Locus 4090

Sequence ID	2R_DroMel_CAF1
Location	13,475,841 – 13,475,936
Length	95
Max. P	0.846521

overview

Window 4

Location	13,475,841 – 13,475,936
Length	95
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	87.44
Mean single sequence MFE	-33.94
Consensus MFE	-27.33
Energy contribution	-28.13
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.79
Structure conservation index	0.81
SVM decision value	0.73
SVM RNA-class probability	0.833947
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13475841 95 + 20766785
----------CCUGCAGUCAAGCUGUGCAAUUGACUCGCAAGUCGAGUCGCCUGCGAGGCUUAUCCUCAUCGCCAUUUUGUCUGCUCGACUCGGCUCUGCAUUCG
----------..(((((..(((((.((((..(((((((.....)))))))..)))).))))).........(((.....(((.....)))..))).))))).... ( -31.30)
>DroSec_CAF1 24497 105 + 1
UGGCCCCCGUUCUGCAGUCAAGCUGUGCAGUUGACUCGCAAGUCGAGUCGCCUGCGAGGCUUAUCCUCAUCGCCAUUUUGUCUGCUCGGCUCGGCUCUGCAUUCG
.((((.(((....((((.((((.((.((((.(((((((.....))))))).))))((((.....)))).....)).)))).)))).)))...))))......... ( -39.00)
>DroSim_CAF1 24522 105 + 1
UGGCCCCCGUUCUGCAGUCAAGCUGUGCAGUUGACUCGCAAGUCGAGUCGCCUGCGAGGCUUAUCCUCAUCGCCAUUUUGUCUGCUCGGCUCGGCUCUGCAUUCG
.((((.(((....((((.((((.((.((((.(((((((.....))))))).))))((((.....)))).....)).)))).)))).)))...))))......... ( -39.00)
>DroEre_CAF1 25148 93 + 1
------UCAUCCUGCAG-CAAGCUGUGCAGUUGCCUCGCAAGUCGAGUCGCCUGCCAGGCUUAUCCCCAUCGCCAUUUUGUCUGCGC-----GGCUCUGCAUUCG
------......(((((-..((((((((((..((((.(((.((......)).))).))))...........((......))))))))-----))))))))).... ( -31.50)
>DroYak_CAF1 25967 94 + 1
------UCCUUCUGCAGUCAAGCUGUGCAGUUGACUCGCAAGUCGAGUCGCCUGCGAGGCUUAUCCCCAUCGCCAUUUUGUCUGCUC-----GCCUCUGCAUUCG
------.......((((.((((...(((((.(((((((.....))))))).))))).(((...........)))..)))).))))..-----((....))..... ( -28.90)
>consensus
______CCGUUCUGCAGUCAAGCUGUGCAGUUGACUCGCAAGUCGAGUCGCCUGCGAGGCUUAUCCUCAUCGCCAUUUUGUCUGCUCG_CUCGGCUCUGCAUUCG
............(((((..(((((.(((((.(((((((.....))))))).))))).))))).........(((..................))).))))).... (-27.33 = -28.13 +   0.80)

alignment

secondary structure

dotplot

Window 5

Location	13,475,841 – 13,475,936
Length	95
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	87.44
Mean single sequence MFE	-35.22
Consensus MFE	-29.32
Energy contribution	-30.84
Covariance contribution	1.52
Combinations/Pair	1.11
Mean z-score	-1.73
Structure conservation index	0.83
SVM decision value	0.77
SVM RNA-class probability	0.846521
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13475841 95 - 20766785
CGAAUGCAGAGCCGAGUCGAGCAGACAAAAUGGCGAUGAGGAUAAGCCUCGCAGGCGACUCGACUUGCGAGUCAAUUGCACAGCUUGACUGCAGG----------
..........((..((((((((...............((((.....))))((((..((((((.....))))))..))))...))))))))))...---------- ( -33.60)
>DroSec_CAF1 24497 105 - 1
CGAAUGCAGAGCCGAGCCGAGCAGACAAAAUGGCGAUGAGGAUAAGCCUCGCAGGCGACUCGACUUGCGAGUCAACUGCACAGCUUGACUGCAGAACGGGGGCCA
((..(((((...(((((.(.((((.......(.(..(((((.....)))))..).)((((((.....))))))..)))).).))))).)))))...))....... ( -37.90)
>DroSim_CAF1 24522 105 - 1
CGAAUGCAGAGCCGAGCCGAGCAGACAAAAUGGCGAUGAGGAUAAGCCUCGCAGGCGACUCGACUUGCGAGUCAACUGCACAGCUUGACUGCAGAACGGGGGCCA
((..(((((...(((((.(.((((.......(.(..(((((.....)))))..).)((((((.....))))))..)))).).))))).)))))...))....... ( -37.90)
>DroEre_CAF1 25148 93 - 1
CGAAUGCAGAGCC-----GCGCAGACAAAAUGGCGAUGGGGAUAAGCCUGGCAGGCGACUCGACUUGCGAGGCAACUGCACAGCUUG-CUGCAGGAUGA------
....((((((((.-----(.((((.(.....).............((((.(((((((...)).))))).))))..)))).).)))..-)))))......------ ( -31.30)
>DroYak_CAF1 25967 94 - 1
CGAAUGCAGAGGC-----GAGCAGACAAAAUGGCGAUGGGGAUAAGCCUCGCAGGCGACUCGACUUGCGAGUCAACUGCACAGCUUGACUGCAGAAGGA------
(...(((((...(-----((((...............((((.....))))((((..((((((.....))))))..))))...))))).)))))...)..------ ( -35.40)
>consensus
CGAAUGCAGAGCCGAG_CGAGCAGACAAAAUGGCGAUGAGGAUAAGCCUCGCAGGCGACUCGACUUGCGAGUCAACUGCACAGCUUGACUGCAGAACGA______
....(((((...(((((.(.((((.......(.(..(((((.....)))))..).)((((((.....))))))..)))).).))))).)))))............ (-29.32 = -30.84 +   1.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:30 2006