Locus 743

Sequence ID	3R_DroMel_CAF1
Location	2,635,189 – 2,635,342
Length	153
Max. P	0.999908

overview

Window 5

Location	2,635,189 – 2,635,309
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.17
Mean single sequence MFE	-32.15
Consensus MFE	-28.61
Energy contribution	-29.41
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.99
Structure conservation index	0.89
SVM decision value	3.60
SVM RNA-class probability	0.999436
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2635189 120 + 27905053
CGCUUGCCAUCAGCAACACUUUUUCGAUGGAUAUUGAACCACACAAACCUCUCUAGAACCGAAUUUGUCCUUAAAGCUAGUAUAAAACAAAUUCGGAUCUACAGGGUAGACGUGGAGCAA
.(((..(((((..............)))))........((((....(((.((.((((.((((((((((..................)))))))))).)))).)))))....))))))).. ( -33.31)
>DroSec_CAF1 35507 120 + 1
CGCUUGCCAUCAGCUACACUUUUUCGAUGGAUAUUGAACCACACAAACCUCUCUAGAACCGAAUUUGUCCUUAAAGCUAGUAUAAAACAAAUUCGGAUCUACAGGGUAGACGUGGAGCAA
.(((..(((((..............)))))........((((....(((.((.((((.((((((((((..................)))))))))).)))).)))))....))))))).. ( -33.31)
>DroSim_CAF1 23724 120 + 1
CGCUUGCCAUAAGCUACACUUUUUCGAUGGAUAUUGAACCACACAAACCUCUCUAGAACCGAAUUUGUCCUUAAAGCUAGUAUAAAACAAAUUCGGAUCUACAGGGUAGACGUGGAGCAA
............(((.......((((((....))))))((((....(((.((.((((.((((((((((..................)))))))))).)))).)))))....))))))).. ( -30.87)
>DroEre_CAF1 26210 120 + 1
CGCUUGACAUCAGCUUCACUUUUCCGAUGGAUAUUGAACCACACAAACCUCUCUAGAACCGAAUUUGUCCUUAAAGCUAGUAUAAAACAAAUUCGGAUCUACAGGGUAGACGUAGAGCAA
.((((.((.((.(.((((....(((...)))...)))).)......(((.((.((((.((((((((((..................)))))))))).)))).))))).)).)).)))).. ( -30.57)
>DroYak_CAF1 17160 120 + 1
CGCUUGACAUCAGCUUCACUUUUCCGAUGGAUAUUGAACCACACAAACCUCUCUAGAACCGAAUUUGUCCUUAAAACUAGUAUAAAACAAAUUCGGAUCUACAGGGUAGACGUGGAGCAA
.((((.((.((.(.((((....(((...)))...)))).)......(((.((.((((.((((((((((..................)))))))))).)))).))))).)).)).)))).. ( -32.67)
>consensus
CGCUUGCCAUCAGCUACACUUUUUCGAUGGAUAUUGAACCACACAAACCUCUCUAGAACCGAAUUUGUCCUUAAAGCUAGUAUAAAACAAAUUCGGAUCUACAGGGUAGACGUGGAGCAA
.(((..(((((..............)))))........((((....(((.((.((((.((((((((((..................)))))))))).)))).)))))....))))))).. (-28.61 = -29.41 +   0.80)

alignment

secondary structure

dotplot

Window 6

Location	2,635,189 – 2,635,309
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.17
Mean single sequence MFE	-38.38
Consensus MFE	-36.14
Energy contribution	-35.98
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-3.00
Structure conservation index	0.94
SVM decision value	4.49
SVM RNA-class probability	0.999908
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2635189 120 - 27905053
UUGCUCCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGUGGUUCAAUAUCCAUCGAAAAAGUGUUGCUGAUGGCAAGCG
..((((((((...(((((.((((.(((((((((((((............))))))))))))).)))).)).)))...)))))........((((((..((....))..))))))..))). ( -39.00)
>DroSec_CAF1 35507 120 - 1
UUGCUCCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGUGGUUCAAUAUCCAUCGAAAAAGUGUAGCUGAUGGCAAGCG
..((((((((...(((((.((((.(((((((((((((............))))))))))))).)))).)).)))...)))))........((((((............))))))..))). ( -38.80)
>DroSim_CAF1 23724 120 - 1
UUGCUCCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGUGGUUCAAUAUCCAUCGAAAAAGUGUAGCUUAUGGCAAGCG
(((..(((((...(((((.((((.(((((((((((((............))))))))))))).)))).)).)))...)))))..)))...................((((.....)))). ( -36.80)
>DroEre_CAF1 26210 120 - 1
UUGCUCUACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGUGGUUCAAUAUCCAUCGGAAAAGUGAAGCUGAUGUCAAGCG
..(((..(((((.(((((.((((.(((((((((((((............))))))))))))).)))).)).)))......(.((((...(((...)))....)))).).)))))..))). ( -38.30)
>DroYak_CAF1 17160 120 - 1
UUGCUCCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGUUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGUGGUUCAAUAUCCAUCGGAAAAGUGAAGCUGAUGUCAAGCG
..((((((((...(((((.((((.(((((((((((((............))))))))))))).)))).)).)))...))))).........((((((..........))))))...))). ( -39.00)
>consensus
UUGCUCCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGUGGUUCAAUAUCCAUCGAAAAAGUGUAGCUGAUGGCAAGCG
(((..(((((...(((((.((((.(((((((((((((............))))))))))))).)))).)).)))...)))))..)))...................(((.......))). (-36.14 = -35.98 +  -0.16)

alignment

secondary structure

dotplot

Window 7

Location	2,635,229 – 2,635,342
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.32
Mean single sequence MFE	-29.49
Consensus MFE	-25.15
Energy contribution	-25.59
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.82
Structure conservation index	0.85
SVM decision value	1.55
SVM RNA-class probability	0.963511
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2635229 113 + 27905053
ACACAAACCUCUCUAGAACCGAAUUUGUCCUUAAAGCUAGUAUAAAACAAAUUCGGAUCUACAGGGUAGACGUGGAGCAAACUGAUGAGGAACA-------GUCGCUGGGGCGAAAUGAA
.......((((..(((..((((((((((..................)))))))))).(((((.(......)))))).....)))..))))....-------.((((....))))...... ( -28.17)
>DroSec_CAF1 35547 113 + 1
ACACAAACCUCUCUAGAACCGAAUUUGUCCUUAAAGCUAGUAUAAAACAAAUUCGGAUCUACAGGGUAGACGUGGAGCAAACUGAUGAGGAACA-------GUCGCUGGGGCGAAAUGAA
.......((((..(((..((((((((((..................)))))))))).(((((.(......)))))).....)))..))))....-------.((((....))))...... ( -28.17)
>DroSim_CAF1 23764 113 + 1
ACACAAACCUCUCUAGAACCGAAUUUGUCCUUAAAGCUAGUAUAAAACAAAUUCGGAUCUACAGGGUAGACGUGGAGCAAACUGAUGAGGAACA-------GUCGCUGGGGCGAAAUGAA
.......((((..(((..((((((((((..................)))))))))).(((((.(......)))))).....)))..))))....-------.((((....))))...... ( -28.17)
>DroEre_CAF1 26250 112 + 1
ACACAAACCUCUCUAGAACCGAAUUUGUCCUUAAAGCUAGUAUAAAACAAAUUCGGAUCUACAGGGUAGACGUAGAGCAAACUGAUGAGGAACGU--------CGGAGGGGCGAAAUGAA
.......((((((((((.((((((((((..................)))))))))).)))........(((((....((......))....))))--------))))))))......... ( -29.57)
>DroYak_CAF1 17200 120 + 1
ACACAAACCUCUCUAGAACCGAAUUUGUCCUUAAAACUAGUAUAAAACAAAUUCGGAUCUACAGGGUAGACGUGGAGCAAAGUGAUGAGGAACGUCAGUUCGUCGCAGGGGCGAAAUGAA
......(((.((.((((.((((((((((..................)))))))))).)))).))))).(((((....((......))....)))))..((((((.....))))))..... ( -33.37)
>consensus
ACACAAACCUCUCUAGAACCGAAUUUGUCCUUAAAGCUAGUAUAAAACAAAUUCGGAUCUACAGGGUAGACGUGGAGCAAACUGAUGAGGAACA_______GUCGCUGGGGCGAAAUGAA
.......((((..(((..((((((((((..................)))))))))).(((((.(......)))))).....)))..))))............((((....))))...... (-25.15 = -25.59 +   0.44)

alignment

secondary structure

dotplot

Window 8

Location	2,635,229 – 2,635,342
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.32
Mean single sequence MFE	-34.44
Consensus MFE	-30.26
Energy contribution	-30.50
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-3.55
Structure conservation index	0.88
SVM decision value	4.36
SVM RNA-class probability	0.999880
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2635229 113 - 27905053
UUCAUUUCGCCCCAGCGAC-------UGUUCCUCAUCAGUUUGCUCCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGU
.............((((((-------((........))).))))).((((...(((((.((((.(((((((((((((............))))))))))))).)))).)).))).)))). ( -35.20)
>DroSec_CAF1 35547 113 - 1
UUCAUUUCGCCCCAGCGAC-------UGUUCCUCAUCAGUUUGCUCCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGU
.............((((((-------((........))).))))).((((...(((((.((((.(((((((((((((............))))))))))))).)))).)).))).)))). ( -35.20)
>DroSim_CAF1 23764 113 - 1
UUCAUUUCGCCCCAGCGAC-------UGUUCCUCAUCAGUUUGCUCCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGU
.............((((((-------((........))).))))).((((...(((((.((((.(((((((((((((............))))))))))))).)))).)).))).)))). ( -35.20)
>DroEre_CAF1 26250 112 - 1
UUCAUUUCGCCCCUCCG--------ACGUUCCUCAUCAGUUUGCUCUACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGU
.......(((......(--------((((....((......))....))))).(((((.((((.(((((((((((((............))))))))))))).)))).)).)))..))). ( -31.50)
>DroYak_CAF1 17200 120 - 1
UUCAUUUCGCCCCUGCGACGAACUGACGUUCCUCAUCACUUUGCUCCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGUUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGU
.......(((....)))((((((((((((....((......))....)))))....((.((((.(((((((((((((............))))))))))))).)))).)).))))))).. ( -35.10)
>consensus
UUCAUUUCGCCCCAGCGAC_______UGUUCCUCAUCAGUUUGCUCCACGUCUACCCUGUAGAUCCGAAUUUGUUUUAUACUAGCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGU
......((((....))))............................((((...(((((.((((.(((((((((((((............))))))))))))).)))).)).))).)))). (-30.26 = -30.50 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:52 2006