Locus 6519

Sequence ID	3L_DroMel_CAF1
Location	17,271,436 – 17,271,633
Length	197
Max. P	0.999949

overview

Window 0

Location	17,271,436 – 17,271,556
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.15
Mean single sequence MFE	-28.27
Consensus MFE	-24.90
Energy contribution	-25.10
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.58
Structure conservation index	0.88
SVM decision value	1.09
SVM RNA-class probability	0.913796
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17271436 120 - 23771897
GCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCAAGGCAAAAACUCAAACGGCGUUGGCAUGACGCCCGAAAACGAAAACGAGUGAACGAAUCAGCGGGCCAACUCAAAUGAAAC
((((.(((.(((....(((....(((..........))).)))....((((....((((((.....))))))((....)).....)))).....))).)))))))............... ( -27.40)
>DroSec_CAF1 154952 120 - 1
GCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCAAGGCAAAAACUCAAACGGCGUUGGCAUGACGCCCGAAAACGAAAACGAGUGAACGAAUCAGCGGGCCAACUCAAAUGAAAC
((((.(((.(((....(((....(((..........))).)))....((((....((((((.....))))))((....)).....)))).....))).)))))))............... ( -27.40)
>DroSim_CAF1 149985 120 - 1
GCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCAAGGCAAAAACUCAAACGGCGUUGGCAUGACGCCCGAAAACGAAAACGAGUGAACGAAUCAGCGGGCCAACUCAAAUGAAAC
((((.(((.(((....(((....(((..........))).)))....((((....((((((.....))))))((....)).....)))).....))).)))))))............... ( -27.40)
>DroEre_CAF1 157801 114 - 1
GCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCAAGGCAAAAACUCAAACGGCGUUGGCAUGACGCCCGAAA------ACGAGUGAGCGAAUCAGCGGGCCAACUCAAAUGAAAC
((((.(((((((.....(((.(.(((..........))).)..............((((((.....)))))))))..------...)))))))(......)))))............... ( -29.90)
>DroYak_CAF1 162606 114 - 1
GCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCCAGGCAAAAACUCAAACGGCGUUGGCAUGACGCCCGAAA------ACGAGUGAGCGAAUCAGCGGGCCAACUCAAAUGAAAC
((((.(((((((.....(((...(((...............)))...........((((((.....)))))))))..------...)))))))(......)))))............... ( -29.26)
>consensus
GCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCAAGGCAAAAACUCAAACGGCGUUGGCAUGACGCCCGAAAACGAAAACGAGUGAACGAAUCAGCGGGCCAACUCAAAUGAAAC
((((.((((.....((((...(.(((..........))).)......))))....((((((.....)))))).............))))((.....))...))))............... (-24.90 = -25.10 +   0.20)

alignment

secondary structure

dotplot

Window 1

Location	17,271,476 – 17,271,596
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.83
Mean single sequence MFE	-36.16
Consensus MFE	-34.72
Energy contribution	-34.76
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-2.62
Structure conservation index	0.96
SVM decision value	4.08
SVM RNA-class probability	0.999787
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17271476 120 - 23771897
CUUUUCGCUGUUUGCUCAGCGAAAGUACAAAUUGCAUGGCGCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCAAGGCAAAAACUCAAACGGCGUUGGCAUGACGCCCGAAAACG
.((((((((..(((((..((....))...(((((((((.((....((((.....)))))).))))))))).....))))))))............((((((.....)))))).))))).. ( -36.50)
>DroSec_CAF1 154992 120 - 1
CUUUUUGCUGUUUGCUCAGCGAAAGUACAAAUUGCAUGGCGCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCAAGGCAAAAACUCAAACGGCGUUGGCAUGACGCCCGAAAACG
.((((((((..(((((..((....))...(((((((((.((....((((.....)))))).))))))))).....))))))))))))).......((((((.....))))))........ ( -37.70)
>DroSim_CAF1 150025 120 - 1
CUUUUCGCUGUUUGCUCAGCGAAAGUACAAAUUGCAUGGCGCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCAAGGCAAAAACUCAAACGGCGUUGGCAUGACGCCCGAAAACG
.((((((((..(((((..((....))...(((((((((.((....((((.....)))))).))))))))).....))))))))............((((((.....)))))).))))).. ( -36.50)
>DroEre_CAF1 157838 117 - 1
CUUUUCGCUGUUUGCUCAGCGAAAGUACAAAUUGCAUGGCGCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCAAGGCAAAAACUCAAACGGCGUUGGCAUGACGCCCGAAA---
..(((((((..(((((..((....))...(((((((((.((....((((.....)))))).))))))))).....))))))))............((((((.....)))))).))))--- ( -35.20)
>DroYak_CAF1 162643 117 - 1
CUUUUCGCUGUUUGCUCAGCGAAAGUACAAAUUGCAUGGCGCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCCAGGCAAAAACUCAAACGGCGUUGGCAUGACGCCCGAAA---
.(((((((((......)))))))))....(((((((((.((....((((.....)))))).))))))))).........................((((((.....)))))).....--- ( -34.90)
>consensus
CUUUUCGCUGUUUGCUCAGCGAAAGUACAAAUUGCAUGGCGCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCAAGGCAAAAACUCAAACGGCGUUGGCAUGACGCCCGAAAACG
..(((((((...((((..((....))...(((((((((.((....((((.....)))))).))))))))).....)))).)))............((((((.....)))))).))))... (-34.72 = -34.76 +   0.04)

alignment

secondary structure

dotplot

Window 2

Location	17,271,516 – 17,271,633
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.97
Mean single sequence MFE	-34.80
Consensus MFE	-32.34
Energy contribution	-32.94
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.27
Structure conservation index	0.93
SVM decision value	3.02
SVM RNA-class probability	0.998140
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17271516 117 + 23771897
UUGCUUUUAUAAUUGCAUGUCGACUCUUAAUGAGCUGGGCGCCAUGCAAUUUGUACUUUCGCUGAGCAAACAGCGAAAAGCGAACAGG---AGGCUAAAAGCAAAGGAUUUCCCAUUUUC
(((((((((...(((((((.((.(((..........))))).)))))))(((((..((((((((......)))))))).)))))....---....))))))))).((.....))...... ( -34.90)
>DroSec_CAF1 155032 117 + 1
UUGCUUUUAUAAUUGCAUGUCGACUCUUAAUGAGCUGGGCGCCAUGCAAUUUGUACUUUCGCUGAGCAAACAGCAAAAAGCGAACAGG---AGGCUAAAAGCAAAGGAUUUCCCAUUUUC
(((((((((.(((((((((.((.(((..........))))).))))))))).((.((((((((..((.....))....)))))).)).---..))))))))))).((.....))...... ( -33.30)
>DroSim_CAF1 150065 117 + 1
UUGCUUUUAUAAUUGCAUGUCGACUCUUAAUGAGCUGGGCGCCAUGCAAUUUGUACUUUCGCUGAGCAAACAGCGAAAAGCGAACAGG---AGGCUAAAAGCAAAGGAUUUCCCAUUUUC
(((((((((...(((((((.((.(((..........))))).)))))))(((((..((((((((......)))))))).)))))....---....))))))))).((.....))...... ( -34.90)
>DroEre_CAF1 157875 117 + 1
UUGCUUUUAUAAUUGCAUGUCGACUCUUAAUGAGCUGGGCGCCAUGCAAUUUGUACUUUCGCUGAGCAAACAGCGAAAAGCGAACAGG---AGGCUAAAAGCAAAGGAUUUCCCAUUUUC
(((((((((...(((((((.((.(((..........))))).)))))))(((((..((((((((......)))))))).)))))....---....))))))))).((.....))...... ( -34.90)
>DroYak_CAF1 162680 120 + 1
UGGCUUUUAUAAUUGCAUGUCGACUCUUAAUGAGCUGGGCGCCAUGCAAUUUGUACUUUCGCUGAGCAAACAGCGAAAAGCGAACAGGAGGAGGCCAAAAGCAAAGGAUUUCCCAUUUUC
((((((((....(((((((.((.(((..........))))).)))))))(((((..((((((((......)))))))).))))).....))))))))........((.....))...... ( -36.00)
>consensus
UUGCUUUUAUAAUUGCAUGUCGACUCUUAAUGAGCUGGGCGCCAUGCAAUUUGUACUUUCGCUGAGCAAACAGCGAAAAGCGAACAGG___AGGCUAAAAGCAAAGGAUUUCCCAUUUUC
(((((((((...(((((((.((.(((..........))))).)))))))(((((..((((((((......)))))))).)))))...........))))))))).((.....))...... (-32.34 = -32.94 +   0.60)

alignment

secondary structure

dotplot

Window 3

Location	17,271,516 – 17,271,633
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.97
Mean single sequence MFE	-36.04
Consensus MFE	-35.94
Energy contribution	-35.82
Covariance contribution	-0.12
Combinations/Pair	1.05
Mean z-score	-3.00
Structure conservation index	1.00
SVM decision value	4.78
SVM RNA-class probability	0.999949
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17271516 117 - 23771897
GAAAAUGGGAAAUCCUUUGCUUUUAGCCU---CCUGUUCGCUUUUCGCUGUUUGCUCAGCGAAAGUACAAAUUGCAUGGCGCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCAA
......(((....)))(((((((((....---..(((..(((((.(((((......)))))))))))))(((((((((.((....((((.....)))))).))))))))).))))))))) ( -36.90)
>DroSec_CAF1 155032 117 - 1
GAAAAUGGGAAAUCCUUUGCUUUUAGCCU---CCUGUUCGCUUUUUGCUGUUUGCUCAGCGAAAGUACAAAUUGCAUGGCGCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCAA
......(((....)))(((((((((....---..(((..((((((.((((......)))))))))))))(((((((((.((....((((.....)))))).))))))))).))))))))) ( -34.80)
>DroSim_CAF1 150065 117 - 1
GAAAAUGGGAAAUCCUUUGCUUUUAGCCU---CCUGUUCGCUUUUCGCUGUUUGCUCAGCGAAAGUACAAAUUGCAUGGCGCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCAA
......(((....)))(((((((((....---..(((..(((((.(((((......)))))))))))))(((((((((.((....((((.....)))))).))))))))).))))))))) ( -36.90)
>DroEre_CAF1 157875 117 - 1
GAAAAUGGGAAAUCCUUUGCUUUUAGCCU---CCUGUUCGCUUUUCGCUGUUUGCUCAGCGAAAGUACAAAUUGCAUGGCGCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCAA
......(((....)))(((((((((....---..(((..(((((.(((((......)))))))))))))(((((((((.((....((((.....)))))).))))))))).))))))))) ( -36.90)
>DroYak_CAF1 162680 120 - 1
GAAAAUGGGAAAUCCUUUGCUUUUGGCCUCCUCCUGUUCGCUUUUCGCUGUUUGCUCAGCGAAAGUACAAAUUGCAUGGCGCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCCA
......(((....)))..(((((((.........(((..(((((.(((((......)))))))))))))(((((((((.((....((((.....)))))).))))))))).))))))).. ( -34.70)
>consensus
GAAAAUGGGAAAUCCUUUGCUUUUAGCCU___CCUGUUCGCUUUUCGCUGUUUGCUCAGCGAAAGUACAAAUUGCAUGGCGCCCAGCUCAUUAAGAGUCGACAUGCAAUUAUAAAAGCAA
......(((....)))(((((((((.........(((..(((((.(((((......)))))))))))))(((((((((.((....((((.....)))))).))))))))).))))))))) (-35.94 = -35.82 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:22:30 2006