Locus 5871

Sequence ID	X_DroMel_CAF1
Location	15,134,310 – 15,134,426
Length	116
Max. P	0.834730

overview

Window 1

Location	15,134,310 – 15,134,426
Length	116
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	89.30
Mean single sequence MFE	-34.90
Consensus MFE	-25.01
Energy contribution	-24.83
Covariance contribution	-0.19
Combinations/Pair	1.16
Mean z-score	-2.44
Structure conservation index	0.72
SVM decision value	0.73
SVM RNA-class probability	0.834730
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15134310 116 + 22224390
ACAAAACAAGCGUGAAGAACUCG-AG--UCUCUCGACUUCGGCAUACCCAAAAAGCACGAAAGCGGGAAGUGUGAUUAUGGCCAAAAUUCCAGAUCUGCGCUUUAAUGGGUGUGCGAAG
............(((((...(((-((--...))))))))))(((((((((.....(.(....).).(((((((((((.(((........))))))).)))))))..))))))))).... ( -36.00)
>DroSec_CAF1 45745 119 + 1
ACAAAACAAGCGAGAAGAACUCGGAGUCUCUCUCGACUUCGGCAUACCCAAAAAGCACGAAAGCGGGAAGUGUGAACAUGGCCAAAAUUCCAGAUCUGCGCUUUAAUGGGUGUGCGGAG
........((((((((((........))).))))).))((.(((((((((.(((((.(....)..((..(((....)))..))................)))))..))))))))).)). ( -38.20)
>DroEre_CAF1 52668 110 + 1
--AAAACAAACC---AGAACUCG-AG--UCUAUCGACUUCGGUAUACCCAAAGACCACGAAAGCGGGAAAUGUGAAUAUGGCCAA-AUUCCAGAUCUGUGCUUUAAUGGGUGUGCGGAG
--........((---.(((.(((-(.--....)))).))).(((((((((....((.(....).))((..((.((((........-))))))..))..........))))))))))).. ( -31.10)
>DroYak_CAF1 53400 112 + 1
ACAAAACAAACC---AGAACUCG-AG--UCUAUCGACUGCGGCAUACCCAAAAAGCACGAAAGCGGAAAAUGUGAAUAUGGCCAA-AUUCCAGAUCUGCGCUUUAAUGGGUGUGCGGAG
..........((---......((-((--((....)))).))(((((((((.(((((......(((((...((.((((........-))))))..))))))))))..))))))))))).. ( -34.30)
>consensus
ACAAAACAAACC___AGAACUCG_AG__UCUAUCGACUUCGGCAUACCCAAAAAGCACGAAAGCGGGAAAUGUGAAUAUGGCCAA_AUUCCAGAUCUGCGCUUUAAUGGGUGUGCGGAG
....................................(((((.((((((((.(((((.(....).((((....((........))...))))........)))))..))))))))))))) (-25.01 = -24.83 +  -0.19)

alignment

secondary structure

dotplot

Window 2

Location	15,134,310 – 15,134,426
Length	116
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	89.30
Mean single sequence MFE	-32.65
Consensus MFE	-24.05
Energy contribution	-24.67
Covariance contribution	0.63
Combinations/Pair	1.06
Mean z-score	-1.67
Structure conservation index	0.74
SVM decision value	0.18
SVM RNA-class probability	0.622595
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15134310 116 - 22224390
CUUCGCACACCCAUUAAAGCGCAGAUCUGGAAUUUUGGCCAUAAUCACACUUCCCGCUUUCGUGCUUUUUGGGUAUGCCGAAGUCGAGAGA--CU-CGAGUUCUUCACGCUUGUUUUGU
....(((.(((((..((((((((((.(.((((.(.(((......))).).)))).).))).))))))).))))).))).(((.(((((...--))-))).)))................ ( -33.30)
>DroSec_CAF1 45745 119 - 1
CUCCGCACACCCAUUAAAGCGCAGAUCUGGAAUUUUGGCCAUGUUCACACUUCCCGCUUUCGUGCUUUUUGGGUAUGCCGAAGUCGAGAGAGACUCCGAGUUCUUCUCGCUUGUUUUGU
....(((.(((((..((((((((((.(.((((.(.(((......))).).)))).).))).))))))).))))).)))..(((.((((((..((.....))..)))))))))....... ( -36.20)
>DroEre_CAF1 52668 110 - 1
CUCCGCACACCCAUUAAAGCACAGAUCUGGAAU-UUGGCCAUAUUCACAUUUCCCGCUUUCGUGGUCUUUGGGUAUACCGAAGUCGAUAGA--CU-CGAGUUCU---GGUUUGUUUU--
....((............))(((((((.(((((-((((...((((.((.....((((....))))..(((((.....))))))).))))..--.)-))))))))---)))))))...-- ( -25.60)
>DroYak_CAF1 53400 112 - 1
CUCCGCACACCCAUUAAAGCGCAGAUCUGGAAU-UUGGCCAUAUUCACAUUUUCCGCUUUCGUGCUUUUUGGGUAUGCCGCAGUCGAUAGA--CU-CGAGUUCU---GGUUUGUUUUGU
..(((((.(((((..(((((((..(..(((((.-.((..........))..)))))..)..))))))).))))).)))((.((((....))--))-))......---)).......... ( -35.50)
>consensus
CUCCGCACACCCAUUAAAGCGCAGAUCUGGAAU_UUGGCCAUAUUCACACUUCCCGCUUUCGUGCUUUUUGGGUAUGCCGAAGUCGAGAGA__CU_CGAGUUCU___CGCUUGUUUUGU
....(((.(((((..((((((((((.(.((((...(((......)))...)))).).))).))))))).))))).))).(((.(((..........))).)))................ (-24.05 = -24.67 +   0.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:28 2006