Locus 3326

Sequence ID	2R_DroMel_CAF1
Location	11,331,217 – 11,331,363
Length	146
Max. P	0.999951

overview

Window 9

Location	11,331,217 – 11,331,328
Length	111
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	93.09
Mean single sequence MFE	-33.58
Consensus MFE	-31.34
Energy contribution	-31.78
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-2.73
Structure conservation index	0.93
SVM decision value	4.80
SVM RNA-class probability	0.999951
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11331217 111 + 20766785
CUUGCGGUUUUUUAUUACGCAUUUCGGUCAGGCGAUUAAGAUACGAAAUACCGAGAUACGGGCGUAAUUAAGUUUAAAGACCGCAUCUCGGCGAUCUUUCGUUU-UUAUGUU
..((((((((((.((((((((((((((((..........))).)))))).(((.....)))))))))).......))))))))))....(((((....))))).-....... ( -31.40)
>DroSec_CAF1 118621 112 + 1
CUUGCGGUUUUUUAUUACGCAUUUCGGUGAGCCGAUUAAGAUACGGAAUACCGAGAUACGGGCGUAAUUAAGUUUAAAGACCGCAUCUCGACGAUCUUUCGUUUUUUAUGUU
..((((((((((.((((((((((((((((..(((.........)))..)))))))))....))))))).......))))))))))....(((((....)))))......... ( -37.00)
>DroSim_CAF1 122466 112 + 1
CUUGCGGUUUUUUAUUACGCAUUUCGGUCAGCCGAUUAAGAUACGGAAUACCGAGAUACGGGCGUAAUUAAGUUUAAAGACCGCAUCUCGACGAUCUUUCGUUUUUUAUGAU
..((((((((((.(((((((((((((((...(((.........)))...))))))))....))))))).......))))))))))....(((((....)))))......... ( -35.10)
>DroEre_CAF1 119912 104 + 1
CUUGCGGUU-UUUAUUACGCAUUUCGGUCAGCCGAUUAAGAUACGGGAUACCGAGAUACGGGCGUAAUUAAGUUUAAAGACCGCAUCUCGACGAUCUUUCGU-UUU------
..(((((((-((((((((((((((((((...(((.........)))...))))))))....)))))).......)))))))))))....(((((....))))-)..------ ( -33.91)
>DroYak_CAF1 121494 106 + 1
CUUGCGGUUUUUUAUUACGCAUUUCGGUCAGCCGAUUAAGAUACGGAAUACCGAGAUACGGGCGCAAUUAAGUUUAAAGACCGCAUCUCGACGAUCUUUCGUGUUU------
..((((((((((.....((.((((((((...(((.........)))...)))))))).))(((........))).)))))))))).....((((....))))....------ ( -30.50)
>consensus
CUUGCGGUUUUUUAUUACGCAUUUCGGUCAGCCGAUUAAGAUACGGAAUACCGAGAUACGGGCGUAAUUAAGUUUAAAGACCGCAUCUCGACGAUCUUUCGUUUUUUAUG_U
..((((((((((.(((((((((((((((...(((.........)))...))))))))....))))))).......)))))))))).....((((....)))).......... (-31.34 = -31.78 +   0.44)

alignment

secondary structure

dotplot

Window 0

Location	11,331,217 – 11,331,328
Length	111
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	93.09
Mean single sequence MFE	-26.93
Consensus MFE	-25.40
Energy contribution	-25.28
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-2.06
Structure conservation index	0.94
SVM decision value	3.48
SVM RNA-class probability	0.999273
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11331217 111 - 20766785
AACAUAA-AAACGAAAGAUCGCCGAGAUGCGGUCUUUAAACUUAAUUACGCCCGUAUCUCGGUAUUUCGUAUCUUAAUCGCCUGACCGAAAUGCGUAAUAAAAAACCGCAAG
.......-..((((((....((((((((((((.(...............).)))))))))))).)))))).......(((......)))..((((...........)))).. ( -28.76)
>DroSec_CAF1 118621 112 - 1
AACAUAAAAAACGAAAGAUCGUCGAGAUGCGGUCUUUAAACUUAAUUACGCCCGUAUCUCGGUAUUCCGUAUCUUAAUCGGCUCACCGAAAUGCGUAAUAAAAAACCGCAAG
..............((((((((((((((((((.(...............).))))))))))).....)).)))))..((((....))))..((((...........)))).. ( -25.76)
>DroSim_CAF1 122466 112 - 1
AUCAUAAAAAACGAAAGAUCGUCGAGAUGCGGUCUUUAAACUUAAUUACGCCCGUAUCUCGGUAUUCCGUAUCUUAAUCGGCUGACCGAAAUGCGUAAUAAAAAACCGCAAG
...........(((((((((((......))))))))).......(((((((....((.(((((...(((.........)))...))))).))))))))).......)).... ( -26.00)
>DroEre_CAF1 119912 104 - 1
------AAA-ACGAAAGAUCGUCGAGAUGCGGUCUUUAAACUUAAUUACGCCCGUAUCUCGGUAUCCCGUAUCUUAAUCGGCUGACCGAAAUGCGUAAUAAA-AACCGCAAG
------...-((((....)))).....((((((.((((.......((((((....((.(((((...(((.........)))...))))).))))))))))))-.)))))).. ( -26.41)
>DroYak_CAF1 121494 106 - 1
------AAACACGAAAGAUCGUCGAGAUGCGGUCUUUAAACUUAAUUGCGCCCGUAUCUCGGUAUUCCGUAUCUUAAUCGGCUGACCGAAAUGCGUAAUAAAAAACCGCAAG
------.......(((((((((......)))))))))........(((((..(((((.(((((...(((.........)))...))))).)))))...........))))). ( -27.72)
>consensus
A_CAUAAAAAACGAAAGAUCGUCGAGAUGCGGUCUUUAAACUUAAUUACGCCCGUAUCUCGGUAUUCCGUAUCUUAAUCGGCUGACCGAAAUGCGUAAUAAAAAACCGCAAG
...........(((((((((((......))))))))).......(((((((....((.(((((...(((.........)))...))))).))))))))).......)).... (-25.40 = -25.28 +  -0.12)

alignment

secondary structure

dotplot

Window 1

Location	11,331,249 – 11,331,363
Length	114
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	89.04
Mean single sequence MFE	-24.49
Consensus MFE	-20.98
Energy contribution	-21.82
Covariance contribution	0.84
Combinations/Pair	1.03
Mean z-score	-1.39
Structure conservation index	0.86
SVM decision value	0.24
SVM RNA-class probability	0.649417
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11331249 114 - 20766785
AUUGUGUAACUAACCGUUGUCACCGUUGUCAUUAAAACAUAA-AAACGAAAGAUCGCCGAGAUGCGGUCUUUAAACUUAAUUACGCCCGUAUCUCGGUAUUUCGUAUCUUAAUCG
...(((((((.....)))).))).(((........)))....-..((((((....((((((((((((.(...............).)))))))))))).)))))).......... ( -29.76)
>DroSec_CAF1 118653 106 - 1
AUUGUGUAACUAACCGU---------UGUCAUCAAAACAUAAAAAACGAAAGAUCGUCGAGAUGCGGUCUUUAAACUUAAUUACGCCCGUAUCUCGGUAUUCCGUAUCUUAAUCG
.(((((((((.....))---------)).)).)))...........(((((((((((((((((((((.(...............).))))))))))).....)).)))))..))) ( -22.36)
>DroSim_CAF1 122498 115 - 1
AUUGUGUAACUAACCGUUGUCACCGUUGUCAUCAAAUCAUAAAAAACGAAAGAUCGUCGAGAUGCGGUCUUUAAACUUAAUUACGCCCGUAUCUCGGUAUUCCGUAUCUUAAUCG
...(((((((.....)))).)))((((.................)))).((((((((((((((((((.(...............).))))))))))).....)).)))))..... ( -23.59)
>DroEre_CAF1 119943 105 - 1
AUUGUGUAACUAACCGUUGUCACCGU---CAUUAA------AAA-ACGAAAGAUCGUCGAGAUGCGGUCUUUAAACUUAAUUACGCCCGUAUCUCGGUAUCCCGUAUCUUAAUCG
...(((((((.....)))).)))...---......------...-.(((((((((((((((((((((.(...............).))))))))))).....)).)))))..))) ( -23.36)
>DroYak_CAF1 121526 106 - 1
AUUGUGUAACUAACCGUUGUCACCGU---CAUUAA------AAACACGAAAGAUCGUCGAGAUGCGGUCUUUAAACUUAAUUGCGCCCGUAUCUCGGUAUUCCGUAUCUUAAUCG
...(((((((.....)))).)))...---......------.....(((((((((((((((((((((.(...............).))))))))))).....)).)))))..))) ( -23.36)
>consensus
AUUGUGUAACUAACCGUUGUCACCGUUGUCAUUAAA_CAUAAAAAACGAAAGAUCGUCGAGAUGCGGUCUUUAAACUUAAUUACGCCCGUAUCUCGGUAUUCCGUAUCUUAAUCG
...(((((((.....)))).))).......................(((((((((((((((((((((.(...............).))))))))))).....)).)))))..))) (-20.98 = -21.82 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:47 2006