Locus 131

Sequence ID	2L_DroMel_CAF1
Location	400,008 – 400,151
Length	143
Max. P	0.872471

overview

Window 2

Location	400,008 – 400,120
Length	112
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	89.67
Mean single sequence MFE	-33.34
Consensus MFE	-29.61
Energy contribution	-29.58
Covariance contribution	-0.03
Combinations/Pair	1.06
Mean z-score	-1.28
Structure conservation index	0.89
SVM decision value	0.00
SVM RNA-class probability	0.534646
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 400008 112 - 22407834
--------GCCACUGCGGCUUCGUUAAAAAGCCAUGAGCCCGAAAUUAUGGGAAAAGUUGCCUCGGCCCAAGAAAUUAUUGGCAACUUGCCAAAAGUUUGGAAAGUGUUGAUGGAGCUCU
--------((....))(((((((((((...((.....))(((((.((.(((...((((((((..................)))))))).))).)).)))))......))))))))))).. ( -30.97)
>DroVir_CAF1 40774 112 - 1
--------AGCGCUGCGGCUACGUUAAAAAGCCAUGAGCCCGAAAUUAUGGGAAAAGUUGCUACGGCCCAAGAAAUCAUUGGCAACUUGCCAAAAGUUUGGAAAGUGUUGAUGGAGCUCU
--------(((((((..((.((.........((((((........)))))).....)).))..))))........((((..(((.(((.((((....)))).))))))..)))).))).. ( -31.14)
>DroPse_CAF1 37028 120 - 1
CUGCAGGAGCUGUUGCGGCUUCGUUAAAAUGCCAUGAGCCCGAAAUUAUGGGAAAAGUUGCCUCGGCCCAAGAAAUCAUUGGCAACUUGCCGAAAGUUUGGAAAGUGUUGAUGGAGCUCU
..((.((.((((..((((((((((....)))((((((........))))))...)))))))..))))))......((((..(((.(((.((((....)))).))))))..)))).))... ( -37.00)
>DroGri_CAF1 41457 112 - 1
--------GCUGGUGUGGCUUCGUUAAAAAGCCAUGAGCCCGAAAUUAUGGGAAAAGUUGCCAUGGCUCAAGAAAUCAUUGGCAACUUGCCAAAAGUUUGGAAAGUGUUGAUGGAACUCU
--------......(((((((.......)))))))(((((.......((((.(.....).)))))))))......((((..(((.(((.((((....)))).))))))..))))...... ( -32.01)
>DroWil_CAF1 48682 110 - 1
----------UGCUGUGGCUUCGUUAAAAGGCCAUGAGCCCGAAAUUAUGGGAAAAGUUGCAACAGCCCAAGAAAUCAUUGGCAACUUGCCAAAAGUUUGGAAAGUGUUGAUGGAGCUCU
----------....(((((((.......)))))))((((((((..((.((((....((....))..)))).))..))((..(((.(((.((((....)))).))))))..)))).)))). ( -31.90)
>DroPer_CAF1 37517 120 - 1
CUGCAGGAGCUGUUGCGGCUUCGUUAAAAUGCCAUGAGCCCGAAAUUAUGGGAAAAGUUGCCUCGGCCCAAGAAAUCAUUGGCAACUUGCCGAAAGUUUGGAAAGUGUUGAUGGAGCUCU
..((.((.((((..((((((((((....)))((((((........))))))...)))))))..))))))......((((..(((.(((.((((....)))).))))))..)))).))... ( -37.00)
>consensus
________GCUGCUGCGGCUUCGUUAAAAAGCCAUGAGCCCGAAAUUAUGGGAAAAGUUGCCACGGCCCAAGAAAUCAUUGGCAACUUGCCAAAAGUUUGGAAAGUGUUGAUGGAGCUCU
................(((((((((((...(((((((.((((......)))).......((....))........))).)))).((((.((((....)))).)))).))))))))))).. (-29.61 = -29.58 +  -0.03)

alignment

secondary structure

dotplot

Window 3

Location	400,048 – 400,151
Length	103
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	77.98
Mean single sequence MFE	-32.88
Consensus MFE	-16.09
Energy contribution	-16.57
Covariance contribution	0.47
Combinations/Pair	1.13
Mean z-score	-2.34
Structure conservation index	0.49
SVM decision value	0.88
SVM RNA-class probability	0.872471
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 400048 103 + 22407834
AAUAAUUUCUUGGGCCGAGGCAACUUUUCCCAUAAUUUCGGGCUCAUGGCUUUUUAACGAAGCCGCAGUGGCAUCCACACC------CGAG---CCCGAGCGCGAGCUCCCC
..........((((..(((....)))..)))).......((((((..((((((.....))))))...((((...))))...------.)))---)))((((....))))... ( -42.80)
>DroVir_CAF1 40814 97 + 1
AAUGAUUUCUUGGGCCGUAGCAACUUUUCCCAUAAUUUCGGGCUCAUGGCUUUUUAACGUAGCCGCAGCGCUUGCACCACCA--ACUCCUC-------------CACUGCGC
..........((((((((.((.......(((........))).....((((.........)))))).)))...)).)))...--.......-------------........ ( -17.80)
>DroEre_CAF1 23020 99 + 1
AAUAAUUUCUUGGGCCGAGGCAACUUUUCCCAUAAUUUCGGGCUCAUGGCUUUUUAACGAAGCCGCAGUGGCAUCCACACCCGAGCUCGAG---CCCGAA----------CC
..........((((..(((....)))..))))....(((((((((..((((((.....))))))...((((...))))..........)))---))))))----------.. ( -38.60)
>DroYak_CAF1 15959 109 + 1
AAUAAUUUCUUGGGCCGAGGCAACUUUUCCCAUAAUUUCGGGCUCAUGGCUUUUUAACGAAGCCGCAGUGGCAUCCACACCCGAGCUCGAG---CCCGAGUGCGAGCUCCCC
........(((((((.(((....)))...........((((((((..((((((.....))))))...((((...))))....)))))))))---))))))............ ( -39.70)
>DroMoj_CAF1 18873 109 + 1
AAUGAUUUCUUCGGCCGUGGCAACUUUUCCCAUAAUUUCGGGCUCAUGGCUUUUUAACGAAGCCACAGCAGCGGUCACUCCA--GCUCCACCCGCUCCU-CCUGCACUGCGC
............((((((.((.......(((........)))....(((((((.....)))))))..)).))))))......--........(((....-........))). ( -26.50)
>DroAna_CAF1 37665 103 + 1
AAUGAUUUCUUGGGCCGAGGCAACUUUUCCCAUAAUUUCGGGCUCAUGGCUUUUUAACGAAGCCGCAGUGCCACCCGCA-----GCUCCAG---CACCU-CCAGAGCUCCUC
...((..(..((((..(((....)))..))))..)..))((((((..((((((.....))))))(((((((.....)))-----.))...)---)....-...))))))... ( -31.90)
>consensus
AAUAAUUUCUUGGGCCGAGGCAACUUUUCCCAUAAUUUCGGGCUCAUGGCUUUUUAACGAAGCCGCAGUGGCAUCCACACC___GCUCCAG___CCCGA_C__GAGCUCCCC
.............((((..((.......(((........))).....((((((.....))))))))..))))........................................ (-16.09 = -16.57 +   0.47)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:26:57 2006