Locus 1658

Sequence ID	X_DroMel_CAF1
Location	4,672,530 – 4,672,680
Length	150
Max. P	0.992800

overview

Window 8

Location	4,672,530 – 4,672,645
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	79.17
Mean single sequence MFE	-28.43
Consensus MFE	-20.80
Energy contribution	-20.30
Covariance contribution	-0.50
Combinations/Pair	1.27
Mean z-score	-1.92
Structure conservation index	0.73
SVM decision value	1.01
SVM RNA-class probability	0.899625
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4672530 115 - 22224390
CUUGCUUCACUGGUUCCUUUGGUUGUCCGGCAACUAUUGUUGCUGGAUAUUUAGCAUUAGCUGGUGUCCGAUUUCUACUUUUUAACGA-----UUUAAGCUAGUUUAAAGUUGCAAAAGA
.(((...(((..(((...((((.(((((((((((....))))))))))).))))....)))..)))..)))......(((((((((..-----.(((((....))))).)))).))))). ( -31.10)
>DroSec_CAF1 33572 112 - 1
CUUGCUUCACUGGUUCCUUUGGUUGUCCGGCAACUAUUGUUGCUGGAUAUUUAGCAUUAGCUGGUGUCCGAUUUCUACUUUUUAACGA-----UUUGAACUA---UCAAGUUUCAGAAGA
.(((...(((..(((...((((.(((((((((((....))))))))))).))))....)))..)))..)))......(((((....((-----(((((....---)))))))..))))). ( -31.30)
>DroEre_CAF1 33974 114 - 1
UUUGCUUCACUGGUUCUUUUGGUUGUCCAGCAACUUUUGUUGUUGGGUAUUUAGCAUUAGUUCGUGCCCGGUUUCUACUUUUUAACGAUCUGAUUUCCACUC---GAAAUAUUAA---AA
..((((..((..(.....)..))(..((((((((....))))))))..)...))))((((.((((....(((....))).....)))).)))).........---..........---.. ( -23.90)
>DroYak_CAF1 30766 112 - 1
CUCGCAUCACUGCUUCCAUUGGUUGUCCGGCAACUAUUGUUGCUCGAUAUUUAGCAUUAACUGGUGUCCGAUGUCGGCUUUUUAACGG-----UUUUCUCUU---GAAAUAUGGACAUGA
...(((....)))..........(((((((((((....))))))(((((((..(((((....)))))..)))))))...((((((.((-----....)).))---))))...)))))... ( -27.40)
>consensus
CUUGCUUCACUGGUUCCUUUGGUUGUCCGGCAACUAUUGUUGCUGGAUAUUUAGCAUUAGCUGGUGUCCGAUUUCUACUUUUUAACGA_____UUUAAACUA___GAAAGAUGCA_AAGA
.(((...((((((((...((((.(((((((((((....))))))))))).))))....))))))))..)))................................................. (-20.80 = -20.30 +  -0.50)

alignment

secondary structure

dotplot

Window 9

Location	4,672,565 – 4,672,680
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	79.94
Mean single sequence MFE	-26.41
Consensus MFE	-20.80
Energy contribution	-20.30
Covariance contribution	-0.50
Combinations/Pair	1.27
Mean z-score	-2.49
Structure conservation index	0.79
SVM decision value	2.35
SVM RNA-class probability	0.992800
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4672565 115 - 22224390
UAGACAUUUCACCAUUUCUACUUA----CUCU-CACUUACCUUGCUUCACUGGUUCCUUUGGUUGUCCGGCAACUAUUGUUGCUGGAUAUUUAGCAUUAGCUGGUGUCCGAUUUCUACUU
((((.(((.((((...........----....-.....(((..(((.....)))......)))(((((((((((....)))))))))))...(((....)))))))...))).))))... ( -28.30)
>DroSec_CAF1 33604 115 - 1
UAGAAAUUUCCCCAUUUCUACUUA----CCUC-CACUUACCUUGCUUCACUGGUUCCUUUGGUUGUCCGGCAACUAUUGUUGCUGGAUAUUUAGCAUUAGCUGGUGUCCGAUUUCUACUU
((((((((.(.((..........(----((..-.....(((..........)))......)))(((((((((((....)))))))))))...(((....))))).)...))))))))... ( -29.22)
>DroEre_CAF1 34008 119 - 1
UAGACAUUUCCAC-UUUCCACUCAGCCACUACUUACAUAUUUUGCUUCACUGGUUCUUUUGGUUGUCCAGCAACUUUUGUUGUUGGGUAUUUAGCAUUAGUUCGUGCCCGGUUUCUACUU
..((((...(((.-...(((...(((.................)))....)))......))).)))).((((((....))))))((((((..(((....))).))))))........... ( -21.83)
>DroYak_CAF1 30798 111 - 1
UAGACAUUUCUAU-UUACC-------CAUUGC-UACUUACCUCGCAUCACUGCUUCCAUUGGUUGUCCGGCAACUAUUGUUGCUCGAUAUUUAGCAUUAACUGGUGUCCGAUGUCGGCUU
..((((((.....-.((((-------...(((-((........(((....)))..........((((.((((((....)))))).))))..)))))......))))...))))))..... ( -26.30)
>consensus
UAGACAUUUCCAC_UUUCCACUUA____CUAC_CACUUACCUUGCUUCACUGGUUCCUUUGGUUGUCCGGCAACUAUUGUUGCUGGAUAUUUAGCAUUAGCUGGUGUCCGAUUUCUACUU
.........................................(((...((((((((...((((.(((((((((((....))))))))))).))))....))))))))..)))......... (-20.80 = -20.30 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:01 2006