Locus 8478

Sequence ID	X_DroMel_CAF1
Location	21,043,491 – 21,043,677
Length	186
Max. P	0.954275

overview

Window 8

Location	21,043,491 – 21,043,606
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.19
Mean single sequence MFE	-42.74
Consensus MFE	-30.67
Energy contribution	-30.07
Covariance contribution	-0.60
Combinations/Pair	1.11
Mean z-score	-1.93
Structure conservation index	0.72
SVM decision value	0.33
SVM RNA-class probability	0.690657
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21043491 115 - 22224390
GGCCUCCUUCUCCUGUUCGGCCAACUUCUCGAUAAGCGUUUAAUUGCUGGUCGAGGACCCAAUGU----CCCAUCUUCUGGGAUGCCUGGGAUUUUGGGUGGCCCAGAACG-GUCUGUUA
............(((((((((((..((((((((.((((......)))).))))))))(((((.((----(((((((....)))....)))))).))))))))))..)))))-)....... ( -46.00)
>DroSec_CAF1 13931 113 - 1
GGCCUCCUUCUCCUCUUCGGCCAACUUCUCGAUAAGCGUUUAAUUGCUGGUCGAGGACCCAACGU----CCCGUCUUCUGGGAUGCCCG--AUAUUGGGUGGCACAGAACG-GGCUGUUG
((((..............))))...((((((((.((((......)))).))))))))..(((((.----(((((..((((...((((((--....))))))...)))))))-)).))))) ( -44.94)
>DroSim_CAF1 14449 114 - 1
GGCCUCCUUCUCCUCUUCGGCCAACUUCUCGAUAAGCGUUUAAUUGCUGGUCGAGGACCCAACGU----CCCGUCUUCUGGGAUGCCCG--AUAUUGAGUGGCACAGAACGAGGCUGUUG
((((((.((((((((.((((.....((((((((.((((......)))).)))))))).....(((----((((.....))))))).)))--)....))).)....)))).)))))).... ( -42.60)
>DroEre_CAF1 14679 115 - 1
GGCCUCCUUCUCCUCUUCGGCCAACUUCUCGAUAAGCGUUUAAUUGCUGGUCGAGGACCCAACGUCCGUCCUGUCUUCUGGGAUGCCCG--AUUGUGGGUGGUG---AACUGGGCGGUUG
.((((..(((.((.............(((((((.((((......)))).)))))))(((((.((..((((((.......))))))..))--....))))))).)---))..))))..... ( -41.80)
>DroYak_CAF1 15886 109 - 1
GGCCUCCUUCUCCUCUUUGGCCAACUUCUCGAUAAGCGUUUAAUUGCUGGUCGAGGACCCAACGU----CCUGUCUUCUGGGAUGCCCG--AUUGUGGGUGGUU-----CGGGGCUGUGA
((((..............))))...((((((((.((((......)))).))))))))((((((((----(((.......)))))(((((--....))))).)))-----.)))....... ( -38.34)
>consensus
GGCCUCCUUCUCCUCUUCGGCCAACUUCUCGAUAAGCGUUUAAUUGCUGGUCGAGGACCCAACGU____CCCGUCUUCUGGGAUGCCCG__AUUUUGGGUGGCACAGAACG_GGCUGUUG
.(((.(((..........(((....((((((((.((((......)))).))))))))(((((((.......)))....))))..))).........))).)))................. (-30.67 = -30.07 +  -0.60)

alignment

secondary structure

dotplot

Window 9

Location	21,043,566 – 21,043,677
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.23
Mean single sequence MFE	-34.61
Consensus MFE	-29.78
Energy contribution	-30.46
Covariance contribution	0.68
Combinations/Pair	1.04
Mean z-score	-1.72
Structure conservation index	0.86
SVM decision value	1.44
SVM RNA-class probability	0.954275
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21043566 111 + 22224390
AACGCUUAUCGAGAAGUUGGCCGAACAGGAGAAGGAGGCCGGCCAGCGGAGAG---------GCAGGGCAGAAAACAGACGACAAUGAGCUGCCUUGCAUAUAAUUGAGGUUAUGGCCGA
........((((...((((((((..(..........)..))))))))......---------(((((((((....((........))..)))))))))......))))(((....))).. ( -36.20)
>DroSec_CAF1 14004 107 + 1
AACGCUUAUCGAGAAGUUGGCCGAAGAGGAGAAGGAGGCCGGCCAGCGCAGAG---------GCAGGGCGGAAAACAGACGACAAUGAGC----UUGCAUAUAAUUGAGGUUAUGGCCGA
..(((((........((((((((................))))))))((....---------)).))))).........((.((...(((----((.((......))))))).))..)). ( -25.99)
>DroSim_CAF1 14523 111 + 1
AACGCUUAUCGAGAAGUUGGCCGAAGAGGAGAAGGAGGCCGGCCAGCGCAGAG---------GCAGGGCGGAAAACAGACGACAAUGAGCUGCCUUGCAUAUAAUUGAGGUUAUGGCCGA
........((((...((((((((................))))))))......---------(((((((((....((........))..)))))))))......))))(((....))).. ( -34.19)
>DroEre_CAF1 14754 119 + 1
AACGCUUAUCGAGAAGUUGGCCGAAGAGGAGAAGGAGGCCGGCCAGGGCAG-GCAGUGCAGUGCAGGGCAGAAAACAGACGACAAUGAGCUGCCUUGCAUAUAAUUGAGGUUAUGGCCGA
...((((......)))).((((..............))))(((((..((..-.((((...(((((((((((....((........))..)))))))))))...))))..))..))))).. ( -43.74)
>DroYak_CAF1 15955 110 + 1
AACGCUUAUCGAGAAGUUGGCCAAAGAGGAGAAGGAGGCCGGCCAGGGUGG-G---------GCAGGGCAGAAAACAGACGACAAUGAGCUGCCUUGCAUAUAAUUGAGGUUAUGGCCGA
....((((((.....(((((((..............)))))))...)))))-)---------(((((((((....((........))..)))))))))..........(((....))).. ( -32.94)
>consensus
AACGCUUAUCGAGAAGUUGGCCGAAGAGGAGAAGGAGGCCGGCCAGCGCAGAG_________GCAGGGCAGAAAACAGACGACAAUGAGCUGCCUUGCAUAUAAUUGAGGUUAUGGCCGA
...((((......)))).((((..............))))((((..................(((((((((....((........))..)))))))))..(((((....))))))))).. (-29.78 = -30.46 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:05:09 2006