Locus 4179

Sequence ID	X_DroMel_CAF1
Location	10,983,051 – 10,983,186
Length	135
Max. P	0.999931

overview

Window 1

Location	10,983,051 – 10,983,158
Length	107
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	95.08
Mean single sequence MFE	-30.62
Consensus MFE	-24.32
Energy contribution	-24.28
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-3.04
Structure conservation index	0.79
SVM decision value	2.06
SVM RNA-class probability	0.987033
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10983051 107 + 22224390
GACUUUUGUUGGUGG-GGGUGUAUUUGUUUGUGCGUUGAAGGGAAAGCGUAAUAACGCCUCCUGAUAUCGAUAUCGAUAUCAUAUCACAAAAAACAAUAAACCAAAAA
........(((((((-((((((...(((...((((((........)))))))))))))))))((((((((....))))))))..................)))))... ( -30.70)
>DroSec_CAF1 6910 107 + 1
GACUUUUGUUGGUGG-GGGUGUAUUUGUUUGUGCGUUGAAGGGAAAGCGUAAUAACGCCUCCUGAUAUCGAUAUCGAUAUCAUAUCACAAAAAACAAUAAACCCCAAA
.(((......))).(-((((.((((..((((((.......((((..((((....)))).))))(((((((....)))))))....))))))....)))).)))))... ( -33.50)
>DroSim_CAF1 6957 107 + 1
GACUUUUGUUGGUGG-GGGUGUAUUUGUUUGUGCGUUGAAGGGAAAGCGUAAUAACGCCUCCUGAUAUCGAUAUCGAUAUCAUAUCACAAAAAACAAUAAACCCUAAA
.(((......))).(-((((.((((..((((((.......((((..((((....)))).))))(((((((....)))))))....))))))....)))).)))))... ( -31.20)
>DroEre_CAF1 7603 108 + 1
GACUUUUGUUGGUGGUGGGUGCAUUUGUUUGUGCGUAGAAAGGAAAGCGUAAUAACCCCUCCUGAUAUCGAUAUCGAUAUCACAUCACAAAAAACAAUAAACCAAAAA
.....(((((.((((((.(..((......))..)......((((..(.((....)))..))))(((((((....))))))).))))))....)))))........... ( -27.10)
>DroYak_CAF1 7250 107 + 1
GACUUUUGUUGGUGGUGGGUGCAUUUGUUUGUACGUAGAAAGGAAAGCGUAAUAACGCCUCCUGAUAUCGAUAUCGAUAUCAUAUCACAAAAAACAAUAAACCAAAA-
.....(((((.((((((.(((((......)))))......((((..((((....)))).))))(((((((....))))))).))))))....)))))..........- ( -30.60)
>consensus
GACUUUUGUUGGUGG_GGGUGUAUUUGUUUGUGCGUUGAAGGGAAAGCGUAAUAACGCCUCCUGAUAUCGAUAUCGAUAUCAUAUCACAAAAAACAAUAAACCAAAAA
.(((......)))....(((....((((((....((.((.((((..((((....)))).))))(((((((....)))))))...))))...))))))...)))..... (-24.32 = -24.28 +  -0.04)

alignment

secondary structure

dotplot

Window 2

Location	10,983,051 – 10,983,158
Length	107
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	95.08
Mean single sequence MFE	-30.40
Consensus MFE	-27.62
Energy contribution	-27.42
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-4.07
Structure conservation index	0.91
SVM decision value	4.63
SVM RNA-class probability	0.999931
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10983051 107 - 22224390
UUUUUGGUUUAUUGUUUUUUGUGAUAUGAUAUCGAUAUCGAUAUCAGGAGGCGUUAUUACGCUUUCCCUUCAACGCACAAACAAAUACACCC-CCACCAACAAAAGUC
.....(((.((((((((..((((...((((((((....))))))))((((((((....)))))))).......)))).)))).)))).))).-............... ( -29.10)
>DroSec_CAF1 6910 107 - 1
UUUGGGGUUUAUUGUUUUUUGUGAUAUGAUAUCGAUAUCGAUAUCAGGAGGCGUUAUUACGCUUUCCCUUCAACGCACAAACAAAUACACCC-CCACCAACAAAAGUC
...(((((.((((((((..((((...((((((((....))))))))((((((((....)))))))).......)))).)))).)))).))))-).............. ( -35.70)
>DroSim_CAF1 6957 107 - 1
UUUAGGGUUUAUUGUUUUUUGUGAUAUGAUAUCGAUAUCGAUAUCAGGAGGCGUUAUUACGCUUUCCCUUCAACGCACAAACAAAUACACCC-CCACCAACAAAAGUC
....((((.((((((((..((((...((((((((....))))))))((((((((....)))))))).......)))).)))).)))).))))-............... ( -32.60)
>DroEre_CAF1 7603 108 - 1
UUUUUGGUUUAUUGUUUUUUGUGAUGUGAUAUCGAUAUCGAUAUCAGGAGGGGUUAUUACGCUUUCCUUUCUACGCACAAACAAAUGCACCCACCACCAACAAAAGUC
.....(((.((((....((((((.((((((((((....)))))))(((((((((....)).)))))))....)))))))))..)))).)))................. ( -27.30)
>DroYak_CAF1 7250 107 - 1
-UUUUGGUUUAUUGUUUUUUGUGAUAUGAUAUCGAUAUCGAUAUCAGGAGGCGUUAUUACGCUUUCCUUUCUACGUACAAACAAAUGCACCCACCACCAACAAAAGUC
-..(((((....(((..(((((....((((((((....))))))))((((((((....))))))))..............))))).)))......)))))........ ( -27.30)
>consensus
UUUUUGGUUUAUUGUUUUUUGUGAUAUGAUAUCGAUAUCGAUAUCAGGAGGCGUUAUUACGCUUUCCCUUCAACGCACAAACAAAUACACCC_CCACCAACAAAAGUC
.....(((.((((....((((((...((((((((....))))))))((((((((....)))))))).........))))))..)))).)))................. (-27.62 = -27.42 +  -0.20)

alignment

secondary structure

dotplot

Window 3

Location	10,983,079 – 10,983,186
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	93.36
Mean single sequence MFE	-22.86
Consensus MFE	-19.50
Energy contribution	-20.06
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-3.07
Structure conservation index	0.85
SVM decision value	3.71
SVM RNA-class probability	0.999547
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10983079 107 + 22224390
UGUGCGUUGAAGGGAAAGCGUAAUAACGCCUCCUGAUAUCGAUAUCGAUAUCAUAUCACAAAAAACAAUAAACCAAAAAAGAAACGCUAAAAACUAGUAGUUUUGUG
(((...(((..((((..((((....)))).))))(((((((....)))))))......)))...))).............(((((((((.....)))).)))))... ( -24.60)
>DroSec_CAF1 6938 107 + 1
UGUGCGUUGAAGGGAAAGCGUAAUAACGCCUCCUGAUAUCGAUAUCGAUAUCAUAUCACAAAAAACAAUAAACCCCAAAAGAAACGCUAAAAACUAGUAGUUUUGUG
...(((((...(((...((((....))))....((((((((....))))))))....................)))......)))))..(((((.....)))))... ( -24.90)
>DroSim_CAF1 6985 107 + 1
UGUGCGUUGAAGGGAAAGCGUAAUAACGCCUCCUGAUAUCGAUAUCGAUAUCAUAUCACAAAAAACAAUAAACCCUAAAAGAAACGCUAAAAACUAGUAGUUUUGUG
...(((((..((((...((((....))))....((((((((....))))))))...................))))......)))))..(((((.....)))))... ( -26.10)
>DroEre_CAF1 7632 106 + 1
UGUGCGUAGAAAGGAAAGCGUAAUAACCCCUCCUGAUAUCGAUAUCGAUAUCACAUCACAAAAAACAAUAAACCAAAAAAAAAACGCUACAAACUAUUAU-UUUGUC
(((((((....((((..(.((....)))..))))(((((((....)))))))...............................)))).))).........-...... ( -18.80)
>DroYak_CAF1 7279 105 + 1
UGUACGUAGAAAGGAAAGCGUAAUAACGCCUCCUGAUAUCGAUAUCGAUAUCAUAUCACAAAAAACAAUAAACCAAAA-AGAAACGCUAAAAACUAUUAG-UUUGUC
.....((.((.((((..((((....)))).))))(((((((....)))))))...))))...................-.((...(((((......))))-)...)) ( -19.90)
>consensus
UGUGCGUUGAAGGGAAAGCGUAAUAACGCCUCCUGAUAUCGAUAUCGAUAUCAUAUCACAAAAAACAAUAAACCAAAAAAGAAACGCUAAAAACUAGUAGUUUUGUG
...(((((...((((..((((....)))).))))(((((((....)))))))..............................))))).................... (-19.50 = -20.06 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	10,983,079 – 10,983,186
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	93.36
Mean single sequence MFE	-26.25
Consensus MFE	-23.20
Energy contribution	-23.48
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-2.60
Structure conservation index	0.88
SVM decision value	3.76
SVM RNA-class probability	0.999589
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10983079 107 - 22224390
CACAAAACUACUAGUUUUUAGCGUUUCUUUUUUGGUUUAUUGUUUUUUGUGAUAUGAUAUCGAUAUCGAUAUCAGGAGGCGUUAUUACGCUUUCCCUUCAACGCACA
...(((((.....)))))..(((((............(((..(.....)..)))((((((((....))))))))((((((((....)))))))).....)))))... ( -26.60)
>DroSec_CAF1 6938 107 - 1
CACAAAACUACUAGUUUUUAGCGUUUCUUUUGGGGUUUAUUGUUUUUUGUGAUAUGAUAUCGAUAUCGAUAUCAGGAGGCGUUAUUACGCUUUCCCUUCAACGCACA
...(((((.....)))))..(((((......(((...(((..(.....)..)))((((((((....))))))))((((((((....)))))))))))..)))))... ( -28.70)
>DroSim_CAF1 6985 107 - 1
CACAAAACUACUAGUUUUUAGCGUUUCUUUUAGGGUUUAUUGUUUUUUGUGAUAUGAUAUCGAUAUCGAUAUCAGGAGGCGUUAUUACGCUUUCCCUUCAACGCACA
...(((((.....)))))..(((((......(((...(((..(.....)..)))((((((((....))))))))((((((((....)))))))))))..)))))... ( -28.70)
>DroEre_CAF1 7632 106 - 1
GACAAA-AUAAUAGUUUGUAGCGUUUUUUUUUUGGUUUAUUGUUUUUUGUGAUGUGAUAUCGAUAUCGAUAUCAGGAGGGGUUAUUACGCUUUCCUUUCUACGCACA
...(((-(((((((......................)))))))))).((((.((((((((((....)))))))(((((((((....)).)))))))....))))))) ( -23.55)
>DroYak_CAF1 7279 105 - 1
GACAAA-CUAAUAGUUUUUAGCGUUUCU-UUUUGGUUUAUUGUUUUUUGUGAUAUGAUAUCGAUAUCGAUAUCAGGAGGCGUUAUUACGCUUUCCUUUCUACGUACA
.(((((-..((((((....(.((.....-...)).)..)))))).)))))....((((((((....))))))))((((((((....))))))))............. ( -23.70)
>consensus
CACAAAACUACUAGUUUUUAGCGUUUCUUUUUUGGUUUAUUGUUUUUUGUGAUAUGAUAUCGAUAUCGAUAUCAGGAGGCGUUAUUACGCUUUCCCUUCAACGCACA
....................(((((............(((..(.....)..)))((((((((....))))))))((((((((....)))))))).....)))))... (-23.20 = -23.48 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:22 2006