Locus 4001

Sequence ID	3R_DroMel_CAF1
Location	10,900,945 – 10,901,079
Length	134
Max. P	0.923763

overview

Window 3

Location	10,900,945 – 10,901,039
Length	94
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	90.21
Mean single sequence MFE	-24.06
Consensus MFE	-19.76
Energy contribution	-19.72
Covariance contribution	-0.04
Combinations/Pair	1.24
Mean z-score	-1.83
Structure conservation index	0.82
SVM decision value	1.16
SVM RNA-class probability	0.923763
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10900945 94 + 27905053
UAAUGGUGUUGGGAAAGUGGUCAAAGGUGUAGCAUCUAAGCAUAUUUUCUAAGGCAAUCUCAGUAAUGGAAAUUUGUGGUGGAUGCCACAGAAA
.....((.((((((((...((...(((((...)))))..))...)))))))).))..((.((....))))..((((((((....)))))))).. ( -24.30)
>DroSec_CAF1 166202 94 + 1
UAAUGGUGUUGGGAAAGUGGUCAAAGGUGUAGCAUCUAAACAUAUUUUCUAAGGUAAUCUCAGUAAUGGAAAUUUGUGGUGGAUGCCACAGAAA
....(((....((((((((.....(((((...))))).....))))))))......)))(((....)))...((((((((....)))))))).. ( -20.10)
>DroSim_CAF1 174671 94 + 1
UAAUGGUGUUGGGAAAGUGGUCAAAGGUGUAGCAUCUAAGCAUAUUUUCUAAGGCAAUCUCAGUAAUGGAAAUUUGUGGUGGAUGCCACAGAAA
.....((.((((((((...((...(((((...)))))..))...)))))))).))..((.((....))))..((((((((....)))))))).. ( -24.30)
>DroEre_CAF1 169413 92 + 1
AAAUGGUGUUGGAAAAGCGGUCAAAGGUGCAGCUU--AAGCAUAUUUUCUAAGGCAAUCUUGGUAAUGGAAAUUUGUGGCGGUCGCCUCAGAAA
.....((.(((((((((((.(....).))).((..--..))...)))))))).)).................((((.(((....))).)))).. ( -20.80)
>DroYak_CAF1 178494 94 + 1
CAAUGGUGUUGGAAAAGUGGUCAAAGGUGUACCUUCUGGGCAUAUUUUCCAAGGCAAUCUCAGUAAUGGAAAUUUGUGGUGGUGGCCACAGGAA
.....((.(((((((((((.(((((((....)))).))).))).)))))))).))..((.((....))))..((((((((....)))))))).. ( -30.80)
>consensus
UAAUGGUGUUGGGAAAGUGGUCAAAGGUGUAGCAUCUAAGCAUAUUUUCUAAGGCAAUCUCAGUAAUGGAAAUUUGUGGUGGAUGCCACAGAAA
.....((.((((((((...((...(((((...)))))..))...)))))))).)).................((((((((....)))))))).. (-19.76 = -19.72 +  -0.04)

alignment

secondary structure

dotplot

Window 4

Location	10,900,965 – 10,901,079
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	90.44
Mean single sequence MFE	-27.62
Consensus MFE	-23.90
Energy contribution	-22.02
Covariance contribution	-1.88
Combinations/Pair	1.31
Mean z-score	-1.43
Structure conservation index	0.87
SVM decision value	0.54
SVM RNA-class probability	0.775720
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10900965 114 + 27905053
UCAAAGGUGUAGCAUCUAAGCAUAUUUUCUAAGGCAAUCUCAGUAAUGGAAAUUUGUGGUGGAUGCCACAGAAAUAUGUGCCACAUGAGUGGAAAGCUACGACUCUUAGUAAAA
...((((((((((......((((((((((((..((.......))..))))).((((((((....))))))))))))))).((((....))))...))))).)).)))....... ( -32.50)
>DroSec_CAF1 166222 114 + 1
UCAAAGGUGUAGCAUCUAAACAUAUUUUCUAAGGUAAUCUCAGUAAUGGAAAUUUGUGGUGGAUGCCACAGAAAUAUGUGCCACAUGAGUGAAAAACUACGACUCUUAGUAAAA
...(((((((((.......(((((((((.........((.((....))))....((((((....)))))))))))))))..(((....))).....)))).)).)))....... ( -23.10)
>DroSim_CAF1 174691 114 + 1
UCAAAGGUGUAGCAUCUAAGCAUAUUUUCUAAGGCAAUCUCAGUAAUGGAAAUUUGUGGUGGAUGCCACAGAAAUAUGUGCCACAUGAGUGAAAAACUACGACUCUUAGUAAAA
...(((((((((.......(((((((((((..((((.(((((..(((....)))..))).)).))))..))))).))))))(((....))).....)))).)).)))....... ( -26.00)
>DroEre_CAF1 169433 112 + 1
UCAAAGGUGCAGCUU--AAGCAUAUUUUCUAAGGCAAUCUUGGUAAUGGAAAUUUGUGGCGGUCGCCUCAGAAAUAUGUGCUGCAUGACUGGAAAACUACGACUCUUAGUAAAA
......(((((((..--..((((((((.((.((((.(((.....(((....)))......))).)))).))))))))))))))))).((((((..........)).)))).... ( -27.30)
>DroYak_CAF1 178514 114 + 1
UCAAAGGUGUACCUUCUGGGCAUAUUUUCCAAGGCAAUCUCAGUAAUGGAAAUUUGUGGUGGUGGCCACAGGAAUAUGUGGUGCAUGAGUGAAAAACUACGACUCUUGGUAAAA
((((..(((((((......((((((((((((..((.......))..))))).((((((((....))))))))))))))))))))))((((...........))))))))..... ( -29.20)
>consensus
UCAAAGGUGUAGCAUCUAAGCAUAUUUUCUAAGGCAAUCUCAGUAAUGGAAAUUUGUGGUGGAUGCCACAGAAAUAUGUGCCACAUGAGUGAAAAACUACGACUCUUAGUAAAA
(((...((((.((......((((((((((((..((.......))..))))).((((((((....))))))))))))))))).))))...)))...((((.......)))).... (-23.90 = -22.02 +  -1.88)

alignment

secondary structure

dotplot

Window 5

Location	10,900,965 – 10,901,079
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	90.44
Mean single sequence MFE	-24.34
Consensus MFE	-19.52
Energy contribution	-19.60
Covariance contribution	0.08
Combinations/Pair	1.21
Mean z-score	-1.74
Structure conservation index	0.80
SVM decision value	0.77
SVM RNA-class probability	0.846393
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10900965 114 - 27905053
UUUUACUAAGAGUCGUAGCUUUCCACUCAUGUGGCACAUAUUUCUGUGGCAUCCACCACAAAUUUCCAUUACUGAGAUUGCCUUAGAAAAUAUGCUUAGAUGCUACACCUUUGA
........((((..(((((...((((....))))..(((((((.(((((......)))))...........(((((.....))))).))))))).......)))))..)))).. ( -27.50)
>DroSec_CAF1 166222 114 - 1
UUUUACUAAGAGUCGUAGUUUUUCACUCAUGUGGCACAUAUUUCUGUGGCAUCCACCACAAAUUUCCAUUACUGAGAUUACCUUAGAAAAUAUGUUUAGAUGCUACACCUUUGA
........((((..(((((...((((....)))).((((((((.(((((......)))))...........(((((.....))))).))))))))......)))))..)))).. ( -24.30)
>DroSim_CAF1 174691 114 - 1
UUUUACUAAGAGUCGUAGUUUUUCACUCAUGUGGCACAUAUUUCUGUGGCAUCCACCACAAAUUUCCAUUACUGAGAUUGCCUUAGAAAAUAUGCUUAGAUGCUACACCUUUGA
.........((((.(........))))).((((((((((((((.(((((......)))))...........(((((.....))))).)))))))......)))))))....... ( -23.60)
>DroEre_CAF1 169433 112 - 1
UUUUACUAAGAGUCGUAGUUUUCCAGUCAUGCAGCACAUAUUUCUGAGGCGACCGCCACAAAUUUCCAUUACCAAGAUUGCCUUAGAAAAUAUGCUU--AAGCUGCACCUUUGA
..((((........)))).....(((...((((((.((((((((((((((((.(.....................).))))))))).)))))))...--..))))))...))). ( -26.40)
>DroYak_CAF1 178514 114 - 1
UUUUACCAAGAGUCGUAGUUUUUCACUCAUGCACCACAUAUUCCUGUGGCCACCACCACAAAUUUCCAUUACUGAGAUUGCCUUGGAAAAUAUGCCCAGAAGGUACACCUUUGA
.....(((((((((.((((.........(((.....))).....(((((......)))))..........)))).))))..)))))............(((((....))))).. ( -19.90)
>consensus
UUUUACUAAGAGUCGUAGUUUUUCACUCAUGUGGCACAUAUUUCUGUGGCAUCCACCACAAAUUUCCAUUACUGAGAUUGCCUUAGAAAAUAUGCUUAGAUGCUACACCUUUGA
.........((((.(.......).)))).((((((((((((((.(((((......)))))...........(((((.....))))).)))))))......)))))))....... (-19.52 = -19.60 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:36 2006