Locus 997

Sequence ID	X_DroMel_CAF1
Location	2,894,346 – 2,894,479
Length	133
Max. P	0.938708

overview

Window 1

Location	2,894,346 – 2,894,458
Length	112
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	75.51
Mean single sequence MFE	-24.53
Consensus MFE	-17.40
Energy contribution	-18.10
Covariance contribution	0.70
Combinations/Pair	1.20
Mean z-score	-1.57
Structure conservation index	0.71
SVM decision value	1.27
SVM RNA-class probability	0.938708
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2894346 112 - 22224390
AAAUGCUAACAAAUAACAAGCCGCUUUGAGUAACUACUCGAGUUGGCUAACUCGCCAAGUUGUCAG-UGGGCAAAUGGCAAGGAAAUGAAACGAAACGGAACGAAAAUAGUCA
....((((..........(((((.(((((((....))))))).)))))..((.((((..(((((..-..))))).)))).)).........................)))).. ( -26.90)
>DroSec_CAF1 281133 112 - 1
AAAUGCUAACAAAUAACAAGCCGCUUUGAGUAACUACUCGAGUUGGCUAACUCGCCAAGUUGUCAG-UGGGCAAAAGGCAAGGAAAUGAAACGAAACGGAACGAAAAUAGUCA
....((((..........(((((.(((((((....))))))).)))))..((.(((...(((((..-..)))))..))).)).........................)))).. ( -26.00)
>DroSim_CAF1 251465 112 - 1
AAAUGCUAACAAAUAACAAGCCGCUUUGAGUAACUACUCGAGUUGGCUAACUCGCCAAGUUGUCAG-UGGGCAAAAGGCAAGGAAAUGAAACGAAACGGAACGAAAAUAGUCA
....((((..........(((((.(((((((....))))))).)))))..((.(((...(((((..-..)))))..))).)).........................)))).. ( -26.00)
>DroEre_CAF1 304756 96 - 1
AAAUGCUAACAAAUAACGAGCCGCUUUGAGUAACUACUUGAGUUGGCUAACUCGCCAAGUUGUCAGUGGGGCAAAAGGCGCGGAGAGG---------------AAAAUAGU--
....((((..........(((((.((..(((....)))..)).)))))..(.((((...(((((.....)))))..)))).)......---------------....))))-- ( -25.20)
>DroYak_CAF1 289420 93 - 1
AAAUGCUAACAAAUAACGAGCCGCUUUGAGUAACUACUUGAGUUGGCUAACUCACCAAGUUGUCAG-GGGGCAAAAGGC--AAAGAGG---------------AAACAAGU--
...((((..(.......).(((.((((((.(((((...((((((....))))))...)))))))))-)))))....)))--)....(.---------------...)....-- ( -23.50)
>DroAna_CAF1 446911 99 - 1
AAGUGGCAAUAAUUU--AGGUAGCAGAAAGUAACUACUUAAGUUAACUAACUCGCCAAGUUGUCAG-UG----ACAGGCCCAGA-----CCCAGUGCUAGACCAAAAUUGU--
...(((((.((((((--((((((..........))))))))))))........(((....((((..-.)----)))))).....-----.....)))))............-- ( -19.60)
>consensus
AAAUGCUAACAAAUAACAAGCCGCUUUGAGUAACUACUCGAGUUGGCUAACUCGCCAAGUUGUCAG_UGGGCAAAAGGCAAGGAAAUG_AACGAAACGGAACGAAAAUAGU__
..................(((((.(((((((....))))))).))))).....(((...(((((.....)))))..))).................................. (-17.40 = -18.10 +   0.70)

alignment

secondary structure

dotplot

Window 2

Location	2,894,386 – 2,894,479
Length	93
Sequences	6
Columns	94
Reading direction	forward
Mean pairwise identity	83.07
Mean single sequence MFE	-22.40
Consensus MFE	-15.62
Energy contribution	-18.07
Covariance contribution	2.45
Combinations/Pair	1.18
Mean z-score	-1.52
Structure conservation index	0.70
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2894386 93 + 22224390
UGCCCA-CUGACAACUUGGCGAGUUAGCCAACUCGAGUAGUUACUCAAAGCGGCUUGUUAUUUGUUAGCAUUUUCGCUUUUUCGUUGUCGACUU
......-.((((((((((((......)))))...((((....))))(((((((..(((((.....)))))...)))))))...))))))).... ( -28.40)
>DroSec_CAF1 281173 93 + 1
UGCCCA-CUGACAACUUGGCGAGUUAGCCAACUCGAGUAGUUACUCAAAGCGGCUUGUUAUUUGUUAGCAUUUUCGCUUUUUCGUCGUCGACUU
......-.((((.(((((((......)))))...((((....))))(((((((..(((((.....)))))...)))))))...)).)))).... ( -24.30)
>DroSim_CAF1 251505 93 + 1
UGCCCA-CUGACAACUUGGCGAGUUAGCCAACUCGAGUAGUUACUCAAAGCGGCUUGUUAUUUGUUAGCAUUUUCGCUUUUUCGUCGUCGACUU
......-.((((.(((((((......)))))...((((....))))(((((((..(((((.....)))))...)))))))...)).)))).... ( -24.30)
>DroEre_CAF1 304779 94 + 1
UGCCCCACUGACAACUUGGCGAGUUAGCCAACUCAAGUAGUUACUCAAAGCGGCUCGUUAUUUGUUAGCAUUUUCGCUUUUUCGCUGUCGACUU
........(((((.((((((......)))))...............(((((((...((((.....))))....)))))))...).))))).... ( -18.50)
>DroYak_CAF1 289441 93 + 1
UGCCCC-CUGACAACUUGGUGAGUUAGCCAACUCAAGUAGUUACUCAAAGCGGCUCGUUAUUUGUUAGCAUUUUCGCUUUUUCGUUGUUGACUU
.((((.-.(((.((((...((((((....))))))...))))..)))..).))).........(((((((....((......)).))))))).. ( -20.20)
>DroAna_CAF1 446944 73 + 1
----CA-CUGACAACUUGGCGAGUUAGUUAACUUAAGUAGUUACUUUCUGCUACCU--AAAUUAUUGCCACUU---------C--UGUCGG---
----..-((((((...(((((((((....)))))..(((((........)))))..--........))))...---------.--))))))--- ( -18.70)
>consensus
UGCCCA_CUGACAACUUGGCGAGUUAGCCAACUCAAGUAGUUACUCAAAGCGGCUUGUUAUUUGUUAGCAUUUUCGCUUUUUCGUUGUCGACUU
........((((((((((((......)))))...((((....))))(((((((..(((((.....)))))...)))))))...))))))).... (-15.62 = -18.07 +   2.45)

alignment

secondary structure

dotplot

Window 3

Location	2,894,386 – 2,894,479
Length	93
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	83.07
Mean single sequence MFE	-24.78
Consensus MFE	-18.39
Energy contribution	-18.92
Covariance contribution	0.53
Combinations/Pair	1.29
Mean z-score	-2.48
Structure conservation index	0.74
SVM decision value	0.71
SVM RNA-class probability	0.828711
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2894386 93 - 22224390
AAGUCGACAACGAAAAAGCGAAAAUGCUAACAAAUAACAAGCCGCUUUGAGUAACUACUCGAGUUGGCUAACUCGCCAAGUUGUCAG-UGGGCA
..(((((((((......((((...((....)).......(((((.(((((((....))))))).)))))...))))...))))))..-..))). ( -25.40)
>DroSec_CAF1 281173 93 - 1
AAGUCGACGACGAAAAAGCGAAAAUGCUAACAAAUAACAAGCCGCUUUGAGUAACUACUCGAGUUGGCUAACUCGCCAAGUUGUCAG-UGGGCA
..(((.(((((((....((((...((....)).......(((((.(((((((....))))))).)))))...))))....))))).)-).))). ( -29.20)
>DroSim_CAF1 251505 93 - 1
AAGUCGACGACGAAAAAGCGAAAAUGCUAACAAAUAACAAGCCGCUUUGAGUAACUACUCGAGUUGGCUAACUCGCCAAGUUGUCAG-UGGGCA
..(((.(((((((....((((...((....)).......(((((.(((((((....))))))).)))))...))))....))))).)-).))). ( -29.20)
>DroEre_CAF1 304779 94 - 1
AAGUCGACAGCGAAAAAGCGAAAAUGCUAACAAAUAACGAGCCGCUUUGAGUAACUACUUGAGUUGGCUAACUCGCCAAGUUGUCAGUGGGGCA
.....((((((......((((...((....)).......(((((.((..(((....)))..)).)))))...))))...))))))......... ( -23.00)
>DroYak_CAF1 289441 93 - 1
AAGUCAACAACGAAAAAGCGAAAAUGCUAACAAAUAACGAGCCGCUUUGAGUAACUACUUGAGUUGGCUAACUCACCAAGUUGUCAG-GGGGCA
................(((......)))............(((.((((((.(((((...((((((....))))))...)))))))))-))))). ( -22.20)
>DroAna_CAF1 446944 73 - 1
---CCGACA--G---------AAGUGGCAAUAAUUU--AGGUAGCAGAAAGUAACUACUUAAGUUAACUAACUCGCCAAGUUGUCAG-UG----
---..((((--(---------...((((..((((((--((((((..........))))))))))))........))))..)))))..-..---- ( -19.70)
>consensus
AAGUCGACAACGAAAAAGCGAAAAUGCUAACAAAUAACAAGCCGCUUUGAGUAACUACUCGAGUUGGCUAACUCGCCAAGUUGUCAG_UGGGCA
.....((((((.....(((......)))...........(((((.(((((((....))))))).)))))..........))))))......... (-18.39 = -18.92 +   0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:58 2006