Locus 3127

Sequence ID	3R_DroMel_CAF1
Location	8,240,030 – 8,240,135
Length	105
Max. P	0.970939

overview

Window 7

Location	8,240,030 – 8,240,135
Length	105
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	78.67
Mean single sequence MFE	-29.83
Consensus MFE	-21.99
Energy contribution	-21.88
Covariance contribution	-0.11
Combinations/Pair	1.10
Mean z-score	-2.09
Structure conservation index	0.74
SVM decision value	1.39
SVM RNA-class probability	0.949455
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8240030 105 + 27905053
ACACACGCUCA-UUGCUCCCCACACUGACA-UGGG-CUU-GUUGCAGAGGAAAAAUCGAUUUCCACCAUUAGCGUGGUGCGGAUUACAUCGCCCACGCCGAGCAUGGUG
.....(((.((-(.((((...........(-((((-(..-...))...(((((......))))).))))..((((((.((((......)))))))))).)))))))))) ( -34.80)
>DroPse_CAF1 5263 99 + 1
----AAUAACA-UUUCUGCUC-UACUAAAAAUUAU----AUUUUUAGAGGAAAAAUCGAUUUCCACCAUCAGCGUUGUGCGAAUAACUUCGCCCACGCCUAGCAUGGUA
----.......-.........-..((((((((...----)))))))).(((((......)))))((((((.((((.(.(((((....)))))).))))...).))))). ( -23.10)
>DroSec_CAF1 7518 105 + 1
ACACACGCUCA-UUGCUCCCCACACUUACA-UGUG-CUU-CUUGCAGAGGAAAAAUCGAUUUCCACCAUUAGCGUGGUGCGGAUUACAUCGCCCACGCCGAGCAUGGUG
.(((..((((.-((((......(((.....-.)))-...-...)))).(((((......))))).......((((((.((((......)))))))))).))))...))) ( -34.00)
>DroEre_CAF1 7402 105 + 1
UCACAAUGUCA-UUGCU-CCCAAGCUGACA-UGAGACUU-CUUGCAGAGGAAAAAUCGAUUUCCACUAUUAGCGUGGUGCGGAUUACGUCGCCCACGCCGAGCAUGGUG
.....((((((-..(((-....))))))))-)...(((.-..(((((.(((((......))))).)).(..((((((.((((......))))))))))..)))).))). ( -33.40)
>DroYak_CAF1 7497 105 + 1
UCAUAAACCCACUUGCG-CCCAAACUAACA-UUGG-UUU-UAUGCAGAGGAAAAAUCGAUUUCCACUAUUAGCGUGGUGCGGAUUACGUCGCCCACGCCGAGUAUGGUG
......(((.(((((.(-(..((((((...-.)))-)))-...))((.(((((......))))).))....((((((.((((......)))))))))))))))..))). ( -30.60)
>DroPer_CAF1 5249 99 + 1
----AAUAACA-UUUCUGCUC-UACUAAAAAUUAU----AUUUUUAGAGGAAAAAUCGAUUUCCACCAUCAGCGUUGUGCGAAUAACUUCGCCCACGCCUAGCAUGGUG
----.......-.........-..((((((((...----)))))))).(((((......)))))((((((.((((.(.(((((....)))))).))))...).))))). ( -23.10)
>consensus
_CACAAUCUCA_UUGCU_CCCAAACUAACA_UGAG_CUU_UUUGCAGAGGAAAAAUCGAUUUCCACCAUUAGCGUGGUGCGGAUUACAUCGCCCACGCCGAGCAUGGUG
................................................(((((......)))))(((((..((((((.((((......)))))))))).....))))). (-21.99 = -21.88 +  -0.11)

alignment

secondary structure

dotplot

Window 8

Location	8,240,030 – 8,240,135
Length	105
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	78.67
Mean single sequence MFE	-34.98
Consensus MFE	-27.15
Energy contribution	-27.65
Covariance contribution	0.50
Combinations/Pair	1.20
Mean z-score	-2.54
Structure conservation index	0.78
SVM decision value	1.67
SVM RNA-class probability	0.970939
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8240030 105 - 27905053
CACCAUGCUCGGCGUGGGCGAUGUAAUCCGCACCACGCUAAUGGUGGAAAUCGAUUUUUCCUCUGCAAC-AAG-CCCA-UGUCAGUGUGGGGAGCAA-UGAGCGUGUGU
.(((((((((((((((((((........))).)))))))...((.(((((......))))).)).....-...-((((-(......)))))......-.))))))).)) ( -41.10)
>DroPse_CAF1 5263 99 - 1
UACCAUGCUAGGCGUGGGCGAAGUUAUUCGCACAACGCUGAUGGUGGAAAUCGAUUUUUCCUCUAAAAAU----AUAAUUUUUAGUA-GAGCAGAAA-UGUUAUU----
.(((((....(((((..(((((....)))))...))))).)))))(((((......))))).((((((((----...))))))))..-.((((....-))))...---- ( -29.70)
>DroSec_CAF1 7518 105 - 1
CACCAUGCUCGGCGUGGGCGAUGUAAUCCGCACCACGCUAAUGGUGGAAAUCGAUUUUUCCUCUGCAAG-AAG-CACA-UGUAAGUGUGGGGAGCAA-UGAGCGUGUGU
.(((((((((((((((((((........))).)))))))..((((....))))(((.((((((.((...-..)-)(((-(....)))))))))).))-)))))))).)) ( -40.20)
>DroEre_CAF1 7402 105 - 1
CACCAUGCUCGGCGUGGGCGACGUAAUCCGCACCACGCUAAUAGUGGAAAUCGAUUUUUCCUCUGCAAG-AAGUCUCA-UGUCAGCUUGGG-AGCAA-UGACAUUGUGA
...(((((((((((((((((........))).)))))))..(((.(((((......))))).)))((((-..(.(...-.).)..)))).)-))).)-))......... ( -34.90)
>DroYak_CAF1 7497 105 - 1
CACCAUACUCGGCGUGGGCGACGUAAUCCGCACCACGCUAAUAGUGGAAAUCGAUUUUUCCUCUGCAUA-AAA-CCAA-UGUUAGUUUGGG-CGCAAGUGGGUUUAUGA
..........((((((((((........))).)))))))..(((.(((((......))))).)))((((-((.-((((-.......))))(-(....))...)))))). ( -33.60)
>DroPer_CAF1 5249 99 - 1
CACCAUGCUAGGCGUGGGCGAAGUUAUUCGCACAACGCUGAUGGUGGAAAUCGAUUUUUCCUCUAAAAAU----AUAAUUUUUAGUA-GAGCAGAAA-UGUUAUU----
((((((....(((((..(((((....)))))...))))).))))))((((......))))((((((((((----...)))))))).)-)((((....-))))...---- ( -30.40)
>consensus
CACCAUGCUCGGCGUGGGCGAAGUAAUCCGCACCACGCUAAUGGUGGAAAUCGAUUUUUCCUCUGCAAA_AAG_CUAA_UGUUAGUAUGGG_AGCAA_UGAGAUUGUG_
..(((((((.((((((((((........))).)))))))..(((.(((((......))))).)))..................)))))))................... (-27.15 = -27.65 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:42 2006