Locus 9560

Sequence ID	3R_DroMel_CAF1
Location	25,257,441 – 25,257,555
Length	114
Max. P	0.991407

overview

Window 8

Location	25,257,441 – 25,257,555
Length	114
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	95.30
Mean single sequence MFE	-30.50
Consensus MFE	-25.24
Energy contribution	-24.96
Covariance contribution	-0.28
Combinations/Pair	1.06
Mean z-score	-2.53
Structure conservation index	0.83
SVM decision value	2.27
SVM RNA-class probability	0.991407
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25257441 114 + 27905053
AAACAAAUAAAAGUUUAACUCCGGCCAGAGGCUAAGGAAAAUAUGUUGCAAUUUUUCAUAUUUUUCC--CACCCUUUUUGCCCGGAUGAGGAAAAAGCAUCCAGCUUCUUGCCCGG
((((........))))....(((((.(((((((..((((((((((...........)))))))))).--..............(((((.........)))))))))))).).)))) ( -29.10)
>DroSec_CAF1 114666 113 + 1
AAACAAAUAAAAGUUUAACUCCGGCCAGAGGCUAAGGAAAAUAUGUUGCAAUUUUUCAUAUU-UUCC--CACCCUUUUUGCCCGGAUGGGGAAAAAGCAUCCAGCUUCUUGCCCGG
((((........))))....(((((.(((((((..((((((((((...........))))))-))))--....((((((.(((....))).)))))).....))))))).).)))) ( -35.70)
>DroSim_CAF1 116845 114 + 1
AAACAAAUAAAAGUUUAACUCCGGCCAGAGGCUAAGGAAAAUAUGUUGCAAUUUUUCAUAUUUUUCC--CACCCUUUUUGCCCGGAUGGGGAAAAAGCAUCCAGCUUCUUGCCCGG
((((........))))....(((((.(((((((..((((((((((...........)))))))))).--....((((((.(((....))).)))))).....))))))).).)))) ( -32.80)
>DroEre_CAF1 131509 113 + 1
AAACAAAUAAAAGUUUAACUCCGGCCAGAGGCUAAGGAAAAUAUGUUGCAAUUUUUCAUAUUCUUCU--CACCCUU-UUGGCCGGAUGGGGAAAAACCAUUCAGCUUCUUGCCCGG
((((........))))...((((((((((((...((((.((((((...........)))))).))))--....)))-)))))))))((((.((.((.(.....).)).)).)))). ( -30.80)
>DroYak_CAF1 118997 116 + 1
AAACAAAUAAAAGUUUAACUCCGUCCAGAGGCUAAGGAAAAUAUGUUGCAAUUUUUCAUAUUCUUCUCUCACCCUUUUUGCCCGGAUGGAGAAAAACCAUUCAGCUUCUUGCCCGG
............((((..((((((((.(.(((.((((..((((((...........))))))..........))))...))))))))))))..))))......((.....)).... ( -24.10)
>consensus
AAACAAAUAAAAGUUUAACUCCGGCCAGAGGCUAAGGAAAAUAUGUUGCAAUUUUUCAUAUUCUUCC__CACCCUUUUUGCCCGGAUGGGGAAAAAGCAUCCAGCUUCUUGCCCGG
((((........))))....(((((.(((((((..((((((((((...........)))))).))))................(((((.........)))))))))))).).)))) (-25.24 = -24.96 +  -0.28)

alignment

secondary structure

dotplot

Window 9

Location	25,257,441 – 25,257,555
Length	114
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	95.30
Mean single sequence MFE	-35.96
Consensus MFE	-28.88
Energy contribution	-28.96
Covariance contribution	0.08
Combinations/Pair	1.11
Mean z-score	-2.99
Structure conservation index	0.80
SVM decision value	2.19
SVM RNA-class probability	0.990035
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25257441 114 - 27905053
CCGGGCAAGAAGCUGGAUGCUUUUUCCUCAUCCGGGCAAAAAGGGUG--GGAAAAAUAUGAAAAAUUGCAACAUAUUUUCCUUAGCCUCUGGCCGGAGUUAAACUUUUAUUUGUUU
..(((.(((((((.....))))))).))).(((((.((...(((.((--((.((((((((...........)))))))).)))).))).)).)))))...((((........)))) ( -34.00)
>DroSec_CAF1 114666 113 - 1
CCGGGCAAGAAGCUGGAUGCUUUUUCCCCAUCCGGGCAAAAAGGGUG--GGAA-AAUAUGAAAAAUUGCAACAUAUUUUCCUUAGCCUCUGGCCGGAGUUAAACUUUUAUUUGUUU
..(((.(((((((.....))))))).))).(((((.((...(((.((--((((-((((((...........)))))))))).)).))).)).)))))...((((........)))) ( -39.50)
>DroSim_CAF1 116845 114 - 1
CCGGGCAAGAAGCUGGAUGCUUUUUCCCCAUCCGGGCAAAAAGGGUG--GGAAAAAUAUGAAAAAUUGCAACAUAUUUUCCUUAGCCUCUGGCCGGAGUUAAACUUUUAUUUGUUU
..(((.(((((((.....))))))).))).(((((.((...(((.((--((.((((((((...........)))))))).)))).))).)).)))))...((((........)))) ( -37.00)
>DroEre_CAF1 131509 113 - 1
CCGGGCAAGAAGCUGAAUGGUUUUUCCCCAUCCGGCCAA-AAGGGUG--AGAAGAAUAUGAAAAAUUGCAACAUAUUUUCCUUAGCCUCUGGCCGGAGUUAAACUUUUAUUUGUUU
..(((..(((((((....))))))).))).((((((((.-.(((.((--((.((((((((...........)))))))).)))).))).))))))))...((((........)))) ( -38.40)
>DroYak_CAF1 118997 116 - 1
CCGGGCAAGAAGCUGAAUGGUUUUUCUCCAUCCGGGCAAAAAGGGUGAGAGAAGAAUAUGAAAAAUUGCAACAUAUUUUCCUUAGCCUCUGGACGGAGUUAAACUUUUAUUUGUUU
..(((((((....((((.(((((..((((.(((((......(((.((((.(((((.((((...........))))))))))))).)))))))).))))..)))))))))))))))) ( -30.90)
>consensus
CCGGGCAAGAAGCUGGAUGCUUUUUCCCCAUCCGGGCAAAAAGGGUG__GGAAAAAUAUGAAAAAUUGCAACAUAUUUUCCUUAGCCUCUGGCCGGAGUUAAACUUUUAUUUGUUU
..(((.(((((((.....))))))).))).(((((.((....((((...((.((((((((...........)))))))).))..)))).)).)))))...((((........)))) (-28.88 = -28.96 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:37:10 2006