Locus 6321

Sequence ID	2R_DroMel_CAF1
Location	19,814,035 – 19,814,131
Length	96
Max. P	0.924754

overview

Window 0

Location	19,814,035 – 19,814,131
Length	96
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	75.57
Mean single sequence MFE	-23.34
Consensus MFE	-18.25
Energy contribution	-18.42
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.32
Structure conservation index	0.78
SVM decision value	1.16
SVM RNA-class probability	0.924754
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19814035 96 + 20766785
CCCUUUCUGCUUCGCAAAAUUCGCUCAAGACGAA----------------------GAAAAAAAGAAAACGGGUUGGGCCGGCUGCAGAUCACGAAAAGUGAUUCAUGGCAAACCCUG
((((((((.((((((.............).))))----------------------)......)))))..)))..(((...((((..((((((.....))))))..))))...))).. ( -24.82)
>DroSec_CAF1 56432 83 + 1
CCCUUUCUGCUUCGC-------------GACGAA----------------------GAAAAAAAGAAAACGGGUUGGGCCGGCUGCAGAUCACGAAAAGUGAUUCAUGGCAAACCCUG
((((((((.(((((.-------------..))))----------------------)......)))))..)))..(((...((((..((((((.....))))))..))))...))).. ( -24.80)
>DroSim_CAF1 35186 83 + 1
CCCUUUCUGCUGCGC-------------GACGAA----------------------GAAAAAAAGAAAACGGGUUGGGCCGGCUGCAGAUCACGAAAAGUGAUUCAUGGCAAACCCUG
((((((((......(-------------......----------------------)......)))))..)))..(((...((((..((((((.....))))))..))))...))).. ( -21.50)
>DroEre_CAF1 57453 93 + 1
CCCUUUCUGCUUCGCAAAAAUCGCAAAAAAUAUA-------A------------------AAAAGAAAACGGGUUGGGCCGGCUGCAGAUCACGAAAAGUGAUUCAUGGCAAACCCUC
.............((.......))..........-------.------------------..........(((((..((((......((((((.....))))))..)))).))))).. ( -20.20)
>DroYak_CAF1 53903 111 + 1
CCCUUUCUGCUUCGCAAAAAUCACAAAAAACACA-------GAAAUCACAAAAAACGAAGAAAAGAAAACGGGUUGGGCCGGCUGCAGAUCACGAAAAGUGAUUCAUGGCAAACCCUC
((((((((.(((((....................-------..............)))))...)))))..)))..(((...((((..((((((.....))))))..))))...))).. ( -25.78)
>DroAna_CAF1 52959 105 + 1
CCCUUUCUGCUCCUCUCGACCGGCU--GGACGAAAGAAAAAAAAAUCUCU-----------AAAAAAAACGGGUUGGGCCGGCUGCAGAUCACGAAAAGUGAUUCAUUGCAAACCCUC
.................(.((((((--.(((...................-----------...........))).)))))))((((((((((.....))))))...))))....... ( -22.91)
>consensus
CCCUUUCUGCUUCGCAAAA_UCGC___AGACGAA______________________GAAAAAAAGAAAACGGGUUGGGCCGGCUGCAGAUCACGAAAAGUGAUUCAUGGCAAACCCUC
......................................................................(((((..((((......((((((.....))))))..)))).))))).. (-18.25 = -18.42 +   0.17)

alignment

secondary structure

dotplot

Window 1

Location	19,814,035 – 19,814,131
Length	96
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	75.57
Mean single sequence MFE	-25.97
Consensus MFE	-17.99
Energy contribution	-17.91
Covariance contribution	-0.08
Combinations/Pair	1.09
Mean z-score	-0.94
Structure conservation index	0.69
SVM decision value	-0.00
SVM RNA-class probability	0.533353
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19814035 96 - 20766785
CAGGGUUUGCCAUGAAUCACUUUUCGUGAUCUGCAGCCGGCCCAACCCGUUUUCUUUUUUUC----------------------UUCGUCUUGAGCGAAUUUUGCGAAGCAGAAAGGG
..(((((.(((.((.(((((.....)))))...))...)))..))))).....(((((((.(----------------------(((((...((.....))..)))))).))))))). ( -27.20)
>DroSec_CAF1 56432 83 - 1
CAGGGUUUGCCAUGAAUCACUUUUCGUGAUCUGCAGCCGGCCCAACCCGUUUUCUUUUUUUC----------------------UUCGUC-------------GCGAAGCAGAAAGGG
..(((((.(((.((.(((((.....)))))...))...)))..))))).....(((((((.(----------------------((((..-------------.))))).))))))). ( -25.20)
>DroSim_CAF1 35186 83 - 1
CAGGGUUUGCCAUGAAUCACUUUUCGUGAUCUGCAGCCGGCCCAACCCGUUUUCUUUUUUUC----------------------UUCGUC-------------GCGCAGCAGAAAGGG
..(((((.(((.((.(((((.....)))))...))...)))..))))).....(((((((.(----------------------(.((..-------------.)).)).))))))). ( -20.80)
>DroEre_CAF1 57453 93 - 1
GAGGGUUUGCCAUGAAUCACUUUUCGUGAUCUGCAGCCGGCCCAACCCGUUUUCUUUU------------------U-------UAUAUUUUUUGCGAUUUUUGCGAAGCAGAAAGGG
..(((((.(((.((.(((((.....)))))...))...)))..))))).....(((((------------------(-------(.....((((((((...)))))))).))))))). ( -22.90)
>DroYak_CAF1 53903 111 - 1
GAGGGUUUGCCAUGAAUCACUUUUCGUGAUCUGCAGCCGGCCCAACCCGUUUUCUUUUCUUCGUUUUUUGUGAUUUC-------UGUGUUUUUUGUGAUUUUUGCGAAGCAGAAAGGG
..((((..((..(..(((((.....)))))..)..))..))))..(((...((((...((((((...(((..(....-------........)..))).....)))))).)))).))) ( -26.90)
>DroAna_CAF1 52959 105 - 1
GAGGGUUUGCAAUGAAUCACUUUUCGUGAUCUGCAGCCGGCCCAACCCGUUUUUUUU-----------AGAGAUUUUUUUUUCUUUCGUCC--AGCCGGUCGAGAGGAGCAGAAAGGG
..((((..((..(..(((((.....)))))..)..))..))))..((((((((....-----------.)))))((((((((((((((.((--....)).))))))))).)))))))) ( -32.80)
>consensus
CAGGGUUUGCCAUGAAUCACUUUUCGUGAUCUGCAGCCGGCCCAACCCGUUUUCUUUUUUUC______________________UUCGUCU___GCGA_UUUUGCGAAGCAGAAAGGG
..((((..((..(..(((((.....)))))..)..))..))))..(((.((((((((................................................)))).)))).))) (-17.99 = -17.91 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:13 2006