Locus 3484

Sequence ID	3L_DroMel_CAF1
Location	10,232,223 – 10,232,314
Length	91
Max. P	0.984452

overview

Window 1

Location	10,232,223 – 10,232,314
Length	91
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	77.38
Mean single sequence MFE	-27.60
Consensus MFE	-15.76
Energy contribution	-18.27
Covariance contribution	2.50
Combinations/Pair	1.15
Mean z-score	-2.71
Structure conservation index	0.57
SVM decision value	1.97
SVM RNA-class probability	0.984452
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10232223 91 + 23771897
--------------CUAGCAAGAAAGCCAUAGUAAGCUCAAAAUAAACCCCCUUCGUCCACGCAGGCAGCGCAAAAGUUGUCUGCGAUGGCAAACAGGGAGGAAA
--------------..........(((........))).........((((((....(((((((((((((......)))))))))).))).....)))).))... ( -30.10)
>DroGri_CAF1 121278 93 + 1
GGCUGCUUACGGCUGUAGAAAGAAAGCCAAAGUAAGCAUGAAAUAAACCCUCAUCGUCUACG---GCAGC---AGCGUUGUCUGCAGU-GCAAGCA-----AAAA
.((((((....((((((((......((........))((((.........))))..))))))---)))))---))).(((..(((...-)))..))-----)... ( -26.30)
>DroSec_CAF1 108141 91 + 1
--------------CUAGCAAGAAAGCCAAAGUAAGCUCGAAAUAAACCCCCAUCGUCCACGCAGGCAGCGCAAACGUUGUCUGCGAUUGCAAACAGGGAGGAAU
--------------..........(((........))).........(((((........(((((((((((....)))))))))))..((....))))).))... ( -25.90)
>DroSim_CAF1 113519 91 + 1
--------------CUAGCAAGAAAGCCAAAGUAAGCUCGAAAUAAACCCCCAUCGUCCACGCAGGCAGCGCAAACGUUGUCUGCGAUGGCAAACAGGGAGGAAU
--------------..........(((........))).........(((((.....((((((((((((((....))))))))))).)))......))).))... ( -29.60)
>DroEre_CAF1 116384 88 + 1
--------------CUGGCAAGAAAGCCAAAGUAAGCUCGAAAUAAACCCCCAGCGUCCACGCAGGCGAUGU---UGUUGUCUGCGAUGGCAAACAGGGAGGAAA
--------------.((((......))))..................(((((.(..((((((((((((((..---.)))))))))).))).)..).))).))... ( -28.90)
>DroYak_CAF1 114214 81 + 1
--------------UGGGCAAGAAAGCCAAAGUAAGCUCGAAAUAAACCCCCAUCGGCCACGCAA----------UGUUGUCUGCGAUGGCAAACGGGGAGGAAA
--------------..(((......)))...................(((((....((((((((.----------.......)))).)))).....))).))... ( -24.80)
>consensus
______________CUAGCAAGAAAGCCAAAGUAAGCUCGAAAUAAACCCCCAUCGUCCACGCAGGCAGCGC_AACGUUGUCUGCGAUGGCAAACAGGGAGGAAA
.........................((........))..........(((((.....(((((((((((((......)))))))))).)))......))).))... (-15.76 = -18.27 +   2.50)

alignment

secondary structure

dotplot

Window 2

Location	10,232,223 – 10,232,314
Length	91
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	77.38
Mean single sequence MFE	-29.29
Consensus MFE	-14.98
Energy contribution	-17.45
Covariance contribution	2.47
Combinations/Pair	1.17
Mean z-score	-2.44
Structure conservation index	0.51
SVM decision value	1.35
SVM RNA-class probability	0.945495
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10232223 91 - 23771897
UUUCCUCCCUGUUUGCCAUCGCAGACAACUUUUGCGCUGCCUGCGUGGACGAAGGGGGUUUAUUUUGAGCUUACUAUGGCUUUCUUGCUAG--------------
....((((((((((((....))))))..(.((..(((.....)))..)).).))))))........(((((......))))).........-------------- ( -27.70)
>DroGri_CAF1 121278 93 - 1
UUUU-----UGCUUGC-ACUGCAGACAACGCU---GCUGC---CGUAGACGAUGAGGGUUUAUUUCAUGCUUACUUUGGCUUUCUUUCUACAGCCGUAAGCAGCC
...(-----(((((((-...((((......))---)).((---.(((((..((((((.....))))))(((......)))......))))).)).)))))))).. ( -27.00)
>DroSec_CAF1 108141 91 - 1
AUUCCUCCCUGUUUGCAAUCGCAGACAACGUUUGCGCUGCCUGCGUGGACGAUGGGGGUUUAUUUCGAGCUUACUUUGGCUUUCUUGCUAG--------------
....((((((((((((....))))))).((((..(((.....)))..))))..)))))........(((((......))))).........-------------- ( -33.50)
>DroSim_CAF1 113519 91 - 1
AUUCCUCCCUGUUUGCCAUCGCAGACAACGUUUGCGCUGCCUGCGUGGACGAUGGGGGUUUAUUUCGAGCUUACUUUGGCUUUCUUGCUAG--------------
....((((((((((((....))))))).((((..(((.....)))..))))..)))))........(((((......))))).........-------------- ( -32.90)
>DroEre_CAF1 116384 88 - 1
UUUCCUCCCUGUUUGCCAUCGCAGACAACA---ACAUCGCCUGCGUGGACGCUGGGGGUUUAUUUCGAGCUUACUUUGGCUUUCUUGCCAG--------------
....(((((.((...(((.(((((......---.......))))))))..)).)))))..................((((......)))).-------------- ( -25.72)
>DroYak_CAF1 114214 81 - 1
UUUCCUCCCCGUUUGCCAUCGCAGACAACA----------UUGCGUGGCCGAUGGGGGUUUAUUUCGAGCUUACUUUGGCUUUCUUGCCCA--------------
.....((((((((.((((.(((((......----------))))))))).))))))))........(((((......))))).........-------------- ( -28.90)
>consensus
UUUCCUCCCUGUUUGCCAUCGCAGACAACGUU_GCGCUGCCUGCGUGGACGAUGGGGGUUUAUUUCGAGCUUACUUUGGCUUUCUUGCUAG______________
.....((((((((..(((.(((((.((.(......).)).))))))))..))))))))........(((((......)))))....................... (-14.98 = -17.45 +   2.47)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:16 2006