Locus 7824

Sequence ID	2L_DroMel_CAF1
Location	22,227,890 – 22,228,170
Length	280
Max. P	0.889390

overview

Window 8

Location	22,227,890 – 22,228,010
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-37.73
Consensus MFE	-35.79
Energy contribution	-35.47
Covariance contribution	-0.33
Combinations/Pair	1.09
Mean z-score	-1.64
Structure conservation index	0.95
SVM decision value	0.23
SVM RNA-class probability	0.645344
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 22227890 120 + 22407834
ACUACAAUGUAAAGUGCUUGUCUAUGGGCAUGCUGACACCUGUAGAGACCUCUGUUAUCUGGCGAGGUCCUCUUGUAAUGUCAGCAAUACAACGACUGCUAAAAGGUACUGAUUGGGGGC
.(..((((....((((((((((....))).((((((((.....(((((((((.(((....)))))))).)))).....)))))))).................))))))).))))..).. ( -37.70)
>DroSim_CAF1 27648 120 + 1
ACUACAAUGUAAAGUGCUUGUCUAUGGGCAUGCUGACACCUGUAGAGGCCUCUGUUAUCUGGCGAGGUCCUCUUGUAAUGUCAGCAAUACAACGACUGUUAAAAGGUACUGAUUGGGGAC
.(..((((....((((((((((....))).((((((((.....(((((((((.(((....))))))).))))).....)))))))).................))))))).))))..).. ( -39.60)
>DroYak_CAF1 223718 120 + 1
ACUACAAUGUAAAGUGCUUGUCUAUGGGCAUGUUGACACCUGUUGAGACCUCUGUUAUAUGGCGAGGUCCUCUUGUAAUGUCAGCAAUACGACGGCUGCUAAAAGGUGCUGAUUGGGGAC
.(..(((((((..((((((......))))))(((((((......((((((((.(((....)))))))).)))......)))))))..)))..((((.(((....)))))))))))..).. ( -35.90)
>consensus
ACUACAAUGUAAAGUGCUUGUCUAUGGGCAUGCUGACACCUGUAGAGACCUCUGUUAUCUGGCGAGGUCCUCUUGUAAUGUCAGCAAUACAACGACUGCUAAAAGGUACUGAUUGGGGAC
.(..((((....((((((((((....))).((((((((.....(((((((((.(((....)))))))).)))).....)))))))).................))))))).))))..).. (-35.79 = -35.47 +  -0.33)

alignment

secondary structure

dotplot

Window 9

Location	22,228,010 – 22,228,130
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	93.89
Mean single sequence MFE	-40.00
Consensus MFE	-34.64
Energy contribution	-34.20
Covariance contribution	-0.44
Combinations/Pair	1.05
Mean z-score	-2.64
Structure conservation index	0.87
SVM decision value	0.96
SVM RNA-class probability	0.889390
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 22228010 120 - 22407834
GAACAGCUGCAGUAUGAGGUGUUGUUACCAGGAUAACCCCUGUGAUAGGUGCAUGCUGGGAUAGUGAGAGAUGUACAUCUCCAGUGCCCGGUGGAGUAUCUAUAACUAGGACAUCUAGAA
.((((((.((........)))))))).(((((......)))).)((((((((.(((((((.((.((.(((((....))))))).)))))))))..))))))))..((((.....)))).. ( -39.50)
>DroSim_CAF1 27768 120 - 1
GAACUGCUGCAGUAUGAGGUGUUGUUACAAGGAUAACCCCAGUGAUGGGUGUAUGCUGGGAUAGUGAGAGAUGCACAUCUCCAGUGCCCGGUGGAGUAUCUAUAACCAGGACAUCUAAAA
..((((...))))...(((((((((((...(((((((((((....)))).))..((((((.((.((.(((((....))))))).))))))))....))))).))))...))))))).... ( -38.00)
>DroYak_CAF1 223838 120 - 1
GAACAGCUGCAGUAUGAGGUGUUGUUACAAGGAUAACACCUGUGAUAGGUGCAUGCUGGGAUAGUGAGAGAUGUACAUCUCCAGUGCCCGGUGGAGUAUCUAUAACCAAUACAUCUAAAA
...........((((.((((((((((.....))))))))))((.((((((((.(((((((.((.((.(((((....))))))).)))))))))..)))))))).))..))))........ ( -42.50)
>consensus
GAACAGCUGCAGUAUGAGGUGUUGUUACAAGGAUAACCCCUGUGAUAGGUGCAUGCUGGGAUAGUGAGAGAUGUACAUCUCCAGUGCCCGGUGGAGUAUCUAUAACCAGGACAUCUAAAA
..........((.(((.((.((((((.....)))))).)).((.((((((((.(((((((.((.((.(((((....))))))).)))))))))..)))))))).)).....))))).... (-34.64 = -34.20 +  -0.44)

alignment

secondary structure

dotplot

Window 0

Location	22,228,050 – 22,228,170
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	93.89
Mean single sequence MFE	-34.52
Consensus MFE	-26.12
Energy contribution	-27.57
Covariance contribution	1.45
Combinations/Pair	1.03
Mean z-score	-2.83
Structure conservation index	0.76
SVM decision value	0.21
SVM RNA-class probability	0.634583
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 22228050 120 + 22407834
AGAUGUACAUCUCUCACUAUCCCAGCAUGCACCUAUCACAGGGGUUAUCCUGGUAACAACACCUCAUACUGCAGCUGUUCAGGUGACCUUGAAAGGUGCAAGCAUGUACGAAAAGUUAAA
...(((((((..............((.(((((((.(((.(((.(((((....)))))..(((((...((.......))..))))).)))))).))))))).))))))))).......... ( -35.33)
>DroSim_CAF1 27808 120 + 1
AGAUGUGCAUCUCUCACUAUCCCAGCAUACACCCAUCACUGGGGUUAUCCUUGUAACAACACCUCAUACUGCAGCAGUUCAGGUGACCUUGAAAGGUGCAAGGAUGUACGAAAAGCUAAA
...(((((..........(((((((.............))))))).((((((((.....(((((...((((...))))..)))))((((....))))))))))))))))).......... ( -35.12)
>DroYak_CAF1 223878 120 + 1
AGAUGUACAUCUCUCACUAUCCCAGCAUGCACCUAUCACAGGUGUUAUCCUUGUAACAACACCUCAUACUGCAGCUGUUCAGGUGACCUUAAAAGGUGCCAGGAUGUACGAAAAGUUAAA
...(((((((((..........((((.((((........(((((((...........))))))).....))))))))....(((.((((....))))))).))))))))).......... ( -33.12)
>consensus
AGAUGUACAUCUCUCACUAUCCCAGCAUGCACCUAUCACAGGGGUUAUCCUUGUAACAACACCUCAUACUGCAGCUGUUCAGGUGACCUUGAAAGGUGCAAGGAUGUACGAAAAGUUAAA
...(((((((((....((.....))...((((((.(((.(((.(((((....)))))..(((((...((.......))..))))).)))))).))))))..))))))))).......... (-26.12 = -27.57 +   1.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:45:44 2006