Locus 8854

Sequence ID 3R_DroMel_CAF1
Location 23,749,690 – 23,749,793
Length 103
Max. P 0.733872
window14215 window14216

overview

Window 5

Location 23,749,690 – 23,749,793
Length 103
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 74.70
Mean single sequence MFE -29.22
Consensus MFE -18.01
Energy contribution -17.93
Covariance contribution -0.08
Combinations/Pair 1.26
Mean z-score -1.34
Structure conservation index 0.62
SVM decision value 0.24
SVM RNA-class probability 0.650730
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23749690 103 + 27905053
-GAUCUCCUGCGUUGCCAGAUAAAAUGCUCUUCUUGGCGUUACGAUUGAAACUUGAUUCACGGCUUCCAUCGUGGUAACGGAAGAGCAACAGCUGUUGUAUUCA-------
-.........(((((((......((((((......))))))(((((.(((.((........)).))).))))))))))))(((..(((((....))))).))).------- ( -27.80)
>DroSec_CAF1 2698 103 + 1
-GAUCUCCUGCGUUGUCAGAUAAAAUGCUCUUCUUGGCGUUACGAUUGAAAUUUGAUUCACGGCUUCCAUCGUGGUAACGGAAGAGCAACAGCUGUAGUAUUCA-------
-((....(((((((((.........((((((((....(((((((((..(...)..)))(((((......)))))))))))))))))))))))).))))...)).------- ( -28.40)
>DroSim_CAF1 2617 103 + 1
-GAUCUCCUGCGUUGCCAGAUAAAAUGCUCUUCUUGGCGUUACGAUUGAAAUUUGAUUCACGGCUUCCAUCGUGGUAACGGAAGAGCAACAGCUGUUGUAUUUA-------
-...(((.(.(((((((......((((((......))))))(((((.(((..(((.....))).))).)))))))))))).).)))((((....))))......------- ( -25.20)
>DroYak_CAF1 868 110 + 1
-GAUAUCCUGCGUUGCCAGAUAAAAUGCUCUUCUAGGCGUUACGAUUGAAACUUGUUUCACGGCUUCCAUCGUGGUAACGGAAGAGCUACAUCUUUUGAACCCUUUCAAAC
-....((.(.(((((((......((((((......))))))(((((.(((.((........)).))).)))))))))))).).)).........((((((....)))))). ( -25.00)
>DroMoj_CAF1 2129 98 + 1
AGCAAUAAUGCGUUGCUAAAUAAACUGCCCUCCUAGGCGUUACGAUUGCAGCCUGAUUCCAAGGUGCCAUCGUUUGCAGUGGAGGGCCACAGCUGCA---U----------
((((((.....)))))).........(((((((...(((..(((((.(((.(((.......)))))).))))).)))...)))))))..........---.---------- ( -37.10)
>DroPer_CAF1 2589 102 + 1
AGCAUUGGUGCGUUGCCAGAAUAACUGCUCUCCUAGGCGUUACGAGUGUAACCUGAUUCAAAGUUGCAGACGUUUGCAGUGGAGAGCCACAGCUU--AUUUUUA-------
(((.(((((.....))))).......(((((((...(((..(((..((((((.(......).))))))..))).)))...)))))))....))).--.......------- ( -31.80)
>consensus
_GAUCUCCUGCGUUGCCAGAUAAAAUGCUCUUCUAGGCGUUACGAUUGAAACUUGAUUCACGGCUUCCAUCGUGGUAACGGAAGAGCAACAGCUGUUGUAUUCA_______
..........................((((((((......((((((.(((.((........)).))).)))))).....))))))))........................ (-18.01 = -17.93 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 23,749,690 – 23,749,793
Length 103
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 74.70
Mean single sequence MFE -27.10
Consensus MFE -17.96
Energy contribution -18.24
Covariance contribution 0.28
Combinations/Pair 1.20
Mean z-score -1.23
Structure conservation index 0.66
SVM decision value 0.43
SVM RNA-class probability 0.733872
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23749690 103 - 27905053
-------UGAAUACAACAGCUGUUGCUCUUCCGUUACCACGAUGGAAGCCGUGAAUCAAGUUUCAAUCGUAACGCCAAGAAGAGCAUUUUAUCUGGCAACGCAGGAGAUC-
-------............((((((((((((((((...(((((.(((((..........))))).)))))))))....))))))))........(....)))))......- ( -25.80)
>DroSec_CAF1 2698 103 - 1
-------UGAAUACUACAGCUGUUGCUCUUCCGUUACCACGAUGGAAGCCGUGAAUCAAAUUUCAAUCGUAACGCCAAGAAGAGCAUUUUAUCUGACAACGCAGGAGAUC-
-------.........(((.((.((((((((((((((....((((...))))(((......)))....))))))....))))))))...)).)))...............- ( -22.00)
>DroSim_CAF1 2617 103 - 1
-------UAAAUACAACAGCUGUUGCUCUUCCGUUACCACGAUGGAAGCCGUGAAUCAAAUUUCAAUCGUAACGCCAAGAAGAGCAUUUUAUCUGGCAACGCAGGAGAUC-
-------......((((....))))(((((.((((.(((.(((((((((..((((......))))...))...((........)).)))))))))).)))).)))))...- ( -24.00)
>DroYak_CAF1 868 110 - 1
GUUUGAAAGGGUUCAAAAGAUGUAGCUCUUCCGUUACCACGAUGGAAGCCGUGAAACAAGUUUCAAUCGUAACGCCUAGAAGAGCAUUUUAUCUGGCAACGCAGGAUAUC-
.((((((....)))))).(((((.(((((((((((...(((((.(((((..........))))).)))))))))....)))))))......((((......)))))))))- ( -27.60)
>DroMoj_CAF1 2129 98 - 1
----------A---UGCAGCUGUGGCCCUCCACUGCAAACGAUGGCACCUUGGAAUCAGGCUGCAAUCGUAACGCCUAGGAGGGCAGUUUAUUUAGCAACGCAUUAUUGCU
----------.---.((((.(((((((((((...((..(((((.(((.((((....)))).))).)))))...))...))))))).(((.....)))..))))...)))). ( -36.30)
>DroPer_CAF1 2589 102 - 1
-------UAAAAAU--AAGCUGUGGCUCUCCACUGCAAACGUCUGCAACUUUGAAUCAGGUUACACUCGUAACGCCUAGGAGAGCAGUUAUUCUGGCAACGCACCAAUGCU
-------.......--.(((.((((((((((..((((......))))............(((((....))))).....))))))).........(....).)))....))) ( -26.90)
>consensus
_______UGAAUACAACAGCUGUUGCUCUUCCGUUACCACGAUGGAAGCCGUGAAUCAAGUUUCAAUCGUAACGCCAAGAAGAGCAUUUUAUCUGGCAACGCAGGAGAUC_
..................((....(((((((.......(((((.(((((..........))))).)))))........))))))).........(....)))......... (-17.96 = -18.24 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:21:21 2006