Locus 998

Sequence ID 3R_DroMel_CAF1
Location 3,183,721 – 3,183,819
Length 98
Max. P 0.919644
window1616 window1617

overview

Window 6

Location 3,183,721 – 3,183,819
Length 98
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.66
Mean single sequence MFE -33.18
Consensus MFE -23.26
Energy contribution -22.87
Covariance contribution -0.38
Combinations/Pair 1.35
Mean z-score -2.10
Structure conservation index 0.70
SVM decision value 1.13
SVM RNA-class probability 0.919644
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3183721 98 + 27905053
---GCCGGAAAACCUUGGAAAAAAG-GCAGCAAAGCGUUAAGCCGUUAGCAGCUAGAUUGAGCCCAGCAGCUGCUGGCGACACCUUGCAACAGUUGCCU--G---------------AA-
---.((((......)))).....((-(((((...((.....))(((((((((((.(.(((....))))))))))))))).............)))))))--.---------------..- ( -33.00)
>DroVir_CAF1 4275 117 + 1
AACAUG-GAUAGCACAAGAAAAAAGCGCAGCACAGCGUCAAACCGUUGGCGGUUGCGUUAAGC--AACAGCUGCCAGCGACACCUUGCAAGAGUUGCUGUUGUAAAGUGUUGGGCGGAAA
....((-..((((((........((((((((.(((((......)))))...))))))))..((--((((((.(((.((((....))))..).)).))))))))...))))))..)).... ( -39.50)
>DroSec_CAF1 3065 98 + 1
---GCCGGAAAACCUUGGAAAAAAG-GCAGCAAAGCGUUAAACCGUUAGCAGCUAGAUUGAGCCCAGCAGCUGCUGGCGACACCUUGCAACAGUUGCCU--G---------------AA-
---.((((......)))).....((-(((((...(((......(((((((((((.(.(((....)))))))))))))))......)))....)))))))--.---------------..- ( -32.70)
>DroSim_CAF1 9097 98 + 1
---GCCGGAAAACCUUGGAAAAAAG-GCAGCAAAGCGUUAAACCGUUAGCAGCUAGAUUGAGCCCAGCAGCUGCUGGCGACACCUUGCAACAGUUGCCU--G---------------AA-
---.((((......)))).....((-(((((...(((......(((((((((((.(.(((....)))))))))))))))......)))....)))))))--.---------------..- ( -32.70)
>DroEre_CAF1 3932 95 + 1
---GCCGGAAGUCCUUGGAAAAAAG-GCAGCAAAGCAUUAAACCGUUA---GCUAGAUUGAGCCCAGCAGCUGCUGGCGACACCUUGCAACAGUUGCCU--G---------------AG-
---.((((......)))).....((-(((((...(((......(((((---((.((.(((.......))))))))))))......)))....)))))))--.---------------..- ( -25.30)
>DroYak_CAF1 8904 104 + 1
---GCCGGGAAUCCUUGGAA-AAAG-GCAGCAAAGUGUUAAACCGUUAGCAGCUAGAUUGAGCCGAGCAGCUGCUGGCGACACCUUGCAACAGUUGCCU--GGAAAA--------GGAA-
---.(((((...((((....-.)))-)..((((.((((.....(((((((((((...(((...)))..))))))))))))))).))))........)))--))....--------....- ( -35.90)
>consensus
___GCCGGAAAACCUUGGAAAAAAG_GCAGCAAAGCGUUAAACCGUUAGCAGCUAGAUUGAGCCCAGCAGCUGCUGGCGACACCUUGCAACAGUUGCCU__G_______________AA_
....((((......))))........(((((...(((......(((((((((((..............)))))))))))......)))....)))))....................... (-23.26 = -22.87 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,183,721 – 3,183,819
Length 98
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.66
Mean single sequence MFE -31.60
Consensus MFE -21.45
Energy contribution -21.54
Covariance contribution 0.09
Combinations/Pair 1.28
Mean z-score -1.54
Structure conservation index 0.68
SVM decision value 0.46
SVM RNA-class probability 0.745164
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3183721 98 - 27905053
-UU---------------C--AGGCAACUGUUGCAAGGUGUCGCCAGCAGCUGCUGGGCUCAAUCUAGCUGCUAACGGCUUAACGCUUUGCUGC-CUUUUUUCCAAGGUUUUCCGGC---
-..---------------(--((....)))..(((((((((.(((...(((.((((((.....)))))).)))...)))...))))))))).((-(((......)))))........--- ( -34.20)
>DroVir_CAF1 4275 117 - 1
UUUCCGCCCAACACUUUACAACAGCAACUCUUGCAAGGUGUCGCUGGCAGCUGUU--GCUUAACGCAACCGCCAACGGUUUGACGCUGUGCUGCGCUUUUUUCUUGUGCUAUC-CAUGUU
......................((((......(((.((((((((((...((.(((--((.....))))).))...))))..)))))).))).((((.........))))....-..)))) ( -29.90)
>DroSec_CAF1 3065 98 - 1
-UU---------------C--AGGCAACUGUUGCAAGGUGUCGCCAGCAGCUGCUGGGCUCAAUCUAGCUGCUAACGGUUUAACGCUUUGCUGC-CUUUUUUCCAAGGUUUUCCGGC---
-..---------------(--((....)))..(((((((((.(((...(((.((((((.....)))))).)))...)))...))))))))).((-(((......)))))........--- ( -32.60)
>DroSim_CAF1 9097 98 - 1
-UU---------------C--AGGCAACUGUUGCAAGGUGUCGCCAGCAGCUGCUGGGCUCAAUCUAGCUGCUAACGGUUUAACGCUUUGCUGC-CUUUUUUCCAAGGUUUUCCGGC---
-..---------------(--((....)))..(((((((((.(((...(((.((((((.....)))))).)))...)))...))))))))).((-(((......)))))........--- ( -32.60)
>DroEre_CAF1 3932 95 - 1
-CU---------------C--AGGCAACUGUUGCAAGGUGUCGCCAGCAGCUGCUGGGCUCAAUCUAGC---UAACGGUUUAAUGCUUUGCUGC-CUUUUUUCCAAGGACUUCCGGC---
-..---------------.--(((((((((((((.((((...((((((....))).)))...)))).))---.))))))....))))).(((((-(((......)))).....))))--- ( -26.90)
>DroYak_CAF1 8904 104 - 1
-UUCC--------UUUUCC--AGGCAACUGUUGCAAGGUGUCGCCAGCAGCUGCUCGGCUCAAUCUAGCUGCUAACGGUUUAACACUUUGCUGC-CUUU-UUCCAAGGAUUCCCGGC---
-.(((--------((....--(((((......(((((((((.(((((((((((............))))))))...)))...))))))))))))-))..-....)))))........--- ( -33.40)
>consensus
_UU_______________C__AGGCAACUGUUGCAAGGUGUCGCCAGCAGCUGCUGGGCUCAAUCUAGCUGCUAACGGUUUAACGCUUUGCUGC_CUUUUUUCCAAGGUUUUCCGGC___
......................((.....((.(((((((((.(((...(((.((((((.....)))))).)))...)))...))))))))).))........))................ (-21.45 = -21.54 +   0.09)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:59 2006