Locus 5578

Sequence ID	3L_DroMel_CAF1
Location	15,301,911 – 15,302,008
Length	97
Max. P	0.864998

overview

Window 2

Location	15,301,911 – 15,302,008
Length	97
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	76.21
Mean single sequence MFE	-28.27
Consensus MFE	-19.78
Energy contribution	-19.45
Covariance contribution	-0.33
Combinations/Pair	1.19
Mean z-score	-1.39
Structure conservation index	0.70
SVM decision value	0.84
SVM RNA-class probability	0.864998
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15301911 97 + 23771897
-U-GGACGACUCUCCAUUUAAAAGAGAAGUUGCGCACGUUGCGGCAGUCAGUCGAAAAUCAGCCAACGUGCGCGUUACAUUAC--GAACCGG--AAAAUAUCG
-.-((..(((((((.........))).))))((((((((((((((.....)))).........))))))))))..........--...))..--......... ( -26.10)
>DroVir_CAF1 34208 90 + 1
GUGUACCGUCUCUCUAUUUAAGUGAG-AGCUGCGCACGUUGCGGCAGUCAGUCGACACUCAGCCAACGUGCGCGCCAGAC-----AUACCAA--AAA-----G
((((....((((.((.....)).)))-)((.(((((((((((....(((....))).....).))))))))))))...))-----)).....--...-----. ( -29.00)
>DroGri_CAF1 35294 87 + 1
---GCCCGUCUCUCUAUUUAAAUGAG-AGUUGCGCACGUUGCGGCAGUCAGUCGACACUCAGCCAACGUGCGCGCCACAC-----AUACCGA--AAA-----G
---((....(((((.........)))-))..(((((((((((....(((....))).....).)))))))))))).....-----.......--...-----. ( -27.10)
>DroSim_CAF1 34061 97 + 1
-U-GGACGACUCUCCAUUUAAAAGAGAAGUUGCGCACGUUGCGGCAGUCAGUCGAAAAUCAGCCAACGUGCGCGUUACAUUAC--GAACCGG--AAAGUAUCG
-.-.((..(((.(((................((((((((((((((.....)))).........))))))))))((......))--.....))--).))).)). ( -26.60)
>DroMoj_CAF1 32830 92 + 1
GAGGACCGUCUCUCUAUUUAAGUGAG-AGUUGCGCACGUUGCGGCAGUCAGUCGACACUCAGCUAACGUGCGCGCCACAU-----AUACCACAUAGA-----G
..((.....(((((.........)))-))..(((((((((((....(((....))).....)).))))))))).......-----...)).......-----. ( -28.60)
>DroAna_CAF1 31985 87 + 1
-U-GU----------AUUUAAGUGAG-AGUUGCGCACGUUGCGACAGUCAGUCGAAAGUCAGCCAUCGUGCGCGCCACAUUACCGGAACCGG--A-AUUCUCG
-.-..----------........(((-(((((((((((..(((((..((....))..))).))...))))))).........(((....)))--)-)))))). ( -32.20)
>consensus
_U_GACCGUCUCUCUAUUUAAAUGAG_AGUUGCGCACGUUGCGGCAGUCAGUCGAAACUCAGCCAACGUGCGCGCCACAU_____AAACCGG__AAA_____G
............................(.(((((((((((((((.....)))).........))))))))))).)........................... (-19.78 = -19.45 +  -0.33)

alignment

secondary structure

dotplot

Window 3

Location	15,301,911 – 15,302,008
Length	97
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	76.21
Mean single sequence MFE	-30.13
Consensus MFE	-17.59
Energy contribution	-17.79
Covariance contribution	0.20
Combinations/Pair	1.08
Mean z-score	-1.50
Structure conservation index	0.58
SVM decision value	0.16
SVM RNA-class probability	0.610884
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15301911 97 - 23771897
CGAUAUUUU--CCGGUUC--GUAAUGUAACGCGCACGUUGGCUGAUUUUCGACUGACUGCCGCAACGUGCGCAACUUCUCUUUUAAAUGGAGAGUCGUCC-A-
.((((((((--(((....--((......))((((((((((((................)))..)))))))))...............)))))))).))).-.- ( -27.79)
>DroVir_CAF1 34208 90 - 1
C-----UUU--UUGGUAU-----GUCUGGCGCGCACGUUGGCUGAGUGUCGACUGACUGCCGCAACGUGCGCAGCU-CUCACUUAAAUAGAGAGACGGUACAC
.-----...--...((((-----(((((((((((((((((.(.(...(((....)))..).))))))))))).)))-(((.........))))))).)))).. ( -31.50)
>DroGri_CAF1 35294 87 - 1
C-----UUU--UCGGUAU-----GUGUGGCGCGCACGUUGGCUGAGUGUCGACUGACUGCCGCAACGUGCGCAACU-CUCAUUUAAAUAGAGAGACGGGC---
.-----..(--(((((((-----((((((((..((.((((((.....))))))))..)))))).))))))....((-(((.........))))).)))).--- ( -32.30)
>DroSim_CAF1 34061 97 - 1
CGAUACUUU--CCGGUUC--GUAAUGUAACGCGCACGUUGGCUGAUUUUCGACUGACUGCCGCAACGUGCGCAACUUCUCUUUUAAAUGGAGAGUCGUCC-A-
.((((((((--(((....--((......))((((((((((((................)))..)))))))))...............)))))))).))).-.- ( -30.09)
>DroMoj_CAF1 32830 92 - 1
C-----UCUAUGUGGUAU-----AUGUGGCGCGCACGUUAGCUGAGUGUCGACUGACUGCCGCAACGUGCGCAACU-CUCACUUAAAUAGAGAGACGGUCCUC
(-----(((((..(((..-----..((...(((((((((.((.(...(((....)))..).))))))))))).)).-...)))...))))))........... ( -30.00)
>DroAna_CAF1 31985 87 - 1
CGAGAAU-U--CCGGUUCCGGUAAUGUGGCGCGCACGAUGGCUGACUUUCGACUGACUGUCGCAACGUGCGCAACU-CUCACUUAAAU----------AC-A-
.((((((-(--(((....))).))).....(((((((...((.(((..((....))..)))))..)))))))...)-)))........----------..-.- ( -29.10)
>consensus
C_____UUU__CCGGUAC_____AUGUGGCGCGCACGUUGGCUGAGUGUCGACUGACUGCCGCAACGUGCGCAACU_CUCACUUAAAUAGAGAGACGGCC_A_
..............................((((((((((((................)))..)))))))))............................... (-17.59 = -17.79 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:52 2006