Locus 10038

Sequence ID	3R_DroMel_CAF1
Location	26,887,188 – 26,887,304
Length	116
Max. P	0.901685

overview

Window 8

Location	26,887,188 – 26,887,304
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	65.04
Mean single sequence MFE	-36.44
Consensus MFE	-15.38
Energy contribution	-15.58
Covariance contribution	0.20
Combinations/Pair	1.15
Mean z-score	-1.95
Structure conservation index	0.42
SVM decision value	0.80
SVM RNA-class probability	0.854304
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26887188 116 + 27905053
UAGA---CCCAGUGCUGCCAGAUGGACGAAAAAUAUUUUUGAGCUGCGCCACCUAGCGGAUGAGUUGGCGA-AAGUGGUAUCCAGGUGGCGCCCGAAACAAAAGGUGGCGCCUUAUUUCA
....---....((((..((.......(((((.....)))))....(((((((((...(((((...(.((..-..)).)))))))))))))))...........))..))))......... ( -39.50)
>DroSec_CAF1 95449 108 + 1
UACA---CCCAGUGCUGCCAGAUGGAGGCAAACUACUUGUGAGCUGCGCCACCUAGCGGAUGAGUACGCGAAAAGUGGUACCCAGAUGGCGCCUAAUAUU---------UCUGUAUUUCU
....---...((.((.((((..(((.(((..((.....))..)))..(((((...(((........))).....)))))..)))..))))))))......---------........... ( -29.40)
>DroSim_CAF1 99139 108 + 1
CAGA---CCCAGUGCUGCCAGAUGGAGGCAAACUACUUGUAAGCUGCGCCACCUAGCGGAUGAGUAGGCGAAAAGUGGUACCCAGGUGGCGCCUACAAUU---------UCAGUAUAUCU
....---....(((((((.((.(((.(((..((.....))..)))...))).)).))(((...(((((((..(..(((...)))..)..)))))))...)---------))))))).... ( -31.40)
>DroEre_CAF1 104142 119 + 1
UAACCUGGCCAGUGUUGCCAGAUAGGCGCAAGCUAUUUUGGAAGCGCGCCACCUAGCGGUCGUACAUGCGA-AUGUGACAUAUAGGUGGCGCUUCAAGCAAAAGUUGGCGCAAUAUUUCA
.....(((((((.(((.(((((..(((....)))..))))).)))((((((((((...(((..((((....-)))))))...))))))))))............))))).))........ ( -47.50)
>DroYak_CAF1 110411 92 + 1
UAA---------------------------AAAUAUUUUUAAGGUGCGCCACCUAGCGGAUGCCCAGACGA-AUGUGGUACAUAGGUGGCGCACAAAACAAAAGGUGGCGCCAUUUUUCA
...---------------------------.............((((((((((((...(.((((((.....-.)).))))).))))))))))))......(((((((....))))))).. ( -34.40)
>consensus
UAAA___CCCAGUGCUGCCAGAUGGACGCAAACUAUUUUUGAGCUGCGCCACCUAGCGGAUGAGUAGGCGA_AAGUGGUACCCAGGUGGCGCCUAAAACAAAAG_UGGCGCAAUAUUUCA
.............................................(((((((((.((......))..((.....)).......)))))))))............................ (-15.38 = -15.58 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	26,887,188 – 26,887,304
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	65.04
Mean single sequence MFE	-33.65
Consensus MFE	-19.13
Energy contribution	-19.13
Covariance contribution	0.00
Combinations/Pair	1.18
Mean z-score	-1.69
Structure conservation index	0.57
SVM decision value	1.02
SVM RNA-class probability	0.901685
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26887188 116 - 27905053
UGAAAUAAGGCGCCACCUUUUGUUUCGGGCGCCACCUGGAUACCACUU-UCGCCAACUCAUCCGCUAGGUGGCGCAGCUCAAAAAUAUUUUUCGUCCAUCUGGCAGCACUGGG---UCUA
........((((((.............))))))((((((((.......-..........))))(((((((((((..................)).)))))))))......)))---)... ( -31.62)
>DroSec_CAF1 95449 108 - 1
AGAAAUACAGA---------AAUAUUAGGCGCCAUCUGGGUACCACUUUUCGCGUACUCAUCCGCUAGGUGGCGCAGCUCACAAGUAGUUUGCCUCCAUCUGGCAGCACUGGG---UGUA
...........---------........((((((((((((((((.......).)))).......))))))))))).....(((..(((((((((.......))))).))))..---))). ( -32.91)
>DroSim_CAF1 99139 108 - 1
AGAUAUACUGA---------AAUUGUAGGCGCCACCUGGGUACCACUUUUCGCCUACUCAUCCGCUAGGUGGCGCAGCUUACAAGUAGUUUGCCUCCAUCUGGCAGCACUGGG---UCUG
((((.......---------..(((((((((((((((((.........................)))))))))...)))))))).(((((((((.......))))).)))).)---))). ( -34.31)
>DroEre_CAF1 104142 119 - 1
UGAAAUAUUGCGCCAACUUUUGCUUGAAGCGCCACCUAUAUGUCACAU-UCGCAUGUACGACCGCUAGGUGGCGCGCUUCCAAAAUAGCUUGCGCCUAUCUGGCAACACUGGCCAGGUUA
.........((((...............((((((((((...(((((((-....))))..)))...))))))))))(((........)))..))))..(((((((.......))))))).. ( -41.40)
>DroYak_CAF1 110411 92 - 1
UGAAAAAUGGCGCCACCUUUUGUUUUGUGCGCCACCUAUGUACCACAU-UCGUCUGGGCAUCCGCUAGGUGGCGCACCUUAAAAAUAUUU---------------------------UUA
.........(((((((((...((...((((.(((...(((.....)))-.....)))))))..)).)))))))))...............---------------------------... ( -28.00)
>consensus
UGAAAUACGGCGCCA_CUUUUGUUUUAGGCGCCACCUGGGUACCACUU_UCGCCUACUCAUCCGCUAGGUGGCGCAGCUCAAAAAUAGUUUGCCUCCAUCUGGCAGCACUGGG___UCUA
............................(((((((((((.........................)))))))))))............................................. (-19.13 = -19.13 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:47:29 2006