Locus 275

Sequence ID	3L_DroMel_CAF1
Location	782,593 – 782,714
Length	121
Max. P	0.915527

overview

Window 4

Location	782,593 – 782,684
Length	91
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	78.70
Mean single sequence MFE	-23.91
Consensus MFE	-15.11
Energy contribution	-16.47
Covariance contribution	1.36
Combinations/Pair	1.04
Mean z-score	-2.08
Structure conservation index	0.63
SVM decision value	1.10
SVM RNA-class probability	0.915527
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 782593 91 + 23771897
------------------UCACAGUGGAAGCAGCAU------AAAGAAGCGCUAAUGUUGCAUUAAAUUCAGCUGAAAUCAACUGUUAAGUGGCUUUCAGUGAGCUAUUUAAUUC
------------------..(((((.((.(((((((------..((.....)).)))))))......(((....))).)).)))))((((((((((.....)))))))))).... ( -23.30)
>DroVir_CAF1 163401 91 + 1
U------------------------GGCAGUGGCAUUUCAAAAAAAAAACGCUAAUGUUGCAUUAAAUUCAAAUGAAAUCAACUGUUAAGUGGCUUUCAGUGAGCUAUUUAAUUU
.------------------------.(((((.(.((((((..........((.......))............))))))).)))))((((((((((.....)))))))))).... ( -18.05)
>DroGri_CAF1 182127 100 + 1
UGGCCGG---------AUUUCUUGUGGCAGUGGCAU------AAAAAAUAGCUAAUGUUGCAUUAAAUUCAAAUGAAAUCAACUGGUAAGUGGCUUUCAGUGAGCUAUUUAAUUU
..(((((---------((((..((..(((.((((..------........)))).)))..))..))))))...((....))...)))(((((((((.....)))))))))..... ( -27.80)
>DroWil_CAF1 159541 106 + 1
UUUCCCU---UUUUUGUUUCGCUGUGGCAGUGGCAU------AAAAAAGCGCUAAUGUUGCAUUAAAUUCAAAUGAAAUCAACUGUUAAGUGGCUUUCAGUGAGCUAUUUAAUUU
((((.((---(((((((.((((((...)))))).))------))))))).((.......)).............))))......((((((((((((.....)))))))))))).. ( -25.30)
>DroMoj_CAF1 159978 85 + 1
U------------------------GGCAAUGGCAU------AAAAAAGCGCUAAUGUUGCAUUAAAUUCAAAUGAAAUCAACUGUUAAGCGGCUUUCAGUGAGCUAUUUAAUUU
.------------------------...((((((.(------(..(((((((((((((((((((.......))))....)))).))).))).)))))...)).))))))...... ( -14.80)
>DroPer_CAF1 158459 109 + 1
UGCCUCUGCCUCUGCCUCUGCCUGUGGCAGGGGCAU------AAAAAAACGCUAAUGUUGCAUUAAAUUCAACUGAAAUCAACUGUUAAGUGGCUUUCAGUGAGCUAUUUAAUUU
((((((((((.(.((....))..).)))))))))).------........((.......))(((((((...(((((((.(.(((....))).).))))))).....))))))).. ( -34.20)
>consensus
U_________________U__CUGUGGCAGUGGCAU______AAAAAAGCGCUAAUGUUGCAUUAAAUUCAAAUGAAAUCAACUGUUAAGUGGCUUUCAGUGAGCUAUUUAAUUU
.......................((((((.((((................)))).))))))......(((....))).......((((((((((((.....)))))))))))).. (-15.11 = -16.47 +   1.36)

alignment

secondary structure

dotplot

Window 5

Location	782,610 – 782,714
Length	104
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.42
Mean single sequence MFE	-18.06
Consensus MFE	-14.52
Energy contribution	-14.85
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.39
Structure conservation index	0.80
SVM decision value	-0.05
SVM RNA-class probability	0.507797
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 782610 104 + 23771897
U------AAAGAAGCGCUAAUGUUGCAUUAAAUUCAGCUGAAAUCAACUGUUAAGUGGCUUUCAGUGAGCUAUUUAAUUCUCGAACACCC-----AAAAAGAGCAAAGGC-GAUUC----
.------...(((.((((....((((........(((.((....)).)))(((((((((((.....))))))))))).............-----.......)))).)))-).)))---- ( -23.30)
>DroVir_CAF1 163412 108 + 1
UUUCAAAAAAAAAACGCUAAUGUUGCAUUAAAUUCAAAUGAAAUCAACUGUUAAGUGGCUUUCAGUGAGCUAUUUAAUUUUCCAACACCA-----AAAAAGAGCUAAGAA-AAU------
...............(((..(((((.......(((....))).......((((((((((((.....))))))))))))....)))))...-----......)))......-...------ ( -16.00)
>DroPse_CAF1 152622 107 + 1
U------AAAAAAACGCUAAUGUUGCAUUAAAUUCAACUGAAAUCAACUGUUAAGUGGCUUUCAGUGAGCUAUUUAAUUUCAAAACAUCC-----AAAAAGAGCAAAUAA-AAA-UAAAC
.------........(((....(((.......(((....))).......((((((((((((.....))))))))))))...........)-----))....)))......-...-..... ( -16.60)
>DroGri_CAF1 182153 103 + 1
U------AAAAAAUAGCUAAUGUUGCAUUAAAUUCAAAUGAAAUCAACUGGUAAGUGGCUUUCAGUGAGCUAUUUAAUUUUCCAACACCAA----AAAAAGAGCUAAGCA-AAU------
.------......(((((...((((((((.......))))....))))(((((((((((((.....)))))))))).....))).......----......)))))....-...------ ( -17.60)
>DroMoj_CAF1 159989 108 + 1
U------AAAAAAGCGCUAAUGUUGCAUUAAAUUCAAAUGAAAUCAACUGUUAAGCGGCUUUCAGUGAGCUAUUUAAUUUCCCUACGCCGAGCUGAAAAAGAGCUGCGAAAAAU------
.------.....(((((.......))......(((....))).......)))..((((((((((((..((................))...)))))....))))))).......------ ( -18.29)
>DroPer_CAF1 158494 107 + 1
U------AAAAAAACGCUAAUGUUGCAUUAAAUUCAACUGAAAUCAACUGUUAAGUGGCUUUCAGUGAGCUAUUUAAUUUCAAAACAUCC-----AAAAAGAGCAAAUAA-AAA-UAUAC
.------........(((....(((.......(((....))).......((((((((((((.....))))))))))))...........)-----))....)))......-...-..... ( -16.60)
>consensus
U______AAAAAAACGCUAAUGUUGCAUUAAAUUCAAAUGAAAUCAACUGUUAAGUGGCUUUCAGUGAGCUAUUUAAUUUCCCAACACCC_____AAAAAGAGCAAAGAA_AAU______
...............(((...((((.(((....((....))))))))).((((((((((((.....)))))))))))).......................)))................ (-14.52 = -14.85 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:06 2006