Locus 506

Sequence ID 2R_DroMel_CAF1
Location 2,760,899 – 2,761,020
Length 121
Max. P 0.644160
window961 window962 window963

overview

Window 1

Location 2,760,899 – 2,760,990
Length 91
Sequences 6
Columns 93
Reading direction forward
Mean pairwise identity 80.51
Mean single sequence MFE -28.89
Consensus MFE -15.80
Energy contribution -17.17
Covariance contribution 1.36
Combinations/Pair 1.14
Mean z-score -2.02
Structure conservation index 0.55
SVM decision value 0.12
SVM RNA-class probability 0.595162
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2760899 91 + 20766785
--CAUUUCUGAUGAAAUUCAGUGGAAUUCUCAGGCGGCGGAGAGCGCGGCUAUAAAAGCGUUCGCUCGCCAACCGAAAGCAUUCAUUGUGAAA
--.(((((....))))).(((((((.......((.(((((.((((((..........))))))..)))))..)).......)))))))..... ( -26.04)
>DroVir_CAF1 50079 82 + 1
AUGCGCUCUUAUGAAAUUCG----------UUGGCGGC-GAGAGCGCAGCUAUAAAAGCGUGCGCUCGCCAGUGUCUGGCAUUCAUUGUGAAA
...(((....(((((..(((----------(.....))-))((((((((((.....))).)))))))(((((...))))).))))).)))... ( -31.10)
>DroSim_CAF1 11723 91 + 1
--CAUUUCUGAUGAAAUUCAGUGGAAUUCGCAGGCGGCGGAGAGCGCGGCUAUAAAAGCGCUCGCUCGCCAACCGAAAGCAUUCAUUGUGAAA
--.....((((......)))).....(((((((..(((((.((((((..........))))))..)))))...(....)......))))))). ( -30.40)
>DroEre_CAF1 11667 91 + 1
--CAUUUCUUAUGAAAUUCAUUGGAAUUCUCAGGCGGCAGAGAGCGCGGCUAUAAAAGCGCUCGCUCGCCAACCGAAAGCAUUCAUUGUGAAA
--..((((....))))(((((..((((.((..((.(((((.((((((..........)))))).)).)))..))...)).))))...))))). ( -28.30)
>DroYak_CAF1 11049 91 + 1
--CAUUUCUGAUGAAAUUCAGUGGAAUUCUUAGGCGGCGGAGAGCGCGGCUAUAAAAGCGCUCGCUCGCCAACCGAAAGCAUUCAUUGUGAAA
--.(((((....))))).(((((((...(((.((.(((((.((((((..........))))))..)))))..))..)))..)))))))..... ( -29.10)
>DroPer_CAF1 10357 91 + 1
--CGUUGCUGAUGAAAUUCAGUGGGAAACGCACGUUUUGGAGAGCACUGCUAUAAAAGCGCGCGUUCGCCCGGUUGGAGCAUUCAUUGUGAAA
--..(..(.((((((.((((.((((.(((((.((((((....(((...)))...)))))).)))))..)))).).)))...)))))))..).. ( -28.40)
>consensus
__CAUUUCUGAUGAAAUUCAGUGGAAUUCUCAGGCGGCGGAGAGCGCGGCUAUAAAAGCGCUCGCUCGCCAACCGAAAGCAUUCAUUGUGAAA
.....((((((((((.................(((((....((((((..........))))))..)))))...(....)..))))))).))). (-15.80 = -17.17 +   1.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 2,760,899 – 2,760,990
Length 91
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 80.51
Mean single sequence MFE -26.42
Consensus MFE -14.90
Energy contribution -14.98
Covariance contribution 0.08
Combinations/Pair 1.15
Mean z-score -2.00
Structure conservation index 0.56
SVM decision value 0.23
SVM RNA-class probability 0.644160
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2760899 91 - 20766785
UUUCACAAUGAAUGCUUUCGGUUGGCGAGCGAACGCUUUUAUAGCCGCGCUCUCCGCCGCCUGAGAAUUCCACUGAAUUUCAUCAGAAAUG--
.........((((.(((.((((.((.(((((...(((.....)))..))))).))))))...))).))))..((((......)))).....-- ( -26.80)
>DroVir_CAF1 50079 82 - 1
UUUCACAAUGAAUGCCAGACACUGGCGAGCGCACGCUUUUAUAGCUGCGCUCUC-GCCGCCAA----------CGAAUUUCAUAAGAGCGCAU
.......(((((.(((((...)))))(((((((.(((.....))))))))))..-........----------.....))))).......... ( -25.90)
>DroSim_CAF1 11723 91 - 1
UUUCACAAUGAAUGCUUUCGGUUGGCGAGCGAGCGCUUUUAUAGCCGCGCUCUCCGCCGCCUGCGAAUUCCACUGAAUUUCAUCAGAAAUG--
.(((.((..(((....)))(((.((((.(.((((((..........)))))).)))))))))).))).....((((......)))).....-- ( -27.60)
>DroEre_CAF1 11667 91 - 1
UUUCACAAUGAAUGCUUUCGGUUGGCGAGCGAGCGCUUUUAUAGCCGCGCUCUCUGCCGCCUGAGAAUUCCAAUGAAUUUCAUAAGAAAUG--
..(((....((((..((((((.((((.((.((((((..........)))))).)))))).))))))))))...)))(((((....))))).-- ( -27.70)
>DroYak_CAF1 11049 91 - 1
UUUCACAAUGAAUGCUUUCGGUUGGCGAGCGAGCGCUUUUAUAGCCGCGCUCUCCGCCGCCUAAGAAUUCCACUGAAUUUCAUCAGAAAUG--
.........((((.(((..(((.((((.(.((((((..........)))))).)))))))).))).))))..((((......)))).....-- ( -28.30)
>DroPer_CAF1 10357 91 - 1
UUUCACAAUGAAUGCUCCAACCGGGCGAACGCGCGCUUUUAUAGCAGUGCUCUCCAAAACGUGCGUUUCCCACUGAAUUUCAUCAGCAACG--
............(((.......(((.(((((((((((.....))).((..........)))))))))))))..(((......))))))...-- ( -22.20)
>consensus
UUUCACAAUGAAUGCUUUCGGUUGGCGAGCGAGCGCUUUUAUAGCCGCGCUCUCCGCCGCCUGAGAAUUCCACUGAAUUUCAUCAGAAAUG__
((((...(((((.(((.......)))(((((...(((.....)))..)))))..........................)))))..)))).... (-14.90 = -14.98 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 2,760,911 – 2,761,020
Length 109
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 82.61
Mean single sequence MFE -32.13
Consensus MFE -21.08
Energy contribution -22.25
Covariance contribution 1.17
Combinations/Pair 1.13
Mean z-score -1.77
Structure conservation index 0.66
SVM decision value 0.05
SVM RNA-class probability 0.559345
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2760911 109 + 20766785
AAUUCAGUGGAAUUCUCAGGCGGCGGAGAGCGCGGCUAUAAAAGCGUUCGCUCGCCAACCGAAAGCAUUCAUUGUGAAAUUGCCACUCAAAAUUGAAACAG-CGCG--GACA-------
.....(((((..(((.(((..(((((.((((((..........))))))..)))))...(....)......))).)))....)))))..............-....--....------- ( -27.80)
>DroVir_CAF1 50093 101 + 1
AAUUCG----------UUGGCGGC-GAGAGCGCAGCUAUAAAAGCGUGCGCUCGCCAGUGUCUGGCAUUCAUUGUGAAAUUGCAAAUCAAAAUUGAAACAAGCACAAAGCAA-------
......----------...(((((-(((.((((.(((.....))))))).)))))).(((..((((((((.....)))..)))...(((....)))..))..)))...))..------- ( -33.80)
>DroSim_CAF1 11735 109 + 1
AAUUCAGUGGAAUUCGCAGGCGGCGGAGAGCGCGGCUAUAAAAGCGCUCGCUCGCCAACCGAAAGCAUUCAUUGUGAAAUUGCCACUCAAAAUUGAAACAG-CGCG--GACA-------
.....(((((..(((((((..(((((.((((((..........))))))..)))))...(....)......)))))))....)))))..............-....--....------- ( -33.80)
>DroEre_CAF1 11679 109 + 1
AAUUCAUUGGAAUUCUCAGGCGGCAGAGAGCGCGGCUAUAAAAGCGCUCGCUCGCCAACCGAAAGCAUUCAUUGUGAAAUUGCCACUCAAAAUUGAAACAA-CGCG--GACA-------
..(((((..((((.((..((.(((((.((((((..........)))))).)).)))..))...)).))))...))))).((((...(((....))).....-.)))--)...------- ( -27.80)
>DroYak_CAF1 11061 109 + 1
AAUUCAGUGGAAUUCUUAGGCGGCGGAGAGCGCGGCUAUAAAAGCGCUCGCUCGCCAACCGAAAGCAUUCAUUGUGAAAUCGCCACUCAAAAUUGAAACAA-CGCG--GACA-------
...((.(((.........((((((((.((((((..........))))))..)))))....((...(((.....)))...)))))..(((....))).....-))).--))..------- ( -31.00)
>DroAna_CAF1 19421 116 + 1
AAUUCAGUGGAAUCGGUUGGUGGCGGAGAGGGCAGCUAUAAAAGCGCUCGCUCGCCACCAGGCGGCAUUCAUUGUGAAAUUGAAAAUCAAAAUUGAAACAA-CGCG--GACGACACUAG
.....((((...(((.(((((((((.((.((((.(((.....))))))).)))))))))))(((...((((...(((.........)))....))))....-))).--..))))))).. ( -38.60)
>consensus
AAUUCAGUGGAAUUCUCAGGCGGCGGAGAGCGCGGCUAUAAAAGCGCUCGCUCGCCAACCGAAAGCAUUCAUUGUGAAAUUGCCACUCAAAAUUGAAACAA_CGCG__GACA_______
..((((((..........((((((((.((((((..........))))))..)))))........(((.....)))......))).......))))))...................... (-21.08 = -22.25 +   1.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:40:29 2006