Locus 7552

Sequence ID	3L_DroMel_CAF1
Location	20,278,709 – 20,278,885
Length	176
Max. P	0.999314

overview

Window 3

Location	20,278,709 – 20,278,825
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.58
Mean single sequence MFE	-24.02
Consensus MFE	-18.50
Energy contribution	-19.94
Covariance contribution	1.44
Combinations/Pair	1.10
Mean z-score	-1.85
Structure conservation index	0.77
SVM decision value	0.63
SVM RNA-class probability	0.804269
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20278709 116 - 23771897
UUUUAAAGCUGAUUUUCGUGCACUUGACUUUAAUAUUUUAAUUUGAGUAUCGUGGU---UUGCAUUAUUGAUUAUAUUAUUCGAAUUGUAUUAUCUUCCUGUGCAUGCG-UUCGAUUCUA
.........(((....(((((((..((...((((((...((((((((((..(((((---(.........))))))..))))))))))))))))...))..)))))))..-.)))...... ( -24.70)
>DroSec_CAF1 17309 116 - 1
UUUUGAAGUUGCUUUUCGUGCACAUGACUUUAAUAUUUCAAUUUUAGUAUCGUGGU---UUGCAUUAUUGACUAUAUUACUCGAAUUGUAUUAUCUUCCUGUGCAUGCG-UUCGAUCCUA
..(((((..(((.....(((((((.((...(((((...((((((.((((..(((((---(.........))))))..)))).)))))))))))...)).))))))))))-)))))..... ( -26.50)
>DroSim_CAF1 17273 116 - 1
UUUUGAAGCUGCUGUUCGUGCACAUGACUUUAAUAUUUCAAUUUUAGUAUCGUGGU---UUGCAUUAUUGACUAUAUUAUUCGAAUUGUAUUAUCUUCCUGUGCAUGCG-UUCGAUCCUA
..(((((((....)).((((((((.((...(((((...((((((.((((..(((((---(.........))))))..)))).)))))))))))...)).))))))))..-)))))..... ( -24.30)
>DroYak_CAF1 8989 120 - 1
AAAUCAAUUUUCAGCUCGGGCACAUGACUUUAAUAUUUCAACUUGAGCAUCGUUGUUGCUUGCAUUAUUGACUAUAUUAUUCGAAUGGUAUUAUUUUCCUGUGCAUGCGGUUUUAUCUUA
(((((........(((((((....(((..(....)..))).))))))).........((.(((((....((..(((((((....)))))))..)).....))))).)))))))....... ( -20.60)
>consensus
UUUUGAAGCUGCUGUUCGUGCACAUGACUUUAAUAUUUCAAUUUGAGUAUCGUGGU___UUGCAUUAUUGACUAUAUUAUUCGAAUUGUAUUAUCUUCCUGUGCAUGCG_UUCGAUCCUA
................((((((((.((...(((((...(((((((((((..(((((..............)))))..))))))))))))))))...)).))))))))............. (-18.50 = -19.94 +   1.44)

alignment

secondary structure

dotplot

Window 4

Location	20,278,785 – 20,278,885
Length	100
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	72.60
Mean single sequence MFE	-28.50
Consensus MFE	-19.52
Energy contribution	-20.40
Covariance contribution	0.88
Combinations/Pair	1.14
Mean z-score	-2.45
Structure conservation index	0.69
SVM decision value	3.51
SVM RNA-class probability	0.999314
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20278785 100 + 23771897
UAAAAUAUUAAAGUCAAGUGCACGAAAAUCAGCUUUAAAAUGUGGAGCUGUA----GGUCUUGCUGUUUGCAGUUCGGAGAGCAUGGCUUGGAAUAUUGAA--CAA--------------
...((((((.((((((.((...((((...((((((((.....))))))))..----....((((.....))))))))....)).))))))..))))))...--...-------------- ( -25.40)
>DroSec_CAF1 17385 104 + 1
UGAAAUAUUAAAGUCAUGUGCACGAAAAGCAACUUCAAAAUGUGGAGCUGAAAGUUGAUCUUGCUGUUUGCAGUUCGGAGAGCAUGGCUUGGAAUAUUGAG--CAA--------------
((.((((((.(((((((((...((((..(((((((((.....))))).....(((.......)))..))))..))))....)))))))))..))))))...--)).-------------- ( -27.70)
>DroSim_CAF1 17349 104 + 1
UGAAAUAUUAAAGUCAUGUGCACGAACAGCAGCUUCAAAAUGUGGAGCUGAAAGUUGAUCUUGCUGUUUGCAGUUCGGAGAGCAUGGCUUGGAAUAUAGAA--CAA--------------
....(((((.(((((((((...(((((..((((((((.....))))))))...........(((.....))))))))....)))))))))..)))))....--...-------------- ( -34.80)
>DroYak_CAF1 9069 111 + 1
UGAAAUAUUAAAGUCAUGUGCCCGAGCUGAAAAUUGAUUUUGCUGAUUUGU------GUGGUGCUGUUUG---GUCAGAGCGCAUGGCUUUCAAUAUAUAGAGUUAAAGUUUAUAAUAGU
....(((((((((((((((((.(..((..((....(...(..(........------)..)..)..))..---))..).)))))))))))).)))))....................... ( -26.10)
>consensus
UGAAAUAUUAAAGUCAUGUGCACGAAAAGCAACUUCAAAAUGUGGAGCUGAA____GAUCUUGCUGUUUGCAGUUCGGAGAGCAUGGCUUGGAAUAUAGAA__CAA______________
....(((((.(((((((((...((((...((((((((.....))))))))...........(((.....))).))))....)))))))))..)))))....................... (-19.52 = -20.40 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:50:04 2006