Locus 6505

Sequence ID 2L_DroMel_CAF1
Location 18,290,462 – 18,290,552
Length 90
Max. P 0.889484
window10381 window10382

overview

Window 1

Location 18,290,462 – 18,290,552
Length 90
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 66.52
Mean single sequence MFE -25.83
Consensus MFE -12.89
Energy contribution -13.83
Covariance contribution 0.95
Combinations/Pair 1.24
Mean z-score -1.72
Structure conservation index 0.50
SVM decision value 0.96
SVM RNA-class probability 0.889484
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18290462 90 + 22407834
GGACACUUGCAGGAUCCACUCCUGCGAAGGUAAACUGCACGCGUCUGA----AAACA---AAAGCAA--------GCAUGUUGCCGCUAGGUGGCGACACCGUGC
...(((((((((((.....)))))))).(((....(((..((...((.----...))---...))..--------))).((((((((...)))))))))))))). ( -31.50)
>DroSec_CAF1 134235 74 + 1
GGACACUUGCAGGAUCCACUCCUGCAAAGGUAA--------------------AACA---ACAGCAA--------GCAUGUUGCCGCUAGGUGGCGACACCGUGC
..((..((((((((.....))))))))..))..--------------------....---...(((.--------...(((((((((...)))))))))...))) ( -27.50)
>DroSim_CAF1 141250 74 + 1
GGACACUUGCAGGAUCCACUCCUGCAAAGGUAA--------------------AACA---ACAGCAA--------GCAUGUUGCCGCUAGGUGGCGACACCGUGC
..((..((((((((.....))))))))..))..--------------------....---...(((.--------...(((((((((...)))))))))...))) ( -27.50)
>DroEre_CAF1 135442 90 + 1
AAACACUUUCAGGGUUCCCUCCUGCAAGAGUAAGCUCCAUGCAUCUGA----GAACA---ACAACAG--------ACACGUUGCCGCUAGGUGGCGACACCGUAC
...........((((((.(...((((.(((....)))..))))...).----)))).---.......--------....((((((((...)))))))).)).... ( -24.90)
>DroAna_CAF1 124214 94 + 1
GGACAGUUUUAGUGUCAGGACCUGUAACGGUAAAUUGCAUUCACAGGAGCAGGAACAGGAACAACUA--------GCA---CGCCGCUAGGUGGCGACACCGUAC
...........(((((.(..(((((..(.((...(((......)))..)).)..)))))..).....--------((.---((((....)))))))))))..... ( -25.80)
>DroPer_CAF1 156951 97 + 1
GGACAGUUUUAGUGUCAAGCCCUGUAACGGUAAAUUGCAUACGAAAAA-----AAAA---ACAAUAAAGAAUAGAAAAAGUCACCGCUCGAGGGCGACACCGUAC
...........(((((..(((((....((((...(((....)))....-----....---.............((.....))))))....))))))))))..... ( -17.80)
>consensus
GGACACUUGCAGGAUCCACUCCUGCAAAGGUAAA_UGCAU_C____GA_____AACA___ACAACAA________GCAUGUUGCCGCUAGGUGGCGACACCGUAC
((((.....(((((.....))))).....))................................................((((((((...)))))))).)).... (-12.89 = -13.83 +   0.95)

alignment

Postscript

secondary structure

Postscript

dotplot

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Window 2

Location 18,290,462 – 18,290,552
Length 90
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 66.52
Mean single sequence MFE -28.00
Consensus MFE -11.57
Energy contribution -11.47
Covariance contribution -0.11
Combinations/Pair 1.37
Mean z-score -1.73
Structure conservation index 0.41
SVM decision value 0.50
SVM RNA-class probability 0.758785
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18290462 90 - 22407834
GCACGGUGUCGCCACCUAGCGGCAACAUGC--------UUGCUUU---UGUUU----UCAGACGCGUGCAGUUUACCUUCGCAGGAGUGGAUCCUGCAAGUGUCC
((((((((((((......)))))(((.(((--------.(((.((---((...----.)))).))).)))))).)))...((((((.....))))))..)))).. ( -33.70)
>DroSec_CAF1 134235 74 - 1
GCACGGUGUCGCCACCUAGCGGCAACAUGC--------UUGCUGU---UGUU--------------------UUACCUUUGCAGGAGUGGAUCCUGCAAGUGUCC
((((((((....))))(((((((((.....--------)))))))---))..--------------------......((((((((.....)))))))))))).. ( -28.90)
>DroSim_CAF1 141250 74 - 1
GCACGGUGUCGCCACCUAGCGGCAACAUGC--------UUGCUGU---UGUU--------------------UUACCUUUGCAGGAGUGGAUCCUGCAAGUGUCC
((((((((....))))(((((((((.....--------)))))))---))..--------------------......((((((((.....)))))))))))).. ( -28.90)
>DroEre_CAF1 135442 90 - 1
GUACGGUGUCGCCACCUAGCGGCAACGUGU--------CUGUUGU---UGUUC----UCAGAUGCAUGGAGCUUACUCUUGCAGGAGGGAACCCUGAAAGUGUUU
.((((.((((((......)))))).)))).--------.......---.((((----((...((((.((((....))))))))...))))))............. ( -27.10)
>DroAna_CAF1 124214 94 - 1
GUACGGUGUCGCCACCUAGCGGCG---UGC--------UAGUUGUUCCUGUUCCUGCUCCUGUGAAUGCAAUUUACCGUUACAGGUCCUGACACUAAAACUGUCC
....(((((((..((((.(..(((---.(.--------.((((((....(((((.......).))))))))))..))))..)))))..))))))).......... ( -23.80)
>DroPer_CAF1 156951 97 - 1
GUACGGUGUCGCCCUCGAGCGGUGACUUUUUCUAUUCUUUAUUGU---UUUU-----UUUUUCGUAUGCAAUUUACCGUUACAGGGCUUGACACUAAAACUGUCC
....(((((((((((..((((((((...............(((((---....-----..........)))))))))))))..)))))..)))))).......... ( -25.60)
>consensus
GCACGGUGUCGCCACCUAGCGGCAACAUGC________UUGCUGU___UGUU_____UC____G_AUGCA_UUUACCUUUGCAGGAGUGGACCCUGAAAGUGUCC
(((...((((((......))))))...)))............................................((.(((.(((((.....))))).))).)).. (-11.57 = -11.47 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:49 2006