Locus 4886

Sequence ID	2R_DroMel_CAF1
Location	15,978,429 – 15,978,572
Length	143
Max. P	0.940299

overview

Window 6

Location	15,978,429 – 15,978,538
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.77
Mean single sequence MFE	-24.44
Consensus MFE	-18.56
Energy contribution	-18.80
Covariance contribution	0.24
Combinations/Pair	1.15
Mean z-score	-1.51
Structure conservation index	0.76
SVM decision value	-0.01
SVM RNA-class probability	0.530177
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15978429 109 + 20766785
AAUUAAAGCUCCGCAGGGA----AAAUAGAGGAAAUUCCUCGUUCAACUUUGACUGCACCUGUUCGAACAUCUUUCCU-------UUUAUUUUCCACUUUGCUAAGUGGCAACAGCAUAA
............(((((((----((...((((.....))))(((((((..((....))...))).))))...))))))-------).......((((((....)))))).....)).... ( -25.50)
>DroSec_CAF1 34197 109 + 1
AAUUAAAGCUCCGCAGGGA----AAACAGAGGAAAUUCCUCGCUCAACUUUGACUGCACCUGUUCGAAGUUCUUUCCU-------UUUAUUUUCCACUUUGCUAAGUGGCAACAGCAUAA
............(((((((----((...((((.....))))....((((((((..((....)))))))))).))))))-------).......((((((....)))))).....)).... ( -27.10)
>DroSim_CAF1 34370 109 + 1
AAUUAAAGCUCCGCAGGGA----AAACAGAGGAAAUUCCUCGCUCAACUUUGACUGCACCUGUUCGAAGUUCUUUCCU-------UUUAUUUUCCACUUUGCUAAGUGGCAACAGCAUAA
............(((((((----((...((((.....))))....((((((((..((....)))))))))).))))))-------).......((((((....)))))).....)).... ( -27.10)
>DroEre_CAF1 40587 109 + 1
AAUUAAAGCUCCGCAGGGA----AAAAAGUUGAAAUUCCUCGCUUAACUUCGACUGCACCUGCCCGAAGUUCGUUCCU-------UUUAUUUUUCACUUUGCAAAGUGGCAACAGCAUAA
.......(((..(((((((----(..((((.((......))))))(((((((...((....)).)))))))..)))))-------)........(((((....)))))))...))).... ( -22.10)
>DroYak_CAF1 42333 120 + 1
AAUUAAAGCUCCGCAGGGAGAAAAAAAAGUUGAAAUUCCUCGCUUAACUUUGACUGCACCUGUUCGAACUUCCUUCCUCUUAGUUUUUAUUUUUCACUUUGCCAAGUGGCAACAGCAUAA
.......(((..(((((..(.....((((((((..........)))))))).....).)))))..(((((...........)))))............(((((....))))).))).... ( -20.40)
>consensus
AAUUAAAGCUCCGCAGGGA____AAAAAGAGGAAAUUCCUCGCUCAACUUUGACUGCACCUGUUCGAAGUUCUUUCCU_______UUUAUUUUCCACUUUGCUAAGUGGCAACAGCAUAA
.......(((..(((((...........((((.....))))((............)).)))))..............................((((((....))))))....))).... (-18.56 = -18.80 +   0.24)

alignment

secondary structure

dotplot

Window 7

Location	15,978,465 – 15,978,572
Length	107
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	89.71
Mean single sequence MFE	-27.75
Consensus MFE	-23.72
Energy contribution	-23.56
Covariance contribution	-0.16
Combinations/Pair	1.17
Mean z-score	-1.77
Structure conservation index	0.85
SVM decision value	1.29
SVM RNA-class probability	0.940299
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15978465 107 - 20766785
AAAGGCUUGACUGUCACAGCUUUAAGAGGACUACUUAUGCUGUUGCCACUUAGCAAAGUGGAAAAUAAA-------AGGAAAGAUGUUCGAACAGGUGCAGUCAAAGUUGAACG
...((((((((((.(((........(((.....)))...(((((.((((((....))))))........-------..(((.....))).))))))))))))).)))))..... ( -26.60)
>DroSec_CAF1 34233 107 - 1
AAAGGCUUGACUGUCACAGCUUUAAAAGGACAACUUAUGCUGUUGCCACUUAGCAAAGUGGAAAAUAAA-------AGGAAAGAACUUCGAACAGGUGCAGUCAAAGUUGAGCG
...((((((((((.(((........(((.....)))...(((((.((((((....))))))........-------..(((.....))).))))))))))))).)))))..... ( -26.40)
>DroSim_CAF1 34406 107 - 1
AAAGGCUUGACUGUCACAGCUUUAAAAGGACUACUUAUGCUGUUGCCACUUAGCAAAGUGGAAAAUAAA-------AGGAAAGAACUUCGAACAGGUGCAGUCAAAGUUGAGCG
...((((((((((.(((........(((.....)))...(((((.((((((....))))))........-------..(((.....))).))))))))))))).)))))..... ( -26.40)
>DroEre_CAF1 40623 106 - 1
GAAGGCUUGGCUGUCACUGCUUUAA-AGUACUACUUAUGCUGUUGCCACUUUGCAAAGUGAAAAAUAAA-------AGGAACGAACUUCGGGCAGGUGCAGUCGAAGUUAAGCG
....((((((((.(((((((....(-((.....)))...(((((..(((((....))))).........-------.....((.....)))))))..))))).)))))))))). ( -27.00)
>DroYak_CAF1 42373 114 - 1
AAGGGCUUGACUGUCACUGCUUUAAAAGGACUACUUAUGCUGUUGCCACUUGGCAAAGUGAAAAAUAAAAACUAAGAGGAAGGAAGUUCGAACAGGUGCAGUCAAAGUUAAGCG
....((((((((...(((((.......(((((.(((...((.(((((....)))))(((...........))).))...)))..)))))........)))))...)))))))). ( -32.36)
>consensus
AAAGGCUUGACUGUCACAGCUUUAAAAGGACUACUUAUGCUGUUGCCACUUAGCAAAGUGGAAAAUAAA_______AGGAAAGAACUUCGAACAGGUGCAGUCAAAGUUGAGCG
...((((((((((.(((........(((.....)))...(((((.((((((....)))))).................(((.....))).)))))))))))))).))))..... (-23.72 = -23.56 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:30 2006