Locus 6230

Sequence ID	3R_DroMel_CAF1
Location	16,281,512 – 16,281,684
Length	172
Max. P	0.997700

overview

Window 8

Location	16,281,512 – 16,281,604
Length	92
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	78.31
Mean single sequence MFE	-35.20
Consensus MFE	-27.51
Energy contribution	-27.40
Covariance contribution	-0.11
Combinations/Pair	1.10
Mean z-score	-2.15
Structure conservation index	0.78
SVM decision value	2.04
SVM RNA-class probability	0.986397
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16281512 92 + 27905053
UGCCAUGCCGGCAGGGCCAACAAGGACAACCAGUGCCACGACAAUGGUAAGAAAUGGAGUUGGCUGGCUGGAGGCG----------------------------UAGGAGGAGGACAGGA
.(((...(((((..(((((((..((....))..(((((......))))).........))))))).))))).))).----------------------------................ ( -31.50)
>DroSec_CAF1 2262 92 + 1
UGCCAUGCCGGCAGGGCCAACAAGGACAACCAGUGCCACGACAAUGGUAAGAAAUGGAGUUGGCUGGCUGGAGGCG----------------------------UAGGAGGAGGACAGGA
.(((...(((((..(((((((..((....))..(((((......))))).........))))))).))))).))).----------------------------................ ( -31.50)
>DroYak_CAF1 3270 120 + 1
UGCCAUGCCGGCAGCGCCAACAAGGACAACCACUGCCACGACAAUGGGGAGAAAUGGAGUUGGCUGGUUGGUGGCGUAGUAGGAGCUAGUUGGCGUAGAAGGCGUAGGAGGAGGAUUGGA
..(((((((..(.((((((((.....((((((..(((((..((.(.......).))..).)))))))))).((((.........)))))))))))).)..))))).))............ ( -42.60)
>consensus
UGCCAUGCCGGCAGGGCCAACAAGGACAACCAGUGCCACGACAAUGGUAAGAAAUGGAGUUGGCUGGCUGGAGGCG____________________________UAGGAGGAGGACAGGA
.(((...(((((...((((((..((....))..(((((......))))).........))))))..))))).)))............................................. (-27.51 = -27.40 +  -0.11)

alignment

secondary structure

dotplot

Window 9

Location	16,281,512 – 16,281,604
Length	92
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	78.31
Mean single sequence MFE	-27.28
Consensus MFE	-25.29
Energy contribution	-25.07
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-2.00
Structure conservation index	0.93
SVM decision value	2.91
SVM RNA-class probability	0.997700
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16281512 92 - 27905053
UCCUGUCCUCCUCCUA----------------------------CGCCUCCAGCCAGCCAACUCCAUUUCUUACCAUUGUCGUGGCACUGGUUGUCCUUGUUGGCCCUGCCGGCAUGGCA
................----------------------------.(((.((.((..((((((..........((((.(((....))).)))).......))))))...)).))...))). ( -25.33)
>DroSec_CAF1 2262 92 - 1
UCCUGUCCUCCUCCUA----------------------------CGCCUCCAGCCAGCCAACUCCAUUUCUUACCAUUGUCGUGGCACUGGUUGUCCUUGUUGGCCCUGCCGGCAUGGCA
................----------------------------.(((.((.((..((((((..........((((.(((....))).)))).......))))))...)).))...))). ( -25.33)
>DroYak_CAF1 3270 120 - 1
UCCAAUCCUCCUCCUACGCCUUCUACGCCAACUAGCUCCUACUACGCCACCAACCAGCCAACUCCAUUUCUCCCCAUUGUCGUGGCAGUGGUUGUCCUUGUUGGCGCUGCCGGCAUGGCA
.............(((.(((..(..(((((((.((..(..((((((((((...............................))))).))))).)..)).)))))))..)..))).))).. ( -31.18)
>consensus
UCCUGUCCUCCUCCUA____________________________CGCCUCCAGCCAGCCAACUCCAUUUCUUACCAUUGUCGUGGCACUGGUUGUCCUUGUUGGCCCUGCCGGCAUGGCA
.............................................(((..((((((((((.(..((...........))..)))))..))))))....(((((((...))))))).))). (-25.29 = -25.07 +  -0.22)

alignment

secondary structure

dotplot

Window 0

Location	16,281,588 – 16,281,684
Length	96
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	81.55
Mean single sequence MFE	-31.53
Consensus MFE	-25.39
Energy contribution	-25.50
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-1.52
Structure conservation index	0.81
SVM decision value	0.26
SVM RNA-class probability	0.658064
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16281588 96 - 27905053
CCAACUAUCUUGGCAGGCUGACUGCCUUCAGCGCUGGGCUCCGACUUGGUGGCAUCUUAUCCUGUUGCCGUCGUCGCGGUUCCUGUCCUCCUCCUA------------------------
...........((((((((((......)))))...(((((.((((.(((..(((........)))..)))..)))).)))))))))).........------------------------ ( -31.20)
>DroSec_CAF1 2338 96 - 1
CCAACUAUCUUGGCAGGCUGACUGCCUUCAGCGCUGGGCUCCGACUUGGUGGCAUCUUAUCCUGUCGCCGUCGUCGCGGUUCCUGUCCUCCUCCUA------------------------
...........((((((((((......)))))...(((((.((((.((((((((........))))))))..)))).)))))))))).........------------------------ ( -32.70)
>DroYak_CAF1 3350 117 - 1
CCAACUAUCUUGGCAGGCUGACUGCCUUCAGCGCUGGGCUCCGACUUAGUGGCAUCUUAUCCUGUCGCCG---UCGCGGUUCCAAUCCUCCUCCUACGCCUUCUACGCCAACUAGCUCCU
....(((..(((((((((.....))))...(((.((((...((((...((((((........)))))).)---))).((.......))....))))))).......))))).)))..... ( -30.70)
>consensus
CCAACUAUCUUGGCAGGCUGACUGCCUUCAGCGCUGGGCUCCGACUUGGUGGCAUCUUAUCCUGUCGCCGUCGUCGCGGUUCCUGUCCUCCUCCUA________________________
((((.....))))((((((((......))))).)))((..(((...((((((((........))))))))......)))..))..................................... (-25.39 = -25.50 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:16:09 2006