Locus 7781

Sequence ID	X_DroMel_CAF1
Location	19,364,314 – 19,364,461
Length	147
Max. P	0.991903

overview

Window 7

Location	19,364,314 – 19,364,421
Length	107
Sequences	4
Columns	107
Reading direction	forward
Mean pairwise identity	84.99
Mean single sequence MFE	-22.08
Consensus MFE	-17.15
Energy contribution	-17.27
Covariance contribution	0.12
Combinations/Pair	1.13
Mean z-score	-2.33
Structure conservation index	0.78
SVM decision value	1.43
SVM RNA-class probability	0.952757
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19364314 107 + 22224390
CAUCAUUUUUUUUUUUUUUUCGUGACAUUACCUAGCAUAUAACAAGUAAGUGGGGUAGCCCUGCUGCCAACGCAGCUACCCCAGCUAAUACAAUCUGGAAUAUCACC
.....................((((.(((.((((((.(((.....)))..(((((((((..(((.......)))))))))))))))).........))))).)))). ( -26.20)
>DroSec_CAF1 7245 102 + 1
CAUCAUUUUUU-----UUUUCUUGACAUUACCUAGCAUAUAACAAGUAACUGGGGUAGCCCUGCUGCCAUCACAGCUACCCUGCCUAAUACAAUCUGGAAUAUCACC
...........-----..((((.((......((((..(((.....))).))))(((((....((((......))))....)))))........)).))))....... ( -16.00)
>DroSim_CAF1 7124 104 + 1
CAUCAUUUUUU---UUUUUUCGUGACAUUACCUAGCAUAUAACAAGUAACUGGGGUAGCCCUGCUGCCAUCGCAGCUACCCCGCCUAAUACAAUCUGGAAUAUCACC
...........---.......((((.(((.((.....(((.....)))...((((((((..(((.......)))))))))))..............))))).)))). ( -23.10)
>DroEre_CAF1 7270 88 + 1
---------UU---UUUUUUCGUGACAUUACUUAGCAUAUAACA----AUUGGGGUAGCCCU---GCCACCGCAGCUACCCCACGUAAUACAAUCUGGAAUAUCACC
---------..---.......((((.(((.((.....(((.((.----..(((((((((..(---((....)))))))))))).)).)))......))))).)))). ( -23.00)
>consensus
CAUCAUUUUUU___UUUUUUCGUGACAUUACCUAGCAUAUAACAAGUAACUGGGGUAGCCCUGCUGCCAUCGCAGCUACCCCACCUAAUACAAUCUGGAAUAUCACC
.....................((((.(((.((.((...............(((((((((.....(((....))))))))))))...........))))))).)))). (-17.15 = -17.27 +   0.12)

alignment

secondary structure

dotplot

Window 8

Location	19,364,314 – 19,364,421
Length	107
Sequences	4
Columns	107
Reading direction	reverse
Mean pairwise identity	84.99
Mean single sequence MFE	-30.65
Consensus MFE	-25.06
Energy contribution	-26.88
Covariance contribution	1.81
Combinations/Pair	1.03
Mean z-score	-2.83
Structure conservation index	0.82
SVM decision value	2.29
SVM RNA-class probability	0.991903
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19364314 107 - 22224390
GGUGAUAUUCCAGAUUGUAUUAGCUGGGGUAGCUGCGUUGGCAGCAGGGCUACCCCACUUACUUGUUAUAUGCUAGGUAAUGUCACGAAAAAAAAAAAAAAAUGAUG
.((((((((((((..((((..((.((((((((((((.......))..))))))))))....))...))))..)).)).))))))))..................... ( -32.60)
>DroSec_CAF1 7245 102 - 1
GGUGAUAUUCCAGAUUGUAUUAGGCAGGGUAGCUGUGAUGGCAGCAGGGCUACCCCAGUUACUUGUUAUAUGCUAGGUAAUGUCAAGAAAA-----AAAAAAUGAUG
..(((((((((((..((((.((((..((((((((.((.......)).))))))))......)))).))))..)).)).)))))))......-----........... ( -27.20)
>DroSim_CAF1 7124 104 - 1
GGUGAUAUUCCAGAUUGUAUUAGGCGGGGUAGCUGCGAUGGCAGCAGGGCUACCCCAGUUACUUGUUAUAUGCUAGGUAAUGUCACGAAAAAA---AAAAAAUGAUG
.((((((((((((..((((.((((.(((((((((((.......))..))))))))).....)))).))))..)).)).)))))))).......---........... ( -32.70)
>DroEre_CAF1 7270 88 - 1
GGUGAUAUUCCAGAUUGUAUUACGUGGGGUAGCUGCGGUGGC---AGGGCUACCCCAAU----UGUUAUAUGCUAAGUAAUGUCACGAAAAAA---AA---------
.((((((((.(.....((((.((.((((((((((((....))---..))))))))))..----.))...))))...).)))))))).......---..--------- ( -30.10)
>consensus
GGUGAUAUUCCAGAUUGUAUUAGGCGGGGUAGCUGCGAUGGCAGCAGGGCUACCCCAGUUACUUGUUAUAUGCUAGGUAAUGUCACGAAAAAA___AAAAAAUGAUG
.((((((((((((..((((.((((((((((((((((....)).....))))))))))....)))).))))..)).)).))))))))..................... (-25.06 = -26.88 +   1.81)

alignment

secondary structure

dotplot

Window 9

Location	19,364,350 – 19,364,461
Length	111
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	87.24
Mean single sequence MFE	-27.22
Consensus MFE	-19.00
Energy contribution	-19.75
Covariance contribution	0.75
Combinations/Pair	1.14
Mean z-score	-1.84
Structure conservation index	0.70
SVM decision value	0.34
SVM RNA-class probability	0.696665
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19364350 111 + 22224390
AUAUAACAAGUAAGUGGGGUAGCCCUGCUGCCAACGCAGCUACCCCAGCUAAUACAAUCUGGAAUAUCACCCAUCCGGCCUCACCACUUCGGCACUUCGGCAGGGAGUUUC
....(((..((((((((((((((..(((.......)))))))))))).))..)))..............(((..((((((..........)))....)))..))).))).. ( -31.10)
>DroSec_CAF1 7276 111 + 1
AUAUAACAAGUAACUGGGGUAGCCCUGCUGCCAUCACAGCUACCCUGCCUAAUACAAUCUGGAAUAUCACCCAUCCGGCCUCACCACUUCGGCACUUCGGCGAGUAGUUUC
..............(((((((((...)))))).))).((((((..((((..........(((........)))....(((..........))).....)))).)))))).. ( -24.50)
>DroSim_CAF1 7157 111 + 1
AUAUAACAAGUAACUGGGGUAGCCCUGCUGCCAUCGCAGCUACCCCGCCUAAUACAAUCUGGAAUAUCACCCAUCCGGCCUCACCACUUCGGCACUUCGGCGAGUAGUUUC
............(((((((((((..(((.......)))))))))))(((..........(((........)))....(((..........))).....))).)))...... ( -29.50)
>DroEre_CAF1 7294 101 + 1
AUAUAACA----AUUGGGGUAGCCCU---GCCACCGCAGCUACCCCACGUAAUACAAUCUGGAAUAUCACCCAUCCGGCCUCACCACA---CCACUCCAUCAACGAGUUUC
........----..(((((((((..(---((....))))))))))))...........(((((..........)))))..........---..((((.......))))... ( -23.80)
>consensus
AUAUAACAAGUAACUGGGGUAGCCCUGCUGCCAUCGCAGCUACCCCACCUAAUACAAUCUGGAAUAUCACCCAUCCGGCCUCACCACUUCGGCACUUCGGCAAGGAGUUUC
..............(((((((((.....(((....))))))))))))...........(((((..........)))))...............(((((.....)))))... (-19.00 = -19.75 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:47:25 2006