Locus 506

Sequence ID	X_DroMel_CAF1
Location	1,448,825 – 1,448,935
Length	110
Max. P	0.982977

overview

Window 5

Location	1,448,825 – 1,448,935
Length	110
Sequences	3
Columns	117
Reading direction	forward
Mean pairwise identity	82.06
Mean single sequence MFE	-33.76
Consensus MFE	-23.58
Energy contribution	-24.24
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.56
Structure conservation index	0.70
SVM decision value	1.42
SVM RNA-class probability	0.951966
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1448825 110 + 22224390
GCCGCGUUUACUUAGUUAGUCCGAAA-GAGGCAGAGAAACAAGAGGAGCGAGGGGGGGGGGGGAA------AAGUCGCGGAUUGCGACAGCUCCAAAAUGCGGCGACAAAGGUAAAA
(((((((((.........((((....-).)))............(((((................------..(((((.....))))).))))).)))))))))............. ( -33.61)
>DroSim_CAF1 35799 106 + 1
GCCGCGUUUACUUAGUUAGUCCGAAA-AAGGGAGAGAAACGAGAGGAGCGAGGGA----GAGGAA------AAGUCGCGGAUUGCGACAGCUCCAAAAUGCGGCGACAAAGGUAAAA
(((((((((.(((..((..(((....-..)))....))..))).(((((......----......------..(((((.....))))).))))).)))))))))............. ( -32.66)
>DroAna_CAF1 65572 113 + 1
GCCGCGUUUACUUAGUUAGUCCGGACGGACAAAAAGAGAUAGGUGGAGAGAGGGG----AGGGAAUACCCGGAGUCGCGGAUUGCGACAGCUCCGAAAUGCCGCGACAAAGGUAAAA
((.((((((.(((..((.((((....)))).))..))).....(((((...(((.----........)))...(((((.....)))))..))))))))))).))............. ( -35.00)
>consensus
GCCGCGUUUACUUAGUUAGUCCGAAA_GAGGAAGAGAAACAAGAGGAGCGAGGGG____GGGGAA______AAGUCGCGGAUUGCGACAGCUCCAAAAUGCGGCGACAAAGGUAAAA
((((((((((((.....)))........................(((((........................(((((.....))))).))))).)))))))))............. (-23.58 = -24.24 +   0.67)

alignment

secondary structure

dotplot

Window 6

Location	1,448,825 – 1,448,935
Length	110
Sequences	3
Columns	117
Reading direction	reverse
Mean pairwise identity	82.06
Mean single sequence MFE	-28.29
Consensus MFE	-19.38
Energy contribution	-20.04
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-3.01
Structure conservation index	0.68
SVM decision value	1.93
SVM RNA-class probability	0.982977
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1448825 110 - 22224390
UUUUACCUUUGUCGCCGCAUUUUGGAGCUGUCGCAAUCCGCGACUU------UUCCCCCCCCCCCCUCGCUCCUCUUGUUUCUCUGCCUC-UUUCGGACUAACUAAGUAAACGCGGC
.............(((((.....(((((.(((((.....)))))..------................))))).((((((..((((....-...))))..))).))).....))))) ( -27.41)
>DroSim_CAF1 35799 106 - 1
UUUUACCUUUGUCGCCGCAUUUUGGAGCUGUCGCAAUCCGCGACUU------UUCCUC----UCCCUCGCUCCUCUCGUUUCUCUCCCUU-UUUCGGACUAACUAAGUAAACGCGGC
.............(((((.....(((((.(((((.....)))))..------......----......)))))....((((.....((..-....))(((.....)))))))))))) ( -25.36)
>DroAna_CAF1 65572 113 - 1
UUUUACCUUUGUCGCGGCAUUUCGGAGCUGUCGCAAUCCGCGACUCCGGGUAUUCCCU----CCCCUCUCUCCACCUAUCUCUUUUUGUCCGUCCGGACUAACUAAGUAAACGCGGC
..........((((((.......((((..(((((.....)))))...(((....))).----.......))))..............((((....))))............)))))) ( -32.10)
>consensus
UUUUACCUUUGUCGCCGCAUUUUGGAGCUGUCGCAAUCCGCGACUU______UUCCCC____CCCCUCGCUCCUCUUGUUUCUCUCCCUC_UUUCGGACUAACUAAGUAAACGCGGC
.............(((((.....(((((.(((((.....)))))........................)))))......................(.(((.....)))...)))))) (-19.38 = -20.04 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:17 2006