Locus 6728

Sequence ID	3R_DroMel_CAF1
Location	17,720,999 – 17,721,098
Length	99
Max. P	0.753084

overview

Window 4

Location	17,720,999 – 17,721,098
Length	99
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	84.57
Mean single sequence MFE	-37.82
Consensus MFE	-23.91
Energy contribution	-24.68
Covariance contribution	0.78
Combinations/Pair	1.04
Mean z-score	-3.52
Structure conservation index	0.63
SVM decision value	0.48
SVM RNA-class probability	0.753084
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17720999 99 + 27905053
UGGAUCUGGAUCGG-----GGAUCCGGGGCUUAGCCAGCGCGAAUUAUUGAAUUAUUUCGCCAGCAGCUGGUAAAUUCGAUUUGCGCGCUGGCUGCCAUCAUAU
..((((((((((..-----.)))))))(((..((((((((((....((((((((.....(((((...))))).))))))))...)))))))))))))))).... ( -45.00)
>DroPse_CAF1 10366 93 + 1
--GAUGUGGAUACA------GAUCUGGGGUUUAGCCAGCGCGAUUUAUUGAAUUAUUUAGCCAGCAGCUGGUAAAUUCGAUUUGCACGCUGCCAGCC---AUAU
--.((((((.....------...((((((.....))((((.(....((((((((..(((((.....)))))..))))))))...).)))).))))))---)))) ( -26.10)
>DroSim_CAF1 10369 98 + 1
UGGAUCUGGAUCGGGAU------CCGGGGCUUAGCCAGCGCGAAUUAUUGAAUUAUUUCGCCAGCAGCUGGUAAAUUCGAUUUGCGCGCUGGCUGCCACCAUAU
.((((((......))))------))(((((..((((((((((....((((((((.....(((((...))))).))))))))...))))))))))))).)).... ( -47.10)
>DroEre_CAF1 12347 95 + 1
UGGAUCUGGAUCUGGAUCC------GGGGCUUAGCCAGCGCGAAUUAUUGAAUUAUUUCGCCAGCAGCUGGUAAAUUCGAUUUGCGCGCUGGCUGCC---AUAU
.((((((......))))))------..(((..((((((((((....((((((((.....(((((...))))).))))))))...)))))))))))))---.... ( -44.40)
>DroYak_CAF1 10896 98 + 1
UGGAUCUGGAUCUGGAUCCGGAUACGGGGCUUAGCCAGCGCGAAUUAUUGAAUUAUUUCGCCAGCAGCUGGUAAAUUCGAUUUG---GCUGGCUGCC---AUAU
...((((((((....))))))))....(((..(((((((.((((((...(((....)))(((((...)))))......))))))---))))))))))---.... ( -38.20)
>DroPer_CAF1 10379 93 + 1
--GAUGUGGAUACA------GAUCUGGGGUUUAGCCAGCGCGAUUUAUUGAAUUAUUUAGCCAGCAGCUGGUAAAUUCGAUUUGCACGCUGCCAGCC---AUAU
--.((((((.....------...((((((.....))((((.(....((((((((..(((((.....)))))..))))))))...).)))).))))))---)))) ( -26.10)
>consensus
UGGAUCUGGAUCCG______GAUCCGGGGCUUAGCCAGCGCGAAUUAUUGAAUUAUUUCGCCAGCAGCUGGUAAAUUCGAUUUGCGCGCUGGCUGCC___AUAU
...........................(((..((((((((.(....((((((((.....(((((...))))).))))))))...).)))))))))))....... (-23.91 = -24.68 +   0.78)

alignment

secondary structure

dotplot

Window 5

Location	17,720,999 – 17,721,098
Length	99
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	84.57
Mean single sequence MFE	-30.11
Consensus MFE	-20.94
Energy contribution	-22.27
Covariance contribution	1.33
Combinations/Pair	1.05
Mean z-score	-2.82
Structure conservation index	0.70
SVM decision value	0.32
SVM RNA-class probability	0.685653
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17720999 99 - 27905053
AUAUGAUGGCAGCCAGCGCGCAAAUCGAAUUUACCAGCUGCUGGCGAAAUAAUUCAAUAAUUCGCGCUGGCUAAGCCCCGGAUCC-----CCGAUCCAGAUCCA
....((((((((((((((((......(((((.....((.....)).....))))).......))))))))))..)))..(((((.-----..)))))..))).. ( -34.82)
>DroPse_CAF1 10366 93 - 1
AUAU---GGCUGGCAGCGUGCAAAUCGAAUUUACCAGCUGCUGGCUAAAUAAUUCAAUAAAUCGCGCUGGCUAAACCCCAGAUC------UGUAUCCACAUC--
...(---(((..(((((...................)))))..))))...................((((.......))))...------............-- ( -20.91)
>DroSim_CAF1 10369 98 - 1
AUAUGGUGGCAGCCAGCGCGCAAAUCGAAUUUACCAGCUGCUGGCGAAAUAAUUCAAUAAUUCGCGCUGGCUAAGCCCCGG------AUCCCGAUCCAGAUCCA
....((.(((((((((((((......(((((.....((.....)).....))))).......))))))))))..)))))((------(((........))))). ( -39.32)
>DroEre_CAF1 12347 95 - 1
AUAU---GGCAGCCAGCGCGCAAAUCGAAUUUACCAGCUGCUGGCGAAAUAAUUCAAUAAUUCGCGCUGGCUAAGCCCC------GGAUCCAGAUCCAGAUCCA
....---(((((((((((((......(((((.....((.....)).....))))).......))))))))))..)))..------(((((........))))). ( -35.62)
>DroYak_CAF1 10896 98 - 1
AUAU---GGCAGCCAGC---CAAAUCGAAUUUACCAGCUGCUGGCGAAAUAAUUCAAUAAUUCGCGCUGGCUAAGCCCCGUAUCCGGAUCCAGAUCCAGAUCCA
....---((((((((((---..............(((...)))(((((.((......)).))))))))))))..)))........(((((........))))). ( -29.10)
>DroPer_CAF1 10379 93 - 1
AUAU---GGCUGGCAGCGUGCAAAUCGAAUUUACCAGCUGCUGGCUAAAUAAUUCAAUAAAUCGCGCUGGCUAAACCCCAGAUC------UGUAUCCACAUC--
...(---(((..(((((...................)))))..))))...................((((.......))))...------............-- ( -20.91)
>consensus
AUAU___GGCAGCCAGCGCGCAAAUCGAAUUUACCAGCUGCUGGCGAAAUAAUUCAAUAAUUCGCGCUGGCUAAGCCCCGGAUC______CAGAUCCAGAUCCA
.......(((((((((((((......(((((.....((.....)).....))))).......))))))))))..)))........................... (-20.94 = -22.27 +   1.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:27 2006