Locus 5719

Sequence ID	2R_DroMel_CAF1
Location	18,116,125 – 18,116,225
Length	100
Max. P	0.708377

overview

Window 8

Location	18,116,125 – 18,116,225
Length	100
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	81.82
Mean single sequence MFE	-35.38
Consensus MFE	-26.19
Energy contribution	-26.13
Covariance contribution	-0.05
Combinations/Pair	1.19
Mean z-score	-1.59
Structure conservation index	0.74
SVM decision value	0.32
SVM RNA-class probability	0.688937
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18116125 100 + 20766785
-----------------AUGGGAGCUUUGUUUGGAAAAACCAGCAAAAAGACGGCUCCUAGUCGGAUCACCGACCAGGACAAGGCGGUUCUGGUAAGUUGGUGGUAAC-UGAGUAGCC
-----------------.(((((((((((((.((.....)))))))......)))))))).(((((((((((((((((((......))))))))....)))))))..)-)))...... ( -35.90)
>DroSec_CAF1 1 100 + 1
-----------------AUGGGGGCCUUUUUUGGAAAAACCAGCAAAAAGACGGCUCCUAGUCGGAUCACCGACCAGGACAAGGCGGUGCUGGUAAGUUGGUGGUCAC-UGAGUAGCC
-----------------.((((((((((((((((.....)))....))))).))))))))....(((((((((((((.((......)).)))))....))))))))..-......... ( -35.90)
>DroSim_CAF1 1 100 + 1
-----------------AUGGGGGCUUUGUUUGGAAAAACCAGCAAAAAGACGGCUCCUAGUCGGAUCACCGACCAGGACAAGGCGGUGCUGGUAAGUUGGUGGUCCC-UGAGUAGCC
-----------------..(((((((....(..(....(((((((......((.(((((.(((((....))))).))))...).)).)))))))...)..).))))))-)........ ( -37.10)
>DroEre_CAF1 685 117 + 1
CUGCCACGUAGUUAGUCAUGGGAGCUUUGUUUGGAAAAACGAGCAAAAAGACGGCUCCUAGUCGGAUCACCGACCAGGACAAGGCGGUGCUGGUAUGUGGGGGGUCAC-UGAGUUGCC
((.(((((((........(((((((((((((((......)))))))......))))))))(((((....)))))(((.((......)).))).))))))).)).....-......... ( -40.80)
>DroYak_CAF1 1 100 + 1
-----------------AUGGGAGCUUUGUUUGGAAAAACCAGCAAAAAGACGGCUCCUAGUCGGAUCACCGACCAGGACAAGGCGGUGCUGGUGAGUUGGUGGUCAC-UGGGUCGCC
-----------------......(((..((((....)))).)))........(((.((((((..(((((((((((((.((......)).)))))....))))))))))-))))..))) ( -37.00)
>DroAna_CAF1 203 112 + 1
CUA------AUUGAGUCAUGGGGGCUUUGUUUGGGAAAAGUAGCAAAAAAACGGCUCCUAGCCGAAUUACCGACCAGGACAAGGCAGUUUUAGUAAGUAGAUGGCUAAUUUAGAGUCU
...------...((.((.((((((((.(.((((..........))))...).))))))))((((..((((..((.(((((......))))).))..)))).)))).......)).)). ( -25.60)
>consensus
_________________AUGGGAGCUUUGUUUGGAAAAACCAGCAAAAAGACGGCUCCUAGUCGGAUCACCGACCAGGACAAGGCGGUGCUGGUAAGUUGGUGGUCAC_UGAGUAGCC
..................((((((((...((((..........)))).....))))))))....(((((((.(((((.((......)).))))).....)))))))............ (-26.19 = -26.13 +  -0.05)

alignment

secondary structure

dotplot

Window 9

Location	18,116,125 – 18,116,225
Length	100
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	81.82
Mean single sequence MFE	-28.99
Consensus MFE	-21.88
Energy contribution	-22.22
Covariance contribution	0.34
Combinations/Pair	1.16
Mean z-score	-1.61
Structure conservation index	0.75
SVM decision value	0.37
SVM RNA-class probability	0.708377
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18116125 100 - 20766785
GGCUACUCA-GUUACCACCAACUUACCAGAACCGCCUUGUCCUGGUCGGUGAUCCGACUAGGAGCCGUCUUUUUGCUGGUUUUUCCAAACAAAGCUCCCAU-----------------
((((....(-(((......)))).(((((.((.((....((((((((((....)))))))))))).)).......)))))............)))).....----------------- ( -25.90)
>DroSec_CAF1 1 100 - 1
GGCUACUCA-GUGACCACCAACUUACCAGCACCGCCUUGUCCUGGUCGGUGAUCCGACUAGGAGCCGUCUUUUUGCUGGUUUUUCCAAAAAAGGCCCCCAU-----------------
((((....(-((........))).(((((((......((((((((((((....))))))))))..))......)))))))............)))).....----------------- ( -32.30)
>DroSim_CAF1 1 100 - 1
GGCUACUCA-GGGACCACCAACUUACCAGCACCGCCUUGUCCUGGUCGGUGAUCCGACUAGGAGCCGUCUUUUUGCUGGUUUUUCCAAACAAAGCCCCCAU-----------------
((((.....-((.....)).....(((((((......((((((((((((....))))))))))..))......)))))))............)))).....----------------- ( -34.30)
>DroEre_CAF1 685 117 - 1
GGCAACUCA-GUGACCCCCCACAUACCAGCACCGCCUUGUCCUGGUCGGUGAUCCGACUAGGAGCCGUCUUUUUGCUCGUUUUUCCAAACAAAGCUCCCAUGACUAACUACGUGGCAG
(((......-(((......))).................((((((((((....)))))))))))))........(((.((((....))))..)))..(((((........)))))... ( -32.10)
>DroYak_CAF1 1 100 - 1
GGCGACCCA-GUGACCACCAACUCACCAGCACCGCCUUGUCCUGGUCGGUGAUCCGACUAGGAGCCGUCUUUUUGCUGGUUUUUCCAAACAAAGCUCCCAU-----------------
(((.....(-((........))).(((((((......((((((((((((....))))))))))..))......))))))).............))).....----------------- ( -29.30)
>DroAna_CAF1 203 112 - 1
AGACUCUAAAUUAGCCAUCUACUUACUAAAACUGCCUUGUCCUGGUCGGUAAUUCGGCUAGGAGCCGUUUUUUUGCUACUUUUCCCAAACAAAGCCCCCAUGACUCAAU------UAG
.((.((.....((((............(((((.((....((((((((((....)))))))))))).)))))...))))((((........)))).......)).))...------... ( -20.06)
>consensus
GGCUACUCA_GUGACCACCAACUUACCAGCACCGCCUUGUCCUGGUCGGUGAUCCGACUAGGAGCCGUCUUUUUGCUGGUUUUUCCAAACAAAGCCCCCAU_________________
........................(((((((......((((((((((((....))))))))))..))......)))))))...................................... (-21.88 = -22.22 +   0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:38 2006