Locus 735

Sequence ID	3R_DroMel_CAF1
Location	2,614,593 – 2,614,742
Length	149
Max. P	0.697937

overview

Window 2

Location	2,614,593 – 2,614,710
Length	117
Sequences	3
Columns	117
Reading direction	forward
Mean pairwise identity	88.54
Mean single sequence MFE	-31.67
Consensus MFE	-21.22
Energy contribution	-23.22
Covariance contribution	2.00
Combinations/Pair	1.00
Mean z-score	-2.87
Structure conservation index	0.67
SVM decision value	0.29
SVM RNA-class probability	0.672028
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2614593 117 + 27905053
CAGACUGCUUCAGACUAUUUCCUAUAUAAAAUAAUCAAAUUACAACACUCUGCAGUGGUAUCAAACACGCUGGGCGUCUUGGCGUUGCCAAAGUUUAAAAACAAACUUGGGCAGCAU
......(((..(((((((((........)))))..............(((.((.(((........))))).))).)))).)))((((((.((((((......)))))).)))))).. ( -28.70)
>DroSec_CAF1 14365 115 + 1
CAGACGAUUUCU--UUAGCAGCUAUGUGAAAAAAUCAAAUUACAACACUCAGCAGUGGUAUCAAAACCGCUGGGAGUCAUGGCGUUGCCAAAGUUUAAAAACAAACUUGGGCCGCAU
............--...((.(((((((((.....))).........((((..(((((((......))))))).))))))))))...(((.((((((......)))))).))).)).. ( -32.90)
>DroSim_CAF1 2463 115 + 1
CAGACUAUUUCU--UUAGCAGCUAUGUGAAAAAAUCAAAUUACAACACUCAGCAGUGGUAUCAAAACCGCUGGGAGUCAUGGCGUUGCCAAAGUUUAAAAACAAACUUGGGCCGCAU
..(.(((.....--.)))).(((((((((.....))).........((((..(((((((......))))))).))))))))))((.(((.((((((......)))))).))).)).. ( -33.40)
>consensus
CAGACUAUUUCU__UUAGCAGCUAUGUGAAAAAAUCAAAUUACAACACUCAGCAGUGGUAUCAAAACCGCUGGGAGUCAUGGCGUUGCCAAAGUUUAAAAACAAACUUGGGCCGCAU
....................((((((....................((((..(((((((......))))))).))))))))))((.(((.((((((......)))))).))).)).. (-21.22 = -23.22 +   2.00)

alignment

secondary structure

dotplot

Window 3

Location	2,614,630 – 2,614,742
Length	112
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	88.30
Mean single sequence MFE	-31.63
Consensus MFE	-24.81
Energy contribution	-25.70
Covariance contribution	0.89
Combinations/Pair	1.07
Mean z-score	-2.23
Structure conservation index	0.78
SVM decision value	0.34
SVM RNA-class probability	0.697937
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2614630 112 + 27905053
AAUUACAACACUCUGCAGUGGUAUCAAACACGCUGGGCGUCUUGGCGUUGCCAAAGUUUAAAAACAAACUUGGGCAGCAUGUUUUUUUUAUGUGUUGCUAAAAUUUCCAUGU--------
..(((((((((......(((........)))((..((...))..))((((((.((((((......)))))).)))))).............)))))).)))...........-------- ( -29.90)
>DroSec_CAF1 14400 119 + 1
AAUUACAACACUCAGCAGUGGUAUCAAAACCGCUGGGAGUCAUGGCGUUGCCAAAGUUUAAAAACAAACUUGGGCCGCAUGUUAU-GUUAUGUGUUUCCAAAAUCUCCAUAUUGAAUCUG
...........(((((((((((......)))))))((((...(((....(((.((((((......)))))).)))((((((....-..))))))...)))....))))...))))..... ( -32.50)
>DroSim_CAF1 2498 119 + 1
AAUUACAACACUCAGCAGUGGUAUCAAAACCGCUGGGAGUCAUGGCGUUGCCAAAGUUUAAAAACAAACUUGGGCCGCAUGUUAU-GUUAUGUGUUUCCAAAAUCUCCAUAUUGAAUCUG
...........(((((((((((......)))))))((((...(((....(((.((((((......)))))).)))((((((....-..))))))...)))....))))...))))..... ( -32.50)
>consensus
AAUUACAACACUCAGCAGUGGUAUCAAAACCGCUGGGAGUCAUGGCGUUGCCAAAGUUUAAAAACAAACUUGGGCCGCAUGUUAU_GUUAUGUGUUUCCAAAAUCUCCAUAUUGAAUCUG
...............(((((((......)))))))((((...(((....(((.((((((......)))))).)))((((((.......))))))...)))....))))............ (-24.81 = -25.70 +   0.89)

alignment

secondary structure

dotplot

Window 4

Location	2,614,630 – 2,614,742
Length	112
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	88.30
Mean single sequence MFE	-33.50
Consensus MFE	-22.23
Energy contribution	-23.90
Covariance contribution	1.67
Combinations/Pair	1.00
Mean z-score	-2.93
Structure conservation index	0.66
SVM decision value	0.33
SVM RNA-class probability	0.693641
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2614630 112 - 27905053
--------ACAUGGAAAUUUUAGCAACACAUAAAAAAAACAUGCUGCCCAAGUUUGUUUUUAAACUUUGGCAACGCCAAGACGCCCAGCGUGUUUGAUACCACUGCAGAGUGUUGUAAUU
--------..............(((((((.......((((((((((((.(((((((....))))))).)))...((......))..))))))))).......(....).))))))).... ( -29.10)
>DroSec_CAF1 14400 119 - 1
CAGAUUCAAUAUGGAGAUUUUGGAAACACAUAAC-AUAACAUGCGGCCCAAGUUUGUUUUUAAACUUUGGCAACGCCAUGACUCCCAGCGGUUUUGAUACCACUGCUGAGUGUUGUAAUU
..((((((((((((((....((....))......-....(((((((((.(((((((....))))))).)))..)).)))).))))(((((((.........))))))).)))))).)))) ( -35.70)
>DroSim_CAF1 2498 119 - 1
CAGAUUCAAUAUGGAGAUUUUGGAAACACAUAAC-AUAACAUGCGGCCCAAGUUUGUUUUUAAACUUUGGCAACGCCAUGACUCCCAGCGGUUUUGAUACCACUGCUGAGUGUUGUAAUU
..((((((((((((((....((....))......-....(((((((((.(((((((....))))))).)))..)).)))).))))(((((((.........))))))).)))))).)))) ( -35.70)
>consensus
CAGAUUCAAUAUGGAGAUUUUGGAAACACAUAAC_AUAACAUGCGGCCCAAGUUUGUUUUUAAACUUUGGCAACGCCAUGACUCCCAGCGGUUUUGAUACCACUGCUGAGUGUUGUAAUU
........................(((((..........(((((((((.(((((((....))))))).)))..)).)))).....(((((((.........))))))).)))))...... (-22.23 = -23.90 +   1.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:38 2006