Locus 2706

Sequence ID	2R_DroMel_CAF1
Location	9,513,981 – 9,514,126
Length	145
Max. P	0.998008

overview

Window 2

Location	9,513,981 – 9,514,101
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.50
Mean single sequence MFE	-28.39
Consensus MFE	-22.88
Energy contribution	-23.68
Covariance contribution	0.80
Combinations/Pair	1.06
Mean z-score	-1.67
Structure conservation index	0.81
SVM decision value	0.66
SVM RNA-class probability	0.815706
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9513981 120 - 20766785
GAAAGUGAUUUUCCUGCUUAGACAAAUAUCGCUUUGCAUGACUAACGUCGAUUUUCAGUCAUGUAAAGGAUAUUAAAUAGAUACUGUUAUUUGAUUACUGAAGUAACUUGUUUCAAGUGC
...............(((((((((((((((.((((((((((((.............))))))))))))))))))...........(((((((........))))))).))))).)))).. ( -28.82)
>DroSec_CAF1 11006 120 - 1
GAAAGUGAUUUUCCAGCUAAGACAAAUAUCGCUUUGCAUGACUAACGUCGAUUUUCAGUCAUGUAAAGGAUAUUUAAUAGAUACUGUUAUUUGAUUACUCAAGUAACUUGUUUCAAGUGC
...............(((.....(((((((.((((((((((((.............)))))))))))))))))))....((.((.(((((((((....)))))))))..)).)).))).. ( -31.92)
>DroSim_CAF1 11051 120 - 1
GAAAGUGAUUUUCCUGCUAAGACAAAUAUCGCUUUGCAUGACUAAAGUCGAUGUUCAGUCAUGUAAAGGAUAUUUAAUAGAUACUGUUAUUUGAUUACUCUAGUAACUUGUUUCAAGUGC
...............(((.....(((((((.((((((((((((.............)))))))))))))))))))....((.((.((((((.((....)).))))))..)).)).))).. ( -27.72)
>DroEre_CAF1 11240 120 - 1
GAAAGUGAUUUUCCUGCUUAGACAAAUAAUGCUUUGCAUGACUAAGGUCGAUUUUCCGUCAUGUAAAGGAUAUUUAAUAGAUACGGCUAUUUGCUAACUGAAGUAACGUGUUUCAAGUGG
.............(..(((....(((((.(.(((((((((((...((........))))))))))))).))))))...(((((((..(((((........))))).))))))).)))..) ( -26.50)
>DroYak_CAF1 11127 120 - 1
GAAAGUGAUUUUCCUGCUUAGACAAAUAAUGCUUUGCAUGACUAAGGUCGAUUUUCCGUCAUGUAAGGGAUAUUUAAUAGAUACGGUUAUUUGCUUACUGAAGUAACGUGUUUCAAGUGG
.............(..((((((((....((.(((((((((((...((........))))))))))))).))..............(((((((........))))))).))))).)))..) ( -27.00)
>consensus
GAAAGUGAUUUUCCUGCUUAGACAAAUAUCGCUUUGCAUGACUAACGUCGAUUUUCAGUCAUGUAAAGGAUAUUUAAUAGAUACUGUUAUUUGAUUACUGAAGUAACUUGUUUCAAGUGC
...............(((((((((((((((.(((((((((((...............)))))))))))))))))...........(((((((........))))))).))))).)))).. (-22.88 = -23.68 +   0.80)

alignment

secondary structure

dotplot

Window 3

Location	9,514,021 – 9,514,126
Length	105
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	86.61
Mean single sequence MFE	-27.55
Consensus MFE	-24.58
Energy contribution	-25.20
Covariance contribution	0.62
Combinations/Pair	1.06
Mean z-score	-3.36
Structure conservation index	0.89
SVM decision value	2.98
SVM RNA-class probability	0.998008
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9514021 105 + 20766785
CUAUUUAAUAUCCUUUACAUGACUGAAAAUCGACGUUAGUCAUGCAAAGCGAUAUUUGUCUAAGCAGGAAAAUCACUUUCCUCACGUGUAAUUUAUGUGCAUUUG--------------
......((((((((((.(((((((((.........))))))))).)))).)))))).......((((((((.....)))))).(((((.....))))))).....-------------- ( -25.90)
>DroSec_CAF1 11046 105 + 1
CUAUUAAAUAUCCUUUACAUGACUGAAAAUCGACGUUAGUCAUGCAAAGCGAUAUUUGUCUUAGCUGGAAAAUCACUUUCCUCACGUGUAAUUUAUGUGCAUUUG--------------
(((.((((((((((((.(((((((((.........))))))))).)))).))))))))...)))..(((((.....))))).((((((.....))))))......-------------- ( -28.00)
>DroSim_CAF1 11091 105 + 1
CUAUUAAAUAUCCUUUACAUGACUGAACAUCGACUUUAGUCAUGCAAAGCGAUAUUUGUCUUAGCAGGAAAAUCACUUUCCUCACGUGUAAUUUAUGUGCAUUUG--------------
(((.((((((((((((.((((((((((.......)))))))))).)))).))))))))...))).((((((.....))))))((((((.....))))))......-------------- ( -30.10)
>DroEre_CAF1 11280 118 + 1
CUAUUAAAUAUCCUUUACAUGACGGAAAAUCGACCUUAGUCAUGCAAAGCAUUAUUUGUCUAAGCAGGAAAAUCACUUUCCAUACAUGUA-UUCAUGUGCACAUGUACAUAUGUAUGUA
....((((((..((((.((((((((........))...)))))).))))...)))))).....((.(((((.....)))))((((((((.-..((((....))))...)))))))))). ( -26.20)
>consensus
CUAUUAAAUAUCCUUUACAUGACUGAAAAUCGACGUUAGUCAUGCAAAGCGAUAUUUGUCUAAGCAGGAAAAUCACUUUCCUCACGUGUAAUUUAUGUGCAUUUG______________
....((((((((((((.(((((((((.........))))))))).)))).)))))))).....((.(((((.....)))))..(((((.....)))))))................... (-24.58 = -25.20 +   0.62)

alignment

secondary structure

dotplot

Window 4

Location	9,514,021 – 9,514,126
Length	105
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	86.61
Mean single sequence MFE	-28.79
Consensus MFE	-23.96
Energy contribution	-24.64
Covariance contribution	0.69
Combinations/Pair	1.10
Mean z-score	-3.25
Structure conservation index	0.83
SVM decision value	2.56
SVM RNA-class probability	0.995321
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9514021 105 - 20766785
--------------CAAAUGCACAUAAAUUACACGUGAGGAAAGUGAUUUUCCUGCUUAGACAAAUAUCGCUUUGCAUGACUAACGUCGAUUUUCAGUCAUGUAAAGGAUAUUAAAUAG
--------------.....(((...(((((((.(....)....)))))))...))).......((((((.((((((((((((.............))))))))))))))))))...... ( -28.52)
>DroSec_CAF1 11046 105 - 1
--------------CAAAUGCACAUAAAUUACACGUGAGGAAAGUGAUUUUCCAGCUAAGACAAAUAUCGCUUUGCAUGACUAACGUCGAUUUUCAGUCAUGUAAAGGAUAUUUAAUAG
--------------.....((....(((((((.(....)....)))))))....))......(((((((.((((((((((((.............)))))))))))))))))))..... ( -27.72)
>DroSim_CAF1 11091 105 - 1
--------------CAAAUGCACAUAAAUUACACGUGAGGAAAGUGAUUUUCCUGCUAAGACAAAUAUCGCUUUGCAUGACUAAAGUCGAUGUUCAGUCAUGUAAAGGAUAUUUAAUAG
--------------.....(((...(((((((.(....)....)))))))...)))......(((((((.((((((((((((.............)))))))))))))))))))..... ( -29.42)
>DroEre_CAF1 11280 118 - 1
UACAUACAUAUGUACAUGUGCACAUGAA-UACAUGUAUGGAAAGUGAUUUUCCUGCUUAGACAAAUAAUGCUUUGCAUGACUAAGGUCGAUUUUCCGUCAUGUAAAGGAUAUUUAAUAG
..(((((((.(((.((((....)))).)-)).)))))))..((((.........))))....(((((.(.(((((((((((...((........))))))))))))).))))))..... ( -29.50)
>consensus
______________CAAAUGCACAUAAAUUACACGUGAGGAAAGUGAUUUUCCUGCUAAGACAAAUAUCGCUUUGCAUGACUAACGUCGAUUUUCAGUCAUGUAAAGGAUAUUUAAUAG
...................(((...(((((((.(....)....)))))))...)))......(((((((.((((((((((((.............)))))))))))))))))))..... (-23.96 = -24.64 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:12 2006