Locus 7949

Sequence ID	X_DroMel_CAF1
Location	19,825,730 – 19,825,881
Length	151
Max. P	0.969429

overview

Window 1

Location	19,825,730 – 19,825,848
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.87
Mean single sequence MFE	-31.18
Consensus MFE	-29.04
Energy contribution	-29.24
Covariance contribution	0.20
Combinations/Pair	1.11
Mean z-score	-1.52
Structure conservation index	0.93
SVM decision value	1.64
SVM RNA-class probability	0.969429
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19825730 118 + 22224390
AGUUUGGCUUGAUGUUUGUCUUUUGUUUGUUGACACAAUGUUCGCGGAAAGGCG--AGUUGGCUAAAGCCGAAUGCAAAGAGGACUAAUUCAACAUUUUAGUCAAGAUGAAAAUUAACAU
..(((((((.((((((.(((((((.(((((.(((.....))).)))))...(((--..(((((....))))).)))..)))))))......))))))..))))))).............. ( -28.60)
>DroSec_CAF1 31488 118 + 1
AGUUUGGCUUGGUGUUUGUCUUUUGUUUGUUGACACAAUGUUCGCGGGAAGGCG--AGUUGGCUAAAGCCGAAUGCAAAGAGGACUAAUUAAACAUUUUAGCCAAGAUGAAAAUGAACAU
..(((((((.(((((((((((((..(((((..........(((((......)))--))(((((....)))))..))))))))))).....)))))))..))))))).............. ( -31.40)
>DroSim_CAF1 29654 118 + 1
AGUUUGGCUUGCUGUUUGUCUUUUGUUUGUUGACACAAUGUUCGCGGGAAGGCG--AGUUGGCUAAAGCCGAAUGCAAAGAGGACUAAUUAAACAUUUUAGCCAAGAUGAAAAUGAACAU
..(((((((...(((((((((((..(((((..........(((((......)))--))(((((....)))))..))))))))))).....)))))....))))))).............. ( -28.80)
>DroEre_CAF1 21779 118 + 1
AGUUGGGCUUGGUGUUUGUCUUCUGUUUGUUGGCACAGUGUUCGCGGGAAGGCG--AGUUGGCUGAAGCCGAAUGCAAAUAGGACUAAUUAAACAUUUUAGCCAAGAUGAAAAUUAAGAU
.....((((.((((((((..((((((((((((((.((((.(((((......)))--))...))))..))))...)))))))))).....))))))))..))))..(((....)))..... ( -35.50)
>DroYak_CAF1 22624 120 + 1
AGUUUGGCUUGGUGUUUGUCUUUUGUUUGUUGACACAAUGUUCGCGGGAAGGCGAGAGUUGGCUAAAGCCGAAUGCAAAGAGGACUAAUUAAACAUUUUAGCCAAGAUGAAAAUGAACAU
..(((((((.(((((((((((((..(((((..........(((((......)))))..(((((....)))))..))))))))))).....)))))))..))))))).............. ( -31.60)
>consensus
AGUUUGGCUUGGUGUUUGUCUUUUGUUUGUUGACACAAUGUUCGCGGGAAGGCG__AGUUGGCUAAAGCCGAAUGCAAAGAGGACUAAUUAAACAUUUUAGCCAAGAUGAAAAUGAACAU
..(((((((.((((((((((((((.(((((.(((.....))).)))))...(((....(((((....))))).)))..))))))).....)))))))..))))))).............. (-29.04 = -29.24 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	19,825,730 – 19,825,848
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.87
Mean single sequence MFE	-20.72
Consensus MFE	-17.38
Energy contribution	-17.66
Covariance contribution	0.28
Combinations/Pair	1.04
Mean z-score	-1.35
Structure conservation index	0.84
SVM decision value	0.09
SVM RNA-class probability	0.578271
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19825730 118 - 22224390
AUGUUAAUUUUCAUCUUGACUAAAAUGUUGAAUUAGUCCUCUUUGCAUUCGGCUUUAGCCAACU--CGCCUUUCCGCGAACAUUGUGUCAACAAACAAAAGACAAACAUCAAGCCAAACU
.((((..........(((((...(((((((((((((......))).))))(((....)))....--(((......)))))))))..))))).........))))................ ( -18.51)
>DroSec_CAF1 31488 118 - 1
AUGUUCAUUUUCAUCUUGGCUAAAAUGUUUAAUUAGUCCUCUUUGCAUUCGGCUUUAGCCAACU--CGCCUUCCCGCGAACAUUGUGUCAACAAACAAAAGACAAACACCAAGCCAAACU
...............((((((....(((((.....(((...((((.....(((....)))...(--(((......))))...((((....)))).)))).))))))))...))))))... ( -21.20)
>DroSim_CAF1 29654 118 - 1
AUGUUCAUUUUCAUCUUGGCUAAAAUGUUUAAUUAGUCCUCUUUGCAUUCGGCUUUAGCCAACU--CGCCUUCCCGCGAACAUUGUGUCAACAAACAAAAGACAAACAGCAAGCCAAACU
...............((((((....(((((.....(((...((((.....(((....)))...(--(((......))))...((((....)))).)))).))))))))...))))))... ( -22.30)
>DroEre_CAF1 21779 118 - 1
AUCUUAAUUUUCAUCUUGGCUAAAAUGUUUAAUUAGUCCUAUUUGCAUUCGGCUUCAGCCAACU--CGCCUUCCCGCGAACACUGUGCCAACAAACAGAAGACAAACACCAAGCCCAACU
.................((((....(((((.....(((............(((....)))...(--(((......))))...((((........))))..))))))))...))))..... ( -20.40)
>DroYak_CAF1 22624 120 - 1
AUGUUCAUUUUCAUCUUGGCUAAAAUGUUUAAUUAGUCCUCUUUGCAUUCGGCUUUAGCCAACUCUCGCCUUCCCGCGAACAUUGUGUCAACAAACAAAAGACAAACACCAAGCCAAACU
...............((((((....(((((.....(((...((((.....(((....))).....((((......))))...((((....)))).)))).))))))))...))))))... ( -21.20)
>consensus
AUGUUCAUUUUCAUCUUGGCUAAAAUGUUUAAUUAGUCCUCUUUGCAUUCGGCUUUAGCCAACU__CGCCUUCCCGCGAACAUUGUGUCAACAAACAAAAGACAAACACCAAGCCAAACU
...............((((((....(((((.....(((............(((....)))......(((......)))....((((........))))..))))))))...))))))... (-17.38 = -17.66 +   0.28)

alignment

secondary structure

dotplot

Window 3

Location	19,825,770 – 19,825,881
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.19
Mean single sequence MFE	-31.49
Consensus MFE	-27.18
Energy contribution	-27.26
Covariance contribution	0.08
Combinations/Pair	1.04
Mean z-score	-1.77
Structure conservation index	0.86
SVM decision value	1.62
SVM RNA-class probability	0.968363
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19825770 111 + 22224390
UUCGCGGAAAGGCG--AGUUGGCUAAAGCCGAAUGCAAAGAGGACUAAUUCAACAUUUUAGUCAAGAUGAAAAUUAACAUUUUUUGGCUGCCUACGCGAGCAUACGGCUC-------AAC
...(((...(((((--..(((((....)))))...(((((((((((((.........))))))..(((....)))....)))))))..))))).)))((((.....))))-------... ( -32.60)
>DroSec_CAF1 31528 111 + 1
UUCGCGGGAAGGCG--AGUUGGCUAAAGCCGAAUGCAAAGAGGACUAAUUAAACAUUUUAGCCAAGAUGAAAAUGAACAUUUUUUGGCUGCCUACGCGAGCAUACGGCUC-------AAC
...(((...(((((--..(((((....)))))...).......................((((((((((........))))..)))))))))).)))((((.....))))-------... ( -32.20)
>DroSim_CAF1 29694 111 + 1
UUCGCGGGAAGGCG--AGUUGGCUAAAGCCGAAUGCAAAGAGGACUAAUUAAACAUUUUAGCCAAGAUGAAAAUGAACAUUUUUUGGCUGCCUACGCGAGCAUACGGCUC-------AAC
...(((...(((((--..(((((....)))))...).......................((((((((((........))))..)))))))))).)))((((.....))))-------... ( -32.20)
>DroEre_CAF1 21819 111 + 1
UUCGCGGGAAGGCG--AGUUGGCUGAAGCCGAAUGCAAAUAGGACUAAUUAAACAUUUUAGCCAAGAUGAAAAUUAAGAUUUUUUGGCUGCCUACGCGAGCAUACGACUC-------AAC
((((((...(((((--..(((((....)))))...).......................((((((((..............)))))))))))).))))))..........-------... ( -29.84)
>DroYak_CAF1 22664 120 + 1
UUCGCGGGAAGGCGAGAGUUGGCUAAAGCCGAAUGCAAAGAGGACUAAUUAAACAUUUUAGCCAAGAUGAAAAUGAACAUUUUUUGCCUGCCUACGCGAGCAUACGGCUGAAAUACGAAC
.(((((((.((((((((((((((....))))).........((.((((.........)))))).................))))))))).))..)))))((.....))............ ( -30.60)
>consensus
UUCGCGGGAAGGCG__AGUUGGCUAAAGCCGAAUGCAAAGAGGACUAAUUAAACAUUUUAGCCAAGAUGAAAAUGAACAUUUUUUGGCUGCCUACGCGAGCAUACGGCUC_______AAC
((((((...((((.....(((((....)))))...........................((((((((..............)))))))))))).)))))).................... (-27.18 = -27.26 +   0.08)

alignment

secondary structure

dotplot

Window 4

Location	19,825,770 – 19,825,881
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.19
Mean single sequence MFE	-27.78
Consensus MFE	-23.46
Energy contribution	-23.90
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.30
Structure conservation index	0.84
SVM decision value	0.13
SVM RNA-class probability	0.598447
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19825770 111 - 22224390
GUU-------GAGCCGUAUGCUCGCGUAGGCAGCCAAAAAAUGUUAAUUUUCAUCUUGACUAAAAUGUUGAAUUAGUCCUCUUUGCAUUCGGCUUUAGCCAACU--CGCCUUUCCGCGAA
...-------((((.....))))(((.((((.((...(((((....)))))......((((((.........))))))......))....(((....)))....--.))))...)))... ( -25.50)
>DroSec_CAF1 31528 111 - 1
GUU-------GAGCCGUAUGCUCGCGUAGGCAGCCAAAAAAUGUUCAUUUUCAUCUUGGCUAAAAUGUUUAAUUAGUCCUCUUUGCAUUCGGCUUUAGCCAACU--CGCCUUCCCGCGAA
(((-------((((((.((((..((....))((((((...(((........))).)))))).......................)))).)))).)))))....(--(((......)))). ( -28.50)
>DroSim_CAF1 29694 111 - 1
GUU-------GAGCCGUAUGCUCGCGUAGGCAGCCAAAAAAUGUUCAUUUUCAUCUUGGCUAAAAUGUUUAAUUAGUCCUCUUUGCAUUCGGCUUUAGCCAACU--CGCCUUCCCGCGAA
(((-------((((((.((((..((....))((((((...(((........))).)))))).......................)))).)))).)))))....(--(((......)))). ( -28.50)
>DroEre_CAF1 21819 111 - 1
GUU-------GAGUCGUAUGCUCGCGUAGGCAGCCAAAAAAUCUUAAUUUUCAUCUUGGCUAAAAUGUUUAAUUAGUCCUAUUUGCAUUCGGCUUCAGCCAACU--CGCCUUCCCGCGAA
(((-------((((((.((((....(((((((((((((((((....)))))....))))))..(((.....))).).)))))..)))).)))).)))))....(--(((......)))). ( -29.10)
>DroYak_CAF1 22664 120 - 1
GUUCGUAUUUCAGCCGUAUGCUCGCGUAGGCAGGCAAAAAAUGUUCAUUUUCAUCUUGGCUAAAAUGUUUAAUUAGUCCUCUUUGCAUUCGGCUUUAGCCAACUCUCGCCUUCCCGCGAA
.(((((......(((.((((....)))))))((((..(((((....)))))....(((((((((..((..((((((......))).)))..))))))))))).....))))....))))) ( -27.30)
>consensus
GUU_______GAGCCGUAUGCUCGCGUAGGCAGCCAAAAAAUGUUCAUUUUCAUCUUGGCUAAAAUGUUUAAUUAGUCCUCUUUGCAUUCGGCUUUAGCCAACU__CGCCUUCCCGCGAA
..........((((.....))))(((.(((((((((((((((....)))))....)))))).............................(((....))).......))))...)))... (-23.46 = -23.90 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:51:33 2006