Locus 8796

Sequence ID	3R_DroMel_CAF1
Location	23,508,688 – 23,508,778
Length	90
Max. P	0.926688

overview

Window 6

Location	23,508,688 – 23,508,778
Length	90
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	85.81
Mean single sequence MFE	-26.30
Consensus MFE	-19.02
Energy contribution	-19.98
Covariance contribution	0.96
Combinations/Pair	1.05
Mean z-score	-2.42
Structure conservation index	0.72
SVM decision value	1.18
SVM RNA-class probability	0.926688
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23508688 90 + 27905053
UGCCGCCGCCGUUUGAACGAGCGGUGAAAUUGCUGGACAUGCCUGGCAUGGCCAACA----------AAUAGUAAAAAAAAAAGCGUGGAAAAAAAA----AAC
..((((((((((((....))))))))...(((.(((.(((((...))))).))).))----------).................))))........----... ( -26.50)
>DroSec_CAF1 6041 84 + 1
UGCCGCCGCCGUUUGAACGAGCGGUGAAAUUGCUGGACAUGCCUGGCAUGGCCAACA----------AACAGUGAAA---AAAGCGUGGAAA---AA----AAC
..((((((((((((....))))))))...(((.(((.(((((...))))).))).))----------).........---.....))))...---..----... ( -26.50)
>DroSim_CAF1 5349 84 + 1
UGCCGCCGCCGUUUGAACGAGCGGUGAAAUUGCUGGACAUGCCUGGCAUGGCCAACA----------AACAGUGAAU----AAGCGUGGAAAA--AA----AAC
..((((((((((((....))))))))...(((.(((.(((((...))))).))).))----------).........----....))))....--..----... ( -26.50)
>DroEre_CAF1 7568 92 + 1
UGCCG---CCGUUUGAACGAGCGGUGAAAUUGCUGGACAUGCCUGGCAUGGCUAACAGUGAGCGUAAAACAGUGAAA---AAGGCGUGGAAAC--AA----AAC
.((((---((((((....)))))))....(..(((..(((((...)))))(((.......)))......)))..)..---..))).((....)--).----... ( -29.40)
>DroYak_CAF1 5382 86 + 1
UGCCG---CCGUUUGAACGAGCGGUGAAAUUGCUGGACAUGCCUGGCAUGGCUAACA----------AACAGUGAAA---AAAGCGUGGAAAA--AACAACGAC
.((((---((((((....))))))))...(..(((.....(((......))).....----------..)))..)..---...))........--......... ( -22.60)
>consensus
UGCCGCCGCCGUUUGAACGAGCGGUGAAAUUGCUGGACAUGCCUGGCAUGGCCAACA__________AACAGUGAAA___AAAGCGUGGAAAA__AA____AAC
..((((((((((((....))))))))....((.(((.(((((...))))).))).))............................))))............... (-19.02 = -19.98 +   0.96)

alignment

secondary structure

dotplot

Window 7

Location	23,508,688 – 23,508,778
Length	90
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	85.81
Mean single sequence MFE	-22.84
Consensus MFE	-17.88
Energy contribution	-19.32
Covariance contribution	1.44
Combinations/Pair	1.05
Mean z-score	-1.64
Structure conservation index	0.78
SVM decision value	0.25
SVM RNA-class probability	0.652346
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23508688 90 - 27905053
GUU----UUUUUUUUCCACGCUUUUUUUUUUACUAUU----------UGUUGGCCAUGCCAGGCAUGUCCAGCAAUUUCACCGCUCGUUCAAACGGCGGCGGCA
...----............((...............(----------((((((.(((((...))))).)))))))...(.((((.(((....))))))).))). ( -26.10)
>DroSec_CAF1 6041 84 - 1
GUU----UU---UUUCCACGCUUU---UUUCACUGUU----------UGUUGGCCAUGCCAGGCAUGUCCAGCAAUUUCACCGCUCGUUCAAACGGCGGCGGCA
...----..---.......((...---.........(----------((((((.(((((...))))).)))))))...(.((((.(((....))))))).))). ( -26.10)
>DroSim_CAF1 5349 84 - 1
GUU----UU--UUUUCCACGCUU----AUUCACUGUU----------UGUUGGCCAUGCCAGGCAUGUCCAGCAAUUUCACCGCUCGUUCAAACGGCGGCGGCA
...----..--........((..----.........(----------((((((.(((((...))))).)))))))...(.((((.(((....))))))).))). ( -26.10)
>DroEre_CAF1 7568 92 - 1
GUU----UU--GUUUCCACGCCUU---UUUCACUGUUUUACGCUCACUGUUAGCCAUGCCAGGCAUGUCCAGCAAUUUCACCGCUCGUUCAAACGG---CGGCA
...----((--(((..((.((((.---...((..(((..(((.....))).)))..))..)))).))...))))).....((((.(((....))))---))).. ( -17.20)
>DroYak_CAF1 5382 86 - 1
GUCGUUGUU--UUUUCCACGCUUU---UUUCACUGUU----------UGUUAGCCAUGCCAGGCAUGUCCAGCAAUUUCACCGCUCGUUCAAACGG---CGGCA
(((((((((--(.....(((....---.........(----------((((.(.(((((...))))).).)))))..........)))..))))))---)))). ( -18.70)
>consensus
GUU____UU__UUUUCCACGCUUU___UUUCACUGUU__________UGUUGGCCAUGCCAGGCAUGUCCAGCAAUUUCACCGCUCGUUCAAACGGCGGCGGCA
...................(((.........................((((((.(((((...))))).))))))......((((.(((....))))))).))). (-17.88 = -19.32 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:19:57 2006