Locus 4195

Sequence ID	X_DroMel_CAF1
Location	11,012,942 – 11,013,041
Length	99
Max. P	0.974876

overview

Window 5

Location	11,012,942 – 11,013,041
Length	99
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	77.52
Mean single sequence MFE	-24.08
Consensus MFE	-12.85
Energy contribution	-13.30
Covariance contribution	0.45
Combinations/Pair	1.05
Mean z-score	-2.43
Structure conservation index	0.53
SVM decision value	1.42
SVM RNA-class probability	0.952318
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11012942 99 + 22224390
UAAAAAAAAAAAAAG-AAAAAACAACAAAAAUUGUCAAUUAAAGCCAUUAGGGCCAUUGGCAAUUAGUUGCCAGCCAGCCCCAUUAUGCGGAAAGUCAUU---
...............-...........................((.....((((..(((((((....)))))))...))))......))...........--- ( -16.60)
>DroPse_CAF1 4891 96 + 1
AGA-GCC-AUUUGCCCGUUGGCCGACAAAAAUUGUCAAUUAAAGCCAUUAAGGCCAACGGCAAUUAGUUGGCU----GC-CCAUUUUGUGGAAACUCAUUCCG
..(-(((-(.(((((.(((((((((((.....))))..((((.....)))))))))))))))).....)))))----..-.........((((.....)))). ( -33.10)
>DroSec_CAF1 5837 83 + 1
AAAAAAA-------------GCCAACAAAAAUUGUCAAUUAAAGCCAUUAGGGCCAUUGGCAAUUAGUUGCCA----GCCCCAUUAUGCGGAAAGUCAUU---
.......-------------.((.(((.....)))........((.....((((...((((((....))))))----))))......)))).........--- ( -16.20)
>DroSim_CAF1 909 84 + 1
AAAAAAA------------GGCCAACAAAAAUUGUCAAUUAAAGCCAUUAGGGCCAUUGGCAAUUAGUUGCCA----GCCCCAUUAUGCGGAAAGUCAUU---
.......------------(((.(((...((((((((((....(((.....))).)))))))))).)))))).----((........))...........--- ( -18.70)
>DroYak_CAF1 903 94 + 1
AACAACC-CUGUGCU-GGCGGCCAACAGAAAUUGUCAAUUAAAGCCAUUAGGGCCAUUGGCAAUUAGUUGCCA----GCCCCAUUAUGCGGAAAGUCAUU---
.......-(((((((-(((((((....).((((((((((....(((.....))).)))))))))).)))))))----))........)))).........--- ( -26.70)
>DroPer_CAF1 4870 96 + 1
AGA-GCC-AUUUGCCCGUUGGCCGACAAAAAUUGUCAAUUAAAGCCAUUAAGGCCAACGGCAAUUAGUUGGCU----GC-CCAUUAUGUGGAAACUCAUUCCG
..(-(((-(.(((((.(((((((((((.....))))..((((.....)))))))))))))))).....)))))----..-.....(((.(....).))).... ( -33.20)
>consensus
AAAAAAA_AU_UGC__G__GGCCAACAAAAAUUGUCAAUUAAAGCCAUUAGGGCCAUUGGCAAUUAGUUGCCA____GCCCCAUUAUGCGGAAAGUCAUU___
......................((((...((((((((((....(((.....))).)))))))))).))))..........((.......))............ (-12.85 = -13.30 +   0.45)

alignment

secondary structure

dotplot

Window 6

Location	11,012,942 – 11,013,041
Length	99
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	77.52
Mean single sequence MFE	-27.67
Consensus MFE	-13.64
Energy contribution	-14.28
Covariance contribution	0.64
Combinations/Pair	1.20
Mean z-score	-2.76
Structure conservation index	0.49
SVM decision value	1.74
SVM RNA-class probability	0.974876
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11012942 99 - 22224390
---AAUGACUUUCCGCAUAAUGGGGCUGGCUGGCAACUAAUUGCCAAUGGCCCUAAUGGCUUUAAUUGACAAUUUUUGUUGUUUUUU-CUUUUUUUUUUUUUA
---...........((....((((((((..((((((....)))))).))))))))...))...((..((((((....))))))..))-............... ( -24.70)
>DroPse_CAF1 4891 96 - 1
CGGAAUGAGUUUCCACAAAAUGG-GC----AGCCAACUAAUUGCCGUUGGCCUUAAUGGCUUUAAUUGACAAUUUUUGUCGGCCAACGGGCAAAU-GGC-UCU
.((((.....))))........(-(.----(((((.....((((((((((((((((.....))))..((((.....))))))))))).))))).)-)))-))) ( -32.50)
>DroSec_CAF1 5837 83 - 1
---AAUGACUUUCCGCAUAAUGGGGC----UGGCAACUAAUUGCCAAUGGCCCUAAUGGCUUUAAUUGACAAUUUUUGUUGGC-------------UUUUUUU
---..................(((((----..((((..(((((.((((((((.....))))...)))).))))).))))..))-------------))).... ( -21.00)
>DroSim_CAF1 909 84 - 1
---AAUGACUUUCCGCAUAAUGGGGC----UGGCAACUAAUUGCCAAUGGCCCUAAUGGCUUUAAUUGACAAUUUUUGUUGGCC------------UUUUUUU
---..................(((((----..((((..(((((.((((((((.....))))...)))).))))).))))..)))------------))..... ( -23.80)
>DroYak_CAF1 903 94 - 1
---AAUGACUUUCCGCAUAAUGGGGC----UGGCAACUAAUUGCCAAUGGCCCUAAUGGCUUUAAUUGACAAUUUCUGUUGGCCGCC-AGCACAG-GGUUGUU
---...(((..(((......((((((----..(((...(((((.((((((((.....))))...)))).)))))..)))..))).))-).....)-))..))) ( -31.50)
>DroPer_CAF1 4870 96 - 1
CGGAAUGAGUUUCCACAUAAUGG-GC----AGCCAACUAAUUGCCGUUGGCCUUAAUGGCUUUAAUUGACAAUUUUUGUCGGCCAACGGGCAAAU-GGC-UCU
.((((.....))))........(-(.----(((((.....((((((((((((((((.....))))..((((.....))))))))))).))))).)-)))-))) ( -32.50)
>consensus
___AAUGACUUUCCGCAUAAUGGGGC____UGGCAACUAAUUGCCAAUGGCCCUAAUGGCUUUAAUUGACAAUUUUUGUUGGCC__C__GCA_AU_GGUUUUU
....................((((((....((((((....))))))...))))))..((((......((((.....))))))))................... (-13.64 = -14.28 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:53 2006