Locus 2881

Sequence ID	2L_DroMel_CAF1
Location	8,268,129 – 8,268,258
Length	129
Max. P	0.953169

overview

Window 4

Location	8,268,129 – 8,268,237
Length	108
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	80.18
Mean single sequence MFE	-29.67
Consensus MFE	-13.50
Energy contribution	-15.37
Covariance contribution	1.86
Combinations/Pair	1.22
Mean z-score	-2.66
Structure conservation index	0.46
SVM decision value	0.47
SVM RNA-class probability	0.747757
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8268129 108 + 22407834
CGCCAC----UACCGUAAAUUGUUUAGCCAAUUUAUGGCCAGAGAAUGCAUCGAAUUAUGCAUUCGAUUUGGUUUUACACUAUGGCA---UUGCAUUCAAUUAAUGCCAGACGGA
..((..----..((((((((((......))))))))))(((((((((((((......))))))))..)))))..........(((((---(((........))))))))...)). ( -33.00)
>DroSec_CAF1 46174 104 + 1
UGCCAC----AAC----AAUUGGCUAAACAAUUUACGGCCAGAGAAUGCAACAAAUUAUGCAUUCGAUUUGGUUUUGCAUUAUGGCA---UUGCAUUCAAUUAAUGCCAGACGGA
.((((.----...----...))))...........(((((((((((((((........)))))))..)))))).........(((((---(((........))))))))..)).. ( -28.00)
>DroSim_CAF1 46261 108 + 1
UGCCAC----AACCGUAAUUUGUUUAGCCAAUUUACGGCCAGAGAAUGCAACAAAUUAUGCAUUCGAUUUGGUUUUGCAUUAUGGCA---UUGCAUUCAAUUAAUGCCAGACGGA
(((...----..((((((.(((......))).))))))((((((((((((........)))))))..)))))....)))...(((((---(((........))))))))...... ( -30.80)
>DroEre_CAF1 48464 103 + 1
UGCCAC----AACUGUAAAUGGCUUAGCCAAUUUAUGGCAAGAAAAUGCAUCGCAUUAUGCAUUCGAUUUGGUUUUGCAUUCUGGC--------AUUCAAUUAAUGCCAGACGGA
..((..----...........((..((((((......(((....(((((...))))).))).......))))))..))..((((((--------(((.....))))))))).)). ( -28.62)
>DroYak_CAF1 49803 103 + 1
UGCCAC----AACUGUAAAUGGUUUAGCCAAUUUAUGGCAAGAAAAUGCAUCGAAUUAUGCAUUCGAUUUGGUUUUGCAUUCUGGC--------AUUCAAUUAAUGCCAGACGGA
..((..----...........((..((((((......(((......)))(((((((.....)))))))))))))..))..((((((--------(((.....))))))))).)). ( -29.00)
>DroAna_CAF1 54420 110 + 1
UGCUUUGACGAACGGUAAUUUGCUUAGCCAAUUUAUGGCCAG-GAAUGCAACGAAUUAAAUAUUCGAUACUGUCUAGAAACCUGCCACCCUGGCAUUCA----AUGCUAGACGGA
........((((...((((((((((.((((.....)))).))-).......)))))))....))))...((((((((.....((((.....))))....----...)))))))). ( -28.61)
>consensus
UGCCAC____AACCGUAAAUUGUUUAGCCAAUUUAUGGCCAGAGAAUGCAACGAAUUAUGCAUUCGAUUUGGUUUUGCAUUAUGGCA___UUGCAUUCAAUUAAUGCCAGACGGA
.((((.......((((((((((......)))))))))).....(((((((........))))))).................))))....................((....)). (-13.50 = -15.37 +   1.86)

alignment

secondary structure

dotplot

Window 5

Location	8,268,129 – 8,268,237
Length	108
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	80.18
Mean single sequence MFE	-31.10
Consensus MFE	-15.69
Energy contribution	-17.13
Covariance contribution	1.45
Combinations/Pair	1.18
Mean z-score	-3.22
Structure conservation index	0.50
SVM decision value	1.43
SVM RNA-class probability	0.953169
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8268129 108 - 22407834
UCCGUCUGGCAUUAAUUGAAUGCAA---UGCCAUAGUGUAAAACCAAAUCGAAUGCAUAAUUCGAUGCAUUCUCUGGCCAUAAAUUGGCUAAACAAUUUACGGUA----GUGGCG
........(((((.....)))))..---.((((((.((((((........((((((((......))))))))..((((((.....)))))).....)))))).).----))))). ( -34.00)
>DroSec_CAF1 46174 104 - 1
UCCGUCUGGCAUUAAUUGAAUGCAA---UGCCAUAAUGCAAAACCAAAUCGAAUGCAUAAUUUGUUGCAUUCUCUGGCCGUAAAUUGUUUAGCCAAUU----GUU----GUGGCA
........(((((.....)))))..---(((((((((.............(((((((........)))))))..((((.............))))...----)))----)))))) ( -27.82)
>DroSim_CAF1 46261 108 - 1
UCCGUCUGGCAUUAAUUGAAUGCAA---UGCCAUAAUGCAAAACCAAAUCGAAUGCAUAAUUUGUUGCAUUCUCUGGCCGUAAAUUGGCUAAACAAAUUACGGUU----GUGGCA
........(((((.....)))))..---((((((((.......(((....(((((((........)))))))..)))((((((.(((......))).))))))))----)))))) ( -33.20)
>DroEre_CAF1 48464 103 - 1
UCCGUCUGGCAUUAAUUGAAU--------GCCAGAAUGCAAAACCAAAUCGAAUGCAUAAUGCGAUGCAUUUUCUUGCCAUAAAUUGGCUAAGCCAUUUACAGUU----GUGGCA
....(((((((((.....)))--------))))))...............((((((((......))))))))....((((.....))))...(((((........----))))). ( -32.80)
>DroYak_CAF1 49803 103 - 1
UCCGUCUGGCAUUAAUUGAAU--------GCCAGAAUGCAAAACCAAAUCGAAUGCAUAAUUCGAUGCAUUUUCUUGCCAUAAAUUGGCUAAACCAUUUACAGUU----GUGGCA
....(((((((((.....)))--------))))))(((((........((((((.....))))))))))).....((((((((..(((.....))).......))----)))))) ( -31.10)
>DroAna_CAF1 54420 110 - 1
UCCGUCUAGCAU----UGAAUGCCAGGGUGGCAGGUUUCUAGACAGUAUCGAAUAUUUAAUUCGUUGCAUUC-CUGGCCAUAAAUUGGCUAAGCAAAUUACCGUUCGUCAAAGCA
...((((((...----.(..((((.....))))..)..)))))).(((.(((((.....))))).)))....-.((((((.....))))))........................ ( -27.70)
>consensus
UCCGUCUGGCAUUAAUUGAAUGCAA___UGCCAGAAUGCAAAACCAAAUCGAAUGCAUAAUUCGAUGCAUUCUCUGGCCAUAAAUUGGCUAAACAAUUUACAGUU____GUGGCA
........(((((.....)))))......((((.................(((((((........)))))))..((((((.....))))))...................)))). (-15.69 = -17.13 +   1.45)

alignment

secondary structure

dotplot

Window 6

Location	8,268,162 – 8,268,258
Length	96
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	80.34
Mean single sequence MFE	-27.78
Consensus MFE	-12.35
Energy contribution	-15.02
Covariance contribution	2.67
Combinations/Pair	1.10
Mean z-score	-2.50
Structure conservation index	0.44
SVM decision value	0.09
SVM RNA-class probability	0.578146
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8268162 96 + 22407834
GCCAGAGAAUGCAUCGAAUUAUGCAUUCGAUUUGGUUUUACACUAUGGCA---UUGCAUUCAAUUAAUGCCAGACGGAAGUGGCAUUUGAGUGGGCGGU
((((..((((((((......))))))))....((((.....)))))))).---...(((((((...(((((..((....))))))))))))))...... ( -31.40)
>DroSec_CAF1 46203 96 + 1
GCCAGAGAAUGCAACAAAUUAUGCAUUCGAUUUGGUUUUGCAUUAUGGCA---UUGCAUUCAAUUAAUGCCAGACGGAAGUGACAUUUGAGUGGGCAGU
(((((((((((((........)))))))..)))))).((((....(((((---(((........)))))))).((....)).............)))). ( -27.80)
>DroSim_CAF1 46294 96 + 1
GCCAGAGAAUGCAACAAAUUAUGCAUUCGAUUUGGUUUUGCAUUAUGGCA---UUGCAUUCAAUUAAUGCCAGACGGAAGUGACAUUUGAGUGGGCAGU
(((((((((((((........)))))))..)))))).((((....(((((---(((........)))))))).((....)).............)))). ( -27.80)
>DroEre_CAF1 48497 91 + 1
GCAAGAAAAUGCAUCGCAUUAUGCAUUCGAUUUGGUUUUGCAUUCUGGC--------AUUCAAUUAAUGCCAGACGGAAGUGGCAUUUGAGUGGGUAGU
(((......))).....(((((.(((((((........(((...(((((--------(((.....))))))))((....)).))).))))))).))))) ( -27.00)
>DroYak_CAF1 49836 91 + 1
GCAAGAAAAUGCAUCGAAUUAUGCAUUCGAUUUGGUUUUGCAUUCUGGC--------AUUCAAUUAAUGCCAGACGGAAGUGGCAUUUGAGUGGGUUGU
((((...(((((((......)))))))(.(((..(...(((...(((((--------(((.....))))))))((....)).))).)..))).).)))) ( -26.30)
>DroAna_CAF1 54457 85 + 1
GCCAG-GAAUGCAACGAAUUAAAUAUUCGAUACUGUCUAGAAACCUGCCACCCUGGCAUUCA----AUGCUAGACGGAAGUGGCUUAUAA---------
((((.-........(((((.....)))))...((((((((.....((((.....))))....----...))))))))...))))......--------- ( -26.40)
>consensus
GCCAGAGAAUGCAACGAAUUAUGCAUUCGAUUUGGUUUUGCAUUAUGGCA___UUGCAUUCAAUUAAUGCCAGACGGAAGUGGCAUUUGAGUGGGCAGU
((((...((((((.((((((........))))))....)))))).))))........((((((...(((((..((....)))))))))))))....... (-12.35 = -15.02 +   2.67)

alignment

secondary structure

dotplot

Window 7

Location	8,268,162 – 8,268,258
Length	96
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	80.34
Mean single sequence MFE	-22.96
Consensus MFE	-11.33
Energy contribution	-11.58
Covariance contribution	0.25
Combinations/Pair	1.25
Mean z-score	-2.87
Structure conservation index	0.49
SVM decision value	0.94
SVM RNA-class probability	0.886029
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8268162 96 - 22407834
ACCGCCCACUCAAAUGCCACUUCCGUCUGGCAUUAAUUGAAUGCAA---UGCCAUAGUGUAAAACCAAAUCGAAUGCAUAAUUCGAUGCAUUCUCUGGC
...(((......(((((((........)))))))....((((((.(---(((....))))........(((((((.....)))))))))))))...))) ( -25.50)
>DroSec_CAF1 46203 96 - 1
ACUGCCCACUCAAAUGUCACUUCCGUCUGGCAUUAAUUGAAUGCAA---UGCCAUAAUGCAAAACCAAAUCGAAUGCAUAAUUUGUUGCAUUCUCUGGC
...(((......(((((((........)))))))....((((((((---(...((.(((((.............))))).))..)))))))))...))) ( -21.62)
>DroSim_CAF1 46294 96 - 1
ACUGCCCACUCAAAUGUCACUUCCGUCUGGCAUUAAUUGAAUGCAA---UGCCAUAAUGCAAAACCAAAUCGAAUGCAUAAUUUGUUGCAUUCUCUGGC
...(((......(((((((........)))))))....((((((((---(...((.(((((.............))))).))..)))))))))...))) ( -21.62)
>DroEre_CAF1 48497 91 - 1
ACUACCCACUCAAAUGCCACUUCCGUCUGGCAUUAAUUGAAU--------GCCAGAAUGCAAAACCAAAUCGAAUGCAUAAUGCGAUGCAUUUUCUUGC
..............(((........(((((((((.....)))--------))))))..)))....(((...((((((((......))))))))..))). ( -20.60)
>DroYak_CAF1 49836 91 - 1
ACAACCCACUCAAAUGCCACUUCCGUCUGGCAUUAAUUGAAU--------GCCAGAAUGCAAAACCAAAUCGAAUGCAUAAUUCGAUGCAUUUUCUUGC
...........((((((........(((((((((.....)))--------))))))............(((((((.....)))))))))))))...... ( -24.00)
>DroAna_CAF1 54457 85 - 1
---------UUAUAAGCCACUUCCGUCUAGCAU----UGAAUGCCAGGGUGGCAGGUUUCUAGACAGUAUCGAAUAUUUAAUUCGUUGCAUUC-CUGGC
---------......((((.....((((((...----.(..((((.....))))..)..)))))).(((.(((((.....))))).)))....-.)))) ( -24.40)
>consensus
ACUGCCCACUCAAAUGCCACUUCCGUCUGGCAUUAAUUGAAUGCAA___UGCCAGAAUGCAAAACCAAAUCGAAUGCAUAAUUCGAUGCAUUCUCUGGC
............(((((((........)))))))....((((((......((......))..........(((((.....)))))..))))))...... (-11.33 = -11.58 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:36 2006