Locus 6778

Sequence ID	3L_DroMel_CAF1
Location	18,204,116 – 18,204,224
Length	108
Max. P	0.902770

overview

Window 1

Location	18,204,116 – 18,204,224
Length	108
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	94.04
Mean single sequence MFE	-29.35
Consensus MFE	-25.16
Energy contribution	-25.40
Covariance contribution	0.24
Combinations/Pair	1.05
Mean z-score	-1.56
Structure conservation index	0.86
SVM decision value	0.96
SVM RNA-class probability	0.890310
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18204116 108 + 23771897
CCUCAGUGUAGCUGCAAAAACACUUCUCAGCCCAGCAGCCAGCUACUGGGCAUACGCCAAAAAGGAGGCGACCAACGACCACGCCCCUAAGCAAAUAGACCGUAGAGA
.(((.((.((..(((..............((((((.((....)).))))))...........(((.((((...........)))))))..)))..)).))....))). ( -30.80)
>DroSec_CAF1 105991 107 + 1
CCCCAGUGUAGCUGCAAAAACACUUCUCAGCCCAGCAG-CAGCUACUGGGCAUACGCCAAAAAGGAGGCGACCAACGACCACGCCCCUAAGCAAAUAGACCGUAGAGA
.((((((((.(((((...................))))-).)).)))))).....((.....(((.((((...........)))))))..))................ ( -28.21)
>DroEre_CAF1 108030 107 + 1
CCCCAGUGUAGCUGCAAAAACACUUCUCAGCCCAGCAG-CAGCUACUGGGCAUACGCCAAAACGGAGGCGACCGUCGACCACGCCCCUAAGCAAAUAGACCGUAGAGA
.((((((((.(((((...................))))-).)).))))))....((((........))))((.(((......((......)).....))).))..... ( -29.31)
>DroYak_CAF1 112303 107 + 1
CCUCAGUGUAGCUGCAAAAACACUUCUCAGCCCAGCAG-CAGCUACUGGGCAUACGCCAAAAAGGAGGCGACCGUCGACCACGCCCCUAAGCAAAUAGACCGUAGAGA
.(((...((((((((......................)-))))))).((((...((((........))))...((.....))))))..................))). ( -28.65)
>DroAna_CAF1 113149 105 + 1
UUUCAGUGUAACUGCGAAAACACUU--CAGCCCAGCAU-CAGCUACUGGGCAUACGCCAAAAAGGAGGCGACUGGCGACCACGCCUCUAAGCAAAUAGACCGUAGAGA
...........(((((.........--..((((((...-......))))))............(((((((..(((...))))))))))............)))))... ( -29.80)
>consensus
CCUCAGUGUAGCUGCAAAAACACUUCUCAGCCCAGCAG_CAGCUACUGGGCAUACGCCAAAAAGGAGGCGACCGACGACCACGCCCCUAAGCAAAUAGACCGUAGAGA
.....((.((..(((..............((((((.((....)).))))))...........(((.((((...........)))))))..)))..)).))........ (-25.16 = -25.40 +   0.24)

alignment

secondary structure

dotplot

Window 2

Location	18,204,116 – 18,204,224
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	94.04
Mean single sequence MFE	-38.94
Consensus MFE	-34.40
Energy contribution	-34.44
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.48
Structure conservation index	0.88
SVM decision value	1.03
SVM RNA-class probability	0.902770
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18204116 108 - 23771897
UCUCUACGGUCUAUUUGCUUAGGGGCGUGGUCGUUGGUCGCCUCCUUUUUGGCGUAUGCCCAGUAGCUGGCUGCUGGGCUGAGAAGUGUUUUUGCAGCUACACUGAGG
((((............(((.(((((.(((..(...)..))))))))....)))....(((((((((....))))))))).))))(((((..........))))).... ( -39.70)
>DroSec_CAF1 105991 107 - 1
UCUCUACGGUCUAUUUGCUUAGGGGCGUGGUCGUUGGUCGCCUCCUUUUUGGCGUAUGCCCAGUAGCUG-CUGCUGGGCUGAGAAGUGUUUUUGCAGCUACACUGGGG
.................((((((((((((((((..((......))....)))).))))))).(((((((-(....(.(((....))).)....)))))))).))))). ( -38.40)
>DroEre_CAF1 108030 107 - 1
UCUCUACGGUCUAUUUGCUUAGGGGCGUGGUCGACGGUCGCCUCCGUUUUGGCGUAUGCCCAGUAGCUG-CUGCUGGGCUGAGAAGUGUUUUUGCAGCUACACUGGGG
.................((((((((((((((((((((......)))))..))).))))))).(((((((-(....(.(((....))).)....)))))))).))))). ( -41.90)
>DroYak_CAF1 112303 107 - 1
UCUCUACGGUCUAUUUGCUUAGGGGCGUGGUCGACGGUCGCCUCCUUUUUGGCGUAUGCCCAGUAGCUG-CUGCUGGGCUGAGAAGUGUUUUUGCAGCUACACUGAGG
.................(((((((((((((((((.((......))...))))).))))))).(((((((-(....(.(((....))).)....)))))))).))))). ( -39.40)
>DroAna_CAF1 113149 105 - 1
UCUCUACGGUCUAUUUGCUUAGAGGCGUGGUCGCCAGUCGCCUCCUUUUUGGCGUAUGCCCAGUAGCUG-AUGCUGGGCUG--AAGUGUUUUCGCAGUUACACUGAAA
......((((.((.((((.....((((....))))...((((........))))...((((((((....-.))))))))..--..........)))).)).))))... ( -35.30)
>consensus
UCUCUACGGUCUAUUUGCUUAGGGGCGUGGUCGACGGUCGCCUCCUUUUUGGCGUAUGCCCAGUAGCUG_CUGCUGGGCUGAGAAGUGUUUUUGCAGCUACACUGAGG
......((((.((.((((..(((.((............((((........))))...(((((((((....)))))))))......)).)))..)))).)).))))... (-34.40 = -34.44 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:29:43 2006