Locus 2071

Sequence ID	3R_DroMel_CAF1
Location	5,890,607 – 5,890,720
Length	113
Max. P	0.689766

overview

Window 0

Location	5,890,607 – 5,890,720
Length	113
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.56
Mean single sequence MFE	-40.95
Consensus MFE	-27.70
Energy contribution	-29.58
Covariance contribution	1.87
Combinations/Pair	1.08
Mean z-score	-2.15
Structure conservation index	0.68
SVM decision value	0.33
SVM RNA-class probability	0.689766
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5890607 113 + 27905053
UAUCCCCGAACUAAAGAGACUUGCGUGCGGGCUCUUCUUGGGGGGGUUUCUUUGGAUUUCCCGCGGGAUCCUUGCGGUUUUCGCC-------GAAGCCAUAUGCGCAAUUUAGUUAUAAU
..(((((((....(((((.((((....))))))))).)))))))((((((..((((....(((((((...)))))))..))))..-------))))))...................... ( -36.10)
>DroSim_CAF1 15320 113 + 1
UAUCCCCGAACUACAGAGACUUGCGUGUGUGCUCUUCUUCGAGGGGUUUCUUUGGAUUUCCCGCGGGAUCGUUGCGGUUUUCGCC-------GAAGCCAUAUGCGCAAUUUAGUUAUAAU
........(((((....((.(((((((((((.....(((((.((((..((....))..))))(((..((((...))).)..))))-------)))).))))))))))))))))))..... ( -32.80)
>DroEre_CAF1 14500 113 + 1
UAUCCCCGAACAGAGGAGACUUGCGUGAGUACUCUCCUUCGGGGGGUUUCUGUGGAUUUCCCGCGGGAUACUUGCGGUUUUCCCC-------GAAGCCAUAUGCGCAAUUUAGACAUAAU
...((((((....((((((..(((....))).))))))))))))((((((.(.(((....(((((((...)))))))...)))).-------)))))).(((((........).)))).. ( -45.40)
>DroYak_CAF1 14778 120 + 1
UAUCCCCGAACCGAAGAGACUUGCGUGAGUGCUCUUCUUCGGGGGGUUUCUUUGGAUUUCCCGCGGGAUCCUUGCGGUUUUCGCCGCUUUCGGAAGCCAUAUGCGCAAUUUAGCCGUAAU
...(((((((..((((((((((....)))).)))))))))))))(((((((..((((..(....)..))))..(((((....)))))....))))))).((((.((......)))))).. ( -49.50)
>consensus
UAUCCCCGAACUAAAGAGACUUGCGUGAGUGCUCUUCUUCGGGGGGUUUCUUUGGAUUUCCCGCGGGAUCCUUGCGGUUUUCGCC_______GAAGCCAUAUGCGCAAUUUAGUCAUAAU
...(((((((..((((((((((....)))).)))))))))))))((((((...((.....(((((((...)))))))......)).......)))))).(((((........).)))).. (-27.70 = -29.58 +   1.87)

alignment

secondary structure

dotplot

Window 1

Location	5,890,607 – 5,890,720
Length	113
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.56
Mean single sequence MFE	-33.90
Consensus MFE	-26.16
Energy contribution	-26.35
Covariance contribution	0.19
Combinations/Pair	1.12
Mean z-score	-1.56
Structure conservation index	0.77
SVM decision value	0.20
SVM RNA-class probability	0.628920
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5890607 113 - 27905053
AUUAUAACUAAAUUGCGCAUAUGGCUUC-------GGCGAAAACCGCAAGGAUCCCGCGGGAAAUCCAAAGAAACCCCCCCAAGAAGAGCCCGCACGCAAGUCUCUUUAGUUCGGGGAUA
............(((((....(.((...-------.)).)....)))))((((((....)))..))).......((((.....((((((.....((....)))))))).....))))... ( -31.20)
>DroSim_CAF1 15320 113 - 1
AUUAUAACUAAAUUGCGCAUAUGGCUUC-------GGCGAAAACCGCAACGAUCCCGCGGGAAAUCCAAAGAAACCCCUCGAAGAAGAGCACACACGCAAGUCUCUGUAGUUCGGGGAUA
............(((((....(.((...-------.)).)....)))))..((((((.(((...((....))...))).)......(((((((.((....))...))).)))).))))). ( -28.90)
>DroEre_CAF1 14500 113 - 1
AUUAUGUCUAAAUUGCGCAUAUGGCUUC-------GGGGAAAACCGCAAGUAUCCCGCGGGAAAUCCACAGAAACCCCCCGAAGGAGAGUACUCACGCAAGUCUCCUCUGUUCGGGGAUA
............(((((.......((((-------((((....((((.........))))....((....))....))))))))(((....))).)))))((((((.......)))))). ( -34.50)
>DroYak_CAF1 14778 120 - 1
AUUACGGCUAAAUUGCGCAUAUGGCUUCCGAAAGCGGCGAAAACCGCAAGGAUCCCGCGGGAAAUCCAAAGAAACCCCCCGAAGAAGAGCACUCACGCAAGUCUCUUCGGUUCGGGGAUA
......((......)).....(((.((((....((((.((...((....)).)))))).))))..)))........((((((.((((((.(((......)))))))))...))))))... ( -41.00)
>consensus
AUUAUAACUAAAUUGCGCAUAUGGCUUC_______GGCGAAAACCGCAAGGAUCCCGCGGGAAAUCCAAAGAAACCCCCCGAAGAAGAGCACUCACGCAAGUCUCUUCAGUUCGGGGAUA
............((((((.....))..........((......))))))...(((....)))..............(((((((((((((.....((....))))))))..)))))))... (-26.16 = -26.35 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:35 2006