Locus 3778

Sequence ID	X_DroMel_CAF1
Location	10,010,006 – 10,010,136
Length	130
Max. P	0.820955

overview

Window 5

Location	10,010,006 – 10,010,100
Length	94
Sequences	4
Columns	108
Reading direction	forward
Mean pairwise identity	88.76
Mean single sequence MFE	-27.57
Consensus MFE	-25.06
Energy contribution	-24.88
Covariance contribution	-0.19
Combinations/Pair	1.07
Mean z-score	-1.61
Structure conservation index	0.91
SVM decision value	0.68
SVM RNA-class probability	0.820955
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10010006 94 + 22224390
ACACGCACCCUGCUCAACUUUGCCAUCAUUUGUGGUUUUGCAUGUUCCGCGUGCAGCACAUCGCCAAGUGCUGGCAAUAUGGCCACGC-CCCCCC-------------
....((.....((.((...((((((.((((((((((.(((((((.....)))))))...)))).)))))).))))))..))))...))-......------------- ( -27.50)
>DroSec_CAF1 15433 95 + 1
ACACGCACCCUGCACAACUUUGCUAUCAUUUGUGGUUUUGCAUGUGCCGCGUGCAGCACAUCGCCAAGUGCUGGCAAUAUGGCCACGCACCCCCC-------------
....((((..((((.((((..((........)))))).)))).)))).(((((((((((........))))))((......))))))).......------------- ( -29.70)
>DroEre_CAF1 16048 106 + 1
ACACGCACCCUGCUCAACUUUGCUAUCAUUUGUGGUUUUGCAUGUGCCGCAUGCAGCACAUCGCCAAGUGCUGGCAAUAUGGCCACGC-CCC-CUCACUCCAUCCGCC
....((.............((((((.((((((((((.(((((((.....)))))))...)))).)))))).))))))...(((...))-)..-............)). ( -26.40)
>DroYak_CAF1 12845 93 + 1
ACACGCACCCUGCUCAACUUUGCUAUCAUUUGUGGUUUUGCAUGUGCCGCAUGCAGCACAACGCCAAGUGCUGGCAAUAUGGCCACGC-CAC-CC-------------
....((.....))......((((((.((((((..((((((((((.....)))))))...)))..)))))).))))))..((((...))-)).-..------------- ( -26.70)
>consensus
ACACGCACCCUGCUCAACUUUGCUAUCAUUUGUGGUUUUGCAUGUGCCGCAUGCAGCACAUCGCCAAGUGCUGGCAAUAUGGCCACGC_CCC_CC_____________
....((.....((.((...((((((.((((((((((.(((((((.....)))))))...)))).)))))).))))))..))))...)).................... (-25.06 = -24.88 +  -0.19)

alignment

secondary structure

dotplot

Window 6

Location	10,010,034 – 10,010,136
Length	102
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	82.76
Mean single sequence MFE	-37.85
Consensus MFE	-23.30
Energy contribution	-24.42
Covariance contribution	1.13
Combinations/Pair	1.06
Mean z-score	-1.84
Structure conservation index	0.62
SVM decision value	0.11
SVM RNA-class probability	0.589475
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10010034 102 - 22224390
GUCGCAGUCUUUUCCUUUUUU-UCGUAGCGGAAAAGA----------------GGGGGG-GCGUGGCCAUAUUGCCAGCACUUGGCGAUGUGCUGCACGCGGAACAUGCAAAACCACAAA
.((((.(((.(..((((((((-(((...)))))))))----------------))..))-))(..((.((((((((((...))))))))))))..)..)))).................. ( -39.90)
>DroSec_CAF1 15461 101 - 1
UUCGCAGUCUUUUC--UUUUU-UCGAAGCGGCAGAGA----------------GGGGGGUGCGUGGCCAUAUUGCCAGCACUUGGCGAUGUGCUGCACGCGGCACAUGCAAAACCACAAA
...(((.(((((((--(((..-(((...))).)))))----------------))))).)))((((....((((((((...))))))))((((((....))))))........))))... ( -37.00)
>DroEre_CAF1 16076 117 - 1
UUCUCAGUCUUUCCUUUUUUUUU-GGAGCGGAAAAGGUCGGGCGGAUGGAGUGAG-GGG-GCGUGGCCAUAUUGCCAGCACUUGGCGAUGUGCUGCAUGCGGCACAUGCAAAACCACAAA
(((((.((((..((((((((...-.....))))))))..)))).)).)))(((.(-...-((((((((((((((((((...))))))))))((.....))))).)))))....))))... ( -41.30)
>DroYak_CAF1 12873 102 - 1
UUCUCAGUCUUUCAUUUUUUUUUCGCAGCGGAAAAGA----------------GG-GUG-GCGUGGCCAUAUUGCCAGCACUUGGCGUUGUGCUGCAUGCGGCACAUGCAAAACCACAAA
............((((((((((((......)))))))----------------))-)))-((((((((....(((.(((((........))))))))...))).)))))........... ( -33.20)
>consensus
UUCGCAGUCUUUCCUUUUUUU_UCGAAGCGGAAAAGA________________GG_GGG_GCGUGGCCAUAUUGCCAGCACUUGGCGAUGUGCUGCACGCGGCACAUGCAAAACCACAAA
................(((((((((...)))))))))...................((..((((((((((((((((((...))))))))))((.....))))).)))))....))..... (-23.30 = -24.42 +   1.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:14 2006