Locus 7847

Sequence ID	3R_DroMel_CAF1
Location	21,003,827 – 21,003,981
Length	154
Max. P	0.913870

overview

Window 6

Location	21,003,827 – 21,003,944
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.61
Mean single sequence MFE	-35.56
Consensus MFE	-26.76
Energy contribution	-26.80
Covariance contribution	0.04
Combinations/Pair	1.16
Mean z-score	-2.21
Structure conservation index	0.75
SVM decision value	1.09
SVM RNA-class probability	0.913870
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21003827 117 - 27905053
GGACAUUGCAUUAACCAAAGUCUGGACAACAGAUGUCUGGGGUUUGGU---CCCCUGACAAUAUUAGUUCGGAAAUGGAGGCGUAACAUUCCGGGUGAACUGCAGAUGUCACUAAAAUUC
.(((((((((...(((....(((((((......((((.((((......---)))).))))......)))))))..(((((........))))))))....)))).))))).......... ( -37.70)
>DroSec_CAF1 8379 103 - 1
GGACAUUGCAUUAACCAAAGUCUGGACAACAGAUGUCUGGGGUUUGGUGG-----------------UUCGGAAAUGGAGGCGUAACAUUCCGGGUGAAGUGCAGAUGUCACUAAAAUUC
.(((((((((((.((((((.((..((((.....))))..)).)))))).(-----------------..(((((.((.........)))))))..)..)))))).))))).......... ( -37.60)
>DroSim_CAF1 8430 120 - 1
GGACAUUGCAUUAACCAAAGUCUGGACAACAGAUGUCUGGGGUUUGGUGGUCCCCUGACAAUAUGAGUUCGGAAAUGGAGGCGUAACAUUCCGGGUGAAGUGCAGAUGUCACUAAAAUUC
.(((((((((((.((((((.((..((((.....))))..)).))))))..(((((.((...((((..((((....))))..))))....)).))).)))))))).))))).......... ( -40.00)
>DroEre_CAF1 8508 117 - 1
GGACAUUGCAUUAACCCAACGCUGGACAACAGAUGUCUGGGGUUUGGU---CCCCUGACAAUAUAAGUUCGGAAAUGGGGGCGUAACAUUCCGGGUGAACUGCAGAUGUCACCAAAAUUC
.(((((((((...((((....((((((......((((.((((......---)))).))))......))))))....((((........))))))))....)))).))))).......... ( -38.40)
>DroYak_CAF1 9348 112 - 1
GGACAUUGCAUUAACCGAACUCUGGACAACAGAUGUCUGGACUUUGGU---CCCCUGACAAUAUAAU-----AUAAGGAGGCGUUACAUUCCGGCUGAACUACAGAUGUUACUAAAAUUC
....((((((...((((((.((..((((.....))))..)).))))))---....)).)))).((((-----((..((((........))))..(((.....)))))))))......... ( -24.10)
>consensus
GGACAUUGCAUUAACCAAAGUCUGGACAACAGAUGUCUGGGGUUUGGU___CCCCUGACAAUAUAAGUUCGGAAAUGGAGGCGUAACAUUCCGGGUGAACUGCAGAUGUCACUAAAAUUC
.(((((((((...((((((.((..((((.....))))..)).))))))............................((((........))))........)))).))))).......... (-26.76 = -26.80 +   0.04)

alignment

secondary structure

dotplot

Window 7

Location	21,003,867 – 21,003,981
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.20
Mean single sequence MFE	-25.67
Consensus MFE	-15.66
Energy contribution	-16.62
Covariance contribution	0.96
Combinations/Pair	1.10
Mean z-score	-1.73
Structure conservation index	0.61
SVM decision value	0.06
SVM RNA-class probability	0.563062
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21003867 114 - 27905053
CGAAGCUUACAAAAAUUGGUAAAG---AAAAUAAACAAAUGGACAUUGCAUUAACCAAAGUCUGGACAACAGAUGUCUGGGGUUUGGU---CCCCUGACAAUAUUAGUUCGGAAAUGGAG
....((.........(((......---........))).........)).....(((...(((((((......((((.((((......---)))).))))......)))))))..))).. ( -24.91)
>DroSec_CAF1 8419 102 - 1
CGAAGCUUACAGAAAUGGGUAAAAA-AAAAAUAAACAAAUGGACAUUGCAUUAACCAAAGUCUGGACAACAGAUGUCUGGGGUUUGGUGG-----------------UUCGGAAAUGGAG
((((.(...((....))........-...........................((((((.((..((((.....))))..)).))))))).-----------------))))......... ( -23.40)
>DroSim_CAF1 8470 120 - 1
CGAAGCUUAUAAAAAUGGUUAAAAAAAAAAAUAAACAAAUGGACAUUGCAUUAACCAAAGUCUGGACAACAGAUGUCUGGGGUUUGGUGGUCCCCUGACAAUAUGAGUUCGGAAAUGGAG
((((.((((((......(((.............)))....((((.........((((((.((..((((.....))))..)).)))))).))))........))))))))))......... ( -28.32)
>DroEre_CAF1 8548 109 - 1
CGAAGCUUACAGAAAUGGGUAAA--------AAAGCAAAUGGACAUUGCAUUAACCCAACGCUGGACAACAGAUGUCUGGGGUUUGGU---CCCCUGACAAUAUAAGUUCGGAAAUGGGG
.........((....))......--------...((((.......)))).....((((...((((((......((((.((((......---)))).))))......))))))...)))). ( -30.40)
>DroYak_CAF1 9388 108 - 1
CGAAGCUUACAAAAACGGCUGAAAA-UA---AAAGCAAAUGGACAUUGCAUUAACCGAACUCUGGACAACAGAUGUCUGGACUUUGGU---CCCCUGACAAUAUAAU-----AUAAGGAG
.....((((........(((.....-..---..)))........((((((...((((((.((..((((.....))))..)).))))))---....)).)))).....-----.))))... ( -21.30)
>consensus
CGAAGCUUACAAAAAUGGGUAAAAA__AAAAUAAACAAAUGGACAUUGCAUUAACCAAAGUCUGGACAACAGAUGUCUGGGGUUUGGU___CCCCUGACAAUAUAAGUUCGGAAAUGGAG
((((.................................((((.......)))).((((((.((..((((.....))))..)).))))))...................))))......... (-15.66 = -16.62 +   0.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:56:16 2006