Locus 6661

Sequence ID	3L_DroMel_CAF1
Location	17,734,270 – 17,734,402
Length	132
Max. P	0.999940

overview

Window 2

Location	17,734,270 – 17,734,384
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	97.89
Mean single sequence MFE	-26.34
Consensus MFE	-26.30
Energy contribution	-26.14
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.99
Structure conservation index	1.00
SVM decision value	3.11
SVM RNA-class probability	0.998449
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17734270 114 + 23771897
AAGUGCGUGGAGCAGUUUUUGCAUGCUGCAAAUAAAAUGAUGUUAAAACAUUUGUAAGGCCAAACUAACUAGAAUUUCGUUGGCACUACAAACGAACCCACCAUUUUACACCCU
(((((.((((.(((((........)))))...................(.((((((..(((((...((......))...)))))..)))))).)...)))))))))........ ( -26.40)
>DroSec_CAF1 15406 114 + 1
AAGUGCGUGGAGCAGUUUUUGCAUACUGCAAAUAAAAUGAUGUUAAAACAUUUGUAAGGCCAAACUAACUAGAAUUUCGUUGGCACUACAAACGAAGCCACCAUUUUGCACCCU
..((((((((.(((((........)))))...................(.((((((..(((((...((......))...)))))..)))))).)......))))...))))... ( -26.40)
>DroSim_CAF1 18106 114 + 1
AAGUGCGUGGAGCAGUUUUUGCAUACUGCAAAUAAAAUGAUGUUAAAACAUUUGUAAGGCCAAACUAACUAGAAUUUCGUUGGCACUACAAACGAACCCACCAUUUUGCACCCU
..((((((((.(((((........)))))...................(.((((((..(((((...((......))...)))))..)))))).)......))))...))))... ( -26.40)
>DroEre_CAF1 30269 111 + 1
AAGUGCGUGGAGCAGUUUUUGCAUACUGCAAAUAAAAUGAUGUUAAAACAUUUGUAAGGCCAAACUAACUAGAAUUUCGUUGGCACUACAAACGAACCCACCAUUUUGCAC---
(((((.((((.(((((........)))))...................(.((((((..(((((...((......))...)))))..)))))).)...))))))))).....--- ( -26.10)
>DroYak_CAF1 30894 114 + 1
AAGUGCGUGGAGCAGUUUUUGCAUACUGCAAAUAAAAUGAUGUUAAAACAUUUGUAAGGCCAAACUAACUAGAAUUUCGUUGGCACUACAAACGAACCCACCAUUUUGCACCCU
..((((((((.(((((........)))))...................(.((((((..(((((...((......))...)))))..)))))).)......))))...))))... ( -26.40)
>consensus
AAGUGCGUGGAGCAGUUUUUGCAUACUGCAAAUAAAAUGAUGUUAAAACAUUUGUAAGGCCAAACUAACUAGAAUUUCGUUGGCACUACAAACGAACCCACCAUUUUGCACCCU
(((((.((((.(((((........)))))...................(.((((((..(((((...((......))...)))))..)))))).)...)))))))))........ (-26.30 = -26.14 +  -0.16)

alignment

secondary structure

dotplot

Window 3

Location	17,734,270 – 17,734,384
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	97.89
Mean single sequence MFE	-35.36
Consensus MFE	-34.34
Energy contribution	-34.78
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-3.56
Structure conservation index	0.97
SVM decision value	4.70
SVM RNA-class probability	0.999940
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17734270 114 - 23771897
AGGGUGUAAAAUGGUGGGUUCGUUUGUAGUGCCAACGAAAUUCUAGUUAGUUUGGCCUUACAAAUGUUUUAACAUCAUUUUAUUUGCAGCAUGCAAAAACUGCUCCACGCACUU
.(.(((((((((((((....(((((((((.((((((..(((....))).).))))).)))))))))......))))))))))(((((.....)))))........))).).... ( -32.40)
>DroSec_CAF1 15406 114 - 1
AGGGUGCAAAAUGGUGGCUUCGUUUGUAGUGCCAACGAAAUUCUAGUUAGUUUGGCCUUACAAAUGUUUUAACAUCAUUUUAUUUGCAGUAUGCAAAAACUGCUCCACGCACUU
.(((((((((((((((....(((((((((.((((((..(((....))).).))))).)))))))))......)))))))))....(((((........))))).....)))))) ( -36.40)
>DroSim_CAF1 18106 114 - 1
AGGGUGCAAAAUGGUGGGUUCGUUUGUAGUGCCAACGAAAUUCUAGUUAGUUUGGCCUUACAAAUGUUUUAACAUCAUUUUAUUUGCAGUAUGCAAAAACUGCUCCACGCACUU
.(((((((((((((((....(((((((((.((((((..(((....))).).))))).)))))))))......)))))))))....(((((........))))).....)))))) ( -36.40)
>DroEre_CAF1 30269 111 - 1
---GUGCAAAAUGGUGGGUUCGUUUGUAGUGCCAACGAAAUUCUAGUUAGUUUGGCCUUACAAAUGUUUUAACAUCAUUUUAUUUGCAGUAUGCAAAAACUGCUCCACGCACUU
---(((((((((((((....(((((((((.((((((..(((....))).).))))).)))))))))......)))))))))....(((((........))))).....)))).. ( -35.20)
>DroYak_CAF1 30894 114 - 1
AGGGUGCAAAAUGGUGGGUUCGUUUGUAGUGCCAACGAAAUUCUAGUUAGUUUGGCCUUACAAAUGUUUUAACAUCAUUUUAUUUGCAGUAUGCAAAAACUGCUCCACGCACUU
.(((((((((((((((....(((((((((.((((((..(((....))).).))))).)))))))))......)))))))))....(((((........))))).....)))))) ( -36.40)
>consensus
AGGGUGCAAAAUGGUGGGUUCGUUUGUAGUGCCAACGAAAUUCUAGUUAGUUUGGCCUUACAAAUGUUUUAACAUCAUUUUAUUUGCAGUAUGCAAAAACUGCUCCACGCACUU
.(((((((((((((((....(((((((((.((((((..(((....))).).))))).)))))))))......)))))))))....(((((........))))).....)))))) (-34.34 = -34.78 +   0.44)

alignment

secondary structure

dotplot

Window 4

Location	17,734,305 – 17,734,402
Length	97
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	91.65
Mean single sequence MFE	-24.86
Consensus MFE	-21.78
Energy contribution	-22.96
Covariance contribution	1.18
Combinations/Pair	1.03
Mean z-score	-1.34
Structure conservation index	0.88
SVM decision value	0.46
SVM RNA-class probability	0.744683
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17734305 97 - 23771897
GCGGGGUGCAUAUCCAUAAGGGUGUAAAAUGGUGGGUUCGUUUGUAGUGCCAACGAAAUUCUAGUUAGUUUGGCCUUACAAAUGUUUUAACAUCAUU
((.....))((((((....))))))..(((((((....(((((((((.((((((..(((....))).).))))).)))))))))......))))))) ( -26.10)
>DroSec_CAF1 15441 97 - 1
GGGGGGUGCAUUUCCAUAAGGGUGCAAAAUGGUGGCUUCGUUUGUAGUGCCAACGAAAUUCUAGUUAGUUUGGCCUUACAAAUGUUUUAACAUCAUU
......(((((..((....))))))).(((((((....(((((((((.((((((..(((....))).).))))).)))))))))......))))))) ( -25.90)
>DroSim_CAF1 18141 97 - 1
GCGGGGUGCAUUUCCAUAAGGGUGCAAAAUGGUGGGUUCGUUUGUAGUGCCAACGAAAUUCUAGUUAGUUUGGCCUUACAAAUGUUUUAACAUCAUU
......(((((..((....))))))).(((((((....(((((((((.((((((..(((....))).).))))).)))))))))......))))))) ( -25.90)
>DroEre_CAF1 30304 81 - 1
GGGGG----------------GUGCAAAAUGGUGGGUUCGUUUGUAGUGCCAACGAAAUUCUAGUUAGUUUGGCCUUACAAAUGUUUUAACAUCAUU
.....----------------......(((((((....(((((((((.((((((..(((....))).).))))).)))))))))......))))))) ( -20.50)
>DroYak_CAF1 30929 97 - 1
GCGGGGUGCAUUUCCAUAAGGGUGCAAAAUGGUGGGUUCGUUUGUAGUGCCAACGAAAUUCUAGUUAGUUUGGCCUUACAAAUGUUUUAACAUCAUU
......(((((..((....))))))).(((((((....(((((((((.((((((..(((....))).).))))).)))))))))......))))))) ( -25.90)
>consensus
GCGGGGUGCAUUUCCAUAAGGGUGCAAAAUGGUGGGUUCGUUUGUAGUGCCAACGAAAUUCUAGUUAGUUUGGCCUUACAAAUGUUUUAACAUCAUU
......(((((((......))))))).(((((((....(((((((((.((((((..(((....))).).))))).)))))))))......))))))) (-21.78 = -22.96 +   1.18)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:49 2006