Locus 3821

Sequence ID	2R_DroMel_CAF1
Location	12,607,701 – 12,607,805
Length	104
Max. P	0.939936

overview

Window 0

Location	12,607,701 – 12,607,805
Length	104
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	82.52
Mean single sequence MFE	-31.70
Consensus MFE	-20.21
Energy contribution	-21.52
Covariance contribution	1.31
Combinations/Pair	1.12
Mean z-score	-1.97
Structure conservation index	0.64
SVM decision value	0.13
SVM RNA-class probability	0.597831
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12607701 104 + 20766785
AGAUGUGCGAAAAUUUCCAGCUGGGCGACACCAAAGAGGGCAUUGCUAGCUUCUUCGAGAAGCGCCCACCCAACUGGAAGCACCAGUAACCG-----CAACAUACAAUA
..(((((((.....((((((.((((.(....).....((((.......(((((.....))))))))).)))).))))))((....))...))-----).))))...... ( -31.11)
>DroSec_CAF1 776 104 + 1
AGAUGUGCGAAAAUUUCCAGCUGGGUGACACCAAAGAGGGCAUUGCUAGCUUCUUCGAGAAGCGUCCACCCAACUGGAAGCACCAGUAACCG-----CAACCUACAAUG
.....((((.....((((((.((((((((.((.....)).........(((((.....))))))).)))))).))))))((....))...))-----)).......... ( -33.30)
>DroSim_CAF1 761 104 + 1
AGAUGUGCGAAAAUUUCCAGCUGGGCGACACCAAAGAGGGCAUUUCUAGCUUCUUCGAGAAGCGUCCACCCAACUGGAAGCACCAGUAACCG-----CAACCUGCAAUG
....((((......((((((.((((.(((.((.....)).........(((((.....))))))))..)))).))))))))))........(-----(.....)).... ( -31.20)
>DroEre_CAF1 827 103 + 1
AGAUGUGCGAGAACUUCCAGCUGGGCGACACCAAAGAAGGCAUUGCUAGCUUCUUCGAGAAGCGCCCACCCAACUGGAAGCACAACUAA-CA-----UAAUCUAUUAUG
((.(((((......((((((.(((((((..((......))..))))..(((((.....)))))......))).))))))))))).))..-((-----(((....))))) ( -30.70)
>DroYak_CAF1 827 104 + 1
AGAUGUGCGAGAACUUUCAGCUGGGCGACACCAAAGAGGGCAUUGCUAGCUUCUUUGAGAAGCGUCCACCCAACUGGAAGCACAACUAAUCG-----CAACGUACGAUG
..((((((((...(((((((.((((.(((.((.....)).........(((((.....))))))))..)))).))))))).........)))-----).))))...... ( -32.00)
>DroPer_CAF1 6001 109 + 1
AAAUGGAAGAGAACCUGCAAUUGAGCGACUGCCAGGAAGGCAUCGCUAGCUUCAUAGAGAAGCGUGCACCCCACUGGAAGCACGAGUAAUACCUGUAUAUCCUAUCCUU
....(((((.((...((((....(((((.((((.....))))))))).(((((.....)))))((((..((....))..))))..........))))..)))).))).. ( -31.90)
>consensus
AGAUGUGCGAAAACUUCCAGCUGGGCGACACCAAAGAGGGCAUUGCUAGCUUCUUCGAGAAGCGUCCACCCAACUGGAAGCACCAGUAACCG_____CAACCUACAAUG
....((((......((((((.(((((((..((......))..))))..(((((.....)))))......))).)))))))))).......................... (-20.21 = -21.52 +   1.31)

alignment

secondary structure

dotplot

Window 1

Location	12,607,701 – 12,607,805
Length	104
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	82.52
Mean single sequence MFE	-38.88
Consensus MFE	-31.33
Energy contribution	-31.45
Covariance contribution	0.12
Combinations/Pair	1.26
Mean z-score	-2.87
Structure conservation index	0.81
SVM decision value	1.28
SVM RNA-class probability	0.939936
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12607701 104 - 20766785
UAUUGUAUGUUG-----CGGUUACUGGUGCUUCCAGUUGGGUGGGCGCUUCUCGAAGAAGCUAGCAAUGCCCUCUUUGGUGUCGCCCAGCUGGAAAUUUUCGCACAUCU
......((((.(-----((((.......))(((((((((((((((((((((.....)))))..))...(((......))).)))))))))))))).....))))))).. ( -37.80)
>DroSec_CAF1 776 104 - 1
CAUUGUAGGUUG-----CGGUUACUGGUGCUUCCAGUUGGGUGGACGCUUCUCGAAGAAGCUAGCAAUGCCCUCUUUGGUGUCACCCAGCUGGAAAUUUUCGCACAUCU
......((((((-----((((.......))(((((((((((((.((((....((((((.((.......))..))))))))))))))))))))))).....)))).)))) ( -38.60)
>DroSim_CAF1 761 104 - 1
CAUUGCAGGUUG-----CGGUUACUGGUGCUUCCAGUUGGGUGGACGCUUCUCGAAGAAGCUAGAAAUGCCCUCUUUGGUGUCGCCCAGCUGGAAAUUUUCGCACAUCU
.(((((.....)-----)))).....(((((((((((((((((.((((....((((((.((.......))..)))))))))))))))))))))))......)))).... ( -40.00)
>DroEre_CAF1 827 103 - 1
CAUAAUAGAUUA-----UG-UUAGUUGUGCUUCCAGUUGGGUGGGCGCUUCUCGAAGAAGCUAGCAAUGCCUUCUUUGGUGUCGCCCAGCUGGAAGUUCUCGCACAUCU
......((((..-----((-(.((....((((((((((((((((.(((....((((((((.((....)).))))))))))))))))))))))))))).)).))).)))) ( -43.30)
>DroYak_CAF1 827 104 - 1
CAUCGUACGUUG-----CGAUUAGUUGUGCUUCCAGUUGGGUGGACGCUUCUCAAAGAAGCUAGCAAUGCCCUCUUUGGUGUCGCCCAGCUGAAAGUUCUCGCACAUCU
.(((((.....)-----)))).((.(((((...((((((((((.((((....((((((.((.......))..))))))))))))))))))))...(....)))))).)) ( -36.30)
>DroPer_CAF1 6001 109 - 1
AAGGAUAGGAUAUACAGGUAUUACUCGUGCUUCCAGUGGGGUGCACGCUUCUCUAUGAAGCUAGCGAUGCCUUCCUGGCAGUCGCUCAAUUGCAGGUUCUCUUCCAUUU
..(((..(((.....((((((..((.((((.(((....))).))))(((((.....))))).))..)))))).((((.((((......)))))))).)))..))).... ( -37.30)
>consensus
CAUUGUAGGUUG_____CGGUUACUGGUGCUUCCAGUUGGGUGGACGCUUCUCGAAGAAGCUAGCAAUGCCCUCUUUGGUGUCGCCCAGCUGGAAAUUCUCGCACAUCU
..........................(((((((((((((((((.(((((((.....))))).......(((......))))))))))))))))))......)))).... (-31.33 = -31.45 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:47 2006