Locus 5250

Sequence ID	3L_DroMel_CAF1
Location	14,507,373 – 14,507,504
Length	131
Max. P	0.922707

overview

Window 1

Location	14,507,373 – 14,507,467
Length	94
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	74.03
Mean single sequence MFE	-31.90
Consensus MFE	-21.66
Energy contribution	-21.38
Covariance contribution	-0.27
Combinations/Pair	1.41
Mean z-score	-1.50
Structure conservation index	0.68
SVM decision value	1.15
SVM RNA-class probability	0.922707
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14507373 94 + 23771897
----------GAUUUCACCAAUAUGGCGUAUGUGGCUC-CUGG--UGCCAGCCAUUUUGGUCUUGCACCUUGGCCAAGGCAUCGGUCAGGGUGGACCUUAUUUGCUG
----------......(((((.(((((.....((((..-....--.))))))))).)))))....((((((((((........)))))))))).............. ( -34.30)
>DroVir_CAF1 32075 104 + 1
AUAUAACAUAUAUUCUACCAAUAUGGUGUAUUGGACUC-UUGA--GUCCCGUUAGUCUGCUGUUGGACUUUGGCAAGUGCAUCGGUUAAGGUGGAUCGCAUUUGCUG
.............((((((....((((((((((((((.-...)--)))).((((((((......)))))..))).))))))))).....))))))..((....)).. ( -29.40)
>DroPse_CAF1 3890 94 + 1
----------GACUUCACCAAUAUGGUGUAAGCGGCUC-UUGA--UUCCAGCCGUUUUGGUCCUGCACCUUGGCCAGGGCAUCGGUCAGGGUGGACCUCAUUUGCUG
----------.....((((.....)))).((((((((.-....--....)))))))).(((((...(((((((((........)))))))))))))).......... ( -35.40)
>DroWil_CAF1 5684 97 + 1
----------UAAUCUACCAAUAUGGUGUAUUUGUAUCACCGGCACUCCAACCAUUCGAUUCUUGAGCCUUGGACAAAGCAUCGGUUAAGGUUGAACGCAUUUGUUG
----------........((((((((((.........)))))((....(((((..(((((.(((...(....)...))).)))))....)))))...))...))))) ( -20.10)
>DroAna_CAF1 3786 94 + 1
----------GGAGUUACCAAUAGGGGGUAUGGGGCUC-CUGG--UUCCAGCUGUUCUGGUCCUGAACCUUGGCCAUGGCAUCGGUCAGGGUGGACCUCAUUUGCUG
----------(((...((((....(((((.....))))-))))--))))(((......(((((...(((((((((........))))))))))))))......))). ( -36.80)
>DroPer_CAF1 4415 94 + 1
----------GACUUCACCAAUAUGGUGUAAGCGGCUC-UUGA--UUCCAGCCGUUUUGGUCCUGCACCUUGGCCAGGGCAUCGGUCAGGGUGGACCUCAUUUGCUG
----------.....((((.....)))).((((((((.-....--....)))))))).(((((...(((((((((........)))))))))))))).......... ( -35.40)
>consensus
__________GAAUUCACCAAUAUGGUGUAUGCGGCUC_CUGA__UUCCAGCCAUUCUGGUCCUGCACCUUGGCCAGGGCAUCGGUCAGGGUGGACCUCAUUUGCUG
...............((((.....))))....................((((......(((((...(((((((((........))))))))))))))......)))) (-21.66 = -21.38 +  -0.27)

alignment

secondary structure

dotplot

Window 2

Location	14,507,390 – 14,507,504
Length	114
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	77.80
Mean single sequence MFE	-40.22
Consensus MFE	-23.34
Energy contribution	-23.65
Covariance contribution	0.31
Combinations/Pair	1.41
Mean z-score	-1.62
Structure conservation index	0.58
SVM decision value	0.21
SVM RNA-class probability	0.636992
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14507390 114 + 23771897
GUAUGUGGCUC-CUGG--UGCCAGCCAUUUUGGUCUUGCACCUUGGCCAAGGCAUCGGUCAGGGUGGACCUUAUUUGCUGGCUCGAGUUGCGAUUCUGACCCUUAUCAUAGGGCGAC
...((..((((-...(--.((((((......((((...((((((((((........))))))))))))))......)))))).)))))..))....((.((((......)))))).. ( -48.10)
>DroVir_CAF1 32102 114 + 1
GUAUUGGACUC-UUGA--GUCCCGUUAGUCUGCUGUUGGACUUUGGCAAGUGCAUCGGUUAAGGUGGAUCGCAUUUGCUGGCUGGAGUUACGGGUUUGACCCUUAUCAUAGGGCGAC
...(..(((((-.(((--.(((.((((((((......)))))..((((((((((((.(......).))).)))))))))))).))).))).)))))..)((((......)))).... ( -39.10)
>DroPse_CAF1 3907 114 + 1
GUAAGCGGCUC-UUGA--UUCCAGCCGUUUUGGUCCUGCACCUUGGCCAGGGCAUCGGUCAGGGUGGACCUCAUUUGCUGACUGGAGUUGCGAUUCUGACCCUUAUCAUAGGGAGAG
....(((((((-(...--...((((......(((((...(((((((((........))))))))))))))......))))...))))))))...(((..((((......))))))). ( -44.80)
>DroWil_CAF1 5701 117 + 1
GUAUUUGUAUCACCGGCACUCCAACCAUUCGAUUCUUGAGCCUUGGACAAAGCAUCGGUUAAGGUUGAACGCAUUUGUUGACUGGAGUUACGAUUUUGUCCCUUAUCAUAGGGCGAC
....(((((.(.(((((....(((((..(((((.(((...(....)...))).)))))....)))))((((....))))).)))).).)))))..(((.((((......))))))). ( -27.90)
>DroMoj_CAF1 23972 111 + 1
GUAUUUGGUUC-CUGG--GUCCAGUUGUUCU---GUUGUGCUUUGGCAAGUGCAUCGGUUAAAGUGGAUCGCAUUUGCUGGCUGGAACUACGAUUUUGACCCUUAUCAUAGGGCGAC
.....((((((-(..(--(((((.((...((---(.((..(((....)))..)).)))...)).))))))((....)).....))))))).....(((.((((......))))))). ( -36.20)
>DroAna_CAF1 3803 114 + 1
GUAUGGGGCUC-CUGG--UUCCAGCUGUUCUGGUCCUGAACCUUGGCCAUGGCAUCGGUCAGGGUGGACCUCAUUUGCUGGCUAGAGUUGCGAUUCUGACCCUUAUCAUAGGGCGAC
...((.(((((-.(((--..(((((......(((((...(((((((((........))))))))))))))......))))))))))))).))....((.((((......)))))).. ( -45.20)
>consensus
GUAUGUGGCUC_CUGG__UUCCAGCCAUUCUGGUCUUGAACCUUGGCCAGGGCAUCGGUCAAGGUGGACCGCAUUUGCUGGCUGGAGUUACGAUUCUGACCCUUAUCAUAGGGCGAC
......(((((...(.....(((((......(((((...(((((((((........))))))))))))))......))))))..)))))..........((((......)))).... (-23.34 = -23.65 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:30 2006