Locus 7896

Sequence ID X_DroMel_CAF1
Location 19,676,407 – 19,676,534
Length 127
Max. P 0.805040
window12953 window12954

overview

Window 3

Location 19,676,407 – 19,676,500
Length 93
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 88.78
Mean single sequence MFE -19.88
Consensus MFE -17.16
Energy contribution -17.32
Covariance contribution 0.16
Combinations/Pair 1.06
Mean z-score -1.54
Structure conservation index 0.86
SVM decision value 0.63
SVM RNA-class probability 0.805040
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19676407 93 + 22224390
UCUGUACAAUAUAAUCAACAAUAAAUCGGAACCGAGGUUUCGCCCCUUUU-UUUUCGGGGCAACUGCUGCUACGCAUUCAGGCCU------AUA----------CCCAUA
...........................((.....((((...(((((....-.....)))))..(((.(((...)))..)))))))------...----------.))... ( -19.20)
>DroSec_CAF1 50374 99 + 1
CCUGUACAAUAUAAUCAACAAUAAAUCGGAUCCGAGGUUUCGCCCCUAUU-UUUUCGGGGCAACUGCUGCUACGCAUUCAGGCCCGUAUCCAUG----------CCCAUA
...........................((((.((.(((...(((((....-.....)))))..(((.(((...)))..)))))))).))))...----------...... ( -23.90)
>DroSim_CAF1 37896 99 + 1
CCUGUACAAUAUAAUCAACAAUAAAUCGGAUCCGAGGUUUCGCCCCUUUU-UUUUCGGGGCAACUGCUGCUACGCAUUCAGGCCCAUAUCCAUA----------CCCAUA
...........................((((..(.(((...(((((....-.....)))))..(((.(((...)))..)))))))..))))...----------...... ( -20.50)
>DroEre_CAF1 61594 97 + 1
CCUGUACAA--UAAUCAACAAUAAAUCGGAUCCGAGGUUUCGCCCCUUUU-UUUUCGGGGCAACUGCUGCUACGCAUUCAUACCCAUACCCAUA----------CCCAUA
.........--..............(((....)))(((...(((((....-.....)))))...(((......))).....)))..........----------...... ( -16.40)
>DroYak_CAF1 63672 110 + 1
CCUGUACAAUAUAAUCAACAAUAAAUCGGAUCCGAGGUUUCGCCCCUUUUUUUUUCGGGGCAACUGCUGCUACGCAUUCAUACCCAUAACCAUACCUACAUCUACCCAUA
..((((...................(((....)))((((..(((((..........)))))...(((......)))...........)))).....)))).......... ( -19.40)
>consensus
CCUGUACAAUAUAAUCAACAAUAAAUCGGAUCCGAGGUUUCGCCCCUUUU_UUUUCGGGGCAACUGCUGCUACGCAUUCAGGCCCAUAUCCAUA__________CCCAUA
.........................(((....)))(((((.(((((..........)))))...(((......)))...))))).......................... (-17.16 = -17.32 +   0.16)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,676,441 – 19,676,534
Length 93
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 85.86
Mean single sequence MFE -26.68
Consensus MFE -19.42
Energy contribution -19.54
Covariance contribution 0.12
Combinations/Pair 1.11
Mean z-score -1.95
Structure conservation index 0.73
SVM decision value 0.53
SVM RNA-class probability 0.770493
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19676441 93 + 22224390
AGGUUUCGCCCCUUUU-UUUUCGGGGCAACUGCUGCUACGCAUUCAGGCCU------AUA----------CCCAUACCCAUCGCG-----AUGCCCAUAUUGC-AGGGGAACAUCU
((((...(((((....-.....)))))..(((.(((...)))..)))))))------...----------......(((...(((-----(((....))))))-..)))....... ( -26.30)
>DroSec_CAF1 50408 100 + 1
AGGUUUCGCCCCUAUU-UUUUCGGGGCAACUGCUGCUACGCAUUCAGGCCCGUAUCCAUG----------CCCAUACCCAUCGCG-----AUGCCCAUAUUGCCAGGGGAACCUCU
(((((...(((((...-......(((((..(((......)))....((.......)).))----------))).........(((-----(((....)))))).)))))))))).. ( -27.40)
>DroSim_CAF1 37930 100 + 1
AGGUUUCGCCCCUUUU-UUUUCGGGGCAACUGCUGCUACGCAUUCAGGCCCAUAUCCAUA----------CCCAUACCCAUCGCG-----AUGCCCAUAUUGCCAGGGGAACCUCU
((((((.(((((....-.....)))))..(((.(((...)))..))).............----------......(((...(((-----(((....))))))..))))))))).. ( -26.30)
>DroEre_CAF1 61626 99 + 1
AGGUUUCGCCCCUUUU-UUUUCGGGGCAACUGCUGCUACGCAUUCAUACCCAUACCCAUA----------CCCAUACCCAUCGCG-----AUGCCCAUAUCGC-UGAGGAACCUCU
((((((((((((....-.....)))))...(((......)))..................----------..........(((((-----(((....))))))-.))))))))).. ( -26.20)
>DroYak_CAF1 63706 115 + 1
AGGUUUCGCCCCUUUUUUUUUCGGGGCAACUGCUGCUACGCAUUCAUACCCAUAACCAUACCUACAUCUACCCAUACCCAUUGCGAUUCGAUGCCCAUAUCGC-UGGGGAACCUCU
((((((.(((((..........)))))...(((......)))..................................((((..(((((..(.....)..)))))-)))))))))).. ( -27.20)
>consensus
AGGUUUCGCCCCUUUU_UUUUCGGGGCAACUGCUGCUACGCAUUCAGGCCCAUAUCCAUA__________CCCAUACCCAUCGCG_____AUGCCCAUAUUGC_AGGGGAACCUCU
.(((((.(((((..........)))))...(((......)))...)))))..........................(((...(((...............)))...)))....... (-19.42 = -19.54 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:50:14 2006