Locus 222

Sequence ID	X_DroMel_CAF1
Location	778,026 – 778,219
Length	193
Max. P	0.681119

overview

Window 5

Location	778,026 – 778,124
Length	98
Sequences	4
Columns	98
Reading direction	forward
Mean pairwise identity	90.31
Mean single sequence MFE	-27.43
Consensus MFE	-24.46
Energy contribution	-23.90
Covariance contribution	-0.56
Combinations/Pair	1.12
Mean z-score	-1.32
Structure conservation index	0.89
SVM decision value	0.01
SVM RNA-class probability	0.536947
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 778026 98 + 22224390
CGUGGACUGUGGCAAAGUUGUCAUGACUGGGAUACAAAUCCUUAUCGCUAUAAAUUAAUUGAAGCUGGCGUAAAGCGGUCGGCAUCAGUGACCAGCAA
..(((..((((((..((((.....))))(((((....)))))....)))))).....(((((.((((((........)))))).)))))..))).... ( -27.20)
>DroSec_CAF1 93591 98 + 1
CGUGGACCGUGGCAAAGUUGUCAUGACUGGGAUACAAAUCCUUAUCGCUAUAAAUUAAUUGAAGCUGGCGUAAAGCGGUCGGUAUCAGUGACCAGCAA
.......(((((((....))))))).((((((((........))))...........(((((.((((((........)))))).)))))..))))... ( -25.10)
>DroSim_CAF1 54810 98 + 1
CGUGGACCGUGGCAAAGUUGUCAUGACUGGGAUACAAAUCCUUAUCGCUAUAAAUUAAUUGAAGCUGGCGUAAAGCGGUCGGCAUCAGUGACCAGCAA
.......(((((((....))))))).((((((((........))))...........(((((.((((((........)))))).)))))..))))... ( -26.60)
>DroYak_CAF1 94071 93 + 1
-----AUCCAGGUCCAGUUGUCCUGACUGGGAUACAAAUCCCUAUCGCUAUAAAUUAAUUGAAGCUGGCGUACAGCGGUCGGCUUCAAUGAGCAGCAA
-----...........((((..(.((..(((((....)))))..))...........((((((((((((........)))))))))))))..)))).. ( -30.80)
>consensus
CGUGGACCGUGGCAAAGUUGUCAUGACUGGGAUACAAAUCCUUAUCGCUAUAAAUUAAUUGAAGCUGGCGUAAAGCGGUCGGCAUCAGUGACCAGCAA
................((((((..((..(((((....)))))..))...........(((((.((((((........)))))).))))))).)))).. (-24.46 = -23.90 +  -0.56)

alignment

secondary structure

dotplot

Window 6

Location	778,124 – 778,219
Length	95
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	79.16
Mean single sequence MFE	-25.67
Consensus MFE	-14.57
Energy contribution	-15.38
Covariance contribution	0.81
Combinations/Pair	1.12
Mean z-score	-1.85
Structure conservation index	0.57
SVM decision value	0.31
SVM RNA-class probability	0.681119
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 778124 95 - 22224390
AAAGGGUUAACUGAAGUGAAUGUGGGCCUGCAAAAUGGACUGAAAUCAGGGUUAGCCCCGAAAUGGACUUUUGGAAUUUUUCAAAGUU-UUCUGCA
...(((((((((..............((........)).(((....)))))))))))).(....(((((((.(((....)))))))))-)....). ( -21.20)
>DroSec_CAF1 93689 96 - 1
AAAGGGUUAACUGAAGUGAAUGUGGGCCUGGAAAAUGGACUGAAUUCAGGGUUAGGCCCGAAAUGGACUUUUGGAAUUUUUCAAAGUUUUUCUGCA
...(((..(((((((((..((.(((((((((....((((.....))))...)))))))))..))..)))))((((....)))).))))..)))... ( -23.40)
>DroSim_CAF1 54908 96 - 1
AAAGGGUUAACUGAAGUGAAUGUCGGCCUGGAAAAUGGACUGAAUUCAGGGUUAGCCCCGAAAUGGACUUUUGGAAUUUUUCAAAGUUUUUCUGCA
...(((((((((....(((((.((((((........)).))))))))).))))))))).((((..((((((.(((....))))))))))))).... ( -26.40)
>DroEre_CAF1 106498 91 - 1
AAAGGGUUAACUG-----AAUGUGGGCCUGGAAAAUGGUCUGAUUUCAGGGUUAGCCCCGAAAUGGACUUUGGGCAUUUUCCAAAGUUUUUCUGCG
...((((((((((-----((..((((((........))))))..)))..))))))))).((((..(((((((((.....))))))))))))).... ( -31.30)
>DroYak_CAF1 94164 91 - 1
AAAGGGUUAACUG-----AAUGUGGGCCUGGAAAACGGGCCGAUUUCGGGGUUAGCCCCGAAAUGGACUUUUGGCAUUUUGCAAACUUUUUCUGCA
((((((((..(.(-----(((((.((((((.....)))))).(((((((((....))))))))).........)))))).)..))))))))..... ( -35.40)
>DroPer_CAF1 167423 73 - 1
AAAGGGUUAACAGAAAGG-----------------------GGUUCCCGGGUUAGCCCCAAAAUUGACUUUUGGCAUUUUUCAAAGUUUUCUCUCU
...((((((((.....((-----------------------(...)))..)))))))).......((((((.((......))))))))........ ( -16.30)
>consensus
AAAGGGUUAACUGAAGUGAAUGUGGGCCUGGAAAAUGGACUGAAUUCAGGGUUAGCCCCGAAAUGGACUUUUGGAAUUUUUCAAAGUUUUUCUGCA
...(((((((((..............((........)).(((....)))))))))))).((((..((((((.((......)))))))))))).... (-14.57 = -15.38 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:19 2006