Locus 2359

Sequence ID	X_DroMel_CAF1
Location	6,289,298 – 6,289,395
Length	97
Max. P	0.708315

overview

Window 3

Location	6,289,298 – 6,289,395
Length	97
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	80.22
Mean single sequence MFE	-33.05
Consensus MFE	-16.62
Energy contribution	-17.50
Covariance contribution	0.88
Combinations/Pair	1.12
Mean z-score	-2.53
Structure conservation index	0.50
SVM decision value	0.37
SVM RNA-class probability	0.708315
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6289298 97 + 22224390
AAAUUGAAAUGGGAACAGCGUUUACCGGCGAAAAUGGAAAUCGCCGCAAGGUGACUUGGAUUUUGGGGU---GGUUGCUCCAUGCCG--------------------AAAAGGAAUUUUG
....((((.((....))...))))(((((((.........))))).((((....))))..((((((.((---((.....)))).)))--------------------))).))....... ( -29.60)
>DroSec_CAF1 26436 95 + 1
AAAUUGAAAUGGUAGCAGCGUUUACCGCCGA-AAUGGAAAUCGCCGCAAGGUGACUUGGAUUUUG-GGU---GGUUGCUCCACGUCG--------------------AAAAGGAAUUUGG
...((((..(((.((((......((((((((-(((..((.(((((....))))).))..))))).-)))---))))))))))..)))--------------------)............ ( -32.00)
>DroSim_CAF1 24384 95 + 1
AAAUUGAAAUGGUAGCAGCGUUUACCGGCGA-AAUGGAAAUCGCCGCAAGGUGACUUGGAUUUUG-GGU---GGUUGCUCCACGUCG--------------------AAAAGGAAUUUGG
...((((..(((.((((((...(((((((((-........))))).((((....)))).......-)))---))))))))))..)))--------------------)............ ( -33.60)
>DroYak_CAF1 23923 119 + 1
AAAUUGAAAUGGGAACAGCGUUUACCAGCGA-AAUGAAAAUCGCCGCAAGGUGACUCGGAGUUUGGCGUCUGGGCUGCUGGACGGGGCAGAUGGCUGGGUUUAUUGCGAAAGGAAUUUGG
...(((.((((((..((((((((.((.((.(-(((.....(((((....)))))......)))).))(((..(....)..)))..)).)))).))))..)))))).)))........... ( -37.00)
>consensus
AAAUUGAAAUGGGAACAGCGUUUACCGGCGA_AAUGGAAAUCGCCGCAAGGUGACUUGGAUUUUG_GGU___GGUUGCUCCACGUCG____________________AAAAGGAAUUUGG
.........(((.((((((.....(((.......)))...(((((....)))))...................)))))))))...................................... (-16.62 = -17.50 +   0.88)

alignment

secondary structure

dotplot

Window 4

Location	6,289,298 – 6,289,395
Length	97
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	80.22
Mean single sequence MFE	-20.82
Consensus MFE	-14.69
Energy contribution	-15.00
Covariance contribution	0.31
Combinations/Pair	1.25
Mean z-score	-1.67
Structure conservation index	0.71
SVM decision value	0.27
SVM RNA-class probability	0.663467
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6289298 97 - 22224390
CAAAAUUCCUUUU--------------------CGGCAUGGAGCAACC---ACCCCAAAAUCCAAGUCACCUUGCGGCGAUUUCCAUUUUCGCCGGUAAACGCUGUUCCCAUUUCAAUUU
.............--------------------.((.((((((((...---...........((((....))))((((((.........))))))........)))).)))).))..... ( -19.20)
>DroSec_CAF1 26436 95 - 1
CCAAAUUCCUUUU--------------------CGACGUGGAGCAACC---ACC-CAAAAUCCAAGUCACCUUGCGGCGAUUUCCAUU-UCGGCGGUAAACGCUGCUACCAUUUCAAUUU
.............--------------------.((.(((((((((((---.((-..((((..(((((.((....)).)))))..)))-).)).)))......)))).)))).))..... ( -21.40)
>DroSim_CAF1 24384 95 - 1
CCAAAUUCCUUUU--------------------CGACGUGGAGCAACC---ACC-CAAAAUCCAAGUCACCUUGCGGCGAUUUCCAUU-UCGCCGGUAAACGCUGCUACCAUUUCAAUUU
.............--------------------.((.((((((((...---...-.......((((....))))((((((........-))))))........)))).)))).))..... ( -23.60)
>DroYak_CAF1 23923 119 - 1
CCAAAUUCCUUUCGCAAUAAACCCAGCCAUCUGCCCCGUCCAGCAGCCCAGACGCCAAACUCCGAGUCACCUUGCGGCGAUUUUCAUU-UCGCUGGUAAACGCUGUUCCCAUUUCAAUUU
.......................((((....((((.......((((....(((............)))...))))(((((........-)))))))))...))))............... ( -19.10)
>consensus
CCAAAUUCCUUUU____________________CGACGUGGAGCAACC___ACC_CAAAAUCCAAGUCACCUUGCGGCGAUUUCCAUU_UCGCCGGUAAACGCUGCUACCAUUUCAAUUU
..................................((.((((((((.................((((....))))((((((.........))))))........)))).)))).))..... (-14.69 = -15.00 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:42 2006