Locus 7557

Sequence ID	X_DroMel_CAF1
Location	18,829,834 – 18,830,055
Length	221
Max. P	0.570457

overview

Window 0

Location	18,829,834 – 18,829,949
Length	115
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	97.39
Mean single sequence MFE	-29.76
Consensus MFE	-26.57
Energy contribution	-26.77
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.28
Structure conservation index	0.89
SVM decision value	0.07
SVM RNA-class probability	0.570457
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18829834 115 - 22224390
AAAUUGUAUUUUUCCGUUUAGAUAAGCAAAAUUUAUGGCAGGACUUGCGUCCUCGAUCGCUAUUCUGUCCCGUCUCGGUCUGAACUCAAACUUGCAGUCGCAGUCCUGCGGCAAC
....((((..(((..(((((((..............(((((((...(((........)))..)))))))(((...))))))))))..)))..))))((((((....))))))... ( -31.50)
>DroSec_CAF1 66659 115 - 1
AAAUUGUAUUUUUCCGUUUAGAUAAGCAAAAUUUAUGGCAGGACUUGCGUCCUCGAUCGCAAUUCUGUCCCGUCUCGGUCUGAACUCAAACUUUCAGUCGCAGUCCUGCGGCAAC
...............(((((((..............(((((((.(((((........))))))))))))(((...))))))))))...........((((((....))))))... ( -31.20)
>DroSim_CAF1 46915 115 - 1
AAAUUGUAUUUUUCCGUUUAGAUAAGCAAAAUUUAUGGCAGGACUUGCGUCCUCGAUCGCUAUUCUGUCCCGUCUCGGUCUGAACUCAAACUUUCAGUCGCAGUCCUGCGGCAAC
...............(((((((..............(((((((...(((........)))..)))))))(((...))))))))))...........((((((....))))))... ( -28.60)
>DroEre_CAF1 64484 115 - 1
AAAUUGUAUUUUUCCGUUUAGAUAAGCAGAAUUUAUGGCAGGACUUGCGUCCUCGAUCGCUAUUCUGUCCCGUCUCCUUCUGAACUCAAAGUUUCAGUCGCAGUCCUGCGGCAAC
....((...((((..(((((((..((.(((......(((((((...(((........)))..)))))))...))).)))))))))..))))...))((((((....))))))... ( -29.50)
>DroYak_CAF1 63518 115 - 1
AAAUUGUAUUUUUCCGUUUAGAUAAGCAAAAUUUAUGGCAGGACUCGCGUCCUCGAUCGCUAUUCUGUCCCGUCUCGGUCUGAACUCAAAGUUUCAGUCGCAGUCCUGCGGCAAC
....((...((((..(((((((..............(((((((...(((........)))..)))))))(((...))))))))))..))))...))((((((....))))))... ( -28.00)
>consensus
AAAUUGUAUUUUUCCGUUUAGAUAAGCAAAAUUUAUGGCAGGACUUGCGUCCUCGAUCGCUAUUCUGUCCCGUCUCGGUCUGAACUCAAACUUUCAGUCGCAGUCCUGCGGCAAC
...............((((((((.............(((.((((..(((........)))......)))).)))...))))))))...........((((((....))))))... (-26.57 = -26.77 +   0.20)

alignment

secondary structure

dotplot

Window 1

Location	18,829,949 – 18,830,055
Length	106
Sequences	4
Columns	112
Reading direction	reverse
Mean pairwise identity	80.50
Mean single sequence MFE	-18.25
Consensus MFE	-14.05
Energy contribution	-13.43
Covariance contribution	-0.63
Combinations/Pair	1.19
Mean z-score	-1.46
Structure conservation index	0.77
SVM decision value	0.00
SVM RNA-class probability	0.533893
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18829949 106 - 22224390
AAAGAAAAAGGAAUGAAAAU------AAAAACCGAACUUAAAAGCAACUUUUCAGCUCAUGUAAGUGCAAGUGCGAGAGUGUGUGUAUGUGCACGAAAAUAUUUUCAAUUAC
.............(((((((------(......((.((.(((((...))))).)).)).((((.(((((.(..(....)..).))))).))))......))))))))..... ( -20.60)
>DroSec_CAF1 66774 106 - 1
AAAGAAAA------GAAAGAAAGAGAAAAAACCGAACUUAAAAGCAACUUUUCAGCUCAUGUAAGUGCAAGUGCGAGAGUGUGCGAAUGUGCACGAAAAUAUUUUCAAUUAC
........------........(((((......((.((.(((((...))))).)).))......(((((..((((......))))....))))).......)))))...... ( -16.50)
>DroSim_CAF1 47030 100 - 1
AAAGAAAA------GAAAGA------AAAAGCCGAACUUAAAAGCAACUUUUCAGCUCAUGUAAGUGCAAGUGCGAGAGUGUGCGAAUGUGCACGAAAAUAUUUUCAAUUAC
........------....((------(((.((...........))...(((((.((((.((((........)))).))))(((((....))))))))))..)))))...... ( -16.90)
>DroEre_CAF1 64599 84 - 1
--------------AAAAAU------AAAAA--------AAAUCCAACUUUCUAGCGCAUGCAAGUGCAAGUGCGAGAGUGUGUGUAUGUGCACGAAAAUAUUUUCAAUUAC
--------------.(((((------(....--------.......((((((..((((.(((....))).))))))))))((((......)))).....))))))....... ( -19.00)
>consensus
AAAGAAAA______GAAAAA______AAAAACCGAACUUAAAAGCAACUUUUCAGCUCAUGUAAGUGCAAGUGCGAGAGUGUGCGAAUGUGCACGAAAAUAUUUUCAAUUAC
..............(((((...........................((((((..((.(.(((....))).).))))))))((((......)))).......)))))...... (-14.05 = -13.43 +  -0.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:41:55 2006