Locus 5342

Sequence ID X_DroMel_CAF1
Location 13,929,966 – 13,930,096
Length 130
Max. P 0.563588
window8656 window8657

overview

Window 6

Location 13,929,966 – 13,930,060
Length 94
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.09
Mean single sequence MFE -25.40
Consensus MFE -15.31
Energy contribution -15.91
Covariance contribution 0.60
Combinations/Pair 1.10
Mean z-score -1.84
Structure conservation index 0.60
SVM decision value 0.06
SVM RNA-class probability 0.563588
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13929966 94 + 22224390
CCCCAAAGCAUAGCACC------AAAAAAAAGGGACCCCC--------CCUUUGGCAGAGGCUUUCAUUUCGUCAGGAUGGAAAUGUGAAUCUCUCUGCUUUCUUUUU------------
.................------.....((((((.....)--------)))))((((((((..((((((((((....)))))...)))))..))))))))........------------ ( -24.80)
>DroSec_CAF1 10008 90 + 1
CCCCAAAGCAUCGCAGC------AAAAA-AAGGGACC-CC--------CCUUUGGCAGAGGCUUUCAUUUCGUCAGGAUGGAAAUGUGAAUCCCUCUGCUUU--UUUU------------
.......((......))------....(-(((((...-.)--------)))))((((((((..((((((((((....)))))...)))))..))))))))..--....------------ ( -28.60)
>DroSim_CAF1 12588 89 + 1
CCCCAAAGCAUCGCAGC------AAAAA-AAGGGACC-CC--------CCUUUGGCAGAGGCUUUCAUUUCGUCAGGAUGGAAAUGUGAAUCCCUCUGCUUU--U-UU------------
.......((......))------....(-(((((...-.)--------)))))((((((((..((((((((((....)))))...)))))..))))))))..--.-..------------ ( -28.60)
>DroEre_CAF1 11734 98 + 1
CCCCAAAGCAGCGCAGC------AAAAAAAUGGGAGC-CCUCCCCACUCCUUUGGCAGAGGCUUUCAUUUCGUCAGGAUGGAAAUGUGAAUCUCCCGCCUUU--U-UC------------
.......((......))------....(((((..(((-(.((.(((......)))..))))))..)))))....(((..(((.((....)).)))..)))..--.-..------------ ( -22.50)
>DroYak_CAF1 12064 108 + 1
CCCCAAAGCAUCGCAGCGCAAAAAAAAAAAAGGGACC-CC--------CCUUUGGCAGAGGCUUUCAUUUCGUCAGAAUGGAAAUGUGAAUCUCCCUUUUUU--U-UUUCCUUUAACCCC
.......((......))....((((((((((((((..-..--------((((.....)))).((((((((.....)))))))).........))))))))))--)-)))........... ( -22.50)
>consensus
CCCCAAAGCAUCGCAGC______AAAAAAAAGGGACC_CC________CCUUUGGCAGAGGCUUUCAUUUCGUCAGGAUGGAAAUGUGAAUCUCUCUGCUUU__U_UU____________
.(((...........................)))...................((((((((..((((((((((....)))))...)))))..)))))))).................... (-15.31 = -15.91 +   0.60)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,930,000 – 13,930,096
Length 96
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.29
Mean single sequence MFE -20.40
Consensus MFE -16.40
Energy contribution -16.56
Covariance contribution 0.16
Combinations/Pair 1.05
Mean z-score -1.46
Structure conservation index 0.80
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13930000 96 + 22224390
--------CCUUUGGCAGAGGCUUUCAUUUCGUCAGGAUGGAAAUGUGAAUCUCUCUGCUUUCUUUUU----------------UCCCCCAACCAGCCAGCAUUGCCAAAAAAUUUCCAA
--------..(((((((((((..((((((((((....)))))...)))))..))))((((..((....----------------..........))..)))).))))))).......... ( -20.04)
>DroSec_CAF1 10040 94 + 1
--------CCUUUGGCAGAGGCUUUCAUUUCGUCAGGAUGGAAAUGUGAAUCCCUCUGCUUU--UUUU----------------UCCCCCAACCAGCCAGCAUUGCCAAAAAAUCUCCAA
--------..(((((((((((..((((((((((....)))))...)))))..))))((((..--....----------------..............)))).))))))).......... ( -21.85)
>DroSim_CAF1 12620 93 + 1
--------CCUUUGGCAGAGGCUUUCAUUUCGUCAGGAUGGAAAUGUGAAUCCCUCUGCUUU--U-UU----------------UCCCCCAACCAGCCAGCAUUGCCAAAAAAUCUCCAA
--------..(((((((((((..((((((((((....)))))...)))))..))))((((..--.-..----------------..............)))).))))))).......... ( -21.91)
>DroEre_CAF1 11767 103 + 1
UCCCCACUCCUUUGGCAGAGGCUUUCAUUUCGUCAGGAUGGAAAUGUGAAUCUCCCGCCUUU--U-UC--------------CCACCCCCAACCAGCCAGCAUUGCCAAAAAAUCUCCAG
..........((((((((.((((.....(((....))).(((((.(((.......)))...)--)-))--------------)...........))))....)))))))).......... ( -18.60)
>DroYak_CAF1 12103 109 + 1
--------CCUUUGGCAGAGGCUUUCAUUUCGUCAGAAUGGAAAUGUGAAUCUCCCUUUUUU--U-UUUCCUUUAACCCCCACCACCCCAAGCCAGCGAGCAUUGCCAAAAAAUCUCCAA
--------..((((((((.(((((....(((....))).(((((...(((........))).--.-)))))..................))))).(....).)))))))).......... ( -19.60)
>consensus
________CCUUUGGCAGAGGCUUUCAUUUCGUCAGGAUGGAAAUGUGAAUCUCUCUGCUUU__U_UU________________UCCCCCAACCAGCCAGCAUUGCCAAAAAAUCUCCAA
..........(((((((((((..((((((((((....)))))...)))))..)))).......................................(....)..))))))).......... (-16.40 = -16.56 +   0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:29 2006