Locus 6029

Sequence ID	3L_DroMel_CAF1
Location	16,071,876 – 16,072,260
Length	384
Max. P	0.984164

overview

Window 0

Location	16,071,876 – 16,071,995
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.98
Mean single sequence MFE	-27.72
Consensus MFE	-25.16
Energy contribution	-25.72
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.75
Structure conservation index	0.91
SVM decision value	1.97
SVM RNA-class probability	0.984164
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16071876 119 + 23771897
AAAUCCGCUUCGUUCUAGUAUUUGUGUAUAUGAGUGUGAGGGCCAUAAUGUUCACAUUCAAACUGAA-UACAUUGCCUUGCCUUGCACUAAUGCUAGAAAAAUACAAGUUUUAUGAUCCA
......((((..((((((((((.(((((..((((((((((.(......).)))))))))).......-..((......))...))))).))))))))))......))))........... ( -27.80)
>DroSec_CAF1 777 118 + 1
AAAUCCGCUUCGUUCUUGUAUUUGUGUAUAUGAGUGUGAGGG-CAUAAUGUUCACAUUCAAACUGAA-UACAUUGCCUUGCCUUGCACUAAUGCUAGAAAAAUACAAGUUUUAUGAUCCA
......(..((((.(((((((((..((((...(((((.((((-((((((((....((((.....)))-)))))))...))))))))))).)))).....)))))))))....))))..). ( -31.00)
>DroSim_CAF1 6930 119 + 1
AAAUCCGCUUCGUUCUUGUAUUUGUGUAUAUGAGUGUGAGGGCCAUAAUGUUCACAUUCAAACUGAA-UACAUUGCCUUGCCUUGCACUAAUGCUAGAAAAAUACAAGUUUUAUGAUCCA
......(..((((.(((((((((..((((...((((..(((....((((((....((((.....)))-))))))).....)))..)))).)))).....)))))))))....))))..). ( -29.70)
>DroEre_CAF1 806 119 + 1
AAAUCCGCUUUGUUCUUGUAUUUGUGUAAAUGAGUGUGAGGGCCUAAAAGUUCACAUUCAAACUGAA-UACAUUGCCUUGCCUUGCACUAAUGCUAGAAAAAUACAAGUUUUAUGAUCCG
.....((..(..(.(((((((((..(((....((((..(((..............((((.....)))-).((......)))))..))))..))).....)))))))))....)..)..)) ( -23.30)
>DroYak_CAF1 7039 120 + 1
AAAUCCGCUUUGUUCUUGUAUUUGUGUAAAUGAGUGUGAGGGCCAAAAUGUUCACAUUCAAACUGAAUUACAUUGCCUUGCCUUGCACUAAUGCUAAAAAAAUACAAGUUUUAUGAUCCG
.....((..(..(.(((((((((..(((....((((..(((.....(((((....((((.....)))).)))))......)))..))))..))).....)))))))))....)..)..)) ( -26.80)
>consensus
AAAUCCGCUUCGUUCUUGUAUUUGUGUAUAUGAGUGUGAGGGCCAUAAUGUUCACAUUCAAACUGAA_UACAUUGCCUUGCCUUGCACUAAUGCUAGAAAAAUACAAGUUUUAUGAUCCA
......(..((((.(((((((((..((((...((((..(((.....(((((.....(((.....)))..)))))......)))..)))).)))).....)))))))))....))))..). (-25.16 = -25.72 +   0.56)

alignment

secondary structure

dotplot

Window 1

Location	16,071,995 – 16,072,115
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.16
Mean single sequence MFE	-24.82
Consensus MFE	-22.18
Energy contribution	-22.34
Covariance contribution	0.16
Combinations/Pair	1.08
Mean z-score	-1.24
Structure conservation index	0.89
SVM decision value	0.36
SVM RNA-class probability	0.705706
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16071995 120 - 23771897
CUAAUCUAUACACGAGUAUUCAAACCGAUUGGGGCACAAGGAGCUAAGCAUGUCCAACAUGUUGCCCAAUCGGCGAUUAGUGAAUCCCAAAUUACCCCAACUUUAACUAACAAUAUUUAG
((((((.((((....)))).....(((((((((((.......))..((((((.....)))))).))))))))).))))))........................................ ( -27.60)
>DroSec_CAF1 895 120 - 1
CUAAUCUGUACACGAGUAUUCAAACCGAUUGGGGCACAAGUAGCUAAGCAUGUCCAACAUGUUGCCCAAUCGGCGUUUAGUGAAUCCCAAACUACCCCAACUUUAACUAACAAUAUUUAG
.............(((((((....(((((((((((.......))..((((((.....)))))).))))))))).(..((((.........))))..)..............))))))).. ( -25.50)
>DroSim_CAF1 7049 120 - 1
CUAAUCUGUACACGAGUAUUCAAACCGAUUGGGGCACAAGGAGCUAAGCAUGUCCAACAUGUUGCCCAAUCGGCGUUUAGUGAAUCCCAAACUACCACAACUUUAACUAACAAUAUUUAG
.............(((((((....(((((((((((.......))..((((((.....)))))).))))))))).((.((((.........))))..)).............))))))).. ( -25.50)
>DroEre_CAF1 925 119 - 1
CUUAUCUGUACACGAGUAUUCAAACCAAUUUGGGCACAAGGAGCUAAGCAUGUCCAACAUGUUGCCCAAUUGGCGAUUAGUGAAUCCCCA-UUACACGAACUUUAACUAACAAUAUUUAG
.............(((((((....((((((.(((((...........(((((.....))))))))))))))))((..(((((......))-)))..)).............))))))).. ( -22.90)
>DroYak_CAF1 7159 119 - 1
CUUAUCUGUACACGAGUAUUCAAACCAAUUUGGGCACAAGGAGCUAAGCAUGUCCAACAUGUUGCCCAAUUGGCGAUUAGUGAAUCCCCA-AUACACGAACAUUAACUAACCAUAUUUAG
............((.(((((....((((((.(((((...........(((((.....)))))))))))))))).((((....))))...)-)))).))...................... ( -22.60)
>consensus
CUAAUCUGUACACGAGUAUUCAAACCGAUUGGGGCACAAGGAGCUAAGCAUGUCCAACAUGUUGCCCAAUCGGCGAUUAGUGAAUCCCAAACUACCCCAACUUUAACUAACAAUAUUUAG
((((((.((((....)))).....((((((.(((((...........(((((.....)))))))))))))))).))))))........................................ (-22.18 = -22.34 +   0.16)

alignment

secondary structure

dotplot

Window 2

Location	16,072,115 – 16,072,230
Length	115
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	93.22
Mean single sequence MFE	-24.94
Consensus MFE	-21.16
Energy contribution	-21.20
Covariance contribution	0.04
Combinations/Pair	1.13
Mean z-score	-1.27
Structure conservation index	0.85
SVM decision value	0.09
SVM RNA-class probability	0.576396
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16072115 115 - 23771897
ACUCCUGCCAGCACCUAAGCGGCGAGAAUAGGUUAUAUACACGUAGUCGGCUACUAAUAUUACAAUUUCUCUCAAGAUAAAAGCGCGACCAGGCGUCACUUAACUAUAACCAACU
.(((..(((.((......))))))))....(((((((.....((((....))))............................((((......))))........))))))).... ( -23.80)
>DroSec_CAF1 1015 115 - 1
ACUCCUGCCAGCACCUAAGCGGCGAGAAUAGGUUAUAUACACGUAGUCGGCUACUAAUAUUACAAUUUCUCUCAAGAUAAAUGCGCGACCAGGCGUCACUUAACUAUAACCAACU
.(((..(((.((......))))))))....(((((((.....((((....)))).......................(((.(((((......))).)).)))..))))))).... ( -24.20)
>DroSim_CAF1 7169 115 - 1
ACUCCUGCCAGCACCUAAGCGGCGAGAAUAGGUUAUAUACACGUAGUCGGCUACUAAUAUUACAAUUUCUCUCAAGAUAAUUGCGCGAACAGGCGUCACUUAACUAUAACCAACU
.(((..(((.((......))))))))....(((((((.....((((....)))).......................(((.(((((......))).)).)))..))))))).... ( -24.20)
>DroEre_CAF1 1044 115 - 1
ACUGCUGCCAGUGCAUAGGCGGCGAGAAUAGGUUAUUUACACGUAGUCGGCUACUAAAAUUACAAUUUCUCUCAAGAUAAAUGCGCAUCCAAGCGUCACUUAACUAUAACCAACU
...((((((........))))))(((((...((.((((....((((....))))..)))).))...)))))...((.(((.(((((......))).)).))).)).......... ( -27.00)
>DroYak_CAF1 7278 115 - 1
ACUCCUGCCAGUGCCUAAGCGGCGGGAAUAGAUUAUAUACACGUAGUCGGCUACUAAAAUUACAAUUUCUCUUAAGAUAAAUGCGCGUCCAAGCGCCACUUAACUAUAACCAACU
..(((((((.((......)))))))))((((...........((((....)))).................(((((......((((......))))..)))))))))........ ( -25.50)
>consensus
ACUCCUGCCAGCACCUAAGCGGCGAGAAUAGGUUAUAUACACGUAGUCGGCUACUAAUAUUACAAUUUCUCUCAAGAUAAAUGCGCGACCAGGCGUCACUUAACUAUAACCAACU
.(((..(((.((......))))))))....(((((((.....((((....))))............................((((......))))........))))))).... (-21.16 = -21.20 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	16,072,155 – 16,072,260
Length	105
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	94.10
Mean single sequence MFE	-31.94
Consensus MFE	-26.60
Energy contribution	-26.16
Covariance contribution	-0.44
Combinations/Pair	1.19
Mean z-score	-1.55
Structure conservation index	0.83
SVM decision value	0.63
SVM RNA-class probability	0.805783
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16072155 105 - 23771897
AAGGUGGCCAAGAAGGAGGGUGUCGGAGGCACUCCUGCCAGCACCUAAGCGGCGAGAAUAGGUUAUAUACACGUAGUCGGCUACUAAUAUUACAAUUUCUCUCAA
......(((.....(((((((((.....)))).))).)).((......)))))(((((...((.((((....((((....))))..)))).))...))))).... ( -29.60)
>DroSec_CAF1 1055 105 - 1
AAGGUGGCCAAGAAGGAGGGUGCCGGAGUCACUCCUGCCAGCACCUAAGCGGCGAGAAUAGGUUAUAUACACGUAGUCGGCUACUAAUAUUACAAUUUCUCUCAA
..((((.((........)).))))((((...)))).(((.((......)))))(((((...((.((((....((((....))))..)))).))...))))).... ( -28.50)
>DroSim_CAF1 7209 105 - 1
AAGGUGGCCAAGAAGGAGGGUGCUGGAGGCACUCCUGCCAGCACCUAAGCGGCGAGAAUAGGUUAUAUACACGUAGUCGGCUACUAAUAUUACAAUUUCUCUCAA
..(((((((........((((((((((((....))).)))))))))..((.(((.(.(((.....))).).))).)).))))))).................... ( -34.60)
>DroEre_CAF1 1084 105 - 1
AAGGUGGCCAAGAAGGAGGGUGCCGGAGGCACUGCUGCCAGUGCAUAGGCGGCGAGAAUAGGUUAUUUACACGUAGUCGGCUACUAAAAUUACAAUUUCUCUCAA
..(((((((.........((((((...))))))((((((........)))))).......(..(((......)))..)))))))).................... ( -32.20)
>DroYak_CAF1 7318 105 - 1
AAAGUGGCCAAGAAGGAGGGUGCCGGAGGCACUCCUGCCAGUGCCUAAGCGGCGGGAAUAGAUUAUAUACACGUAGUCGGCUACUAAAAUUACAAUUUCUCUUAA
..(((((((..........(((((...)))))(((((((.((......)))))))))...((((((......))))))))))))).................... ( -34.80)
>consensus
AAGGUGGCCAAGAAGGAGGGUGCCGGAGGCACUCCUGCCAGCACCUAAGCGGCGAGAAUAGGUUAUAUACACGUAGUCGGCUACUAAUAUUACAAUUUCUCUCAA
..(((((((.....((.(((((((...)))))))))(((.((......))))).......((((((......))))))))))))).................... (-26.60 = -26.16 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:22 2006