Locus 5610

Sequence ID	3R_DroMel_CAF1
Location	14,796,078 – 14,796,179
Length	101
Max. P	0.978432

overview

Window 9

Location	14,796,078 – 14,796,179
Length	101
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	83.65
Mean single sequence MFE	-26.44
Consensus MFE	-22.30
Energy contribution	-21.91
Covariance contribution	-0.39
Combinations/Pair	1.12
Mean z-score	-3.79
Structure conservation index	0.84
SVM decision value	1.81
SVM RNA-class probability	0.978432
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14796078 101 + 27905053
AAAAAAA-AACACAAACACACAACCGGUAACAAGUCAAGAUCAAAGCAAGUGCUGGCUUUUGGCUGGCUUUUGGCCAAAACUUGCU-CUGAUUGGCAGCCCAC
.......-.................(((.....((((..((((.(((((((..(((((...((....))...)))))..)))))))-.)))))))).)))... ( -27.40)
>DroSec_CAF1 4577 89 + 1
-AAAAAA-UACCCAAUCACACAACCGGUAACAAGUCAAGAUCAAAGCAAGUGCUGGCU-----------UUUGGCCAAAACUUGCU-CUGAUUGGCAGCUCAC
-......-((((.............))))....((((..((((.(((((((..((((.-----------....))))..)))))))-.))))))))....... ( -25.82)
>DroSim_CAF1 1837 90 + 1
-AAAAAA-UACCCAAUCACACAACCGGUAACAAGUCAAGAUCAAAGCAAGUGCUGGCU-----------UUUGGCCAAAACUUGCUUCUGAUUGGCAGCGCAC
-......-((((.............))))....((((..((((((((((((..((((.-----------....))))..)))))))).))))))))....... ( -25.52)
>DroEre_CAF1 11686 89 + 1
-AAAACAGCCCAUAAUCACACAACCGGUAACAAGUCAAGAUCAAAGCAAGUGCUGGCC------------CUGGCCAAAACUUGCU-CUGAUUGGCAGCCCAC
-......(((....(((........)))..........(((((.(((((((..((((.------------...))))..)))))))-.))))))))....... ( -27.10)
>DroYak_CAF1 11934 97 + 1
-AAAAAA-CACCCAAUCACACAACCGGUAACAAGUCAAGAUCAAAGCAAGUGCUGGCCAA-AACUG--CUCUGGCCAAAACUUGCU-CUGAUUGGCAGCCCAC
-......-.................(((.....((((..((((.(((((((..((((((.-.....--...))))))..)))))))-.)))))))).)))... ( -27.90)
>DroAna_CAF1 1678 83 + 1
-AAAA-------CACUAACAUGACCGGUAACAAGUCAAGAUCAAAGCAAGUUAUGGCC-----------UUUGGCCAAAAUUUGCU-CUGAUUGGCAGCACCC
-....-------.............(((.....((((..((((.((((((((.(((((-----------...))))).))))))))-.))))))))...))). ( -24.90)
>consensus
_AAAAAA_CACCCAAUCACACAACCGGUAACAAGUCAAGAUCAAAGCAAGUGCUGGCC___________UUUGGCCAAAACUUGCU_CUGAUUGGCAGCCCAC
.................................(((((......(((((((..(((((..............)))))..))))))).....)))))....... (-22.30 = -21.91 +  -0.39)

alignment

secondary structure

dotplot

Window 0

Location	14,796,078 – 14,796,179
Length	101
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	83.65
Mean single sequence MFE	-29.93
Consensus MFE	-20.74
Energy contribution	-21.24
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.52
Structure conservation index	0.69
SVM decision value	0.38
SVM RNA-class probability	0.714884
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14796078 101 - 27905053
GUGGGCUGCCAAUCAG-AGCAAGUUUUGGCCAAAAGCCAGCCAAAAGCCAGCACUUGCUUUGAUCUUGACUUGUUACCGGUUGUGUGUUUGUGUU-UUUUUUU
(..(((.(((.(((((-(((((((.(((((.....(....).....))))).))))))))))))..(((....)))..))).....)))..)...-....... ( -26.20)
>DroSec_CAF1 4577 89 - 1
GUGAGCUGCCAAUCAG-AGCAAGUUUUGGCCAAA-----------AGCCAGCACUUGCUUUGAUCUUGACUUGUUACCGGUUGUGUGAUUGGGUA-UUUUUU-
(..(((.....(((((-(((((((.(((((....-----------.))))).))))))))))))...).))..)..((((((....))))))...-......- ( -28.70)
>DroSim_CAF1 1837 90 - 1
GUGCGCUGCCAAUCAGAAGCAAGUUUUGGCCAAA-----------AGCCAGCACUUGCUUUGAUCUUGACUUGUUACCGGUUGUGUGAUUGGGUA-UUUUUU-
........((((((((((((((((.(((((....-----------.))))).)))))))))......((((.......))))...)))))))...-......- ( -28.10)
>DroEre_CAF1 11686 89 - 1
GUGGGCUGCCAAUCAG-AGCAAGUUUUGGCCAG------------GGCCAGCACUUGCUUUGAUCUUGACUUGUUACCGGUUGUGUGAUUAUGGGCUGUUUU-
..((((.(((.(((((-(((((((.(((((...------------.))))).)))))))))))).....(..((((((....).)))))...)))).)))).- ( -33.00)
>DroYak_CAF1 11934 97 - 1
GUGGGCUGCCAAUCAG-AGCAAGUUUUGGCCAGAG--CAGUU-UUGGCCAGCACUUGCUUUGAUCUUGACUUGUUACCGGUUGUGUGAUUGGGUG-UUUUUU-
.(((....)))(((((-(((((((.((((((((((--...))-)))))))).))))))))))))............((((((....))))))...-......- ( -36.10)
>DroAna_CAF1 1678 83 - 1
GGGUGCUGCCAAUCAG-AGCAAAUUUUGGCCAAA-----------GGCCAUAACUUGCUUUGAUCUUGACUUGUUACCGGUCAUGUUAGUG-------UUUU-
(((..(((.(((((((-(((((.((.(((((...-----------))))).)).))))))))))..(((((.......))))))).)))..-------))).- ( -27.50)
>consensus
GUGGGCUGCCAAUCAG_AGCAAGUUUUGGCCAAA___________AGCCAGCACUUGCUUUGAUCUUGACUUGUUACCGGUUGUGUGAUUGGGUA_UUUUUU_
....((.(((.(((((.(((((((.(((((................))))).))))))))))))..(((....)))..))).))................... (-20.74 = -21.24 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:18 2006