Locus 4121

Sequence ID	2R_DroMel_CAF1
Location	13,535,937 – 13,536,075
Length	138
Max. P	0.957036

overview

Window 5

Location	13,535,937 – 13,536,035
Length	98
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	74.59
Mean single sequence MFE	-30.62
Consensus MFE	-14.94
Energy contribution	-16.62
Covariance contribution	1.68
Combinations/Pair	1.27
Mean z-score	-2.16
Structure conservation index	0.49
SVM decision value	1.47
SVM RNA-class probability	0.957036
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13535937 98 + 20766785
GUGGGGAAACACCACUACUCAAGGUCCAUGGUGGGGAAAUACUACUACUCAAGGUCCAUGGUGGGGAAACACUACCACUCAAGGUCCAUGGUGGGGAA
(((((....).)))).........(((((.(((((((....((........)).))).(((((((....).))))))........)))).)))))... ( -33.80)
>DroSim_CAF1 87116 98 + 1
GUGGGGAAACACUACCACUCAAGGCCCAUGGUGGGGAAACACAACUACUCAAGGUCCAUGGUGGGGAAACACCACUACUGAAGGUCCAUGGUGGGGAA
(((((....).)))).........(((((.(((((....)..............((..(((((((....).))))))..))....)))).)))))... ( -33.60)
>DroEre_CAF1 84771 98 + 1
GUUGGGAAACACCACUACUCAAGGUCCAUGGUGGGGAAAUAACUCUACUCAAGGUCCAUGGUGGGGAAAUAACUCUACUCAAGGUCCAUGGUGGGGAA
....(....).((((((...........))))))........((((((.((.((.((.((((((((......)))))).)).)).)).)))))))).. ( -30.90)
>DroWil_CAF1 64124 86 + 1
UUGG---AA---CACCACCGAAGGUCCUUGGUGGAAUAACUCCACGGCCUCCCCUCCCCAAUGG---AACACCACAGCAUUACCUCCCCAAUUG---A
((((---..---..(((((((......)))))))......((((.((..........))..)))---)...................))))...---. ( -16.10)
>DroYak_CAF1 87710 98 + 1
GUGGGGAAACACCACCACUCAAGGUCCAUGGUGGGGAAACACCACCACUCAAGGUCCAUGGUGGGGAAACAACUCAACGGAAGGUCCAUGGUGGGGAA
(((((....).)))).........(((.(((((((....).))))))........((((.(((((....).......(....)..)))).))))))). ( -38.70)
>consensus
GUGGGGAAACACCACCACUCAAGGUCCAUGGUGGGGAAACACCACUACUCAAGGUCCAUGGUGGGGAAACACCACAACUCAAGGUCCAUGGUGGGGAA
.........(((((((((.((.((.((.((((((..........)))).)).)).)).))))))(....)..................)))))..... (-14.94 = -16.62 +   1.68)

alignment

secondary structure

dotplot

Window 6

Location	13,535,955 – 13,536,075
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	70.47
Mean single sequence MFE	-37.29
Consensus MFE	-13.72
Energy contribution	-14.81
Covariance contribution	1.09
Combinations/Pair	1.30
Mean z-score	-2.17
Structure conservation index	0.37
SVM decision value	1.11
SVM RNA-class probability	0.916415
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13535955 120 + 20766785
UCAAGGUCCAUGGUGGGGAAAUACUACUACUCAAGGUCCAUGGUGGGGAAACACUACCACUCAAGGUCCAUGGUGGGGAAACACCACUACUCAAGGUCCAUGGUGGGGAAACACCACUAC
....((.((.((((((((........((((.((.((.((.(((((((....).)))))).....)).)).))))))(....).)).)))).)).)).)).(((((((....).)))))). ( -46.80)
>DroPse_CAF1 81255 102 + 1
UGAAUGGCCCUGGUGGAGCAAUACGACCGCU---GGACCAA-AUGUGAAUA-----CAACCCAAGGUCCUUGGUGGGGUAACACCA---CUUCCGGUCCAA-GUGGG-----AACACUAC
....(((((..(((((.(...(((..(((((---(((((..-..((.....-----..))....)))))..))))).))).).)))---))...)).)))(-(((..-----..)))).. ( -33.00)
>DroSim_CAF1 87134 120 + 1
UCAAGGCCCAUGGUGGGGAAACACAACUACUCAAGGUCCAUGGUGGGGAAACACCACUACUGAAGGUCCAUGGUGGGGAAACACUACGACUCAAGGUCCAUGGUGGGGAAACACAACUAC
......(((((.(((((....)...(((...((.((.((.(((((((....).)))))).....)).)).))(((((....).)))).......))))))).)))))............. ( -38.50)
>DroEre_CAF1 84789 120 + 1
UCAAGGUCCAUGGUGGGGAAAUAACUCUACUCAAGGUCCAUGGUGGGGAAAUAACUCUACUCAAGGUCCAUGGUGGGGAAACACCACUACUCAAGGUCCAUGGUGGGGAAAUAACUCCAC
.((.((.((.((((((((......)))))).)).)).)).))((((((......((((((.((.((.((.(((((((....).)))))).....)).)).))))))))......)))))) ( -45.30)
>DroWil_CAF1 64136 111 + 1
CGAAGGUCCUUGGUGGAAUAACUCCACGGCCUCCCCUCCCCAAUGG---AACACCACAGCAUUACCUCCCCAAUUG---AACACCACAACCGAUCGUCCUUGGUGG---AACAACUCGAC
((((((((....(((((.....))))))))))....(((((((.((---(..........................---.................))))))).))---).....))).. ( -20.43)
>DroYak_CAF1 87728 120 + 1
UCAAGGUCCAUGGUGGGGAAACACCACCACUCAAGGUCCAUGGUGGGGAAACAACUCAACGGAAGGUCCAUGGUGGGGAAAUAACUCUACUCAAGGUCCAUGGUGGGGAAACAACUCAAC
......(((.(((((((....).))))))........((((.(((((....).......(....)..((.((((((((......)))))).)).)).)))).)))))))........... ( -39.70)
>consensus
UCAAGGUCCAUGGUGGGGAAACACCACUACUCAAGGUCCAUGGUGGGGAAACACCACAACUCAAGGUCCAUGGUGGGGAAACACCACUACUCAAGGUCCAUGGUGGGGAAACAACACUAC
......(((((.(((((.........(((((...((.((.........................)).))..)))))(....)..............))))).)))))............. (-13.72 = -14.81 +   1.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:19 2006