Locus 4597

Sequence ID	3R_DroMel_CAF1
Location	12,087,103 – 12,087,249
Length	146
Max. P	0.973705

overview

Window 5

Location	12,087,103 – 12,087,209
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.34
Mean single sequence MFE	-28.46
Consensus MFE	-23.52
Energy contribution	-23.92
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.04
Structure conservation index	0.83
SVM decision value	1.72
SVM RNA-class probability	0.973705
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12087103 106 + 27905053
-------AUACUCACAUAUAGGA-AACACUGCGGACAAGUGAAAUUGGUGGAAGAGCCAGCGAGAAGUUUAAUAUAAAUCUCUCACAGUGCUGGCGCGACCGAAUUC------AAUUUAC
-------.............(..-..)............((((.(((((.(....((((((((((..((((...))))..)))).....)))))).).))))).)))------)...... ( -27.90)
>DroSec_CAF1 23706 107 + 1
-------AUACUCAUAUAUAGGAAAACACUGCGGACAAGUGAAAUUGGUGGAAGAGCCAGCGAGAAGUUUAAUAUAAAUCUCUCACAGUGCUGGCGCGACCGAAUUC------AAUUUAC
-------..............(((..((((.......))))...(((((.(....((((((((((..((((...))))..)))).....)))))).).))))).)))------....... ( -27.10)
>DroSim_CAF1 23867 107 + 1
-------AUACUCAUAUAUAGGAAAACACUGCGGACAAGUGAAAUUGGUGGAAGAGCCAGCGAGAAGUUUAAUAUAAAUCUCUCACAGUGCUGGCGCGACCGAAUUC------AAUUUAC
-------..............(((..((((.......))))...(((((.(....((((((((((..((((...))))..)))).....)))))).).))))).)))------....... ( -27.10)
>DroEre_CAF1 25729 114 + 1
AUACUUCAUACUCAUACAUAGGAAAACACUGCGGACAAGUCAAAUUGGUGGAAGCGCCAGCGAGAAGUUUAAUAUAAAUCUCUCACAGUGCUGGCGCGACCGAAUUC------AAUUUAC
.........(((....(.(((.......))).)....))).((((((((((..((((((((((((..((((...))))..)))).....))))))))..)))...))------))))).. ( -29.00)
>DroYak_CAF1 26190 113 + 1
-------AUACUCAUACAUAGGAAAACACUGCGGACAAGUCAAAUUGGUGGAAGCGCCAGCGAGAAGUUUAAUAUAAAUCUCUCACAGUGCUGGCGCGACCGACUUCAACACCAAUUCAC
-------..(((....(.(((.......))).)....)))..((((((((...((((((((((((..((((...))))..)))).....))))))))((......))..))))))))... ( -31.20)
>consensus
_______AUACUCAUAUAUAGGAAAACACUGCGGACAAGUGAAAUUGGUGGAAGAGCCAGCGAGAAGUUUAAUAUAAAUCUCUCACAGUGCUGGCGCGACCGAAUUC______AAUUUAC
..........................((((.......))))...(((((.(....((((((((((..((((...))))..)))).....)))))).).)))))................. (-23.52 = -23.92 +   0.40)

alignment

secondary structure

dotplot

Window 6

Location	12,087,135 – 12,087,249
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.67
Mean single sequence MFE	-28.58
Consensus MFE	-22.78
Energy contribution	-23.18
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.91
Structure conservation index	0.80
SVM decision value	0.78
SVM RNA-class probability	0.849618
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12087135 114 + 27905053
GAAAUUGGUGGAAGAGCCAGCGAGAAGUUUAAUAUAAAUCUCUCACAGUGCUGGCGCGACCGAAUUC------AAUUUACAGUCUACGUCCAAAGCUUUAACAUACGAAAUGCAACGACA
(((.(((((.(....((((((((((..((((...))))..)))).....)))))).).))))).)))------..............(((....(((((........))).))...))). ( -27.70)
>DroSec_CAF1 23739 114 + 1
GAAAUUGGUGGAAGAGCCAGCGAGAAGUUUAAUAUAAAUCUCUCACAGUGCUGGCGCGACCGAAUUC------AAUUUACAGUCUACGUCCAAAGCUUUAACAUACGAAAUGCAACGACA
(((.(((((.(....((((((((((..((((...))))..)))).....)))))).).))))).)))------..............(((....(((((........))).))...))). ( -27.70)
>DroSim_CAF1 23900 112 + 1
GAAAUUGGUGGAAGAGCCAGCGAGAAGUUUAAUAUAAAUCUCUCACAGUGCUGGCGCGACCGAAUUC------AAUUUACAGUCUACGUCCAAAGCUUUAA--UACGAAAUGCAACGACA
(((.(((((.(....((((((((((..((((...))))..)))).....)))))).).))))).)))------..............(((....(((((..--....))).))...))). ( -27.90)
>DroEre_CAF1 25769 114 + 1
CAAAUUGGUGGAAGCGCCAGCGAGAAGUUUAAUAUAAAUCUCUCACAGUGCUGGCGCGACCGAAUUC------AAUUUACAGCCUACGUCCAAAGCUUUAACAUACGAAAUGCAACAACA
.((((((((((..((((((((((((..((((...))))..)))).....))))))))..)))...))------)))))................(((((........))).))....... ( -28.70)
>DroYak_CAF1 26223 120 + 1
CAAAUUGGUGGAAGCGCCAGCGAGAAGUUUAAUAUAAAUCUCUCACAGUGCUGGCGCGACCGACUUCAACACCAAUUCACAGUCUACGUCCAAAGCUUUAACAUACGAAAUGCAACAACA
..((((((((...((((((((((((..((((...))))..)))).....))))))))((......))..)))))))).................(((((........))).))....... ( -30.90)
>consensus
GAAAUUGGUGGAAGAGCCAGCGAGAAGUUUAAUAUAAAUCUCUCACAGUGCUGGCGCGACCGAAUUC______AAUUUACAGUCUACGUCCAAAGCUUUAACAUACGAAAUGCAACGACA
....(((((.(....((((((((((..((((...))))..)))).....)))))).).)))))........................(((....(((((........))).))...))). (-22.78 = -23.18 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:08 2006