Locus 1842

Sequence ID	3R_DroMel_CAF1
Location	5,283,463 – 5,283,559
Length	96
Max. P	0.821245

overview

Window 1

Location	5,283,463 – 5,283,559
Length	96
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	80.62
Mean single sequence MFE	-16.02
Consensus MFE	-14.23
Energy contribution	-14.23
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.55
Structure conservation index	0.89
SVM decision value	0.68
SVM RNA-class probability	0.821245
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5283463 96 + 27905053
-----------UUAUGUU--AUCGAUAGUAUUUUUAUGCAUUUAUGCAUAUUUAAAUGCUGUUAGCAAUUUCU-UAAAUCACAUCCGACUGUUUCUGCUUAAUGGAAUCC--------
-----------...((((--(...(((((((((.((((((....))))))...))))))))))))))......-.........((((...((....))....))))....-------- ( -18.50)
>DroVir_CAF1 1941 100 + 1
-----------UU--UUU--AUCGAUAGUAUUUUUAUGCAUUUAUGCAUAGUUAAAUGCUGUUAGCAAUUUUU-UAAAUCACAUCCGACUGUUUCU-CUCAAUCAAAUCUC-GCUUCU
-----------..--...--...(((((((((((((((((....)))))))..))))))))))..........-............((.((.....-..)).)).......-...... ( -14.60)
>DroGri_CAF1 3652 99 + 1
-----------UU-UUUU--AUCGAUAGUAUUUUUAUGCAUUUAUGCAUAGUUAAAUGCUGUUAGCAAUUUUU-UAAAUCACAUCCGACUGUAUCU-AUCAAUGGAAUUUCCG---CC
-----------..-....--...(((((((((((((((((....)))))))..)))))))))).((.......-......(((......)))....-......((.....)))---). ( -17.20)
>DroWil_CAF1 3241 109 + 1
UCAUUUGUAAUUCAUGUUAAACCGAUAGUAUUUUUAUGCAUUUAUGCAUAGUUAAAUGCUGUUAGCAAAUUUU-UUAAUCACAUCCGACUGUUUCUGCCUAAUCAAAUCU--------
..(((((((((....))).....(((((((((((((((((....)))))))..)))))))))).))))))...-....................................-------- ( -15.40)
>DroMoj_CAF1 1441 88 + 1
-----------UU-UUUU--AUCGAUAGUAUUUUUAUGCAUUUAUGCAUAGUUAAAUGCUGUUAGCAAUUUUU-UGAAUCACAUCCGACUGUUUCU-CUCC-----------G---CC
-----------..-....--...(((((((((((((((((....)))))))..))))))))))..........-.(((.((........)).))).-....-----------.---.. ( -14.40)
>DroAna_CAF1 1485 97 + 1
-----------UUAUACU--AUCGAUAGUAUUUUUAUGCAUUUAUGCAUAUUUAAAUGCUGUUAGCAAUUUCUAUAAAUCACAUCCGACUGUUUCUUCUUAAUGGAAUCC--------
-----------.......--...((((((((((.((((((....))))))...))))))))))...........................(((((........)))))..-------- ( -16.00)
>consensus
___________UU_UUUU__AUCGAUAGUAUUUUUAUGCAUUUAUGCAUAGUUAAAUGCUGUUAGCAAUUUUU_UAAAUCACAUCCGACUGUUUCU_CUCAAUGGAAUCU________
.......................((((((((((.((((((....))))))...))))))))))....................................................... (-14.23 = -14.23 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	5,283,463 – 5,283,559
Length	96
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	80.62
Mean single sequence MFE	-15.40
Consensus MFE	-11.12
Energy contribution	-10.98
Covariance contribution	-0.14
Combinations/Pair	1.06
Mean z-score	-1.14
Structure conservation index	0.72
SVM decision value	-0.02
SVM RNA-class probability	0.522081
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5283463 96 - 27905053
--------GGAUUCCAUUAAGCAGAAACAGUCGGAUGUGAUUUA-AGAAAUUGCUAACAGCAUUUAAAUAUGCAUAAAUGCAUAAAAAUACUAUCGAU--AACAUAA-----------
--------((((..((((..((.......))..))))..)))).-.((...(((.....)))......((((((....)))))).........))...--.......----------- ( -12.80)
>DroVir_CAF1 1941 100 - 1
AGAAGC-GAGAUUUGAUUGAG-AGAAACAGUCGGAUGUGAUUUA-AAAAAUUGCUAACAGCAUUUAACUAUGCAUAAAUGCAUAAAAAUACUAUCGAU--AAA--AA-----------
.((.((-...(((((((((..-.....)))))))))(..(((..-...)))..).....)).......((((((....)))))).........))...--...--..----------- ( -16.40)
>DroGri_CAF1 3652 99 - 1
GG---CGGAAAUUCCAUUGAU-AGAUACAGUCGGAUGUGAUUUA-AAAAAUUGCUAACAGCAUUUAACUAUGCAUAAAUGCAUAAAAAUACUAUCGAU--AAAA-AA-----------
..---.((.....))((((((-((.....((..(((((...(((-.........)))..)))))..))((((((....))))))......))))))))--....-..----------- ( -19.90)
>DroWil_CAF1 3241 109 - 1
--------AGAUUUGAUUAGGCAGAAACAGUCGGAUGUGAUUAA-AAAAUUUGCUAACAGCAUUUAACUAUGCAUAAAUGCAUAAAAAUACUAUCGGUUUAACAUGAAUUACAAAUGA
--------.(((((..((((((.((....((..(((((..(((.-.........)))..)))))..))((((((....)))))).........)).))))))...)))))........ ( -16.10)
>DroMoj_CAF1 1441 88 - 1
GG---C-----------GGAG-AGAAACAGUCGGAUGUGAUUCA-AAAAAUUGCUAACAGCAUUUAACUAUGCAUAAAUGCAUAAAAAUACUAUCGAU--AAAA-AA-----------
..---(-----------((((-.......((..(((((....((-(....)))......)))))..))((((((....))))))......)).)))..--....-..----------- ( -12.60)
>DroAna_CAF1 1485 97 - 1
--------GGAUUCCAUUAAGAAGAAACAGUCGGAUGUGAUUUAUAGAAAUUGCUAACAGCAUUUAAAUAUGCAUAAAUGCAUAAAAAUACUAUCGAU--AGUAUAA-----------
--------..................((.(((((..(..((((....))))..).....(((((((........)))))))............)))))--.))....----------- ( -14.60)
>consensus
________AGAUUCCAUUAAG_AGAAACAGUCGGAUGUGAUUUA_AAAAAUUGCUAACAGCAUUUAACUAUGCAUAAAUGCAUAAAAAUACUAUCGAU__AAAA_AA___________
.............................(((((..(((............(((.....)))......((((((....))))))....)))..))))).................... (-11.12 = -10.98 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:53 2006