Locus 2678

Sequence ID 3R_DroMel_CAF1
Location 7,199,379 – 7,199,556
Length 177
Max. P 0.966771
window4344 window4345

overview

Window 4

Location 7,199,379 – 7,199,477
Length 98
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 76.72
Mean single sequence MFE -43.97
Consensus MFE -28.39
Energy contribution -29.50
Covariance contribution 1.12
Combinations/Pair 1.43
Mean z-score -2.12
Structure conservation index 0.65
SVM decision value 1.60
SVM RNA-class probability 0.966771
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7199379 98 + 27905053
--CUGCUGAUGUUGCUGGUGGCUCGCCGCCACGAGCGGCAUCGGUGAGCUCGCUGAACGGAGGAGCCAGCAGUGGGGAGCAGCACCAGU---CUCAGUUGCAA
--..((((((((((((.(((((.....))))).))))))))))))...(((((((...((.....))..)))))))..(((((......---....))))).. ( -46.20)
>DroPse_CAF1 74602 91 + 1
UGCCGCCGAUGUUGCAGGGGGAUCCCCGCCACGGGCCGCCUCGGUGAGUUCGCUCAACGGCGGCGCCAGCAGCGGCGAUCAGC------------AGCUGCAG
.(((((((.((..((.((((...)))).....(((((((....))).)))))).)).)))))))....(((((.((.....))------------.))))).. ( -46.30)
>DroGri_CAF1 74211 98 + 1
--CAGCAGAUGUUGCUGGCGGUUCACCGCCGCGUGCGGCUUCAGUCAGUUCUUUAAAUGGUGGCGCCAACAAUGAGCAGCAGCAUCAGC---AACAAUUGCAA
--..((((.((((((((((((....)))))((.((((((....))).((((......(((.....))).....)))).)))))...)))---)))).)))).. ( -40.30)
>DroEre_CAF1 45571 98 + 1
--CUGCUGAUGUUGCUGGUGGCUCGCCGCCACGAGCGGCAUCGGUUAGCUCGCUUAACGGUGGUGCCAGCAGUGGGGAGCAGCACCAGU---CGCAGUUGCAA
--.(((...(((.(((((((((((.((((..(..(((.(((((...((....))...))))).)))..)..)))).))))..)))))))---.)))...))). ( -46.20)
>DroYak_CAF1 45772 98 + 1
--CGGCUGAUGUUGCUGGAGGCUCGCCGCCACGAGCGGCAUCGGUCAGCUCGCUGAACGGUGGAGCCAGCAGUGGGGAGCAGCACCAGU---CGCAGUUGCAA
--.(((((((((((((.(.(((.....))).).)))))))))))))..(((((((...((.....))..)))))))..(((((......---....))))).. ( -45.50)
>DroAna_CAF1 39478 101 + 1
--CAGCCGAUGUUGCUGGUGGAUCUCCUCCGAGAGCGGCAUCCGUGAGUUCUUUGAACGGCGGAGCUAGCAGUGGAGAACAGCAACAGCAACAGCAGUUGCAA
--.......((((((((..((....))((((...(((((.(((((..((((...)))).)))))))).))..))))...))))))))(((((....))))).. ( -39.30)
>consensus
__CAGCUGAUGUUGCUGGUGGCUCGCCGCCACGAGCGGCAUCGGUGAGCUCGCUGAACGGUGGAGCCAGCAGUGGGGAGCAGCACCAGU___CGCAGUUGCAA
....((((((((((((.(((((.....))))).))))))))))))...((((((....((.....))...))))))..(((((.............))))).. (-28.39 = -29.50 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 7,199,449 – 7,199,556
Length 107
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 77.47
Mean single sequence MFE -35.07
Consensus MFE -23.87
Energy contribution -23.93
Covariance contribution 0.06
Combinations/Pair 1.33
Mean z-score -1.51
Structure conservation index 0.68
SVM decision value 0.76
SVM RNA-class probability 0.843739
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7199449 107 - 27905053
GCAGCUCCUGAUCCAGUUGCAUCAGCUC-CUUCUUGCCCUGCAGUAUAUUGCGCAGCAUGUGAUGUGCCACCAGGUCGUGUUGCAACUGAG---ACUGGUGCUGCUCCCCA
(((((.((.(.((((((((((.((((..-......))((((..((((((..((.....))..))))))...))))...)).)))))))).)---)).)).)))))...... ( -41.30)
>DroPse_CAF1 74674 98 - 1
GCAGCUCCUGGUCGAGCUGCAUGAGCUC-CUUCUUGCCCUGCAGAAUGUUGCGCAGCAUGUGAUGGGCCACCAGGUCGUGCUGCAGCU------------GCUGAUCGCCG
(((((((......)))))))((.(((..-((.........((((....))))((((((((...(((....)))...))))))))))..------------))).))..... ( -38.40)
>DroGri_CAF1 74281 107 - 1
GCAGCUCUUGAUCCAGCUGCAUUAGCUC-CUUUUUCCCCUGCAAUAUGUUGCGCAGCAUGUGAUGUGCAACUAAAUCGUGUUGCAAUUGUU---GCUGAUGCUGCUGCUCA
((((((........))))))...(((..-...........((((....))))((((((((..((.((((((........))))))...)).---.)..))))))).))).. ( -36.10)
>DroWil_CAF1 66277 95 - 1
GCAACUCCUGAUCAAGUUGCAUUAACUC-CUUCUUGCCUUGAAGAAUAUUUCGUAGCAUAUGAUGGGCCACCAAGUCGUGCUGCAAUU---------------GCUCCCCA
((((((........))))))........-((((.......))))........(((((((....(((....)))....)))))))....---------------........ ( -22.90)
>DroAna_CAF1 39548 110 - 1
GGAGUUCCUGAUCGAGUUGCAUGAGCUC-CUUCUUACCCUGCAGGAUAUUGCGCAGCAUAUGAUGGGCCACGAGAUCGUGUUGCAACUGCUGUUGCUGUUGCUGUUCUCCA
((((..(((.((((.(((((..((..((-((.(.......).))))..))..)))))...)))).)).((((....))))..(((((.((....)).))))).)..)))). ( -33.50)
>DroPer_CAF1 78222 99 - 1
GCAGCUCCUGGUCGAGCUGCAUGAGCUCCCUUCUUGCCCUGCAGAAUGUUGCGCAGCAUGUGAUGGGCCACCAGGUCGUGCUGCAGCU------------GCUGAUCGCCG
(((((((......)))))))((.(((....((((.((...))))))....((((((((((...(((....)))...)))))))).)).------------))).))..... ( -38.20)
>consensus
GCAGCUCCUGAUCGAGCUGCAUGAGCUC_CUUCUUGCCCUGCAGAAUAUUGCGCAGCAUGUGAUGGGCCACCAGGUCGUGCUGCAACU____________GCUGCUCCCCA
((((((........))))))...(((..............((((....))))((((((((...(((....)))...))))))))................)))........ (-23.87 = -23.93 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:59 2006