Locus 5729

Sequence ID	3R_DroMel_CAF1
Location	14,945,231 – 14,945,391
Length	160
Max. P	0.744382

overview

Window 5

Location	14,945,231 – 14,945,351
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.09
Mean single sequence MFE	-31.73
Consensus MFE	-23.64
Energy contribution	-25.70
Covariance contribution	2.06
Combinations/Pair	1.03
Mean z-score	-1.78
Structure conservation index	0.75
SVM decision value	0.46
SVM RNA-class probability	0.744382
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14945231 120 + 27905053
AUCAUGUCGCUGGUGGCAUCUUGGGUGGUCAACAUAAAUAUGUAUGUUCUGGCACUUAACUUCGAGUUAAAUCCAAAACGUGCUGGGCCAAAAGGUACCAUCUAAGGUACCAUCUAACAA
....(((....(((((.((((((((((((............(((((((.(((...(((((.....)))))..))).)))))))...(((....))))))))))))))).)))))..))). ( -38.80)
>DroSec_CAF1 81043 110 + 1
AU-----CGCUGGUGGCAUCUUGGGUGGUCAACAUAAAUA----UGUUCUGGCACUUAACUUCGAGUUAAAUCCAUAACGUGCUGGACCAAAAGGUACC-UCUAAGGUACCAUCUAACAA
..-----...(((((((((..(((((.((((((((....)----)))..))))..(((((.....))))))))))....)))))..))))...((((((-.....))))))......... ( -30.10)
>DroSim_CAF1 73879 115 + 1
AUCAUGUCGCUGGUGGCAUCUUGGGUGGUCAACAUAAAUC----UGUUCUGGCACUUAACUUCGAGUUAAAUCCAUAACGUGCUGGGCCAAAAGGUACC-UCUAAGGUACCAUCUAGCAA
........((((((((.((((((((.(((...........----....(..(((((((((.....))))).........))))..)(((....))))))-)))))))).))).))))).. ( -34.50)
>DroYak_CAF1 77982 108 + 1
AUCAUGUCGCU---GGCAUCUUGGGCGGUCAAAAUAAAUA----UGUUCUGGCACUUAAGUUCGCGUUAAGUCCCAAUCGUGCUGGGCCAAAAGGUACC-UCUC----UCCAUCUAACAA
....(((..(.---.((((.(((((..((((.((((....----)))).))))(((((((....).)))))))))))..))))..)(((....)))...-....----........))). ( -23.50)
>consensus
AUCAUGUCGCUGGUGGCAUCUUGGGUGGUCAACAUAAAUA____UGUUCUGGCACUUAACUUCGAGUUAAAUCCAAAACGUGCUGGGCCAAAAGGUACC_UCUAAGGUACCAUCUAACAA
...........(((((.((((((((.(((...................(..(((((((((.....))))).........))))..)(((....)))))).)))))))).)))))...... (-23.64 = -25.70 +   2.06)

alignment

secondary structure

dotplot

Window 6

Location	14,945,271 – 14,945,391
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	89.65
Mean single sequence MFE	-30.83
Consensus MFE	-24.92
Energy contribution	-26.43
Covariance contribution	1.50
Combinations/Pair	1.12
Mean z-score	-1.47
Structure conservation index	0.81
SVM decision value	0.10
SVM RNA-class probability	0.582279
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14945271 120 - 27905053
AGGCAGCGUGAUUAAAACGGAAAGAUUGGAUAGGGAAAAGUUGUUAGAUGGUACCUUAGAUGGUACCUUUUGGCCCAGCACGUUUUGGAUUUAACUCGAAGUUAAGUGCCAGAACAUACA
..((..(((.......))).......................((((((.((((((......)))))).))))))...))..((((((((((((((.....))))))).)))))))..... ( -32.90)
>DroSec_CAF1 81078 115 - 1
AGGCAGCGUGAUUAAAACGGAAAGAUUGGAUAGGGAAAAGUUGUUAGAUGGUACCUUAGA-GGUACCUUUUGGUCCAGCACGUUAUGGAUUUAACUCGAAGUUAAGUGCCAGAACA----
.(((((((((.......(.....).((((((..(((...(((....)))((((((.....-)))))))))..))))))))))))....(((((((.....))))))))))......---- ( -29.90)
>DroSim_CAF1 73919 115 - 1
AGGCAGCGUGAUUAAAACGGAAAGAUUGGCUAGGGAAAAGUUGCUAGAUGGUACCUUAGA-GGUACCUUUUGGCCCAGCACGUUAUGGAUUUAACUCGAAGUUAAGUGCCAGAACA----
.((((.(((.......)))......((((((.(((.......((((((.((((((.....-)))))).))))))(((........)))......)))..)))))).))))......---- ( -33.40)
>DroYak_CAF1 78019 110 - 1
AGGCA-CGUCAUUAAAGCGGAAAGAUUGGAUUGGGAAAAGUUGUUAGAUGGA----GAGA-GGUACCUUUUGGCCCAGCACGAUUGGGACUUAACGCGAACUUAAGUGCCAGAACA----
.((((-(.........(((..(((((((..(((((....(((....)))...----((((-(....)))))..)))))..)))).....)))..)))........)))))......---- ( -27.13)
>consensus
AGGCAGCGUGAUUAAAACGGAAAGAUUGGAUAGGGAAAAGUUGUUAGAUGGUACCUUAGA_GGUACCUUUUGGCCCAGCACGUUAUGGAUUUAACUCGAAGUUAAGUGCCAGAACA____
..((..(((.......))).............(((........(((((.((((((......)))))).)))))))).))..((((((((((((((.....))))))).)))))))..... (-24.92 = -26.43 +   1.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:03 2006