Locus 1202

Sequence ID	3R_DroMel_CAF1
Location	3,628,842 – 3,628,947
Length	105
Max. P	0.603499

overview

Window 7

Location	3,628,842 – 3,628,947
Length	105
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	82.58
Mean single sequence MFE	-33.45
Consensus MFE	-26.24
Energy contribution	-25.97
Covariance contribution	-0.27
Combinations/Pair	1.30
Mean z-score	-1.47
Structure conservation index	0.78
SVM decision value	0.14
SVM RNA-class probability	0.603499
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3628842 105 + 27905053
CGUUCACAAUGUUUGCUCAGCGCCAAGGCGUCGAUUUCCCGAGAAC---AGCUGUUGGCCAGAAACUGAUUAAUUGGCCCCAGCAGCUCACUCUGGCUAAGAGCUAAA
.((((...............(((....)))(((......)))))))---((((.(((((((((...(((....(((....)))....))).))))))))).))))... ( -32.60)
>DroPse_CAF1 2793 104 + 1
----CGGAGUGUUUAUUUAGGGCCAGGGCACCACUUUCAUGGGAAUAGUAGCUGUGGGCCAGAAGCUGGUUAAUUGGCUCAAACAAUUCGCUUUGACUGAGGGCUAAA
----(((((((........(((((((...((((.((((.(((..((((...))))...))))))).))))...)))))))........)))))))............. ( -29.09)
>DroSec_CAF1 2962 101 + 1
----CACAAUGUUUGCUCAGCGCCAAGGCGUCGAUUUCCCGGGAAC---AACUGUUGGCCAGAAACUGAUUAAUUGGCUUCAGCAGCUCGCUCUGGCUAAGAGCUAAA
----..........((((...((((..(((.....(((....))).---..(((((((((((...........)))))..))))))..)))..))))...)))).... ( -29.50)
>DroSim_CAF1 4286 101 + 1
----CACAAUGUUUGCUCAGCGCCAAGGCGUCGAUUUCCCGGGAAC---AGCUGUUGGCCAGAAAUUGAUUAAUUGGCCUCAGCAGCUCGCUCUGGCUAAGAGCUAAA
----..........((((...((((..(((.....(((....))).---(((((((((((((...........))))))..))))))))))..))))...)))).... ( -34.70)
>DroEre_CAF1 4003 101 + 1
----CACAGUGUUUGUUCAGCGCCAAGCCGUCCAGUUCCCGGGAAC---AGCUGUGGGCCAGAAACUGAUUAACUGGCCUAAGCAGCUCGCCGUGGCUCAGGGCUAGA
----..............(((.(..(((((....((((....))))---(((((((((((((...........)))))))..)))))).....)))))..).)))... ( -35.90)
>DroYak_CAF1 3697 101 + 1
----CACAAUGAUUGCUCAGCGCCAAGGCGUCAAUUUCCCGGGAAC---AGCUGUGGGCCAGAAACUGAUUAACUGGCCCAAGCAGCUCGCUAUGGCUAAGGGCUAAA
----..........((((...((((.((((.....(((....))).---(((((((((((((...........)))))))..)))))))))).))))...)))).... ( -38.90)
>consensus
____CACAAUGUUUGCUCAGCGCCAAGGCGUCGAUUUCCCGGGAAC___AGCUGUGGGCCAGAAACUGAUUAAUUGGCCCAAGCAGCUCGCUCUGGCUAAGAGCUAAA
..............((((...((((.((((.....(((....)))....((((((.((((((...........))))))...)))))))))).))))...)))).... (-26.24 = -25.97 +  -0.27)

alignment

secondary structure

dotplot

Window 8

Location	3,628,842 – 3,628,947
Length	105
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	82.58
Mean single sequence MFE	-33.43
Consensus MFE	-22.69
Energy contribution	-22.67
Covariance contribution	-0.02
Combinations/Pair	1.27
Mean z-score	-1.56
Structure conservation index	0.68
SVM decision value	-0.01
SVM RNA-class probability	0.526897
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3628842 105 - 27905053
UUUAGCUCUUAGCCAGAGUGAGCUGCUGGGGCCAAUUAAUCAGUUUCUGGCCAACAGCU---GUUCUCGGGAAAUCGACGCCUUGGCGCUGAGCAAACAUUGUGAACG
....((((...(((((.((((((.((((.(((((.............)))))..)))).---))))((((....)))).)).)))))...)))).............. ( -36.02)
>DroPse_CAF1 2793 104 - 1
UUUAGCCCUCAGUCAAAGCGAAUUGUUUGAGCCAAUUAACCAGCUUCUGGCCCACAGCUACUAUUCCCAUGAAAGUGGUGCCCUGGCCCUAAAUAAACACUCCG----
(((((..(((((.(((......))).))))).................((((....((((((.(((....))))))))).....)))))))))...........---- ( -19.90)
>DroSec_CAF1 2962 101 - 1
UUUAGCUCUUAGCCAGAGCGAGCUGCUGAAGCCAAUUAAUCAGUUUCUGGCCAACAGUU---GUUCCCGGGAAAUCGACGCCUUGGCGCUGAGCAAACAUUGUG----
....((((...(((((.((((((.((((..((((.............))))...)))).---)))).(((....)))..)).)))))...))))..........---- ( -31.72)
>DroSim_CAF1 4286 101 - 1
UUUAGCUCUUAGCCAGAGCGAGCUGCUGAGGCCAAUUAAUCAAUUUCUGGCCAACAGCU---GUUCCCGGGAAAUCGACGCCUUGGCGCUGAGCAAACAUUGUG----
....((((...(((((.((((((.((((.(((((.............)))))..)))).---)))).(((....)))..)).)))))...))))..........---- ( -36.42)
>DroEre_CAF1 4003 101 - 1
UCUAGCCCUGAGCCACGGCGAGCUGCUUAGGCCAGUUAAUCAGUUUCUGGCCCACAGCU---GUUCCCGGGAACUGGACGGCUUGGCGCUGAACAAACACUGUG----
..((((.(..((((.(((.((((.(((..((((((...........))))))...))).---)))))))(........)))))..).)))).............---- ( -38.30)
>DroYak_CAF1 3697 101 - 1
UUUAGCCCUUAGCCAUAGCGAGCUGCUUGGGCCAGUUAAUCAGUUUCUGGCCCACAGCU---GUUCCCGGGAAAUUGACGCCUUGGCGCUGAGCAAUCAUUGUG----
....((.(...((((..((((((((..((((((((...........)))))))))))))---.(((....))).....)))..))))...).))..........---- ( -38.20)
>consensus
UUUAGCCCUUAGCCAGAGCGAGCUGCUGAGGCCAAUUAAUCAGUUUCUGGCCAACAGCU___GUUCCCGGGAAAUCGACGCCUUGGCGCUGAGCAAACAUUGUG____
((((((.....((((..((((((((....(((((.............)))))..)))))....(((....))).....)))..))))))))))............... (-22.69 = -22.67 +  -0.02)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:31 2006