Locus 4504

Sequence ID	3L_DroMel_CAF1
Location	12,997,710 – 12,997,863
Length	153
Max. P	0.653442

overview

Window 5

Location	12,997,710 – 12,997,830
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	84.14
Mean single sequence MFE	-38.03
Consensus MFE	-30.06
Energy contribution	-29.78
Covariance contribution	-0.27
Combinations/Pair	1.17
Mean z-score	-1.49
Structure conservation index	0.79
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12997710 120 + 23771897
GCGCCAUGGACAUUAACACUGCCCUCCAGGAGGUCUUGAAGAAGUCCCUGAUCGCCGAUGGACUCGUCCAUGGCAUCCACCAGGCCUGCAAGGCCCUGGACAAGUAAGUAGUCCCACAAU
..(((((((((.((((.(((..((....)).))).)))).((.((((.((.....))..))))))))))))))).....(((((((.....)).)))))..................... ( -39.90)
>DroVir_CAF1 4354 120 + 1
GCGCCAUGGACAUAAACACCGCGCUACAGGAAGUUCUAAAGAAGUCGCUGAUCGCUGAUGGACUCGUCCAUGGCAUCCACCAGGCCUGCAAGGCUUUGGACAAGUAAGCAACAACAUCAU
(((((((((((.....(((.(((...(((((..(((....))).)).)))..))).).)).....))))))))).((((..(((((.....))))))))).......))........... ( -39.50)
>DroGri_CAF1 4225 120 + 1
GCGCCAUGGACAUAAACACCGCGCUGCAGGAAGUGCUGAAGAAGUCGCUGAUCGCCGAUGGCCUCGUCCAUGGCAUCCACCAAGCCUGCAAAGCUCUGGACAAGUAAGCAAAAAAUUCAA
(((((((((((.........(((((......))))).((.(..(((((.....).))))..).))))))))))).....((((((.......))).)))........))........... ( -38.20)
>DroWil_CAF1 6281 119 + 1
GUGCCAUGGACAUUAACACCGCUCUCCAGGAAGUUCUGAAGAAGUCUCUGAUUGCCGAUGGUUUGGUCCAUGGCAUCCAUCAGGCUUGCAAGGCUUUGGACAAGUAAGUUUCCC-UCUCU
.((((((((((...(((.(.((....(((..(.(((....))).)..)))...)).)...)))..))))))))))((((..(((((.....)))))))))..............-..... ( -36.20)
>DroMoj_CAF1 4202 116 + 1
GCGCCAUGGACAUAAACACCGCGCUACAGGAAGUGCUGAAGAAGUCGCUGAUCGCCGAUGGACUCGUCCAUGGCAUCCACCAGGCCUGCAAGGCAUUGGACAAGUAAGCAAAAACA----
(((((((((((.........(((((......))))).((....(((((.....).))))....))))))))))).....(((((((.....))).))))........)).......---- ( -39.50)
>DroPer_CAF1 4279 117 + 1
GCGCCAUGGACAUUAACACUGCCCUGCAGGAAGUGCUGAAGAAGUCUCUGAUUGCUGAUGGUCUCGUGCAUGGCAUCCACCAGGCCUGCAAGGCCCUGGACAAGUAAGUAGACCAAG---
..((((((.((.(((.((((..((....)).)))).))).((..((((........)).))..)))).)))))).....(((((((.....)).)))))..................--- ( -34.90)
>consensus
GCGCCAUGGACAUAAACACCGCGCUACAGGAAGUGCUGAAGAAGUCGCUGAUCGCCGAUGGACUCGUCCAUGGCAUCCACCAGGCCUGCAAGGCUCUGGACAAGUAAGCAAAAACAC_AU
(((((((((((.....(((.((....(((((..(.......)..)).)))...)).).)).....))))))))).((((...((((.....)))).)))).......))........... (-30.06 = -29.78 +  -0.27)

alignment

secondary structure

dotplot

Window 6

Location	12,997,750 – 12,997,863
Length	113
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	83.32
Mean single sequence MFE	-42.01
Consensus MFE	-29.20
Energy contribution	-30.56
Covariance contribution	1.36
Combinations/Pair	1.06
Mean z-score	-1.77
Structure conservation index	0.70
SVM decision value	0.25
SVM RNA-class probability	0.653442
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12997750 113 - 23771897
AGAGCCCA---AGUGAAUAACCACGUUGACCGCCAGAUUGUGGGACUACUUACUUGUCCAGGGCCUUGCAGGCCUGGUGGAUGCCAUGGACGAGUCCAUCGGCGAUCAGGGACUUC
.((((((.---.(((......)))..((((((((........((((.........)))).(((((.....)))))))))).(((((((((....))))).)))).)))))).))). ( -44.70)
>DroSec_CAF1 4830 113 - 1
AGAGUCCA---AGUGAAUAACCACGUUGACCGCAAAAUUGUGGGACUACUUACUUGUCCAGGGCCUUGCAGGCCUGGUGGAUGCCAUGGACGAGUCCAUCGGCGAUAAGGGACUUC
.((((((.---.(((......)))((((((((((....)))))........((((((((((((((.....)))))(((....))).)))))))))...)))))......)))))). ( -45.00)
>DroEre_CAF1 4638 116 - 1
AAAUCCCAAGAAGUGAAUAAGCACCUUGAUGUCUGGAUUGUGCGACUACUUACUUGUCCAGGGCCUUGCAGGCCUGGUGGAUGCCAUGGACGAGUCCAUCGGCGAUCAGGGACUUC
...((((..............((((.......((((((.(((........)))..))))))((((.....)))).))))(((((((((((....))))).))).))).)))).... ( -41.40)
>DroYak_CAF1 5078 116 - 1
AAACCCCAAGAAGUGUAUAACCACGUUGAUCUCCGGAUUGUGGGACUACUUACUUGUCCAGGGCCUUGCAGGCCUGGUGGAUGCCAUGGACGAGUCCAUCGGCGAUCAGGGACUUC
....(((.....(((......)))..((((((((((((.(((((....)))))..)))).(((((.....)))))...))).((((((((....))))).)))))))))))..... ( -44.10)
>DroAna_CAF1 9625 104 - 1
-----CCGAACUAUAGAGAAGCAUCCGG-------GUCUCUGGGAGAACUUACUUGUCCAGAGCCUUGCAGGCCUGGUGGAUGCCAUGGACGAGGCCAUCGGCGAUCAGGGACUUC
-----(((.................)))-------((((((((.........((((((((..(((.....))).((((....))))))))))))(((...)))..))))))))... ( -34.83)
>consensus
AAAGCCCAA__AGUGAAUAACCACGUUGACCGCCAGAUUGUGGGACUACUUACUUGUCCAGGGCCUUGCAGGCCUGGUGGAUGCCAUGGACGAGUCCAUCGGCGAUCAGGGACUUC
....(((.....(((......)))...........((((((.((.......((((((((((((((.....)))))(((....))).)))))))))...)).)))))).)))..... (-29.20 = -30.56 +   1.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:11 2006