Locus 1592

Sequence ID	3R_DroMel_CAF1
Location	4,568,858 – 4,568,995
Length	137
Max. P	0.915082

overview

Window 8

Location	4,568,858 – 4,568,969
Length	111
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	92.64
Mean single sequence MFE	-32.55
Consensus MFE	-28.23
Energy contribution	-28.85
Covariance contribution	0.62
Combinations/Pair	1.09
Mean z-score	-1.60
Structure conservation index	0.87
SVM decision value	0.37
SVM RNA-class probability	0.707099
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4568858 111 + 27905053
GAAGGCGCGAUGAAAUGGAAAGUUAAGAUCCCUUUGGAGGAUUGGAUGUGUGUCAGAAGUUGAGAAACAUCCUUUGUUUUAUGUGCCUUCCAUGUGCAUUCGCACUUAACG
((((((((.((((((..((.......((((((....).)))))((((((.(.((((...)))).).))))))))..))))))))))))))...((((....))))...... ( -38.90)
>DroSec_CAF1 25595 111 + 1
GACGGCGCGAUAAAAUGGAAAGUUAAGAUCCCUUUGGGGGAUUGCAUGUGUGUCAGAAGUUGAGAAACAUCCUUUGUUCCAUGUGCCUUCCAUGUGAAUUCACAUUUAACG
((.(((((......((((((......((((((.....))))))(.((((.(.((((...)))).).)))).)....))))))))))).)).(((((....)))))...... ( -28.60)
>DroEre_CAF1 26359 111 + 1
GCCGGCGCGAUGAAAAGGAAAGUUAAGAUCCCUUUGGGGGAUUGGAUGUGUGUCAAAAGUUGAGAAACAUCUUUUGUUUUAUGUGCCUUCCAUGUGCAUUCACACUUAGCG
((.(((((.((((((..(((......((((((.....)))))).(((((.(.(((.....))).).))))))))..))))))))))).....((((....))))....)). ( -31.20)
>DroYak_CAF1 25993 111 + 1
GACGGCGCGAUGAAAUGGAAAGUUAAGAUCCCAUUGGGGCAUUGGAUGUGUGUCAAAAGUUGAGAAACAUCCUUUGUUUUAUGUGCCUUCCAUGUGCAUUCACACUUAACG
((.(((((.((((((..((.......((((((....))).)))((((((.(.(((.....))).).))))))))..))))))))))).))..((((....))))....... ( -31.50)
>consensus
GACGGCGCGAUGAAAUGGAAAGUUAAGAUCCCUUUGGGGGAUUGGAUGUGUGUCAAAAGUUGAGAAACAUCCUUUGUUUUAUGUGCCUUCCAUGUGCAUUCACACUUAACG
...(((((.((((((..((.......((((((.....))))))((((((.(.((((...)))).).))))))))..))))))))))).....((((....))))....... (-28.23 = -28.85 +   0.62)

alignment

secondary structure

dotplot

Window 9

Location	4,568,858 – 4,568,969
Length	111
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	92.64
Mean single sequence MFE	-27.35
Consensus MFE	-22.67
Energy contribution	-23.80
Covariance contribution	1.13
Combinations/Pair	1.06
Mean z-score	-2.28
Structure conservation index	0.83
SVM decision value	1.10
SVM RNA-class probability	0.915082
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4568858 111 - 27905053
CGUUAAGUGCGAAUGCACAUGGAAGGCACAUAAAACAAAGGAUGUUUCUCAACUUCUGACACACAUCCAAUCCUCCAAAGGGAUCUUAACUUUCCAUUUCAUCGCGCCUUC
......((((((.((...((((((((.............((((((.(.(((.....))).).)))))).(((((.....))))).....))))))))..)))))))).... ( -30.70)
>DroSec_CAF1 25595 111 - 1
CGUUAAAUGUGAAUUCACAUGGAAGGCACAUGGAACAAAGGAUGUUUCUCAACUUCUGACACACAUGCAAUCCCCCAAAGGGAUCUUAACUUUCCAUUUUAUCGCGCCGUC
..((..(((((....)))))..))(((.(((((((....(.((((.(.(((.....))).).)))).).(((((.....))))).......))))))......).)))... ( -23.90)
>DroEre_CAF1 26359 111 - 1
CGCUAAGUGUGAAUGCACAUGGAAGGCACAUAAAACAAAAGAUGUUUCUCAACUUUUGACACACAUCCAAUCCCCCAAAGGGAUCUUAACUUUCCUUUUCAUCGCGCCGGC
.(((..((((((.((.....((((((.........((((((.((.....)).))))))...........(((((.....))))).....))))))....)))))))).))) ( -26.50)
>DroYak_CAF1 25993 111 - 1
CGUUAAGUGUGAAUGCACAUGGAAGGCACAUAAAACAAAGGAUGUUUCUCAACUUUUGACACACAUCCAAUGCCCCAAUGGGAUCUUAACUUUCCAUUUCAUCGCGCCGUC
......((((((.((...((((((((.............((((((.(.(((.....))).).))))))....(((....))).......))))))))..)))))))).... ( -28.30)
>consensus
CGUUAAGUGUGAAUGCACAUGGAAGGCACAUAAAACAAAGGAUGUUUCUCAACUUCUGACACACAUCCAAUCCCCCAAAGGGAUCUUAACUUUCCAUUUCAUCGCGCCGUC
......((((((.((...((((((((.............((((((.(.(((.....))).).)))))).(((((.....))))).....))))))))..)))))))).... (-22.67 = -23.80 +   1.13)

alignment

secondary structure

dotplot

Window 0

Location	4,568,891 – 4,568,995
Length	104
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	76.51
Mean single sequence MFE	-31.06
Consensus MFE	-13.58
Energy contribution	-16.22
Covariance contribution	2.64
Combinations/Pair	1.19
Mean z-score	-1.87
Structure conservation index	0.44
SVM decision value	0.18
SVM RNA-class probability	0.621818
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4568891 104 - 27905053
UG-GGUGCUCUUAGGUCCU--GGCAUUGGCGUUAAGUGCGAAUGCACAUGGAA--GGCACAUAAAACAAAGGAUGUUUCUCAACUUCUGACACACAUCCAAUCCUCCAA
((-((((((......((((--((((((.(((.....))).))))).)).))).--)))))..........((((((.(.(((.....))).).))))))......))). ( -31.70)
>DroSec_CAF1 25628 106 - 1
UG-GGUGCUCUUAGCUCCUUUGGCAUUGGCGUUAAAUGUGAAUUCACAUGGAA--GGCACAUGGAACAAAGGAUGUUUCUCAACUUCUGACACACAUGCAAUCCCCCAA
((-(((((.......(((((((....((((.((..(((((....)))))..))--.)).)).....)))))))(((.((.........)).)))...)))....)))). ( -28.20)
>DroEre_CAF1 26392 104 - 1
UG-GGUGGUCUUAGGUCCU--GGCAUUGGCGCUAAGUGUGAAUGCACAUGGAA--GGCACAUAAAACAAAAGAUGUUUCUCAACUUUUGACACACAUCCAAUCCCCCAA
((-((((((((....((((--((((((.((((...)))).))))).)).))))--)))........((((((.((.....)).)))))).....))))))......... ( -30.70)
>DroYak_CAF1 26026 105 - 1
UGGGGUGGACUUAGGUCCU--GGCAUUGGCGUUAAGUGUGAAUGCACAUGGAA--GGCACAUAAAACAAAGGAUGUUUCUCAACUUUUGACACACAUCCAAUGCCCCAA
((((((((((....))))(--(....((((.((..(((((....)))))..))--.)).)).....))..((((((.(.(((.....))).).))))))...)))))). ( -34.70)
>DroAna_CAF1 21584 94 - 1
UG-GGUGCGGCUGGGGGCC--GGAAGGAGAGUU---------UCUAUUUGGGUCCUGCACG-AAAACAAAGGCUGCCUCACA-CAUUUAGGACGCAU-UAAGCCUCCAA
((-((.((((((.((((((--.(((..((....---------.)).))).))))))....(-....)...))))))))))..-......(((.((..-...)).))).. ( -30.00)
>consensus
UG_GGUGCUCUUAGGUCCU__GGCAUUGGCGUUAAGUGUGAAUGCACAUGGAA__GGCACAUAAAACAAAGGAUGUUUCUCAACUUUUGACACACAUCCAAUCCCCCAA
....(((((......(((....(((((.(((.....))).)))))....)))...)))))..........((((((.(.(((.....))).).)))))).......... (-13.58 = -16.22 +   2.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:24 2006