Locus 4466

Sequence ID	2R_DroMel_CAF1
Location	14,686,405 – 14,686,560
Length	155
Max. P	0.668335

overview

Window 4

Location	14,686,405 – 14,686,497
Length	92
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	82.37
Mean single sequence MFE	-32.03
Consensus MFE	-20.42
Energy contribution	-22.15
Covariance contribution	1.73
Combinations/Pair	1.15
Mean z-score	-1.95
Structure conservation index	0.64
SVM decision value	0.15
SVM RNA-class probability	0.609620
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14686405 92 - 20766785
AAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUUCCCAGUUUGCCAGUUGGACGGCGAAGGGGAAA-GAGCUGGAGCCGAAGCAGCU-GAA
................((((((.(((((.(((...(((((..((((((........)))))).))))).-..))).).))))....))))-)). ( -33.60)
>DroSec_CAF1 17491 92 - 1
AAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUUGCCAGUUCGCCAGUUGGACGGCGAAAGGGAAA-GAGCUGGAGCCGAAGCAGCU-GAA
................((((((.(((((.(((......((..((((((........))))))..))...-..))).).))))....))))-)). ( -30.50)
>DroSim_CAF1 12591 92 - 1
AAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUUCCCAGUUCGCCAGUUGGCCGGCGAAGGGGAAA-GAGCUGGAGCCGAAGCAGCU-GAA
................((((((.(((((.(((...(((((..((((((.(....).)))))).))))).-..))).).))))....))))-)). ( -36.00)
>DroEre_CAF1 16263 92 - 1
AAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUUCCCAGUUCGCCAGUUGGCUGGAGGAGGGGAAAAGCGCUGGGGCC-AAGCAGCU-GAA
................((((((..((((.((((..(((((..(((.((((....)))).))).)))))...)))).).)))-....))))-)). ( -34.40)
>DroYak_CAF1 16643 80 - 1
AAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUUCCCAGUUCGCCGGCUGGCUGGAGAAGGGGAAAA-------------AGCAGCU-GAA
.....((.........(((((....)))))((...(((((..(((.((((....)))).))).)))))..-------------.)).)).-... ( -27.00)
>DroAna_CAF1 14145 84 - 1
AAAACGCGUUUUGCCAUCAGUUACGGCUGAGCGAGUUCCCAGCUUG------GAGCUGCGAGGGGCUCG-GAGC---AGCGGAGGCAGCUCUAA
.......((((.(((.........))).))))(((((((((((...------..))))...)))))))(-((((---.((....)).))))).. ( -30.70)
>consensus
AAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUUCCCAGUUCGCCAGUUGGCCGGCGAAGGGGAAA_GAGCUGGAGCCGAAGCAGCU_GAA
.....((((((((...(((((....)))))((...(((((..((((((........)))))).)))))....))......)))))).))..... (-20.42 = -22.15 +   1.73)

alignment

secondary structure

dotplot

Window 5

Location	14,686,422 – 14,686,531
Length	109
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	84.30
Mean single sequence MFE	-33.62
Consensus MFE	-23.96
Energy contribution	-25.13
Covariance contribution	1.17
Combinations/Pair	1.21
Mean z-score	-2.10
Structure conservation index	0.71
SVM decision value	0.08
SVM RNA-class probability	0.572245
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14686422 109 - 20766785
AGCUAAAUACUACACGGUAU----AGAAAACUGAAAACAAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUUCCCAGUUUGCCAGUUGGACGGCGAAGGGGAAA-GAGCUG
((((..(((((....)))))----....((((((...(((((....)))))...))))))..)))).(((...(((((..((((((........)))))).))))).-..))). ( -33.90)
>DroSec_CAF1 17508 109 - 1
AGCUAAAUACUACACGGUAU----AGAAAACUGAAAACAAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUUGCCAGUUCGCCAGUUGGACGGCGAAAGGGAAA-GAGCUG
((((..(((((....)))))----....((((((...(((((....)))))...))))))..)))).(((......((..((((((........))))))..))...-..))). ( -30.80)
>DroSim_CAF1 12608 109 - 1
AGCUAAAUACUACACGGUAU----AGAAAACUGAAAACAAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUUCCCAGUUCGCCAGUUGGCCGGCGAAGGGGAAA-GAGCUG
((((..(((((....)))))----....((((((...(((((....)))))...))))))..)))).(((...(((((..((((((.(....).)))))).))))).-..))). ( -36.30)
>DroEre_CAF1 16279 110 - 1
AGCUAAAUACUACACGGUAU----AGAAAACUGAAAACAAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUUCCCAGUUCGCCAGUUGGCUGGAGGAGGGGAAAAGCGCUG
((((..(((((....)))))----....((((((...(((((....)))))...))))))..)))).((((..(((((..(((.((((....)))).))).)))))...)))). ( -36.80)
>DroYak_CAF1 16653 104 - 1
AGCUAAAUACUACACGGUAU----AGAAAACUGAAAACAAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUUCCCAGUUCGCCGGCUGGCUGGAGAAGGGGAAAA------
((((..(((((....)))))----....((((((...(((((....)))))...))))))..)))).......(((((..(((.((((....)))).))).)))))..------ ( -29.60)
>DroAna_CAF1 14162 102 - 1
CGCCA---GCUAGACGGCGUGGAGAAAAAGUUGAAAACAAAACGCGUUUUGCCAUCAGUUACGGCUGAGCGAGUUCCCAGCUUG------GAGCUGCGAGGGGCUCG-GAGC--
.((((---(((.(((...((((..(((..(((........)))...)))..))))..)))..))))).))(((((((((((...------..))))...))))))).-....-- ( -34.30)
>consensus
AGCUAAAUACUACACGGUAU____AGAAAACUGAAAACAAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUUCCCAGUUCGCCAGUUGGCCGGCGAAGGGGAAA_GAGCUG
((((..(((((....)))))........((((((...(((((....)))))...))))))..)))).(((...(((((..((((((........)))))).)))))....))). (-23.96 = -25.13 +   1.17)

alignment

secondary structure

dotplot

Window 6

Location	14,686,460 – 14,686,560
Length	100
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	85.65
Mean single sequence MFE	-24.92
Consensus MFE	-19.31
Energy contribution	-19.15
Covariance contribution	-0.16
Combinations/Pair	1.20
Mean z-score	-2.27
Structure conservation index	0.78
SVM decision value	0.29
SVM RNA-class probability	0.668335
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14686460 100 - 20766785
UUUUGUAAAUCAUCACUAUCAA-----------CUCGUCGAGCUAAAUACUACACGGUAU----AGAAAACUGAAAACAAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUU
....................((-----------(((((..((((..(((((....)))))----....((((((...(((((....)))))...))))))..))))..))))))) ( -24.20)
>DroSec_CAF1 17546 100 - 1
UUUUGUAAAUGAACACUAUCAA-----------CUCGUCGAGCUAAAUACUACACGGUAU----AGAAAACUGAAAACAAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUU
....................((-----------(((((..((((..(((((....)))))----....((((((...(((((....)))))...))))))..))))..))))))) ( -24.20)
>DroSim_CAF1 12646 100 - 1
UUUUGUAAAUGAACACUAUCAA-----------CUCGUCGAGCUAAAUACUACACGGUAU----AGAAAACUGAAAACAAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUU
....................((-----------(((((..((((..(((((....)))))----....((((((...(((((....)))))...))))))..))))..))))))) ( -24.20)
>DroEre_CAF1 16318 100 - 1
UUUUGUAAACGAACACUAUAAG-----------CUCGUCGAGCUAAAUACUACACGGUAU----AGAAAACUGAAAACAAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUU
.((((....)))).......((-----------(((((..((((..(((((....)))))----....((((((...(((((....)))))...))))))..))))..))))))) ( -24.30)
>DroYak_CAF1 16686 100 - 1
UUUUGUAACUAAACACUAUAAA-----------CUCGUCGAGCUAAAUACUACACGGUAU----AGAAAACUGAAAACAAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUU
....................((-----------(((((..((((..(((((....)))))----....((((((...(((((....)))))...))))))..))))..))))))) ( -24.20)
>DroAna_CAF1 14192 110 - 1
UUUAUUAAACAAA--UUAUAAGCCCAACAUUCACUCUCCUCGCCA---GCUAGACGGCGUGGAGAAAAAGUUGAAAACAAAACGCGUUUUGCCAUCAGUUACGGCUGAGCGAGUU
.............--.........((((......(((((.((((.---.......)))).)))))....)))).......(((.(((((.(((.........))).))))).))) ( -28.40)
>consensus
UUUUGUAAAUGAACACUAUAAA___________CUCGUCGAGCUAAAUACUACACGGUAU____AGAAAACUGAAAACAAAACGCGUUUUGACAUCAGUUACGGCUGAGCGAGUU
.................................(((((..((((..(((((....)))))........((((((...(((((....)))))...))))))..))))..))))).. (-19.31 = -19.15 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:28 2006