Locus 4916

Sequence ID 2L_DroMel_CAF1
Location 14,066,742 – 14,066,832
Length 90
Max. P 0.985049
window7801 window7802

overview

Window 1

Location 14,066,742 – 14,066,832
Length 90
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 71.65
Mean single sequence MFE -19.22
Consensus MFE -12.83
Energy contribution -12.63
Covariance contribution -0.19
Combinations/Pair 1.14
Mean z-score -1.94
Structure conservation index 0.67
SVM decision value 1.99
SVM RNA-class probability 0.985049
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14066742 90 + 22407834
AAAAAA-----UAGGGA--AAAUA-GCGAAACGGAAGUGCAGCCAUUGAAAAGGCAUUUCGAAAUGGCCGCAGACUGUAGGGAAAAUGGU--GUA-UGAAG
.....(-----(((...--.....-.....((....))((.((((((((((.....))))))..)))).))...))))............--...-..... ( -15.80)
>DroVir_CAF1 280336 76 + 1
AC-------A--AAACCAAAAGGCAGCC-AACGGAAGUGCAGCCAUUGAAAAGGCAUUUCAAAAUGGCCGCAAUUUAUGGUGGCAA---------------
..-------.--..........((.(((-(((....))((.((((((((((.....)))))..))))).))......)))).))..--------------- ( -22.00)
>DroGri_CAF1 186558 89 + 1
GC----CGUAAGAGACC--AAGUC-GCCGAACGAAAGUGCAGCUAUUGAAAAGGCAUUUCAAAAUGGCCACAAUUUAUGGUGGCAACUGC--CUG-GGC--
((----(.........(--((...-((.(.((....)).).))..)))...(((((...(.....)(((((........)))))...)))--)).-)))-- ( -23.10)
>DroSec_CAF1 155488 92 + 1
AAAAAA-----UAGGGA--AAAUA-GCGAAACGGAAGUGCAGCCAUUGAAAAGGCAUUUCGAAAUGGCCGCAGGCUGUAGGGAAAAUGGGGAGUG-GGGAG
......-----......--..(((-((...((....))((.((((((((((.....))))))..)))).))..))))).................-..... ( -19.10)
>DroSim_CAF1 156408 92 + 1
AAAAAA-----UAGGGA--AAAUA-GCGAAACGGAAGUGCAGCCAUUGAAAAGGCAUUUCGAAAUGGCCGCAGACUGUAGGGAAAAUGGGGAGUA-AGGAG
.....(-----(((...--.....-.....((....))((.((((((((((.....))))))..)))).))...)))).................-..... ( -15.80)
>DroEre_CAF1 158323 90 + 1
AAAA------AUAGGGA--AAAUA-GCGAAACGGAAGUGCAGCCAUUGAAAAGGCAUUUCGAAAUGGCCGCAGACUGUUGGGAAAAUAGA--GGGGGGGCG
....------.....((--((...-((...((....)))).(((........))).))))......(((.(...(((((.....))))).--...).))). ( -19.50)
>consensus
AAAA_______UAGGGA__AAAUA_GCGAAACGGAAGUGCAGCCAUUGAAAAGGCAUUUCGAAAUGGCCGCAGACUGUAGGGAAAAUGGG__GUG_GGGAG
..............................((....))((.((((((((((.....))))))..)))).)).............................. (-12.83 = -12.63 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,066,742 – 14,066,832
Length 90
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 71.65
Mean single sequence MFE -19.08
Consensus MFE -14.97
Energy contribution -15.00
Covariance contribution 0.03
Combinations/Pair 1.07
Mean z-score -3.40
Structure conservation index 0.78
SVM decision value 1.96
SVM RNA-class probability 0.984115
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14066742 90 - 22407834
CUUCA-UAC--ACCAUUUUCCCUACAGUCUGCGGCCAUUUCGAAAUGCCUUUUCAAUGGCUGCACUUCCGUUUCGC-UAUUU--UCCCUA-----UUUUUU
.....-...--..................((((((((((..((((.....))))))))))))))............-.....--......-----...... ( -16.30)
>DroVir_CAF1 280336 76 - 1
---------------UUGCCACCAUAAAUUGCGGCCAUUUUGAAAUGCCUUUUCAAUGGCUGCACUUCCGUU-GGCUGCCUUUUGGUUU--U-------GU
---------------..((((........(((((((((..(((((.....)))))))))))))).......)-))).(((....)))..--.-------.. ( -24.06)
>DroGri_CAF1 186558 89 - 1
--GCC-CAG--GCAGUUGCCACCAUAAAUUGUGGCCAUUUUGAAAUGCCUUUUCAAUAGCUGCACUUUCGUUCGGC-GACUU--GGUCUCUUACG----GC
--(((-.((--(((((((((.....(((.((..((....((((((.....))))))..))..)).))).....)))-)))).--.)))).....)----)) ( -25.00)
>DroSec_CAF1 155488 92 - 1
CUCCC-CACUCCCCAUUUUCCCUACAGCCUGCGGCCAUUUCGAAAUGCCUUUUCAAUGGCUGCACUUCCGUUUCGC-UAUUU--UCCCUA-----UUUUUU
.....-.......................((((((((((..((((.....))))))))))))))............-.....--......-----...... ( -16.30)
>DroSim_CAF1 156408 92 - 1
CUCCU-UACUCCCCAUUUUCCCUACAGUCUGCGGCCAUUUCGAAAUGCCUUUUCAAUGGCUGCACUUCCGUUUCGC-UAUUU--UCCCUA-----UUUUUU
.....-.......................((((((((((..((((.....))))))))))))))............-.....--......-----...... ( -16.30)
>DroEre_CAF1 158323 90 - 1
CGCCCCCCC--UCUAUUUUCCCAACAGUCUGCGGCCAUUUCGAAAUGCCUUUUCAAUGGCUGCACUUCCGUUUCGC-UAUUU--UCCCUAU------UUUU
.........--...........(((.(..((((((((((..((((.....))))))))))))))...).)))....-.....--.......------.... ( -16.50)
>consensus
CUCCC_CAC__CCCAUUUUCCCUACAGUCUGCGGCCAUUUCGAAAUGCCUUUUCAAUGGCUGCACUUCCGUUUCGC_UAUUU__UCCCUA_______UUUU
.............................((((((((((..((((.....))))))))))))))..................................... (-14.97 = -15.00 +   0.03)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:59 2006