Locus 3356

Sequence ID	2R_DroMel_CAF1
Location	11,380,832 – 11,380,987
Length	155
Max. P	0.990442

overview

Window 5

Location	11,380,832 – 11,380,947
Length	115
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.51
Mean single sequence MFE	-43.29
Consensus MFE	-36.73
Energy contribution	-35.66
Covariance contribution	-1.06
Combinations/Pair	1.20
Mean z-score	-2.87
Structure conservation index	0.85
SVM decision value	2.21
SVM RNA-class probability	0.990442
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11380832 115 + 20766785
GUCUAAUGCGAU-----UUACUUACCAAAUUGUAUAUUCGCGUGCCUGAUUUCUUUGGAGACAUCUCACCGGCAGCCACAGCCCCCGCAGAAGCGGCAGGAUCUCCGCUGCUUCCAGGCA
.....((((((.-----.(((..........)))...))))))(((((.........(((....)))..(((..((....))..)))..((((((((.((....))))))))))))))). ( -39.20)
>DroSec_CAF1 8093 115 + 1
UUCCAAUGCGAU-----UUACUUACCAAAUUGCAUAUUCGUGAGCCGGAUUUCUUUGGAGACAUCUCGCCGGCAGCCACAGCAGCCGCAGAAGCGGCAGGAUCUCCGCUGCUUCCCGGCA
.....(((((((-----((.......)))))))))....(((.(((((.......((....)).....)))))...)))....((((..((((((((.((....)))))))))).)))). ( -45.30)
>DroSim_CAF1 9516 115 + 1
UUCUAAUGCGAU-----UUACUUACCAAAUUGCAUAUUCGUGUGCCGGAUUUCUUUGGAGACAUCUCGCCGGCAGCCACAGCAGCCGCAGAAGCGGCAGGAUCUCCGCUGCUUCCCGGCA
.....(((((((-----((.......)))))))))....(((((((((.......((....)).....))))))..)))....((((..((((((((.((....)))))))))).)))). ( -46.80)
>DroEre_CAF1 8239 120 + 1
UCCUUAUGCGAUUAAAUUUGCUUACCAAGUUGCAUAUUCGUGUGCCAGAUUUCUUCGGCGACGUCUCCCCGGCAGCCACAGCAGCCGCAGAGGAGGCAGGAUCGCCGCUGCUUCCUGGCA
....(((((((((..............)))))))))......((((((....(..((((((.(((((((((((.((....)).))))..).))))))....))))))..)....)))))) ( -41.84)
>consensus
UUCUAAUGCGAU_____UUACUUACCAAAUUGCAUAUUCGUGUGCCGGAUUUCUUUGGAGACAUCUCGCCGGCAGCCACAGCAGCCGCAGAAGCGGCAGGAUCUCCGCUGCUUCCCGGCA
.....(((((((................)))))))........(((((.......((....))......((((.((....)).))))..((((((((.((....))))))))))))))). (-36.73 = -35.66 +  -1.06)

alignment

secondary structure

dotplot

Window 6

Location	11,380,867 – 11,380,987
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.53
Mean single sequence MFE	-53.55
Consensus MFE	-46.49
Energy contribution	-48.17
Covariance contribution	1.69
Combinations/Pair	1.10
Mean z-score	-2.00
Structure conservation index	0.87
SVM decision value	1.15
SVM RNA-class probability	0.922915
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11380867 120 + 20766785
CGUGCCUGAUUUCUUUGGAGACAUCUCACCGGCAGCCACAGCCCCCGCAGAAGCGGCAGGAUCUCCGCUGCUUCCAGGCAGUUGGGUAGAGGGUACAGCUUCCAAGGGUACAUCAGGCGG
..((((((((.(((((((((((.((((.(((((.(((...((....)).((((((((.((....))))))))))..))).)))))...)))))).....)))))))))...)))))))). ( -52.60)
>DroSec_CAF1 8128 120 + 1
UGAGCCGGAUUUCUUUGGAGACAUCUCGCCGGCAGCCACAGCAGCCGCAGAAGCGGCAGGAUCUCCGCUGCUUCCCGGCAGUUGGGUAGAGGGUACAGUUUCCAGGGGUAUAUCAGGCGG
...(((.(((.(((((((((((.....(((..(.(((.((((.((((..((((((((.((....)))))))))).)))).))))))).)..)))...)))))))))))...))).))).. ( -56.90)
>DroSim_CAF1 9551 120 + 1
UGUGCCGGAUUUCUUUGGAGACAUCUCGCCGGCAGCCACAGCAGCCGCAGAAGCGGCAGGAUCUCCGCUGCUUCCCGGCAGUUGGGUAGAGGGUACAGUUUCCAGGGGUAUAUCAGGCGG
..((((.(((.(((((((((((.....(((..(.(((.((((.((((..((((((((.((....)))))))))).)))).))))))).)..)))...)))))))))))...))).)))). ( -56.90)
>DroEre_CAF1 8279 120 + 1
UGUGCCAGAUUUCUUCGGCGACGUCUCCCCGGCAGCCACAGCAGCCGCAGAGGAGGCAGGAUCGCCGCUGCUUCCUGGCAGUUGGGUAGAGGGUACAGCUUCCAUGGGCACAUCAGGCGG
((((((.((.....))(((..(.(((.((((((.(((...((....))..(((((((((........)))))))))))).)))))).))).).....)))......))))))........ ( -47.80)
>consensus
UGUGCCGGAUUUCUUUGGAGACAUCUCGCCGGCAGCCACAGCAGCCGCAGAAGCGGCAGGAUCUCCGCUGCUUCCCGGCAGUUGGGUAGAGGGUACAGCUUCCAGGGGUACAUCAGGCGG
...(((.(((.(((((((((((.....(((..(.(((.((((.((((..((((((((.((....)))))))))).)))).))))))).)..)))...)))))))))))...))).))).. (-46.49 = -48.17 +   1.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:32 2006