Locus 3884

Sequence ID 2R_DroMel_CAF1
Location 12,859,422 – 12,859,544
Length 122
Max. P 0.938188
window6271 window6272 window6273

overview

Window 1

Location 12,859,422 – 12,859,514
Length 92
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.01
Mean single sequence MFE -34.76
Consensus MFE -16.30
Energy contribution -17.83
Covariance contribution 1.53
Combinations/Pair 1.12
Mean z-score -2.08
Structure conservation index 0.47
SVM decision value 0.40
SVM RNA-class probability 0.720974
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12859422 92 + 20766785
AC--------------------GG-------GUGCAUGGGAGCCUGGGCUGU-UGCCCCCGCAGGCUGCAGUCGGUUUACGUUUAAUGCCCAUAUAUAUUGUUGCCUACUUUCGGGCGCA
..--------------------((-------(((.(((..((((..((((((-.(((......))).))))))))))..)))....)))))........(((.((((......))))))) ( -30.90)
>DroGri_CAF1 244230 111 + 1
ACACACACACAUAUAUAUACAUGU-------GUAUAUGUGUGUGUGUGGAGUAUGACUCUUUUGCCUGCAGUCGGUUUACGUUUAAUGCCCAUA--UAUUGUUGCCUACUUUUAGGCGCA
.((((((((((((((((((....)-------)))))))))))))))))(((.....)))....(((((.(((.(((..(((.............--...))).))).)))..)))))... ( -40.39)
>DroSim_CAF1 214786 92 + 1
AC--------------------GG-------GGGCAUGGGAGCCUGGGCUGU-UGCCCCCGCAGGCUGCAGUCGGUUUACGUUUAAUGCCCAUAUAUAUUGUUGCCUACUUUCGGGCGCA
..--------------------((-------(((((..(.(((....))).)-)))))))((.(((......((.....))......))).............((((......)))))). ( -33.90)
>DroEre_CAF1 206963 92 + 1
AC--------------------GG-------GGGCAUGGCAGCCUGGGCUGU-UGCCCCUGCAGGCUGCAGUCGGUUUACGUUUAAUGCCCAUAUAUAUUGUUGCCUACUUUCGGGCACA
..--------------------..-------((((((.(((((((((((...-.))))....)))))))...((.....))....))))))...........(((((......))))).. ( -37.10)
>DroWil_CAF1 311605 93 + 1
AC--------------------GGGUUACGACCGCA-GGACGACGUGGCGGU-AGCCUGUGC---CUGCAGUCGGUUUACGUUUAAUGCCCAUA--UAUUGUUGCCUACUUUUAGGCGCA
..--------------------((((..((((.(((-((.(.(((.(((...-.))))))))---)))).)))).............))))...--...(((.(((((....)))))))) ( -33.46)
>DroYak_CAF1 212701 91 + 1
AC--------------------GG--------GGCAUGGAAGCCUGGGCUGU-UGCCCCUGCAGGCUGCAGUCGGUUUACGUUUAAUGCCCAUAUAUAUUGUUGCCUACUUUCGGGCGCA
..--------------------.(--------(((((..(((((..((((((-.(((......))).))))))))))).......))))))........(((.((((......))))))) ( -32.80)
>consensus
AC____________________GG_______GGGCAUGGGAGCCUGGGCUGU_UGCCCCUGCAGGCUGCAGUCGGUUUACGUUUAAUGCCCAUAUAUAUUGUUGCCUACUUUCGGGCGCA
...................................((((..((((((((.....))))....)))).(((..((.....)).....)))))))......(((.((((......))))))) (-16.30 = -17.83 +   1.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 12,859,422 – 12,859,514
Length 92
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.01
Mean single sequence MFE -31.43
Consensus MFE -15.56
Energy contribution -15.95
Covariance contribution 0.39
Combinations/Pair 1.26
Mean z-score -2.41
Structure conservation index 0.49
SVM decision value 1.29
SVM RNA-class probability 0.938188
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12859422 92 - 20766785
UGCGCCCGAAAGUAGGCAACAAUAUAUAUGGGCAUUAAACGUAAACCGACUGCAGCCUGCGGGGGCA-ACAGCCCAGGCUCCCAUGCAC-------CC--------------------GU
(((((((....)..)))..........(((((........(((.......)))((((((.((.(...-.)..)))))))))))))))).-------..--------------------.. ( -28.50)
>DroGri_CAF1 244230 111 - 1
UGCGCCUAAAAGUAGGCAACAAUA--UAUGGGCAUUAAACGUAAACCGACUGCAGGCAAAAGAGUCAUACUCCACACACACACAUAUAC-------ACAUGUAUAUAUAUGUGUGUGUGU
((((((((.(.((.(....).)).--).))))).......(((.......)))..)))...(((.....))).(((((((((((((((.-------.........))))))))))))))) ( -32.50)
>DroSim_CAF1 214786 92 - 1
UGCGCCCGAAAGUAGGCAACAAUAUAUAUGGGCAUUAAACGUAAACCGACUGCAGCCUGCGGGGGCA-ACAGCCCAGGCUCCCAUGCCC-------CC--------------------GU
((((((((.(.((((....)..))).).)))))......((.....))...)))....(((((((((-..(((....)))....)))))-------))--------------------)) ( -32.70)
>DroEre_CAF1 206963 92 - 1
UGUGCCCGAAAGUAGGCAACAAUAUAUAUGGGCAUUAAACGUAAACCGACUGCAGCCUGCAGGGGCA-ACAGCCCAGGCUGCCAUGCCC-------CC--------------------GU
(((((((....)..))).)))........((((((....((.....))...(((((((....((((.-...))))))))))).))))))-------..--------------------.. ( -34.10)
>DroWil_CAF1 311605 93 - 1
UGCGCCUAAAAGUAGGCAACAAUA--UAUGGGCAUUAAACGUAAACCGACUGCAG---GCACAGGCU-ACCGCCACGUCGUCC-UGCGGUCGUAACCC--------------------GU
...(((((....))))).......--.(((((..(((....)))..(((((((((---((((.(((.-...)))..)).).))-))))))))...)))--------------------)) ( -32.40)
>DroYak_CAF1 212701 91 - 1
UGCGCCCGAAAGUAGGCAACAAUAUAUAUGGGCAUUAAACGUAAACCGACUGCAGCCUGCAGGGGCA-ACAGCCCAGGCUUCCAUGCC--------CC--------------------GU
(((((((....)..)))............((((......((.....))......)))))))((((((-..(((....)))....))))--------))--------------------.. ( -28.40)
>consensus
UGCGCCCGAAAGUAGGCAACAAUAUAUAUGGGCAUUAAACGUAAACCGACUGCAGCCUGCAGGGGCA_ACAGCCCAGGCUCCCAUGCCC_______CC____________________GU
...(((((...((.(....).)).....))))).......(((......((((.....))))((((.....)))).........)))................................. (-15.56 = -15.95 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 12,859,435 – 12,859,544
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.30
Mean single sequence MFE -35.11
Consensus MFE -22.76
Energy contribution -23.77
Covariance contribution 1.00
Combinations/Pair 1.19
Mean z-score -1.58
Structure conservation index 0.65
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12859435 109 - 20766785
-----GAAGCGGGCAAACUGG-----AGGCCAUUGGCCACUGCGCCCGAAAGUAGGCAACAAUAUAUAUGGGCAUUAAACGUAAACCGACUGCAGCCUGCGGGGGCA-ACAGCCCAGGCU
-----...((((((.......-----.((((...))))..((((((((.(.((((....)..))).).)))))......((.....))...)))))))))..((((.-...))))..... ( -37.70)
>DroGri_CAF1 244263 113 - 1
-ACUGGCAACUGGCA-ACUGGCAA--CGGGCACUGA-CACUGCGCCUAAAAGUAGGCAACAAUA--UAUGGGCAUUAAACGUAAACCGACUGCAGGCAAAAGAGUCAUACUCCACACACA
-..(((....((((.-.(((....--)))...((..-..(((((((((....))))).......--..(((..............)))...)))).....)).))))....)))...... ( -25.14)
>DroSim_CAF1 214799 108 - 1
-----GAAACGGGCA-ACUGG-----AGGCCAUUGGCCACUGCGCCCGAAAGUAGGCAACAAUAUAUAUGGGCAUUAAACGUAAACCGACUGCAGCCUGCGGGGGCA-ACAGCCCAGGCU
-----....(((...-.))).-----.((((...))))..((((((((.(.((((....)..))).).)))))......((.....))...)))(((((.((.(...-.)..))))))). ( -35.50)
>DroEre_CAF1 206976 108 - 1
-----GAAACGGGCA-ACUGG-----AGGCCAUUGGCCACUGUGCCCGAAAGUAGGCAACAAUAUAUAUGGGCAUUAAACGUAAACCGACUGCAGCCUGCAGGGGCA-ACAGCCCAGGCU
-----....((((((-...((-----.((((...)))).)).))))))..(((.(....)........(((((................((((.....)))).(...-.).))))).))) ( -37.30)
>DroWil_CAF1 311624 113 - 1
CAGCAGCAGCAGGCA-GCUGGCAGUCAGGCCAAUGGCCAUUGCGCCUAAAAGUAGGCAACAAUA--UAUGGGCAUUAAACGUAAACCGACUGCAG---GCACAGGCU-ACCGCCACGUCG
..((....)).(((.-(((.((((((.((((...))))..((((((((....)))))..((...--..)).))).............)))))).)---))...(((.-...)))..))). ( -39.30)
>DroYak_CAF1 212713 108 - 1
-----GAAACGGGCA-ACUGG-----AGGCCAUUGGCCACUGCGCCCGAAAGUAGGCAACAAUAUAUAUGGGCAUUAAACGUAAACCGACUGCAGCCUGCAGGGGCA-ACAGCCCAGGCU
-----....(((...-.))).-----.((((...)))).(((((((((.(.((((....)..))).).)))))......((.....))...))))...((..((((.-...))))..)). ( -35.70)
>consensus
_____GAAACGGGCA_ACUGG_____AGGCCAUUGGCCACUGCGCCCGAAAGUAGGCAACAAUAUAUAUGGGCAUUAAACGUAAACCGACUGCAGCCUGCAGGGGCA_ACAGCCCAGGCU
.........(((.....))).......((((...)))).(((((((((...((.(....).)).....)))))......((.....))...))))...((..((((.....))))..)). (-22.76 = -23.77 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:24 2006