Locus 5140

Sequence ID	X_DroMel_CAF1
Location	13,412,461 – 13,412,565
Length	104
Max. P	0.887442

overview

Window 9

Location	13,412,461 – 13,412,565
Length	104
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	73.39
Mean single sequence MFE	-27.54
Consensus MFE	-7.26
Energy contribution	-7.62
Covariance contribution	0.36
Combinations/Pair	1.07
Mean z-score	-1.93
Structure conservation index	0.26
SVM decision value	0.95
SVM RNA-class probability	0.887442
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13412461 104 + 22224390
UAGCAUUGGGAAUAUCGAAGGCGGAGGUCAUAAGCAGCUUUCGAAAUGGGUAGCAAAGCUGGAGGGGAUGGGCCCAUCAGAU-------GAAGAUGACGACUCCACAAAAU
..((.((((.....))))..))(((((((((...(((((.((......)).)))....(((..(((......)))..))).)-------)...)))))..))))....... ( -26.80)
>DroSec_CAF1 8207 87 + 1
UAGCAUUGGGAAUAUCGAAGGCGGAGGUCAUAAGCAGCUUUCGACAUGGGGAG-------GGAGCGAA-------AUCG----------GAAGAUGACGACUCCACAAAAU
.....(((......((((((((....((.....)).)))))))).........-------((((((..-------(((.----------...)))..)).)))).)))... ( -24.80)
>DroSim_CAF1 7781 87 + 1
UAGCAUUGGGAAUAUCGAAGGCGGAGGUCAUAAGCAGCUUUCGACAUGGGGAG-------GGAGCGGA-------AUCG----------GAAGAUGACGACUCCACAAAAU
.....(((......((((((((....((.....)).)))))))).........-------((((((..-------(((.----------...)))..)).)))).)))... ( -26.80)
>DroEre_CAF1 2605 92 + 1
UAGCAUUGGGAAUAUCGAAGGCUGAGGUCAUAAGCAGCUUUGGCCAUGUUGGU--AU---GUUGG---------GAU---GUUGGGAGC-CAGGAGAUGACUCCACA-AAU
(((((((..(((((((((.(((..((((........))))..)))...)))))--))---.))..---------)))---))))((((.-((.....)).))))...-... ( -28.20)
>DroYak_CAF1 16663 96 + 1
UAGCAUUGGGAAUAUCGAAGGCGGAGGUCAUAAGCAGCUUUGGCCAUGGUGGC--CA---GCAGU---------CAUCAGCUUAGGUGAGGUGGUGAUGACUCCACA-AAU
..((.((((.....))))..))((((.((.......(((..((((.....)))--))---)).((---------(((((.(((....))).)))))))))))))...-... ( -31.10)
>consensus
UAGCAUUGGGAAUAUCGAAGGCGGAGGUCAUAAGCAGCUUUCGACAUGGGGAG_______GGAGCG_A_______AUCA__U_______GAAGAUGACGACUCCACAAAAU
.....((((((....(....)(((((((........)))))))..........................................................))).)))... ( -7.26 =  -7.62 +   0.36)

alignment

secondary structure

dotplot

Window 0

Location	13,412,461 – 13,412,565
Length	104
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	73.39
Mean single sequence MFE	-20.09
Consensus MFE	-6.84
Energy contribution	-6.80
Covariance contribution	-0.04
Combinations/Pair	1.10
Mean z-score	-1.70
Structure conservation index	0.34
SVM decision value	0.00
SVM RNA-class probability	0.534844
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13412461 104 - 22224390
AUUUUGUGGAGUCGUCAUCUUC-------AUCUGAUGGGCCCAUCCCCUCCAGCUUUGCUACCCAUUUCGAAAGCUGCUUAUGACCUCCGCCUUCGAUAUUCCCAAUGCUA
.....((((((..(((((....-------....((((....)))).....(((((((.............)))))))...))))))))))).................... ( -22.52)
>DroSec_CAF1 8207 87 - 1
AUUUUGUGGAGUCGUCAUCUUC----------CGAU-------UUCGCUCC-------CUCCCCAUGUCGAAAGCUGCUUAUGACCUCCGCCUUCGAUAUUCCCAAUGCUA
.....(((((((((........----------))))-------)))))...-------......((((((((.((..............)).))))))))........... ( -18.44)
>DroSim_CAF1 7781 87 - 1
AUUUUGUGGAGUCGUCAUCUUC----------CGAU-------UCCGCUCC-------CUCCCCAUGUCGAAAGCUGCUUAUGACCUCCGCCUUCGAUAUUCCCAAUGCUA
.....(((((((((........----------))))-------)))))...-------......((((((((.((..............)).))))))))........... ( -21.34)
>DroEre_CAF1 2605 92 - 1
AUU-UGUGGAGUCAUCUCCUG-GCUCCCAAC---AUC---------CCAAC---AU--ACCAACAUGGCCAAAGCUGCUUAUGACCUCAGCCUUCGAUAUUCCCAAUGCUA
..(-((.(((((.(((...((-(((......---...---------.....---..--........)))))..((((..........))))....)))))))))))..... ( -14.86)
>DroYak_CAF1 16663 96 - 1
AUU-UGUGGAGUCAUCACCACCUCACCUAAGCUGAUG---------ACUGC---UG--GCCACCAUGGCCAAAGCUGCUUAUGACCUCCGCCUUCGAUAUUCCCAAUGCUA
...-.((((((((((((.(...........).)))))---------)).((---((--(((.....))))..)))...........))))).................... ( -23.30)
>consensus
AUUUUGUGGAGUCGUCAUCUUC_______A__CGAU_______U_CCCUCC_______CUCCCCAUGUCGAAAGCUGCUUAUGACCUCCGCCUUCGAUAUUCCCAAUGCUA
.....((((((((((.................................................................)))).)))))).................... ( -6.84 =  -6.80 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:56 2006