Locus 1529

Sequence ID	2L_DroMel_CAF1
Location	4,135,884 – 4,136,041
Length	157
Max. P	0.864452

overview

Window 3

Location	4,135,884 – 4,136,001
Length	117
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	97.95
Mean single sequence MFE	-31.82
Consensus MFE	-29.02
Energy contribution	-29.62
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.50
Structure conservation index	0.91
SVM decision value	0.84
SVM RNA-class probability	0.864452
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4135884 117 - 22407834
UAGCUCUGCUAUUAUUCUGACCGCAGCUGUUCAUGCAUGAUAUAUUUGUGGAGACAAAGGCAUUUUUGCCACGCGUUGAUUUUGGCUCAUAAUUAACGCAGAACUUUGGCAAAUUGG
......(((((...((((..((((((.((((((....))).))).)))))).......((((....))))..(((((((((.((...)).)))))))))))))...)))))...... ( -32.00)
>DroSec_CAF1 265347 117 - 1
UAGCUCUGCUAUUAUUCUGACCGCAGCUGUUCAUGCAUGAUAUAUUUGUGGAGACAAAGGCAUUUUUGCCACGCGUUGAUUUUGGCUCAUAAUUAACGCAGAACUUUGGCAAAUUGG
......(((((...((((..((((((.((((((....))).))).)))))).......((((....))))..(((((((((.((...)).)))))))))))))...)))))...... ( -32.00)
>DroSim_CAF1 268987 117 - 1
UAGCUCUGCUAUUAUUCUGACCGCAGCUGUUCAUGCAUGAUAUAUUUGUGGAGACAAAGGCAUUUUUGCCACGCGUUGAUUUUGGCUCAUAAUUAACGCAGAACUUUGGCAAAUUGG
......(((((...((((..((((((.((((((....))).))).)))))).......((((....))))..(((((((((.((...)).)))))))))))))...)))))...... ( -32.00)
>DroEre_CAF1 279289 117 - 1
UGGCGGUGCUAUUACUCUGACCGCAGCUGUUCAUGCAUGAUAUAUUUGUGAAGACAAAGGCAUUUUUGCCACGCGUUGAUUUUGGCUCAUAAUUAACGCAGAACUUUGUCAAAUUGG
..(((((.(.........)))))).((.......))................((((((((((....))))..(((((((((.((...)).))))))))).....))))))....... ( -31.10)
>DroYak_CAF1 283891 117 - 1
UAGCUCUGCUAUUAUUCUGACCGCAGCUGUUCAUGCAUGAUAUAUUUGUGGAGACAAAGGCAUUUUUGCCACGCGUUGAUUUUGGCUCAUAAUUAACGCAGAACUUUGGCAAAUUGG
......(((((...((((..((((((.((((((....))).))).)))))).......((((....))))..(((((((((.((...)).)))))))))))))...)))))...... ( -32.00)
>consensus
UAGCUCUGCUAUUAUUCUGACCGCAGCUGUUCAUGCAUGAUAUAUUUGUGGAGACAAAGGCAUUUUUGCCACGCGUUGAUUUUGGCUCAUAAUUAACGCAGAACUUUGGCAAAUUGG
......(((((...((((..((((((.((((((....))).))).)))))).......((((....))))..(((((((((.((...)).)))))))))))))...)))))...... (-29.02 = -29.62 +   0.60)

alignment

secondary structure

dotplot

Window 4

Location	4,135,923 – 4,136,041
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	96.44
Mean single sequence MFE	-30.62
Consensus MFE	-27.12
Energy contribution	-27.92
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.40
Structure conservation index	0.89
SVM decision value	0.56
SVM RNA-class probability	0.780221
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4135923 118 - 22407834
UUUCUCUCGAAUGUGUGGCAAUUAUUUUGCAACUAAUUGCUAGCUCUGCUAUUAUUCUGACCGCAGCUGUUCAUGCAUGAUAUAUUUGUGGAGACAAAGGCAUUUUUGCCACGCGUUG
.........((((((((((((.......((((....))))......((((.....(((..((((((.((((((....))).))).)))))))))....))))...)))))))))))). ( -31.60)
>DroSec_CAF1 265386 118 - 1
UUGCUCUCGAAUGUGUGGCAAUUAUUUUGCAACUAAUUGCUAGCUCUGCUAUUAUUCUGACCGCAGCUGUUCAUGCAUGAUAUAUUUGUGGAGACAAAGGCAUUUUUGCCACGCGUUG
.........((((((((((((.......((((....))))......((((.....(((..((((((.((((((....))).))).)))))))))....))))...)))))))))))). ( -31.60)
>DroSim_CAF1 269026 118 - 1
UUGCUCUCGAAUGUGUGGCAAUUAUUUUGCAACUAAUUGCUAGCUCUGCUAUUAUUCUGACCGCAGCUGUUCAUGCAUGAUAUAUUUGUGGAGACAAAGGCAUUUUUGCCACGCGUUG
.........((((((((((((.......((((....))))......((((.....(((..((((((.((((((....))).))).)))))))))....))))...)))))))))))). ( -31.60)
>DroEre_CAF1 279328 118 - 1
UUUCCCUCGAAUAUGUAGCAAUUAUUUUGCAACUAAUUGCUGGCGGUGCUAUUACUCUGACCGCAGCUGUUCAUGCAUGAUAUAUUUGUGAAGACAAAGGCAUUUUUGCCACGCGUUG
........(((((.((.((((.....)))).)).....((((.((((.(.........))))))))))))))((((........(((((....)))))((((....))))..)))).. ( -29.50)
>DroYak_CAF1 283930 118 - 1
UUUCCCUCGAAUGUGUAGCAAUUAUUUUGCAACUAAUUGCUAGCUCUGCUAUUAUUCUGACCGCAGCUGUUCAUGCAUGAUAUAUUUGUGGAGACAAAGGCAUUUUUGCCACGCGUUG
(((((..(((((((((.((((.....)))).......(((.(((.((((.............))))..)))...)))..))))))))).)))))....((((....))))........ ( -28.82)
>consensus
UUUCUCUCGAAUGUGUGGCAAUUAUUUUGCAACUAAUUGCUAGCUCUGCUAUUAUUCUGACCGCAGCUGUUCAUGCAUGAUAUAUUUGUGGAGACAAAGGCAUUUUUGCCACGCGUUG
.........((((((((((((.......((((....))))......((((.....(((..((((((.((((((....))).))).)))))))))....))))...)))))))))))). (-27.12 = -27.92 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:47 2006