Locus 9303

Sequence ID	3R_DroMel_CAF1
Location	24,774,848 – 24,775,042
Length	194
Max. P	0.694426

overview

Window 0

Location	24,774,848 – 24,774,962
Length	114
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	91.08
Mean single sequence MFE	-28.04
Consensus MFE	-20.52
Energy contribution	-20.40
Covariance contribution	-0.12
Combinations/Pair	1.09
Mean z-score	-1.91
Structure conservation index	0.73
SVM decision value	0.17
SVM RNA-class probability	0.616643
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24774848 114 - 27905053
UAUCGUAUGCUUCACUGGAGCAGAAUGGGAAUGUCUCAUUCUAUCCGACCCACUAUUCAUUUCACCACCCCACGAAUGCCAGAUCGUCGUGCUCCUCCU--GCUGCUACUGCUGCG
....(((.((..((..(((((((((((((.....))))))))...((((...((...(((((...........)))))..))...)))).)))))...)--)..)))))....... ( -27.60)
>DroSec_CAF1 6064 116 - 1
UUUCGCAUGCUUCACUGGAGCAGAAUGGGAAUGUCUCAUUCUAUCCGACCCACUAUUCAUUUCACCACCCCACGAAUGCCAGAUCGUCCUGCUCCUUCUGUGCUCCUUCUGCUGCG
...((((.((......(((((((((((((.....))))))))...............................(((.((.((......))))...)))...)))))....)))))) ( -27.10)
>DroSim_CAF1 1452 116 - 1
UUUCGCAUGCUUCACUGGAGCAGAAUGGGAAUGUCUCAUUCUAUCCGACCCACUAUUCAUUUCACCACCCCACGAUUGCCAGAUCGUCCUGCUCCUCCUGUGCUCCUUCUGCUGCG
...((((.((......(((((((((((((.....)))))))).............................((((((....))))))..............)))))....)))))) ( -29.60)
>DroEre_CAF1 14931 105 - 1
UUUCGCAUGCUUCACUGGAGCAGAAUGGGAAUGUCUCAUUCUAUCCAACCCACUAUUCAUUUCACCACCCCACGAAUGCCAGAUCGUCCUGCUGCUCCUG-----------CUGCG
...((((.((......(((((((...((((..(((((((((................................)))))..))))..)))).))))))).)-----------))))) ( -27.85)
>consensus
UUUCGCAUGCUUCACUGGAGCAGAAUGGGAAUGUCUCAUUCUAUCCGACCCACUAUUCAUUUCACCACCCCACGAAUGCCAGAUCGUCCUGCUCCUCCUG_GCUCCUUCUGCUGCG
...((((.((.....((((..((((((((.....)))))))).))))........................((((........)))).......................)))))) (-20.52 = -20.40 +  -0.12)

alignment

secondary structure

dotplot

Window 1

Location	24,774,922 – 24,775,042
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.00
Mean single sequence MFE	-31.92
Consensus MFE	-31.78
Energy contribution	-31.82
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.26
Structure conservation index	1.00
SVM decision value	0.34
SVM RNA-class probability	0.694426
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24774922 120 + 27905053
AAUGAGACAUUCCCAUUCUGCUCCAGUGAAGCAUACGAUAUGGCGACAGUUUGUGUGCGCAUAACUGAGCAUAAUCGACGCCUUUUGGUUAUAAUUAACUCAUUAAAGUGAAACGGCAGC
((((((.............((((.(((...((((((((..((....))..)))))))).....)))))))((((((((......))))))))......))))))................ ( -31.40)
>DroSec_CAF1 6140 120 + 1
AAUGAGACAUUCCCAUUCUGCUCCAGUGAAGCAUGCGAAAUGGCGACAGUUUGUGUGCGCAUAACUGAGCAUAAUCGACGCCUUUUGGUUAUAAUUAACUCAUUAAAGUGAAACGGCAGC
((((((.............((((.(((...(((((((((.((....)).))))))))).....)))))))((((((((......))))))))......))))))................ ( -31.80)
>DroSim_CAF1 1528 120 + 1
AAUGAGACAUUCCCAUUCUGCUCCAGUGAAGCAUGCGAAAUGGCGACAGUUUGUGUGCGCAUAACUGAGCAUAAUCGACGCCUUUUGGUUAUAAUUAACUCAUUAAAGUGAAACGGCAGC
((((((.............((((.(((...(((((((((.((....)).))))))))).....)))))))((((((((......))))))))......))))))................ ( -31.80)
>DroEre_CAF1 14996 120 + 1
AAUGAGACAUUCCCAUUCUGCUCCAGUGAAGCAUGCGAAAUGGCGACAGUUUGUGUGCGCAUAACUGAGCAUAAUCGACGCCUUUUGGUUAUAAUUAACUCAUUAAAGUGAAACGGCAGC
((((((.............((((.(((...(((((((((.((....)).))))))))).....)))))))((((((((......))))))))......))))))................ ( -31.80)
>DroYak_CAF1 6697 120 + 1
AAUGAGACAUGCCCAUUCUGCUCCAGUGAAGCAUGCGAAAUGGCGACAGUUUGUGUGCGCAUAACUGAGCAUAAUCGACGCCUUUUGGUUAUAAUUAACUCAUUAAAGUGAAACGGCAGC
.........((((......((((.(((...(((((((((.((....)).))))))))).....)))))))((((((((......)))))))).......((((....))))...)))).. ( -32.80)
>consensus
AAUGAGACAUUCCCAUUCUGCUCCAGUGAAGCAUGCGAAAUGGCGACAGUUUGUGUGCGCAUAACUGAGCAUAAUCGACGCCUUUUGGUUAUAAUUAACUCAUUAAAGUGAAACGGCAGC
((((((.............((((.(((...(((((((((.((....)).))))))))).....)))))))((((((((......))))))))......))))))................ (-31.78 = -31.82 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:31:05 2006