Locus 5139

Sequence ID	2R_DroMel_CAF1
Location	16,726,496 – 16,726,610
Length	114
Max. P	0.566069

overview

Window 7

Location	16,726,496 – 16,726,610
Length	114
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	85.03
Mean single sequence MFE	-36.72
Consensus MFE	-32.54
Energy contribution	-32.35
Covariance contribution	-0.19
Combinations/Pair	1.11
Mean z-score	-1.38
Structure conservation index	0.89
SVM decision value	0.06
SVM RNA-class probability	0.566069
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16726496 114 + 20766785
GCCUUGCGCUUCAGUAUGGUGAAGCGUAUUAACUGCUAAUCGCUGAAGUGCGGCGAAUGCGGCGGCACACGCGGGUACAGCUGCAUAGUGUAUAGAAAGAACGA-AAGGAGUUGG
(((.(((((((((......)))))))))....((((...((((((.....))))))..)))).)))((((((((......))))...))))..........(..-..)....... ( -38.20)
>DroPse_CAF1 37185 106 + 1
GCCUUGCGCUUCAGUAUGGUGAAGCGUAUUAACUGCUAAUCGCCGUAGUGCGGCGACUGCGGCGGCACACGUGGGUACAGCUGUGGA-----UGGGGCG--GCA-GAUAAGUUG-
(((.(((((((((......)))))))))......(((.(((((((((((......))))))))..((((..((....))..))))))-----)..))))--)).-.........- ( -41.70)
>DroEre_CAF1 35435 100 + 1
GCCUUGCGCUUCAGUAUGGUGAAGCGUAUUAACUGCUAAUCGCUGAAGUGCGGCGAAUGCGGCGGCACACGGGGGUACAGCUGUGAA--------------AGA-AAGGAGUUGU
(((.(((((((((......)))))))))....((((...((((((.....))))))..)))).))).(((((........)))))..--------------...-.......... ( -35.30)
>DroYak_CAF1 41037 101 + 1
GCCUUGCGCUUCAGUAUGGUGAAGCGUAUUAACUGCUAAUCGCUGAAGUGCGGCGAAUGCGGCGGCACACGCGGAUACAGCUGUGAA--------------UGAAAAGGAGUUGU
(((.(((((((((......)))))))))....((((...((((((.....))))))..)))).)))...(((((......)))))..--------------.............. ( -35.00)
>DroAna_CAF1 51883 98 + 1
GCCUUGCGCUUCAGUAUCGUGAAGCGUAUUAACUGCUAAUCGCUGAAGUGCGGCGACUGCGGCGGCACACGUGGGUACAGCUGUGAA----------------A-AAGGAGUUCA
(((.(((((((((......)))))))))....((((...((((((.....))))))..)))).))).((((((....))..))))..----------------.-.......... ( -32.50)
>DroPer_CAF1 36334 106 + 1
GCCUUGCGCUUCAGUAUGGUGAAGCGUAUUAACUGCUAAUCGCCGUAGUGCGGCGACUGCGGCGGCACACGUGGGUACAGCUGUGGA-----UGGGGAG--GGA-GAUAAGUUG-
.((.(((((((((......)))))))))....((.((.(((((((((((......))))))))..((((..((....))..))))))-----).)).))--)).-.........- ( -37.60)
>consensus
GCCUUGCGCUUCAGUAUGGUGAAGCGUAUUAACUGCUAAUCGCUGAAGUGCGGCGAAUGCGGCGGCACACGUGGGUACAGCUGUGAA______________GGA_AAGGAGUUG_
(((.(((((((((......)))))))))....((((...((((((.....))))))..)))).)))...(((((......))))).............................. (-32.54 = -32.35 +  -0.19)

alignment

secondary structure

dotplot

Window 8

Location	16,726,496 – 16,726,610
Length	114
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	85.03
Mean single sequence MFE	-28.42
Consensus MFE	-22.57
Energy contribution	-22.57
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.62
Structure conservation index	0.79
SVM decision value	-0.05
SVM RNA-class probability	0.507730
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16726496 114 - 20766785
CCAACUCCUU-UCGUUCUUUCUAUACACUAUGCAGCUGUACCCGCGUGUGCCGCCGCAUUCGCCGCACUUCAGCGAUUAGCAGUUAAUACGCUUCACCAUACUGAAGCGCAAGGC
..........-................((.(((((((((....(((.((((....)))).)))(((......)))....)))))).....((((((......))))))))).)). ( -29.40)
>DroPse_CAF1 37185 106 - 1
-CAACUUAUC-UGC--CGCCCCA-----UCCACAGCUGUACCCACGUGUGCCGCCGCAGUCGCCGCACUACGGCGAUUAGCAGUUAAUACGCUUCACCAUACUGAAGCGCAAGGC
-.........-.((--(......-----......((.((((......)))).)).((((((((((.....)))))))).))........(((((((......)))))))...))) ( -32.80)
>DroEre_CAF1 35435 100 - 1
ACAACUCCUU-UCU--------------UUCACAGCUGUACCCCCGUGUGCCGCCGCAUUCGCCGCACUUCAGCGAUUAGCAGUUAAUACGCUUCACCAUACUGAAGCGCAAGGC
......((((-...--------------.....((((((.....((.((((....)))).)).(((......)))....))))))....(((((((......))))))).)))). ( -24.80)
>DroYak_CAF1 41037 101 - 1
ACAACUCCUUUUCA--------------UUCACAGCUGUAUCCGCGUGUGCCGCCGCAUUCGCCGCACUUCAGCGAUUAGCAGUUAAUACGCUUCACCAUACUGAAGCGCAAGGC
......((((....--------------.....((((((....(((.((((....)))).)))(((......)))....))))))....(((((((......))))))).)))). ( -28.60)
>DroAna_CAF1 51883 98 - 1
UGAACUCCUU-U----------------UUCACAGCUGUACCCACGUGUGCCGCCGCAGUCGCCGCACUUCAGCGAUUAGCAGUUAAUACGCUUCACGAUACUGAAGCGCAAGGC
......((((-.----------------......((.((((......)))).)).((((((((.........)))))).))........(((((((......))))))).)))). ( -24.30)
>DroPer_CAF1 36334 106 - 1
-CAACUUAUC-UCC--CUCCCCA-----UCCACAGCUGUACCCACGUGUGCCGCCGCAGUCGCCGCACUACGGCGAUUAGCAGUUAAUACGCUUCACCAUACUGAAGCGCAAGGC
-.........-...--.......-----..((((..((....))..))))..(((((((((((((.....)))))))).))........(((((((......)))))))...))) ( -30.60)
>consensus
_CAACUCCUU_UCC______________UUCACAGCUGUACCCACGUGUGCCGCCGCAGUCGCCGCACUUCAGCGAUUAGCAGUUAAUACGCUUCACCAUACUGAAGCGCAAGGC
.................................((((((.....(((((((.((.......)).))))....)))....))))))....(((((((......)))))))...... (-22.57 = -22.57 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:32 2006