Locus 2164

Sequence ID	3R_DroMel_CAF1
Location	6,212,417 – 6,212,522
Length	105
Max. P	0.734100

overview

Window 2

Location	6,212,417 – 6,212,522
Length	105
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	77.04
Mean single sequence MFE	-17.12
Consensus MFE	-13.00
Energy contribution	-12.84
Covariance contribution	-0.16
Combinations/Pair	1.20
Mean z-score	-1.33
Structure conservation index	0.76
SVM decision value	0.43
SVM RNA-class probability	0.734100
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6212417 105 + 27905053
AAAUUAAA-CACUUCUUCCAGCAAAACUAUAUAGCAUAUUAGUUCGAGUUAUGGAGCUCGAACUGUUUAAAUCCGAAUCAACCGCAAAACAAAAACAACAGCGUUU
...(((((-(..........((...........)).....((((((((((....))))))))))))))))............(((...............)))... ( -18.36)
>DroSec_CAF1 29078 106 + 1
AAAUUAAAAUUCCUUUGAAAAAAGAAAUCGUUGGUAUAUUAGUUCAUGUUAUGGAGCUCGAACUGUUUAAAUCCGAAUCAACUGCAAAACAAAAACAACAGUGUUU
............((((....))))......((((.....((((((..(((....)))..)))))).......))))....((((..............)))).... ( -13.14)
>DroSim_CAF1 29544 105 + 1
AAAUUAAA-CCCUUUUUCCAGCAAAACUAUUUAGCAUAUUAGUUCGAGUUAUGGAGCUCGAACUGUUUAAAUCCGAAUAAACUACAAAACACAAACAACAGCGUUU
........-........................((.....((((((((((....))))))))))(((((........)))))..................)).... ( -16.80)
>DroEre_CAF1 29856 79 + 1
AAAUA---------------------------AAAAUAUUAGUUCGAGCUAUGGAGCUCGGACUGUAUGAGUCCGAAUCAACUGCAAAACACGAACAACAGCGUUU
.....---------------------------.........(((((.(((....)))(((((((.....)))))))...............))))).......... ( -19.00)
>DroYak_CAF1 26830 105 + 1
AAAGCAAA-CAUUUCUUCGAGCAAAACUAUUUAGCAUAUUAGUUCGAGUUAUGGAGCUCGGACUGUAUAAAUCCGAAUCAACUGCAAAACACAAACAACAGCGUUU
...(((..-...(((.....((...........))((((.((((((((((....))))))))))))))......))).....))).((((.(........).)))) ( -18.30)
>consensus
AAAUUAAA_CACUUCUUCCAGCAAAACUAUUUAGCAUAUUAGUUCGAGUUAUGGAGCUCGAACUGUUUAAAUCCGAAUCAACUGCAAAACACAAACAACAGCGUUU
.......................................(((((((((((....)))))))))))...........................((((......)))) (-13.00 = -12.84 +  -0.16)

alignment

secondary structure

dotplot

Window 3

Location	6,212,417 – 6,212,522
Length	105
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	77.04
Mean single sequence MFE	-20.54
Consensus MFE	-16.00
Energy contribution	-15.52
Covariance contribution	-0.48
Combinations/Pair	1.21
Mean z-score	-0.99
Structure conservation index	0.78
SVM decision value	-0.05
SVM RNA-class probability	0.508932
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6212417 105 - 27905053
AAACGCUGUUGUUUUUGUUUUGCGGUUGAUUCGGAUUUAAACAGUUCGAGCUCCAUAACUCGAACUAAUAUGCUAUAUAGUUUUGCUGGAAGAAGUG-UUUAAUUU
(((((((.((((.........))))....(((((....((((((((((((........)))))))).((((...)))).))))..)))))...))))-)))..... ( -19.80)
>DroSec_CAF1 29078 106 - 1
AAACACUGUUGUUUUUGUUUUGCAGUUGAUUCGGAUUUAAACAGUUCGAGCUCCAUAACAUGAACUAAUAUACCAACGAUUUCUUUUUUCAAAGGAAUUUUAAUUU
......((((((((.((((.((.(((....(((((((.....)))))))))).)).)))).)))).)))).......(((((((((....)))))))))....... ( -17.70)
>DroSim_CAF1 29544 105 - 1
AAACGCUGUUGUUUGUGUUUUGUAGUUUAUUCGGAUUUAAACAGUUCGAGCUCCAUAACUCGAACUAAUAUGCUAAAUAGUUUUGCUGGAAAAAGGG-UUUAAUUU
((((((........)))))).((((((((........)))))((((((((........))))))))....)))(((((..((((......))))..)-)))).... ( -20.40)
>DroEre_CAF1 29856 79 - 1
AAACGCUGUUGUUCGUGUUUUGCAGUUGAUUCGGACUCAUACAGUCCGAGCUCCAUAGCUCGAACUAAUAUUUU---------------------------UAUUU
......(((((((((.(((.((.(((....(((((((.....)))))))))).)).))).))))).))))....---------------------------..... ( -21.90)
>DroYak_CAF1 26830 105 - 1
AAACGCUGUUGUUUGUGUUUUGCAGUUGAUUCGGAUUUAUACAGUCCGAGCUCCAUAACUCGAACUAAUAUGCUAAAUAGUUUUGCUCGAAGAAAUG-UUUGCUUU
....(((((((((((.(((.((.(((....(((((((.....)))))))))).)).))).))))).)))).))((((((.((((......)))).))-)))).... ( -22.90)
>consensus
AAACGCUGUUGUUUGUGUUUUGCAGUUGAUUCGGAUUUAAACAGUUCGAGCUCCAUAACUCGAACUAAUAUGCUAAAUAGUUUUGCUGGAAAAAGUG_UUUAAUUU
......(((((((((.(((.((.(((....(((((((.....)))))))))).)).))).))))).)))).................................... (-16.00 = -15.52 +  -0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:52 2006