Locus 6147

Sequence ID	2L_DroMel_CAF1
Location	17,139,433 – 17,139,673
Length	240
Max. P	0.999509

overview

Window 8

Location	17,139,433 – 17,139,553
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.50
Mean single sequence MFE	-30.62
Consensus MFE	-25.38
Energy contribution	-25.18
Covariance contribution	-0.20
Combinations/Pair	1.08
Mean z-score	-1.81
Structure conservation index	0.83
SVM decision value	0.99
SVM RNA-class probability	0.896780
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17139433 120 + 22407834
UUCCUGGCCUUCAUUUUUCAACUUCAACGACAGUGGCAGCCGCGUGUCUGUGGCUCCUGCCUCAUGGCUUGCGGAAUAUGCAAAUUCUUUGCCACAAUUUUCCCCAGCACUUUUUGUUUU
...((((.....................((((((((...)))).))))((((((....(((....)))(((((.....))))).......)))))).......))))............. ( -30.20)
>DroSec_CAF1 107845 120 + 1
UUCCUGGCCUUCAUUUUUCAACUUCAACGACAGUGGCAGCCGCGUGUCUGUGGCUCCUGCCGCAUGGCUUGUGGAAUAUGCAAAUUCUUUGCCACAAUUUUCCCCAGCACUUUUUGUUUU
...((((..........((.........))..(((((((.((((.(((((((((....)))))).))).))))((((......)))).)))))))........))))............. ( -31.10)
>DroSim_CAF1 120073 120 + 1
UUCCUGGCCUUCAUUUUUCAACUUCAACGACAGUGGCAGCCGCGUGUCUGUGGCUCCUGCCGCAUGGCUUGUGGAAUAUGCAAAUUCUUUGCCACAAUUUUCCCCAGCACUUUUUGUUUU
...((((..........((.........))..(((((((.((((.(((((((((....)))))).))).))))((((......)))).)))))))........))))............. ( -31.10)
>DroEre_CAF1 105452 117 + 1
UUCCUGGCCUUCAUUUUUCAACUUCAACGACAGUGGGAGCCGCGUGUCUGUGGCUCCUGCCUCAUGGCU---GGAAUAUGCAAAUUCUUUGCCACAAUUUUCCCUAGCACUUUUUGUUUU
...((((.....................((..(..(((((((((....)))))))))..).)).((((.---(((((......)))))..)))).........))))............. ( -31.00)
>DroYak_CAF1 107927 120 + 1
UUCCUGGCCUUCAUUUUUCAACUUCAACGACAGUGGGAGCCGCGUGUCUGUGGCUUCUGCCUCAUGCCUUGCGGAAUAUGCAAAUUCUUUGCCACAAUUUUUUCUGGCACUUUUUGUUUU
((((.(((..(((((..((.........)).)))))..)))(((.((.((.(((....))).)).))..)))))))...(((((.....(((((.((....)).)))))...)))))... ( -29.70)
>consensus
UUCCUGGCCUUCAUUUUUCAACUUCAACGACAGUGGCAGCCGCGUGUCUGUGGCUCCUGCCUCAUGGCUUGCGGAAUAUGCAAAUUCUUUGCCACAAUUUUCCCCAGCACUUUUUGUUUU
...((((.....................((((((((...)))).))))((((((....(((....)))....(((((......)))))..)))))).......))))............. (-25.38 = -25.18 +  -0.20)

alignment

secondary structure

dotplot

Window 9

Location	17,139,473 – 17,139,593
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.17
Mean single sequence MFE	-31.18
Consensus MFE	-26.08
Energy contribution	-26.28
Covariance contribution	0.20
Combinations/Pair	1.06
Mean z-score	-1.55
Structure conservation index	0.84
SVM decision value	0.56
SVM RNA-class probability	0.780693
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17139473 120 + 22407834
CGCGUGUCUGUGGCUCCUGCCUCAUGGCUUGCGGAAUAUGCAAAUUCUUUGCCACAAUUUUCCCCAGCACUUUUUGUUUUUAUCCUGUUGCUGUUGUCGAAGUCGUCUUUGAUAAGCAAA
.((.....((((((....(((....)))(((((.....))))).......))))))........((((((................).)))))(((((((((....)))))))))))... ( -31.99)
>DroSec_CAF1 107885 120 + 1
CGCGUGUCUGUGGCUCCUGCCGCAUGGCUUGUGGAAUAUGCAAAUUCUUUGCCACAAUUUUCCCCAGCACUUUUUGUUUUUAUCCUGUUGCUGUUGUCGAAGUCGUCUUUGAUAAGCAAA
...((((.((((((....))))))((((....(((((......)))))..))))............)))).................(((((..((((((((....))))))))))))). ( -32.90)
>DroSim_CAF1 120113 120 + 1
CGCGUGUCUGUGGCUCCUGCCGCAUGGCUUGUGGAAUAUGCAAAUUCUUUGCCACAAUUUUCCCCAGCACUUUUUGUUUUUAUCCUGUUGCUGUUGUCGAAGUCGUCUUUGAUAAGCAAA
...((((.((((((....))))))((((....(((((......)))))..))))............)))).................(((((..((((((((....))))))))))))). ( -32.90)
>DroEre_CAF1 105492 117 + 1
CGCGUGUCUGUGGCUCCUGCCUCAUGGCU---GGAAUAUGCAAAUUCUUUGCCACAAUUUUCCCUAGCACUUUUUGUUUUUAUCCUGUUGCUGUUGCCGAAGUCGUCUUUGAUAAGCAAA
...((((.((.(((....))).))((((.---(((((......)))))..))))............)))).................(((((.....(((((....)))))...))))). ( -25.70)
>DroYak_CAF1 107967 120 + 1
CGCGUGUCUGUGGCUUCUGCCUCAUGCCUUGCGGAAUAUGCAAAUUCUUUGCCACAAUUUUUUCUGGCACUUUUUGUUUUCAUCCUGUUGCUGUUGCCGAAGUCGUCUUUGAUAAGCAAA
.((.((((.((((((((.((..((.((...(((((....(((((.....(((((.((....)).)))))...))))).....))).)).))))..)).))))))).)...)))).))... ( -32.40)
>consensus
CGCGUGUCUGUGGCUCCUGCCUCAUGGCUUGCGGAAUAUGCAAAUUCUUUGCCACAAUUUUCCCCAGCACUUUUUGUUUUUAUCCUGUUGCUGUUGUCGAAGUCGUCUUUGAUAAGCAAA
...(((.(((.(((....)))...((((....(((((......)))))..))))..........)))))).................(((((..((((((((....))))))))))))). (-26.08 = -26.28 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	17,139,553 – 17,139,673
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.08
Mean single sequence MFE	-26.84
Consensus MFE	-23.94
Energy contribution	-24.10
Covariance contribution	0.16
Combinations/Pair	1.03
Mean z-score	-2.49
Structure conservation index	0.89
SVM decision value	3.67
SVM RNA-class probability	0.999509
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17139553 120 - 22407834
AUCAAAUAGCUCAGGCCUUUUCUUCUAAUGCUUUUCGAGCUCGUCAACGCACUAUAAAAAUAUCAUUAUCAGUGCAAAAGUUUGCUUAUCAAAGACGACUUCGACAACAGCAACAGGAUA
........((....))......((((..((((..(((((.(((((...(((((((((........)))).)))))..(((....)))......))))).)))))....))))..)))).. ( -26.30)
>DroSec_CAF1 107965 120 - 1
AUCAAAUAACUCAGGCCUUUUCUCCUAAUGCUUUGCGAGCUCGUCAACGCACUAUAAAAAUAUCAUUAUCAGUGCAAAAGUUUGCUUAUCAAAGACGACUUCGACAACAGCAACAGGAUA
......................((((..(((((((((((.(((((...(((((((((........)))).)))))..(((....)))......))))).)))).))).))))..)))).. ( -30.30)
>DroSim_CAF1 120193 120 - 1
AUCAAAUAACUCAGGCCUUUUCUCCUAAUGCUUUGCGAGCUCGUCAACGCACUAUAAAAAUAUCAUUAUCAGAGCAAAAGUUUGCUUAUCAAAGACGACUUCGACAACAGCAACAGGAUA
......................((((..(((((((((((.(((((..............(((....)))..((((((....))))))......))))).)))).))).))))..)))).. ( -25.70)
>DroEre_CAF1 105569 120 - 1
GUCAAAUAUCGCAGGCCUCUUCUUCUAAUGCUUUUCGAGCUCGUCAACGCACUAUAAAAAUAUCAUUAUCAGUGCAAAAGUUUGCUUAUCAAAGACGACUUCGGCAACAGCAACAGGAUA
......................((((..((((..(((((.(((((...(((((((((........)))).)))))..(((....)))......))))).)))))....))))..)))).. ( -24.80)
>DroYak_CAF1 108047 120 - 1
ACCAAAUAUCACAGGUCUCUUCUCAUCUUGCUUUUCGAGCUCGUCAACGCACUAUAAAAAUAUCAUUAUCAGUGCAAAAGUUUGCUUAUCAAAGACGACUUCGGCAACAGCAACAGGAUG
(((..........))).......(((((((.....((((.(((((...(((((((((........)))).)))))..(((....)))......))))).))))((....))..))))))) ( -27.10)
>consensus
AUCAAAUAACUCAGGCCUUUUCUCCUAAUGCUUUUCGAGCUCGUCAACGCACUAUAAAAAUAUCAUUAUCAGUGCAAAAGUUUGCUUAUCAAAGACGACUUCGACAACAGCAACAGGAUA
......................((((..((((...((((.(((((...(((((((((........)))).)))))..(((....)))......))))).)))).....))))..)))).. (-23.94 = -24.10 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:36 2006