Locus 162

Sequence ID	3L_DroMel_CAF1
Location	507,122 – 507,264
Length	142
Max. P	0.939167

overview

Window 9

Location	507,122 – 507,235
Length	113
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	89.86
Mean single sequence MFE	-31.88
Consensus MFE	-24.42
Energy contribution	-25.46
Covariance contribution	1.04
Combinations/Pair	1.04
Mean z-score	-2.30
Structure conservation index	0.77
SVM decision value	1.28
SVM RNA-class probability	0.939167
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 507122 113 + 23771897
GGCGGGUAAAUGCAGUCAUGGAUACGAUUUUCCUUUUCUGUUUUUCCUCGCCGCUAUUAUGAGUGCAGUGUAUUUCAAGU-----GCGAAUGCACUUAUCAUCUCUGUUUUCCUAACG
((((((.(((.((((....(((........)))....)))).))).))))))......(((((((((.(((((.....))-----)))..)))))))))................... ( -33.60)
>DroSec_CAF1 87312 117 + 1
GGCGGGUAAAUGCAGUCAUGGAUACGAUUUUCCUUUUCUGUU-UUCCUCGCCGCCAUUAUGAGUGCAGUGUAUUUCAAGUGCAGUGCGAUUGCACUUAUCAUCUCUGUUUUCCUAACU
((((((.(((.((((....(((........)))....)))))-)).))))))......((((((((((((((((.(....).))))).)))))))))))................... ( -34.90)
>DroSim_CAF1 88744 118 + 1
GGCGGGUAAAUGCAGUCAUGGAUACGAUUUUCCUUUUCUGUUUUUCCUCGCCGCUAUUAUGAGUGCAAUGUAUUUCAAGUGCAGUGCGAAUGCACUUAUCAUCUCUGUUUUCCUAACG
((((((.(((.((((....(((........)))....)))).))).))))))......(((((((((.((((((.(....).))))))..)))))))))................... ( -33.60)
>DroEre_CAF1 90346 110 + 1
GGCGGGUAAAUGCAGUCAUGGAUACGAUUUUCCUUUUCUGCUUUU-CUCGCCGCUAUUAUGAGU-------ACUUGAAAUGCAGUGCGAAUGCACUUAUCAUCUCUGUUUUUCUAACG
((((((.(((.((((....(((........)))....)))).)))-))))))........(((.-------((..((.(((.(((((....)))))...))).)).))..)))..... ( -29.90)
>DroYak_CAF1 92481 111 + 1
GGCGCGUAAAUGCAGUCAUGGAUACGAUUUUCCUCUUCUGUUUUUCCUCGCCGCUAUUAUGAGU-------AUCUAAAGUGCAGUGCGAAUGCACUUAUCAUCUCUGUUUUCCUAACG
((((.(.(((.((((....(((........)))....)))).))).).))))........(((.-------.....(((((((.......))))))).....)))............. ( -27.40)
>consensus
GGCGGGUAAAUGCAGUCAUGGAUACGAUUUUCCUUUUCUGUUUUUCCUCGCCGCUAUUAUGAGUGCA_UGUAUUUCAAGUGCAGUGCGAAUGCACUUAUCAUCUCUGUUUUCCUAACG
((((((.(((.((((....(((........)))....)))).))).))))))........................(((((((.......)))))))..................... (-24.42 = -25.46 +   1.04)

alignment

secondary structure

dotplot

Window 0

Location	507,160 – 507,264
Length	104
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	82.11
Mean single sequence MFE	-27.68
Consensus MFE	-15.44
Energy contribution	-16.32
Covariance contribution	0.88
Combinations/Pair	1.15
Mean z-score	-2.25
Structure conservation index	0.56
SVM decision value	0.50
SVM RNA-class probability	0.759852
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 507160 104 - 23771897
AAGCCCGUCGUCGCUCCAUUUUAUGGAACCGUUAGGAAAACAGAGAUGAUAAGUGCAUUCGC-----ACUUGAAAUACACUGCACUCAUAAUAGCGGCGAGGAAAAACA
....((.((((((((((((...)))))...((((.((...(((.(((..(((((((....))-----)))))..)).).)))...)).)))).)))))))))....... ( -29.60)
>DroSec_CAF1 87350 97 - 1
-----------CGUUCCAUUUUAUGGAACAGUUAGGAAAACAGAGAUGAUAAGUGCAAUCGCACUGCACUUGAAAUACACUGCACUCAUAAUGGCGGCGAGGAA-AACA
-----------.(((((((...))))))).(((................((((((((.......)))))))).....(.((((.(.......))))).).....-))). ( -22.20)
>DroSim_CAF1 88782 109 - 1
AAUCCCGUAGUCGUUCCAUUUUAUGGAACCGUUAGGAAAACAGAGAUGAUAAGUGCAUUCGCACUGCACUUGAAAUACAUUGCACUCAUAAUAGCGGCGAGGAAAAACA
..((((((....(((((((...)))))))((((((.....).(((......(((((....)))))(((..((.....)).))).)))....)))))))).)))...... ( -28.30)
>DroEre_CAF1 90384 98 - 1
CCGCC---CGCCGUUCCAUUUUAUGGAACCGUUAGAAAAACAGAGAUGAUAAGUGCAUUCGCACUGCAUUUCAAGU-------ACUCAUAAUAGCGGCGAG-AAAAGCA
.((((---.((.(((((((...))))))).............((((((...(((((....))))).))))))....-------..........))))))..-....... ( -29.70)
>DroYak_CAF1 92519 98 - 1
C-GGC---CGCCGCUCCAUAUUAUGGAACCGUUAGGAAAACAGAGAUGAUAAGUGCAUUCGCACUGCACUUUAGAU-------ACUCAUAAUAGCGGCGAGGAAAAACA
.-...---(((((((....(((((((..((....)).....((((.((...(((((....))))).))))))....-------..)))))))))))))).......... ( -28.60)
>consensus
A_GCC___CGCCGUUCCAUUUUAUGGAACCGUUAGGAAAACAGAGAUGAUAAGUGCAUUCGCACUGCACUUGAAAUACA_UGCACUCAUAAUAGCGGCGAGGAAAAACA
........(((((((.....((((((....(((.....))).(((.((...(((((....))))).)))))..............)))))).))))))).......... (-15.44 = -16.32 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:08 2006