Locus 1445

Sequence ID	2R_DroMel_CAF1
Location	5,524,938 – 5,525,067
Length	129
Max. P	0.995724

overview

Window 9

Location	5,524,938 – 5,525,053
Length	115
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	88.09
Mean single sequence MFE	-38.52
Consensus MFE	-29.77
Energy contribution	-30.18
Covariance contribution	0.41
Combinations/Pair	1.09
Mean z-score	-3.27
Structure conservation index	0.77
SVM decision value	2.61
SVM RNA-class probability	0.995724
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5524938 115 + 20766785
CUGGAUGGAUGCUUAAAUUGAUGUCCAUUAGCGUUGAAUUAGUGAGCAAUUAUGUUGCCUGCUCGCUAGGGCGGGCAGCAGAUACAGAUACUCGUCUAUAGAUGGAGAUUCAGAU
((((((...((((((..(..((((......))))..).....))))))....((((((((((((....))))))))))))..........((((((....))).))))))))).. ( -39.60)
>DroSec_CAF1 48224 115 + 1
CUGGAUGGAUGCUUAAAUUGAUGUCCAUUAGCGUUAAAUUAGUGAGCAAUUAUGUUGCCUGCUCGCUGGGGCGGGCAGCAGAUACAGAUACUCGUCUGUAGAUGGAGAUUCAGAU
((((((...((((((..(((((((......))))))).....))))))....((((((((((((....))))))))))))..(((((((....))))))).......)))))).. ( -42.50)
>DroSim_CAF1 25524 115 + 1
CUGGAUGGAUGCUUAAAUUGAUGUCCAUUAGCGUUAAAUUAGUGAGCAAUUAUGUUGCCUGCUCGCUGGGGCGGGCAGCAGAUACAGAUACUCGUCUGUAGAUGGAGAUUCAGAU
((((((...((((((..(((((((......))))))).....))))))....((((((((((((....))))))))))))..(((((((....))))))).......)))))).. ( -42.50)
>DroEre_CAF1 25389 89 + 1
CUGGAUGGAUGCUUAAAUUGAUGUCCAUUAGUGUUAAAUUAGUGAGCAAUUAUGUUGCCUGCUCGCUGGGGCGGGCAGCAGAUACAG--------------------------AU
...(((((((((.......).)))))))).(((((......((((....))))(((((((((((....))))))))))).)))))..--------------------------.. ( -31.70)
>DroYak_CAF1 26639 114 + 1
CUGGAUGGAUGCUGAAAUUGAUGUCCAUUAGCGUUAAAUUAGUGAGCAAUUAUGUUACCUGCUCGCUGGGGCG-GCAGCAGAUACAGAUACUUGUCUGCAGAUGGAGAUUCAGAU
((((((...(((((...(((((((......))))))).((((((((((...........))))))))))..))-)))(((((((........)))))))........)))))).. ( -36.30)
>consensus
CUGGAUGGAUGCUUAAAUUGAUGUCCAUUAGCGUUAAAUUAGUGAGCAAUUAUGUUGCCUGCUCGCUGGGGCGGGCAGCAGAUACAGAUACUCGUCUGUAGAUGGAGAUUCAGAU
(((......((((((..(((((((......))))))).....))))))....((((((((((((....))))))))))))....)))....(((((....))))).......... (-29.77 = -30.18 +   0.41)

alignment

secondary structure

dotplot

Window 0

Location	5,524,976 – 5,525,067
Length	91
Sequences	4
Columns	91
Reading direction	forward
Mean pairwise identity	96.70
Mean single sequence MFE	-27.75
Consensus MFE	-25.23
Energy contribution	-26.23
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.78
Structure conservation index	0.91
SVM decision value	0.37
SVM RNA-class probability	0.709046
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5524976 91 + 20766785
UUAGUGAGCAAUUAUGUUGCCUGCUCGCUAGGGCGGGCAGCAGAUACAGAUACUCGUCUAUAGAUGGAGAUUCAGAUACUUUUAAAGGUGG
....((((......((((((((((((....))))))))))))..........((((((....))).))).))))..(((((....))))). ( -27.80)
>DroSec_CAF1 48262 91 + 1
UUAGUGAGCAAUUAUGUUGCCUGCUCGCUGGGGCGGGCAGCAGAUACAGAUACUCGUCUGUAGAUGGAGAUUCAGAUACUUUUAAAGGUGG
....(((((.....((((((((((((....))))))))))))..(((((((....)))))))......).))))..(((((....))))). ( -30.70)
>DroSim_CAF1 25562 91 + 1
UUAGUGAGCAAUUAUGUUGCCUGCUCGCUGGGGCGGGCAGCAGAUACAGAUACUCGUCUGUAGAUGGAGAUUCAGAUACUUUUAAAGGUGG
....(((((.....((((((((((((....))))))))))))..(((((((....)))))))......).))))..(((((....))))). ( -30.70)
>DroYak_CAF1 26677 90 + 1
UUAGUGAGCAAUUAUGUUACCUGCUCGCUGGGGCG-GCAGCAGAUACAGAUACUUGUCUGCAGAUGGAGAUUCAGAUACUUUUAAAGGUGG
((((((((((...........))))))))))....-...(((((((........)))))))...............(((((....))))). ( -21.80)
>consensus
UUAGUGAGCAAUUAUGUUGCCUGCUCGCUGGGGCGGGCAGCAGAUACAGAUACUCGUCUGUAGAUGGAGAUUCAGAUACUUUUAAAGGUGG
....(((((.....((((((((((((....))))))))))))..(((((((....)))))))......).))))..(((((....))))). (-25.23 = -26.23 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:03 2006