Locus 6065

Sequence ID 3L_DroMel_CAF1
Location 16,144,619 – 16,144,774
Length 155
Max. P 0.568224
window9732 window9733

overview

Window 2

Location 16,144,619 – 16,144,738
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.03
Mean single sequence MFE -32.88
Consensus MFE -28.28
Energy contribution -28.46
Covariance contribution 0.19
Combinations/Pair 1.15
Mean z-score -1.39
Structure conservation index 0.86
SVM decision value 0.07
SVM RNA-class probability 0.568224
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16144619 119 - 23771897
UGAACCCCUUCUCCUGCCGGCAAGCAAAAAUAGGCGGCUGACGUCAAAAUGCAAGCCAGACGGGAAAAA-GGGGAGGGGUGAGUGGGGAAAGAAACCGAAAAAAAACCGAGUUGGAGUCG
....((((((.((((((.(((..(((......((((.....))))....)))..))).).)))))..))-)))).((..(...(.((........)).)....)..))............ ( -34.50)
>DroSec_CAF1 6657 115 - 1
UGAGCCCCUUCUGCUGC-----AACAAAAAUAGGCGGCUGACGUCAAAAUGCAAGCCAGACGGGAAAUGGGGGGAGGGGUGAGUGGGGAACGAAACCGAAAAAAAACCAAGUUGGAGUCG
...(((((((((.((((-----...........))((((..(((....)))..))))...........)).)))))))))..........(((..((((............))))..))) ( -30.10)
>DroSim_CAF1 7455 113 - 1
UGAACCCCUUCUCCUGC-----AACAAAAAUAGGCGGCUGACGUCAAAAUGCAAGCCAGACGGGAAAUGGGGGGAGGGGUGAGUGGGGAACGAAACCGAAA--AAACCAAGUUGGAGUCG
...((((((((((((((-----...........))((((..(((....)))..))))...........))))))))))))..........(((..((((..--........))))..))) ( -33.80)
>DroEre_CAF1 6215 111 - 1
UUGACCCCUCCCCCUGC-----AACAAAAAUAGGCGGCUGACGUCAAAAUGCAAGCCAGACGGGUAAAA-AGGGAGGGGUGUGUGGGGAACGAAACCGAG---AAACCAAGUUGGAGUCG
...(((((((((((((.-----........)))).((((..(((....)))..))))............-.))))))))).....((........))..(---(..((.....))..)). ( -33.10)
>consensus
UGAACCCCUUCUCCUGC_____AACAAAAAUAGGCGGCUGACGUCAAAAUGCAAGCCAGACGGGAAAAA_GGGGAGGGGUGAGUGGGGAACGAAACCGAAA__AAACCAAGUUGGAGUCG
...((((((((((((((................))((((..(((....)))..))))...........))))))))))))...........((..((((............))))..)). (-28.28 = -28.46 +   0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 16,144,659 – 16,144,774
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.64
Mean single sequence MFE -28.35
Consensus MFE -24.76
Energy contribution -24.57
Covariance contribution -0.19
Combinations/Pair 1.18
Mean z-score -1.24
Structure conservation index 0.87
SVM decision value -0.01
SVM RNA-class probability 0.528155
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16144659 115 + 23771897
ACCCCUCCCC-UUUUUCCCGUCUGGCUUGCAUUUUGACGUCAGCCGCCUAUUUUUGCUUGCCGGCAGGAGAAGGGGUUCAAAAGAAUCGAGCAGACAUAAAAAAAC----ACGAGAAAAA
....(((.((-(((((((.(.(((((..(((....(.((.....)).)......)))..)))))).)))))))))((((.........))))..............----..)))..... ( -30.70)
>DroSec_CAF1 6697 115 + 1
ACCCCUCCCCCCAUUUCCCGUCUGGCUUGCAUUUUGACGUCAGCCGCCUAUUUUUGUU-----GCAGCAGAAGGGGCUCAAAAGAAUCGGCCAGACAUUUAAAAAAAGUAAAAAAAAAAA
...................((((((((....((((((.....(((.(((...(((((.-----...))))))))))))))))).....))))))))........................ ( -28.00)
>DroSim_CAF1 7493 103 + 1
ACCCCUCCCCCCAUUUCCCGUCUGGCUUGCAUUUUGACGUCAGCCGCCUAUUUUUGUU-----GCAGGAGAAGGGGUUCAAAAGAAUCGACCAGACAU------------AAAAAAAAUA
...................((((((.(((..((((((.....(((.(((.((((((..-----.)))))).))))))))))))....)))))))))..------------.......... ( -23.20)
>DroEre_CAF1 6252 107 + 1
ACCCCUCCCU-UUUUACCCGUCUGGCUUGCAUUUUGACGUCAGCCGCCUAUUUUUGUU-----GCAGGGGGAGGGGUCAAAAGGAAUCGACCAGACAUAAAAAGGC----AACCAAA---
.......(((-(((((...((((((.(((..(((((((.((..((.(((.........-----..))).))..))))))))).....))))))))).)))))))).----.......--- ( -31.50)
>consensus
ACCCCUCCCC_CAUUUCCCGUCUGGCUUGCAUUUUGACGUCAGCCGCCUAUUUUUGUU_____GCAGGAGAAGGGGUUCAAAAGAAUCGACCAGACAUAAAAAAAC____AAAAAAAAAA
...................((((((.(((.(((((......((((.(((.(((((((......))))))).)))))))....))))))))))))))........................ (-24.76 = -24.57 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:57 2006