Locus 2413

Sequence ID	X_DroMel_CAF1
Location	6,456,276 – 6,456,372
Length	96
Max. P	0.709412

overview

Window 1

Location	6,456,276 – 6,456,372
Length	96
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	83.49
Mean single sequence MFE	-24.23
Consensus MFE	-16.86
Energy contribution	-16.33
Covariance contribution	-0.52
Combinations/Pair	1.31
Mean z-score	-2.40
Structure conservation index	0.70
SVM decision value	0.37
SVM RNA-class probability	0.709412
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6456276 96 + 22224390
CCGAAGUAACCAUCGCAUUUUUUUUUUUUUUGC----AAUCUUUAGCGAUCGCCAAGCAGGCGUGAAAUCAUCGUUAUUAUGAUGAUUAGU-UUUUUGCUC
....(((((...((((.............((((----........))))..(((.....)))))))(((((((((....)))))))))...-...))))). ( -21.70)
>DroPse_CAF1 12463 89 + 1
UCAGAUUUGGCAUAGC---U---------UUGCGGCUGAUAUUUUCCUAUCGCAAAGCAGGCGUGAACUCAUUGCUAAUAUGAUGGUUAUUCUUUUUGCCC
........((((..((---(---------((((((..(........)..))))))))).((((((....)).))))....................)))). ( -22.50)
>DroSec_CAF1 10760 87 + 1
CCGAAGUUACCAUCGCAUUU---------UUGC----GAUCUUUAGCGAUCGCCAAGCAGGCGUGAAAUCAUCGUUAUUAUGAUGAUUAGU-UUUUUGCUU
..((((.....((((((...---------.)))----)))))))(((((.((((.....))))...(((((((((....)))))))))...-...))))). ( -25.10)
>DroSim_CAF1 10740 87 + 1
ACGAAGUUACCAUCGCAUUU---------UUGC----GAUCUUUAGCGAUCGCCAAGCAGGCGUGAAAUCAUCGUUAUUAUGAUGAUUAGU-UUUUUGCUC
..((((.....((((((...---------.)))----)))))))(((((.((((.....))))...(((((((((....)))))))))...-...))))). ( -25.10)
>DroEre_CAF1 10020 87 + 1
GCAGAGUUACCAUCGCAUUU---------UCGC----GAUCUUUAGCGAUCGCCAAGCAGGCGUGAAAUCAUCGUUAUUAUGAUGAUUAGU-UUUUUGCUC
((((((..((..((((....---------((((----........))))..(((.....)))))))(((((((((....))))))))).))-.)))))).. ( -27.60)
>DroYak_CAF1 10999 87 + 1
GCUGAGUUACCAUCACUUUU---------UUGC----GAUCUUUAGCGAUCGCCAAGCAGGCGUGAAAUCAUCGUUAUUAUGAUGAUUAGU-UUUUUGCUC
...((((.....((((....---------....----((((......))))(((.....)))))))(((((((((....)))))))))...-.....)))) ( -23.40)
>consensus
CCGAAGUUACCAUCGCAUUU_________UUGC____GAUCUUUAGCGAUCGCCAAGCAGGCGUGAAAUCAUCGUUAUUAUGAUGAUUAGU_UUUUUGCUC
.((((...((..((((.....................((((......))))(((.....)))))))(((((((((....))))))))).))...))))... (-16.86 = -16.33 +  -0.52)

alignment

secondary structure

dotplot

Window 2

Location	6,456,276 – 6,456,372
Length	96
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	83.49
Mean single sequence MFE	-22.72
Consensus MFE	-14.64
Energy contribution	-14.64
Covariance contribution	0.00
Combinations/Pair	1.26
Mean z-score	-2.73
Structure conservation index	0.64
SVM decision value	0.35
SVM RNA-class probability	0.700341
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6456276 96 - 22224390
GAGCAAAAA-ACUAAUCAUCAUAAUAACGAUGAUUUCACGCCUGCUUGGCGAUCGCUAAAGAUU----GCAAAAAAAAAAAAAAUGCGAUGGUUACUUCGG
(((((....-...(((((((........))))))).......))))).((((((......))))----))................(((.(....).))). ( -21.54)
>DroPse_CAF1 12463 89 - 1
GGGCAAAAAGAAUAACCAUCAUAUUAGCAAUGAGUUCACGCCUGCUUUGCGAUAGGAAAAUAUCAGCCGCAA---------A---GCUAUGCCAAAUCUGA
.((((....((((.....((((.......))))))))......((((((((....((.....))...)))))---------)---))..))))........ ( -20.20)
>DroSec_CAF1 10760 87 - 1
AAGCAAAAA-ACUAAUCAUCAUAAUAACGAUGAUUUCACGCCUGCUUGGCGAUCGCUAAAGAUC----GCAA---------AAAUGCGAUGGUAACUUCGG
(((((....-...(((((((........))))))).......))))).((((((......))))----))..---------.....(((.(....).))). ( -23.24)
>DroSim_CAF1 10740 87 - 1
GAGCAAAAA-ACUAAUCAUCAUAAUAACGAUGAUUUCACGCCUGCUUGGCGAUCGCUAAAGAUC----GCAA---------AAAUGCGAUGGUAACUUCGU
(((((....-...(((((((........))))))).......))))).((((((......))))----))..---------....((((.(....).)))) ( -24.34)
>DroEre_CAF1 10020 87 - 1
GAGCAAAAA-ACUAAUCAUCAUAAUAACGAUGAUUUCACGCCUGCUUGGCGAUCGCUAAAGAUC----GCGA---------AAAUGCGAUGGUAACUCUGC
(((......-...(((((((........)))))))((((((.(..((.((((((......))))----)).)---------).).))).)))...)))... ( -23.00)
>DroYak_CAF1 10999 87 - 1
GAGCAAAAA-ACUAAUCAUCAUAAUAACGAUGAUUUCACGCCUGCUUGGCGAUCGCUAAAGAUC----GCAA---------AAAAGUGAUGGUAACUCAGC
(((......-...(((((((........)))))))....(((.((((.((((((......))))----))..---------..))))...)))..)))... ( -24.00)
>consensus
GAGCAAAAA_ACUAAUCAUCAUAAUAACGAUGAUUUCACGCCUGCUUGGCGAUCGCUAAAGAUC____GCAA_________AAAUGCGAUGGUAACUCCGC
(((((........(((((((........))))))).......))))).((.(((((.............................))))).))........ (-14.64 = -14.64 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:51 2006