGUCCAUUUUUGUGGUUAGCUUCUGAUGUUCUCUCAUUUCUGUU---GGCCCCAACAUGCAAAUGAAAUGGUCAUUCAUUUGCG
...........((.(((...(.((((...(((((.....((((....))))...)))))..)))).)...))).))((((---(....))))).(((((((((.......))))))))). ( -30.20)
>DroSim_CAF1 2167 117 + 1
UUACAUUUAUUGGCGUGUUUGUGCAUAAUGAAGCAAAGUCCAUUUUUGUGGUUAGCUUCUGAUGUUCUCUCAUUUCUGUU---GCCCCCAACAUGCAAAUGAAAUGGCCAUUCAUUUGCG
...........((.(((...(.((((...(((((.....((((....))))...)))))..)))).)...))).))((((---(....))))).(((((((((.......))))))))). ( -28.00)
>DroEre_CAF1 2243 117 + 1
UUACAUUUAUUGGCGUGUUUGUGCAUAAUGAAGCAAAGUCCAUUUUUGUGGUUAGCUUCGGAUAUUCUCUCAUUUCUGUU---GGCCCCAACAUGCAAAUGAAAUGGCCAUUCAUUUGCG
..........((((((((....))))..((((((.....((((....))))...)))))).........(((((((((((---(....))))).).))))))....)))).......... ( -27.00)
>DroYak_CAF1 2305 120 + 1
UUACAUUUAUUGGCGUGUUUGUGCAUAAUGAAGCAAAGUCCAUUUUUGUGGUUAGCUUCGGAUGUUCUCUCAUUUCUGUUUUUACCCUUAGCAUGCAAAUGAAAUGGCCAUUCAUUUGCG
....................((((.....(((((.....((((....))))...)))))(((((......)))))...............))))(((((((((.......))))))))). ( -25.40)
>consensus
UUACAUUUAUUGGCGUGUUUGUGCAUAAUGAAGCAAAGUCCAUUUUUGUGGUUAGCUUCGGAUGUUCUCUCAUUUCUGUU___GCCCCCAACAUGCAAAUGAAAUGGCCAUUCAUUUGCG
...........((.(((...(.((((...(((((.....((((....))))...)))))..)))).)...))).))..................(((((((((.......))))))))). (-24.48 = -24.52 +   0.04)

alignment

secondary structure

dotplot

Window 8

Location	6,133,486 – 6,133,603
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.26
Mean single sequence MFE	-27.86
Consensus MFE	-24.38
Energy contribution	-25.18
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.53
Structure conservation index	0.88
SVM decision value	3.26
SVM RNA-class probability	0.998879
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6133486 117 - 22407834
CGCAAAUGAAUGGCCAUUUCAUUUGCAUGUUGGGAGC---AACAGAAAUGAGAGAGCAUCCGAAGCUAACCACAAAAAUGGACUUUGCUUCAUUAUGCACAAACACGCCAAUAAAUGUAA
.(((((((((.......))))))))).((((((....---..((....)).....((((..(((((...(((......))).....)))))...)))).........))))))....... ( -30.20)
>DroSec_CAF1 2167 117 - 1
CGCAAAUGAAUGACCAUUUCAUUUGCAUGUUGGGGCC---AACAGAAAUGAGAGAACAUCAGAAGCUAACCACAAAAAUGGACUUUGCUUCAUUAUGCACAAACACGCCAAUAAAUGUAA
.(((((((((.......))))))))).((((((.(..---..((....))...........(((((...(((......))).....)))))..............).))))))....... ( -27.70)
>DroSim_CAF1 2167 117 - 1
CGCAAAUGAAUGGCCAUUUCAUUUGCAUGUUGGGGGC---AACAGAAAUGAGAGAACAUCAGAAGCUAACCACAAAAAUGGACUUUGCUUCAUUAUGCACAAACACGCCAAUAAAUGUAA
.(((((((((.......))))))))).((((((.(..---..((....))...........(((((...(((......))).....)))))..............).))))))....... ( -28.60)
>DroEre_CAF1 2243 117 - 1
CGCAAAUGAAUGGCCAUUUCAUUUGCAUGUUGGGGCC---AACAGAAAUGAGAGAAUAUCCGAAGCUAACCACAAAAAUGGACUUUGCUUCAUUAUGCACAAACACGCCAAUAAAUGUAA
.(((((((((.......))))))))).((((((.(..---..((....))...........(((((...(((......))).....)))))..............).))))))....... ( -27.80)
>DroYak_CAF1 2305 120 - 1
CGCAAAUGAAUGGCCAUUUCAUUUGCAUGCUAAGGGUAAAAACAGAAAUGAGAGAACAUCCGAAGCUAACCACAAAAAUGGACUUUGCUUCAUUAUGCACAAACACGCCAAUAAAUGUAA
.(((((((((.......))))))))).(((...((((.....((....)).......))))(((((...(((......))).....))))).....)))..................... ( -25.00)
>consensus
CGCAAAUGAAUGGCCAUUUCAUUUGCAUGUUGGGGGC___AACAGAAAUGAGAGAACAUCCGAAGCUAACCACAAAAAUGGACUUUGCUUCAUUAUGCACAAACACGCCAAUAAAUGUAA
.(((((((((.......))))))))).((((((.(.......((....))...........(((((...(((......))).....)))))..............).))))))....... (-24.38 = -25.18 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:04 2006