Locus 3850

Sequence ID	2R_DroMel_CAF1
Location	12,723,329 – 12,723,439
Length	110
Max. P	0.999766

overview

Window 1

Location	12,723,329 – 12,723,439
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	95.73
Mean single sequence MFE	-27.98
Consensus MFE	-24.56
Energy contribution	-24.60
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-3.57
Structure conservation index	0.88
SVM decision value	4.03
SVM RNA-class probability	0.999766
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12723329 110 + 20766785
CUUGCCAUUUCUGCACAAAUAAAUCAAAUAUGAUUAUUUGAUGACCUUUCUGCCCCAAAUGCUGACGUUGCCACACUCAUAUAUGCAGCAAAUUAGCAUUUGUUCAGGCA
..((((......(((.(((...((((((((....))))))))....))).)))..((((((((((.(((((.............)))))...))))))))))....)))) ( -29.52)
>DroSec_CAF1 69649 110 + 1
CUUGCAAUUUCCGCACAAAUAAAUCAAAUAUGAUUAUUUGAUGACCUUUCUGCCCCAAAUGCUGACGUUGCCACACUCAUAUCUGCAGCAAAUUAGCAUUUGUUCAGGCA
..(((.......))).......((((((((....)))))))).........(((.((((((((((.(((((.............)))))...))))))))))....))). ( -26.32)
>DroSim_CAF1 75517 110 + 1
CUUGCAAUUUCUGCACAAAUAAAUCAAAUAUGAUUAUUUGAUAACCUUUCUGCCCCAAAUGCUGACGUUGCCACACUCAUAUCUGCAGCAAAUUAGCAUUGGUUCGGGCA
..((((.....)))).......((((((((....)))))))).........((((..((((((((.(((((.............)))))...)))))))).....)))). ( -28.02)
>DroEre_CAF1 70504 110 + 1
CUUGCAAUUUCUGGAGAUAUAAAUCAAAUAUGAUUAUUUGAUGACCCUUCUGCCCCAAAUGCUGAUGUUGCCACACUCAUAUCUGCAGCAAAUUAGCAUUUGUUCAGGCA
............((((......((((((((....))))))))....)))).(((.((((((((((((((((.............))))))..))))))))))....))). ( -29.22)
>DroYak_CAF1 77402 110 + 1
CUUGCAAUUUCUGAACAAAUAAAUCAAAUAUGAUUAUUUGAUGACCUUUCUGCCCCAAAUGCUGACGUUGCCACACUCAUAUCUGCAGCAAAUUAGCAUUUGUUCAGGCA
.........(((((((((((..((((((((....))))))))..................(((((.(((((.............)))))...)))))))))))))))).. ( -26.82)
>consensus
CUUGCAAUUUCUGCACAAAUAAAUCAAAUAUGAUUAUUUGAUGACCUUUCUGCCCCAAAUGCUGACGUUGCCACACUCAUAUCUGCAGCAAAUUAGCAUUUGUUCAGGCA
..(((.................((((((((....)))))))).......(((...((((((((((.(((((.............)))))...))))))))))..)))))) (-24.56 = -24.60 +   0.04)

alignment

secondary structure

dotplot

Window 2

Location	12,723,329 – 12,723,439
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	95.73
Mean single sequence MFE	-32.30
Consensus MFE	-28.42
Energy contribution	-28.30
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-2.93
Structure conservation index	0.88
SVM decision value	3.76
SVM RNA-class probability	0.999594
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12723329 110 - 20766785
UGCCUGAACAAAUGCUAAUUUGCUGCAUAUAUGAGUGUGGCAACGUCAGCAUUUGGGGCAGAAAGGUCAUCAAAUAAUCAUAUUUGAUUUAUUUGUGCAGAAAUGGCAAG
((((....((((((((.((((((..(((......)))..)))).)).))))))))..(((.(((....((((((((....))))))))...))).)))......)))).. ( -36.90)
>DroSec_CAF1 69649 110 - 1
UGCCUGAACAAAUGCUAAUUUGCUGCAGAUAUGAGUGUGGCAACGUCAGCAUUUGGGGCAGAAAGGUCAUCAAAUAAUCAUAUUUGAUUUAUUUGUGCGGAAAUUGCAAG
(((.....((((((((.((((((..((........))..)))).)).))))))))..(((.(((....((((((((....))))))))...))).))).......))).. ( -31.30)
>DroSim_CAF1 75517 110 - 1
UGCCCGAACCAAUGCUAAUUUGCUGCAGAUAUGAGUGUGGCAACGUCAGCAUUUGGGGCAGAAAGGUUAUCAAAUAAUCAUAUUUGAUUUAUUUGUGCAGAAAUUGCAAG
(((.....((((((((.((((((..((........))..)))).)).)))).)))).(((.(((....((((((((....))))))))...))).))).......))).. ( -30.60)
>DroEre_CAF1 70504 110 - 1
UGCCUGAACAAAUGCUAAUUUGCUGCAGAUAUGAGUGUGGCAACAUCAGCAUUUGGGGCAGAAGGGUCAUCAAAUAAUCAUAUUUGAUUUAUAUCUCCAGAAAUUGCAAG
(((((...((((((((.((((((..((........))..)))).)).)))))))))))))(.(((...((((((((....)))))))).....))).)............ ( -29.40)
>DroYak_CAF1 77402 110 - 1
UGCCUGAACAAAUGCUAAUUUGCUGCAGAUAUGAGUGUGGCAACGUCAGCAUUUGGGGCAGAAAGGUCAUCAAAUAAUCAUAUUUGAUUUAUUUGUUCAGAAAUUGCAAG
((((((((((((((((..((((((.(((((.(((.(((....))))))..))))).))))))..))).((((((((....))))))))..)))))))))).....))).. ( -33.30)
>consensus
UGCCUGAACAAAUGCUAAUUUGCUGCAGAUAUGAGUGUGGCAACGUCAGCAUUUGGGGCAGAAAGGUCAUCAAAUAAUCAUAUUUGAUUUAUUUGUGCAGAAAUUGCAAG
(((((...((((((((.((((((..((........))..)))).)).)))))))))))))........((((((((....))))))))...................... (-28.42 = -28.30 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:35 2006