Locus 2418

Sequence ID	3R_DroMel_CAF1
Location	6,761,664 – 6,761,844
Length	180
Max. P	0.999206

overview

Window 2

Location	6,761,664 – 6,761,784
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.25
Mean single sequence MFE	-34.48
Consensus MFE	-30.72
Energy contribution	-31.12
Covariance contribution	0.40
Combinations/Pair	1.07
Mean z-score	-1.96
Structure conservation index	0.89
SVM decision value	2.23
SVM RNA-class probability	0.990725
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6761664 120 + 27905053
CAUCCCUGCACGGCUGCUGCCAACAUCAUAUCCAAUUAACAUCAUUGGCUGGCCGCAGUGGACAACUGUGGCGGUGAGAGCAUUUGGCUGGCCAUAAUUAAAACCAACUGCAAUGAAAAA
..((..((((.(((....)))........................((((..((((((((.....)))))....((....))....)))..))))..............))))..)).... ( -33.50)
>DroSec_CAF1 25877 120 + 1
CAUCCCAGCACGACUGCUGCCAACAUCAUAUCCAAUUAACAUCAUUGGCUGGCCGCAGUGGACAACUGUGGCGGUGAGAGCAUUUGGCUGGCCAUAAUUAAAACCAACUACAAUGAAAAA
....(((((.(((.(((((((..........(((((.......)))))...((((((((.....)))))))))))...)))).))))))))............................. ( -35.30)
>DroSim_CAF1 30262 120 + 1
CAUCCCAGCACGACUGCUGCCAACAUCAUAUCCAAUUAACAUCAUUGGCUGGCCGCAGUGGACAACUGUGGCGGUGAGAGCAUUUGGCUGGCCAUAAUUAAAACCAACUGCAAUGAAAAA
....(((((.(((.(((((((..........(((((.......)))))...((((((((.....)))))))))))...)))).))))))))............................. ( -35.30)
>DroEre_CAF1 10346 120 + 1
AGUCCCAGCAUGGCGGAUGCCAACAUCAUAUCCAAUUAACAUCAUUGGCUGGCCGCAGUGGACAACUGUGGCGGUGAGAGCAUUUGGCUGGCCAUAAUUAAAACCAACUGCAAUGGAAAA
....(((((....(((((((...((((....(((((.......)))))...((((((((.....))))))))))))...))))))))))))............(((.......))).... ( -36.20)
>DroYak_CAF1 22507 119 + 1
CAUCCCAGCACGACUGCUGCCAACAUCAUAUCCAAUUAACAUCAUUGGCUGGCCGCAGUGGACAACUAUGGCGGUGAGAGCAUUUGGCUGGCCAUAAUUAAAACCAACUGCAAUG-AAAA
....(((((.(((.((((.............(((((.......)))))((.(((((.((((....)))).))))).)))))).))))))))........................-.... ( -32.10)
>consensus
CAUCCCAGCACGACUGCUGCCAACAUCAUAUCCAAUUAACAUCAUUGGCUGGCCGCAGUGGACAACUGUGGCGGUGAGAGCAUUUGGCUGGCCAUAAUUAAAACCAACUGCAAUGAAAAA
....(((((.(((.(((((((..........(((((.......)))))...((((((((.....)))))))))))...)))).))))))))............................. (-30.72 = -31.12 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	6,761,704 – 6,761,818
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.76
Mean single sequence MFE	-38.44
Consensus MFE	-33.74
Energy contribution	-33.74
Covariance contribution	-0.00
Combinations/Pair	1.06
Mean z-score	-2.55
Structure conservation index	0.88
SVM decision value	3.43
SVM RNA-class probability	0.999206
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6761704 114 + 27905053
AUCAUUGGCUGGCCGCAGUGGACAACUGUGGCGGUGAGAGCAUUUGGCUGGCCAUAAUUAAAACCAACUGCAAUGAAAAAAGGUGAGC-----UGGCUGGCCA-AACCAGAGUGCAGAUA
(((.((.((((.(((((((.....))))))))))).)).(((((((((..((((........(((................)))....-----))))..))))-)......)))).))). ( -38.69)
>DroSec_CAF1 25917 114 + 1
AUCAUUGGCUGGCCGCAGUGGACAACUGUGGCGGUGAGAGCAUUUGGCUGGCCAUAAUUAAAACCAACUACAAUGAAAAAAGGAGAGC-----CGGCUGGCCA-AACCAGAGUGCAGAUA
(((.((.((((.(((((((.....))))))))))).)).(((((((((..(((..............(......)......((....)-----))))..))))-)......)))).))). ( -38.10)
>DroSim_CAF1 30302 114 + 1
AUCAUUGGCUGGCCGCAGUGGACAACUGUGGCGGUGAGAGCAUUUGGCUGGCCAUAAUUAAAACCAACUGCAAUGAAAAAAGGUGAGC-----CGGCUGGCCA-AACCAGAGUGCAGAUA
(((.((.((((.(((((((.....))))))))))).)).(((((((((..(((..............(......)......((....)-----))))..))))-)......)))).))). ( -39.00)
>DroEre_CAF1 10386 119 + 1
AUCAUUGGCUGGCCGCAGUGGACAACUGUGGCGGUGAGAGCAUUUGGCUGGCCAUAAUUAAAACCAACUGCAAUGGAAAAAAGUGAGUGUUCACCGCUGGCCA-AACCAGAGUGCAGAUA
(((.((.((((.(((((((.....))))))))))).)).((((((((.(((((..........(((.......))).....((((.((....)))))))))))-..))))).))).))). ( -40.90)
>DroYak_CAF1 22547 114 + 1
AUCAUUGGCUGGCCGCAGUGGACAACUAUGGCGGUGAGAGCAUUUGGCUGGCCAUAAUUAAAACCAACUGCAAUG-AAAAAAGUGAGC-----CGGCUGGCCAAAACCAGAGUGCAGAUA
.....((((..(((((.((((....)))).)).((....))....)))..)))).............(((((...-.......((.((-----(....))))).........)))))... ( -35.51)
>consensus
AUCAUUGGCUGGCCGCAGUGGACAACUGUGGCGGUGAGAGCAUUUGGCUGGCCAUAAUUAAAACCAACUGCAAUGAAAAAAGGUGAGC_____CGGCUGGCCA_AACCAGAGUGCAGAUA
(((.((.((((.(((((((.....))))))))))).)).((((((((.(((((.............(((............))).(((.......))))))))...))))).))).))). (-33.74 = -33.74 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	6,761,704 – 6,761,818
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.76
Mean single sequence MFE	-33.48
Consensus MFE	-30.70
Energy contribution	-30.74
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-2.08
Structure conservation index	0.92
SVM decision value	3.14
SVM RNA-class probability	0.998544
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6761704 114 - 27905053
UAUCUGCACUCUGGUU-UGGCCAGCCA-----GCUCACCUUUUUUCAUUGCAGUUGGUUUUAAUUAUGGCCAGCCAAAUGCUCUCACCGCCACAGUUGUCCACUGCGGCCAGCCAAUGAU
.....(((...(((((-.(((((((((-----(((((...........)).)))))))........))))))))))..))).......(((.((((.....)))).)))........... ( -32.70)
>DroSec_CAF1 25917 114 - 1
UAUCUGCACUCUGGUU-UGGCCAGCCG-----GCUCUCCUUUUUUCAUUGUAGUUGGUUUUAAUUAUGGCCAGCCAAAUGCUCUCACCGCCACAGUUGUCCACUGCGGCCAGCCAAUGAU
.....(((...(((((-.(((((((((-----((((.............).)))))))........))))))))))..))).......(((.((((.....)))).)))........... ( -31.42)
>DroSim_CAF1 30302 114 - 1
UAUCUGCACUCUGGUU-UGGCCAGCCG-----GCUCACCUUUUUUCAUUGCAGUUGGUUUUAAUUAUGGCCAGCCAAAUGCUCUCACCGCCACAGUUGUCCACUGCGGCCAGCCAAUGAU
........(..(((((-.((((....(-----(....))..........(((((.((...(((((.((((.(((.....)))......)))).))))).))))))))))))))))..).. ( -32.50)
>DroEre_CAF1 10386 119 - 1
UAUCUGCACUCUGGUU-UGGCCAGCGGUGAACACUCACUUUUUUCCAUUGCAGUUGGUUUUAAUUAUGGCCAGCCAAAUGCUCUCACCGCCACAGUUGUCCACUGCGGCCAGCCAAUGAU
........(..(((((-.((((...(((((....)))))..........(((((.((...(((((.((((.(((.....)))......)))).))))).))))))))))))))))..).. ( -35.80)
>DroYak_CAF1 22547 114 - 1
UAUCUGCACUCUGGUUUUGGCCAGCCG-----GCUCACUUUUUU-CAUUGCAGUUGGUUUUAAUUAUGGCCAGCCAAAUGCUCUCACCGCCAUAGUUGUCCACUGCGGCCAGCCAAUGAU
.....((...(((((....)))))...-----)).........(-(((((((((.((...((((((((((.(((.....)))......)))))))))).)))))))((....))))))). ( -35.00)
>consensus
UAUCUGCACUCUGGUU_UGGCCAGCCG_____GCUCACCUUUUUUCAUUGCAGUUGGUUUUAAUUAUGGCCAGCCAAAUGCUCUCACCGCCACAGUUGUCCACUGCGGCCAGCCAAUGAU
........(..((((..((((((((.......)))..............(((((.((...(((((.((((.(((.....)))......)))).))))).))))))))))))))))..).. (-30.70 = -30.74 +   0.04)

alignment

secondary structure

dotplot

Window 5

Location	6,761,744 – 6,761,844
Length	100
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.05
Mean single sequence MFE	-32.30
Consensus MFE	-25.12
Energy contribution	-25.16
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.45
Structure conservation index	0.78
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6761744 100 - 27905053
---ACU-----------GGCAAGGACUGCAGCGGCAUUUGUAUCUGCACUCUGGUU-UGGCCAGCCA-----GCUCACCUUUUUUCAUUGCAGUUGGUUUUAAUUAUGGCCAGCCAAAUG
---..(-----------(((..(((.(((((..((....))..))))).)))....-((((((((((-----(((((...........)).)))))))........)))))))))).... ( -32.70)
>DroSec_CAF1 25957 100 - 1
---ACU-----------GGCAAGGACUGCAGCGGCAUUUGUAUCUGCACUCUGGUU-UGGCCAGCCG-----GCUCUCCUUUUUUCAUUGUAGUUGGUUUUAAUUAUGGCCAGCCAAAUG
---..(-----------(((..(((.(((((..((....))..))))).)))....-((((((((((-----((((.............).)))))))........)))))))))).... ( -31.42)
>DroSim_CAF1 30342 100 - 1
---ACU-----------GGCAAGGACUGCAGCGGCAUUUGUAUCUGCACUCUGGUU-UGGCCAGCCG-----GCUCACCUUUUUUCAUUGCAGUUGGUUUUAAUUAUGGCCAGCCAAAUG
---..(-----------(((..(((.(((((..((....))..))))).)))....-((((((((((-----(((((...........)).)))))))........)))))))))).... ( -31.90)
>DroEre_CAF1 10426 108 - 1
GACACU-----------GGGCAGUACUGCAGCGGCAUUUGUAUCUGCACUCUGGUU-UGGCCAGCGGUGAACACUCACUUUUUUCCAUUGCAGUUGGUUUUAAUUAUGGCCAGCCAAAUG
......-----------.(((...((((((((((.((....)))))).(.((((..-...)))).)((((....))))..........))))))(((((........))))))))..... ( -29.40)
>DroYak_CAF1 22587 114 - 1
GACGCAGGAUGCAGGAUGGCAAGUACUGCAGCGGCAUUUGUAUCUGCACUCUGGUUUUGGCCAGCCG-----GCUCACUUUUUU-CAUUGCAGUUGGUUUUAAUUAUGGCCAGCCAAAUG
(((.(((..((((((...((((((.(((...))).)))))).))))))..))))))(((((((((((-----(((((.......-...)).)))))))........)))))))....... ( -36.10)
>consensus
___ACU___________GGCAAGGACUGCAGCGGCAUUUGUAUCUGCACUCUGGUU_UGGCCAGCCG_____GCUCACCUUUUUUCAUUGCAGUUGGUUUUAAUUAUGGCCAGCCAAAUG
.................(((....((((((((((.((....))))))...(((((....)))))........................))))))(((((........))))))))..... (-25.12 = -25.16 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:22 2006