Locus 667

Sequence ID	3R_DroMel_CAF1
Location	2,437,108 – 2,437,298
Length	190
Max. P	0.738997

overview

Window 6

Location	2,437,108 – 2,437,218
Length	110
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	88.89
Mean single sequence MFE	-30.23
Consensus MFE	-24.67
Energy contribution	-24.65
Covariance contribution	-0.02
Combinations/Pair	1.09
Mean z-score	-1.91
Structure conservation index	0.82
SVM decision value	0.08
SVM RNA-class probability	0.575271
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2437108 110 - 27905053
UUCCGCUUCCGCAAAGAGCUGACCCCAACACCCACGUUACCACAAUAUUCCGCACACACACACACAUAUGUAGCACUUUACCCAAAAGG----------CUACAGUUCGGGCGGAUAGCU
....((((((((...(((((......(((......)))...............................(((((.((((.....)))))----------)))))))))..))))).))). ( -27.70)
>DroSec_CAF1 3464 120 - 1
UUCCGCUUCCGCAAAGAGCUGACCCCAACACCCACGUUACUGGAAUAUUCCGCACACAUACACACACAUGUAGCACUUCAUCCAAAAGGCAGGAUUUGGCCACAGUUCGGGCGGAUAGGU
..((...(((((...((((((...((((...(((......))).....(((.......((((......))))((.(((.......))))).))).))))...))))))..)))))..)). ( -31.70)
>DroSim_CAF1 3557 120 - 1
UUCCGCUUCCGCAAAGAGCUGACCCCAACACCCACGUUACUGGAAUAUUCCGCACACACACACACACAUGUAGCACUUCACCCAAAAGGCAGGAUUUGGCCACGGUUCGGGCGGAUAGCU
....((((((((...((((((...((((...((..(((((.(((....)))(......)..........))))).......((....))..))..))))...))))))..))))).))). ( -31.30)
>consensus
UUCCGCUUCCGCAAAGAGCUGACCCCAACACCCACGUUACUGGAAUAUUCCGCACACACACACACACAUGUAGCACUUCACCCAAAAGGCAGGAUUUGGCCACAGUUCGGGCGGAUAGCU
....((((((((...((((((..............(((((.............................))))).............(((........))).))))))..))))).))). (-24.67 = -24.65 +  -0.02)

alignment

secondary structure

dotplot

Window 7

Location	2,437,178 – 2,437,298
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.25
Mean single sequence MFE	-37.98
Consensus MFE	-33.10
Energy contribution	-33.62
Covariance contribution	0.52
Combinations/Pair	1.12
Mean z-score	-1.33
Structure conservation index	0.87
SVM decision value	0.44
SVM RNA-class probability	0.738997
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2437178 120 + 27905053
GUAACGUGGGUGUUGGGGUCAGCUCUUUGCGGAAGCGGAAACGCCCCACAAAUCGUGGCCUAAUGAUCAUGCCUUUAUUUAAUUAAUUGUUGAUAACAGCCUUAUGCCCAGCGGAAAUGC
....(((((((((((..((((((..((((.((..(((....))).)).)))).((((..(....)..)))).................))))))..)))).....))))).))....... ( -35.50)
>DroSec_CAF1 3544 120 + 1
GUAACGUGGGUGUUGGGGUCAGCUCUUUGCGGAAGCGGAAACGCCCCACAAAUCGUGGCCUAAUGAUCGGGCCUUUAUUUAAUUAAUUGUUGAUAACAGCCUCAUGCCCAGCGGAAAUGC
....(((((((((((..((((((..((((.((..(((....))).)).))))....(((((.......)))))...............))))))..)))).....))))).))....... ( -39.80)
>DroSim_CAF1 3637 120 + 1
GUAACGUGGGUGUUGGGGUCAGCUCUUUGCGGAAGCGGAAACGCCCCACAAAUCGUGGCCUAAUGAUCGUGCCUUUAUUUAAUUAAUUGUUGAUAACAGCCUCAUGCCCAGCGGAUAUGC
....(((((((((((..((((((..((((.((..(((....))).)).))))....((((........).)))...............))))))..)))).....))))).))....... ( -35.30)
>DroEre_CAF1 3641 120 + 1
GGAACGUGGGUGUUGGGAUCAGCUCUUUGCGGAAGCGGAAACGCCCCACAAAUCGCGGCCUAAUGAUCGGGCCUUUACUUAAUUAAUUGUUGAUAACAGCCUCAUGUCCAGCGGAAAUGC
(((.((((((.((((..((((((..((((.((..(((....))).)).))))....(((((.......)))))...............))))))..))))))))))))).(((....))) ( -44.60)
>DroYak_CAF1 3229 120 + 1
GGAACGUGGGUGUUGGGAUCAGCUCUUUGCGUAAGCGGAAACGACCCACAAAUCUUGGCCUAAUGAUCUGGCCAUUAUUUAAUUAAUUGUUGAUAACAGCUUCAUUCCCAGCGGAAAUGC
....((((((.((((..((((((..(((((....)))))..........((((..(((((.........)))))..))))........))))))..))))......)))).))....... ( -34.70)
>consensus
GUAACGUGGGUGUUGGGGUCAGCUCUUUGCGGAAGCGGAAACGCCCCACAAAUCGUGGCCUAAUGAUCGGGCCUUUAUUUAAUUAAUUGUUGAUAACAGCCUCAUGCCCAGCGGAAAUGC
....((((((.((((..((((((..((((.((..(((....))).)).))))....(((((.......)))))...............))))))..))))))))))....(((....))) (-33.10 = -33.62 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:49 2006