Locus 4964

Sequence ID	3R_DroMel_CAF1
Location	13,063,193 – 13,063,310
Length	117
Max. P	0.982744

overview

Window 4

Location	13,063,193 – 13,063,285
Length	92
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	92.39
Mean single sequence MFE	-8.80
Consensus MFE	-8.56
Energy contribution	-8.56
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.39
Structure conservation index	0.97
SVM decision value	1.47
SVM RNA-class probability	0.956927
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13063193 92 - 27905053
-----AAAAAAAAAAGAAAA--ACAUCCAAGAAGAAAACUUAUUAAACGCUUCAUAAAUUUUUAUAUUAUGUCUACCCACAUCAUCAGACAUAACGUGU
-----...............--........((((...............)))).........((..((((((((............))))))))..)). (  -8.56)
>DroSec_CAF1 83259 90 - 1
-----A--AAAAAAAGAAAA--ACAUCCAAGAAGAAAACUUAUUAAACGCUUCAUAAAUUUUUAUAUUAUGUCUACCCACAUCAUCAGACAUAACGUGU
-----.--............--........((((...............)))).........((..((((((((............))))))))..)). (  -8.56)
>DroSim_CAF1 75625 90 - 1
-----A--AAAAAAAGAAAA--ACAUCCAAGAAGAAAACUUAUUAAACGCUUCAUAAAUUUUUAUAUUAUGUCUACCCACAUCAUCAGACAUAACGUGU
-----.--............--........((((...............)))).........((..((((((((............))))))))..)). (  -8.56)
>DroEre_CAF1 83622 97 - 1
CAAAAAAAAAAAAAAGAAAA--ACAACCAAGAAGAAAACUUAUUAAACGCUUCAUAAAUUUUUAUAUUAUGUCUACCCACAUCAUCAGACAUAACGUGU
....................--........((((...............)))).........((..((((((((............))))))))..)). (  -8.56)
>DroAna_CAF1 86191 94 - 1
-----AGAACAAAAAAUAAACCAAAAACGAGAAGAAAACUUAUUAAACGCUUCAUAAAUUUUUAUAUUAUGUCUACCCACAUCAUCAGACAUAACGUGU
-----.....................(((.((((...............)))).............((((((((............))))))))))).. (  -9.76)
>consensus
_____A_AAAAAAAAGAAAA__ACAUCCAAGAAGAAAACUUAUUAAACGCUUCAUAAAUUUUUAUAUUAUGUCUACCCACAUCAUCAGACAUAACGUGU
..............................((((...............)))).........((..((((((((............))))))))..)). ( -8.56 =  -8.56 +  -0.00)

alignment

secondary structure

dotplot

Window 5

Location	13,063,212 – 13,063,310
Length	98
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	84.73
Mean single sequence MFE	-20.16
Consensus MFE	-15.30
Energy contribution	-16.14
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-2.68
Structure conservation index	0.76
SVM decision value	1.92
SVM RNA-class probability	0.982744
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13063212 98 + 27905053
GUGGGUAGACAUAAUAUAAAAAUUUAUGAAGCGUUUAAUAAGUUUUCUUCUUGGAUGU--UUUUCUUUUUUUUUU---------------UUUGCUAUUUUCUCCAUUUGCCCGC
((((((((((((((.........)))))((((((((((.(((....))).))))))))--)).............---------------................))))))))) ( -21.00)
>DroSec_CAF1 83278 96 + 1
GUGGGUAGACAUAAUAUAAAAAUUUAUGAAGCGUUUAAUAAGUUUUCUUCUUGGAUGU--UUUUCUUUUUUU--U---------------UUAGCUAUUUUCUUCUUUUGCCCGC
((((((((((((((.........)))))((((((((((.(((....))).))))))))--))..........--.---------------................))))))))) ( -20.90)
>DroSim_CAF1 75644 95 + 1
GUGGGUAGACAUAAUAUAAAAAUUUAUGAAGCGUUUAAUAAGUUUUCUUCUUGGAUGU--UUUUCUUUUUUU--U---------------UU-GCUAUUUUCUUCUUUUGCCCGC
(((((((((...((((((((((.....(((((((((((.(((....))).))))))))--))).......))--)---------------))-).)))).......))))))))) ( -21.50)
>DroEre_CAF1 83641 113 + 1
GUGGGUAGACAUAAUAUAAAAAUUUAUGAAGCGUUUAAUAAGUUUUCUUCUUGGUUGU--UUUUCUUUUUUUUUUUUUUGCUAUUUGCUAUUUGCUAUUUGCUCCUUUUGCCCGC
(((((((((........(((((.....((((((.((((.(((....))).)))).)))--))).....)))))......((.....((.....)).....))....))))))))) ( -20.30)
>DroAna_CAF1 86210 100 + 1
GUGGGUAGACAUAAUAUAAAAAUUUAUGAAGCGUUUAAUAAGUUUUCUUCUCGUUUUUGGUUUAUUUUUUGUUCU--------------CUU-UAUAUUUUUGUCCUUUGCCCGU
..(((((((((.(((((((((((..(((((.((...((..((.......))..))..)).))))).....)))..--------------.))-))))))..))))...))))).. ( -17.10)
>consensus
GUGGGUAGACAUAAUAUAAAAAUUUAUGAAGCGUUUAAUAAGUUUUCUUCUUGGAUGU__UUUUCUUUUUUUU_U_______________UU_GCUAUUUUCUUCUUUUGCCCGC
((((((((((((((.........)))))..((((((((.(((....))).))))))))................................................))))))))) (-15.30 = -16.14 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:12 2006