Locus 5943

Sequence ID	3L_DroMel_CAF1
Location	15,920,485 – 15,920,645
Length	160
Max. P	0.990340

overview

Window 2

Location	15,920,485 – 15,920,605
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.92
Mean single sequence MFE	-36.69
Consensus MFE	-34.48
Energy contribution	-34.04
Covariance contribution	-0.44
Combinations/Pair	1.13
Mean z-score	-1.65
Structure conservation index	0.94
SVM decision value	2.21
SVM RNA-class probability	0.990340
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15920485 120 + 23771897
UCUCUUGGAUGAAGGUGGCCAUAUACCUUCUUACGUUCCUAACCUACGCCUAUUCAGGCUAUGGAUCCAGCACCAUAGUCCACGUAAGGUGCACCGCUUCUCGUAGGAAAUCUGUGAGAG
((((.((((((((((((......))))))).....((((((.((...((((....))))...)).....(((((.(((....).)).)))))...........))))))))))).)))). ( -37.10)
>DroSec_CAF1 22173 120 + 1
UCUCCUGGAUGAAGGUGGCCAUAUACCUUCUAACGUUCCUAACCUACGCCUAUUCAGGCUAUGGAUCCAGCACCAUAGUCCACGUAAGGUGCACCUCUUCUCGAAGGGAAUCUGUGAGAG
((((.((((((((((((......))))))).....(((((..((...((((....))))...)).....(((((.(((....).)).)))))............)))))))))).)))). ( -35.30)
>DroSim_CAF1 22502 120 + 1
UCUCCUGGAUGAAGGUGGCCAUAUACCUUCUAACGUUCCUAACCUACGCCUAUUCAGGCUAUGGAUCCAGCACCAUAGUCCACGUAAGGUGCACCUCUUCUCGAAGGGAAUCUGUGAGAG
((((.((((((((((((......))))))).....(((((..((...((((....))))...)).....(((((.(((....).)).)))))............)))))))))).)))). ( -35.30)
>DroEre_CAF1 19843 120 + 1
UCUCGUGGAUGAAGGUAGCCAUAUACCUUCUAACGUUCCUAACGUACGCCUAUUCAGGGUAUGGAUCCAGCACCAUAGUCCAUGUAAGGUGCACCUCUUUUCGAAGGGAAUCCGUGAGAG
(((((((((((((((((......))))))).....(((((..(((((.(((....))))))))......(((((.............)))))............))))))))))))))). ( -40.42)
>DroYak_CAF1 20483 120 + 1
UUUCGUGGAUGAAGGUGGCCAUAUACCUUCUAACGUUCCUGACAUACGCCUAUUCAGGCUAUGGAUCCAGCACCAUAGUACAUGUAAGGUGCACCUCUUUUCGAAGGGAAUCCGUAAGAG
(((..((((((((((((......))))))).....(((((..((((.((((....))))))))......(((((.............)))))............))))))))))..))). ( -35.32)
>consensus
UCUCCUGGAUGAAGGUGGCCAUAUACCUUCUAACGUUCCUAACCUACGCCUAUUCAGGCUAUGGAUCCAGCACCAUAGUCCACGUAAGGUGCACCUCUUCUCGAAGGGAAUCUGUGAGAG
((((.((((((((((((......))))))).....(((((......(((((((...((((((((........))))))))...)).)))))....((.....)))))))))))).)))). (-34.48 = -34.04 +  -0.44)

alignment

secondary structure

dotplot

Window 3

Location	15,920,525 – 15,920,645
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.08
Mean single sequence MFE	-33.03
Consensus MFE	-27.48
Energy contribution	-28.16
Covariance contribution	0.68
Combinations/Pair	1.08
Mean z-score	-1.52
Structure conservation index	0.83
SVM decision value	0.59
SVM RNA-class probability	0.792946
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15920525 120 + 23771897
AACCUACGCCUAUUCAGGCUAUGGAUCCAGCACCAUAGUCCACGUAAGGUGCACCGCUUCUCGUAGGAAAUCUGUGAGAGCUAGUAUCUGUUACUCCUGUAUCUUCUCUCCCCGGAUUUA
..(((((((((((...((((((((........))))))))...)).))))((...)).....)))))(((((((.(((((...((((..(.....)..))))...)))))..))))))). ( -32.50)
>DroSec_CAF1 22213 120 + 1
AACCUACGCCUAUUCAGGCUAUGGAUCCAGCACCAUAGUCCACGUAAGGUGCACCUCUUCUCGAAGGGAAUCUGUGAGAGCUGGUAUCUGUUACUCCUGUAUCUUCUCUCCCCGGAUUUA
......(((((((...((((((((........))))))))...)).)))))..(((........)))(((((((.(((((..(((((..(.....)..)))))..)))))..))))))). ( -33.60)
>DroSim_CAF1 22542 120 + 1
AACCUACGCCUAUUCAGGCUAUGGAUCCAGCACCAUAGUCCACGUAAGGUGCACCUCUUCUCGAAGGGAAUCUGUGAGAGCUGGUAUCUGUUACUCCUGUAUCUUCUCUCCCCGGAUUUA
......(((((((...((((((((........))))))))...)).)))))..(((........)))(((((((.(((((..(((((..(.....)..)))))..)))))..))))))). ( -33.60)
>DroEre_CAF1 19883 119 + 1
AACGUACGCCUAUUCAGGGUAUGGAUCCAGCACCAUAGUCCAUGUAAGGUGCACCUCUUUUCGAAGGGAAUCCGUGAGAGAUGCUAUCUG-UACUCCUGUAUCUUCUCUCCCCGGAUUUA
..(((((.(((....))))))))......(((((.............))))).(((........)))(((((((.(((((((((......-.......))))).))))....))))))). ( -33.94)
>DroYak_CAF1 20523 119 + 1
GACAUACGCCUAUUCAGGCUAUGGAUCCAGCACCAUAGUACAUGUAAGGUGCACCUCUUUUCGAAGGGAAUCCGUAAGAGAUGCCAUAUG-UACUCCUGUAUCUUCUCUCCCCGGAUUUA
..((((.((((....))))))))(((((.(((((.............)))))..........((((((.((((....).))).))....(-(((....)))))))).......))))).. ( -31.52)
>consensus
AACCUACGCCUAUUCAGGCUAUGGAUCCAGCACCAUAGUCCACGUAAGGUGCACCUCUUCUCGAAGGGAAUCUGUGAGAGCUGGUAUCUGUUACUCCUGUAUCUUCUCUCCCCGGAUUUA
......(((((((...((((((((........))))))))...)).)))))..((((.....)).))(((((((.(((((..(((((...........)))))..)))))..))))))). (-27.48 = -28.16 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:46 2006