Locus 8479

Sequence ID	3R_DroMel_CAF1
Location	22,621,197 – 22,621,288
Length	91
Max. P	0.915491

overview

Window 1

Location	22,621,197 – 22,621,288
Length	91
Sequences	6
Columns	93
Reading direction	forward
Mean pairwise identity	84.18
Mean single sequence MFE	-30.43
Consensus MFE	-20.67
Energy contribution	-21.55
Covariance contribution	0.88
Combinations/Pair	1.09
Mean z-score	-3.69
Structure conservation index	0.68
SVM decision value	0.89
SVM RNA-class probability	0.874703
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22621197 91 + 27905053
AGCUGCAUUUGCAAAUUAA-GAGUACAACUGCAACUGCAACUGCGAACUGCUAAUGCAACAUUCACAUAUGUUGCGCAUGUGCCGC-UGCAGC
.((((((.(((((.....(-(.......)).....)))))..(((.(((((....(((((((......)))))))))).))..)))-)))))) ( -27.30)
>DroSec_CAF1 69443 85 + 1
AGCUGCACUUGCAAAUUAA-GAGUGCAACUG------CAACUGCAAACUGCUAAUGCAACAUUCACAUAUGUUGCGCAUGUGCCGC-UGCAGC
...(((((((.........-))))))).(((------((.(.(((...(((....(((((((......))))))))))..))).).-))))). ( -29.10)
>DroSim_CAF1 71248 91 + 1
AGCUGCAUUUGCAAAUUAA-GAGUGCAACUGCAACUGCAACUGCAAACUGCUAAUGCAACAUUCACAUAUGUUGCGCAUGUGCCGC-UGCAGC
(((.((((.(((......(-(..((((..(((....)))..))))..))......(((((((......)))))))))).)))).))-)..... ( -30.80)
>DroEre_CAF1 77571 90 + 1
AGCAGCAUUUGCAAAUUAA-GAGUGCAACUGCAACUGCAAGUGC-AACUGCUAAUGCAACAUUCACAUAUGCUGCGCAUGUGCCGC-UGCAGC
.(((((..(((((..(((.-.((((((..(((....)))..)))-.)))..))))))))......(((((((...)))))))..))-)))... ( -30.10)
>DroYak_CAF1 72563 92 + 1
GGCAGCAUUUGCAAAUUAAAAAGUGCAACUGCAAGUGGAAGUGC-AACUGCUAAUGCAACAUUCACAUAUGUUGCGCAUGUGCCGCUUGCAGC
....((((((..........))))))..((((((((((..((((-..........(((((((......)))))))))))...)))))))))). ( -34.40)
>DroAna_CAF1 71661 86 + 1
AGCUGCAAUUGCAGCUCCG-----ACAAUGGCAACUGCAACAUU-CAUUGCAUCUGCAACAUUCACAUAUGUUGCGCAUGUGCGGC-AGCAUC
.(((((..((((((..((.-----.....))...))))))....-...(((((.((((((((......))))))))...)))))))-)))... ( -30.90)
>consensus
AGCUGCAUUUGCAAAUUAA_GAGUGCAACUGCAACUGCAACUGC_AACUGCUAAUGCAACAUUCACAUAUGUUGCGCAUGUGCCGC_UGCAGC
.((.((((.(((............(((..(((....)))..)))...........(((((((......)))))))))).)))).))....... (-20.67 = -21.55 +   0.88)

alignment

secondary structure

dotplot

Window 2

Location	22,621,197 – 22,621,288
Length	91
Sequences	6
Columns	93
Reading direction	reverse
Mean pairwise identity	84.18
Mean single sequence MFE	-33.22
Consensus MFE	-24.44
Energy contribution	-25.52
Covariance contribution	1.07
Combinations/Pair	1.15
Mean z-score	-3.64
Structure conservation index	0.74
SVM decision value	1.10
SVM RNA-class probability	0.915491
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22621197 91 - 27905053
GCUGCA-GCGGCACAUGCGCAACAUAUGUGAAUGUUGCAUUAGCAGUUCGCAGUUGCAGUUGCAGUUGUACUC-UUAAUUUGCAAAUGCAGCU
(((((.-(((.....)))(((((((......)))))))....)))))....(((((((.(((((((((.....-.))).)))))).))))))) ( -33.10)
>DroSec_CAF1 69443 85 - 1
GCUGCA-GCGGCACAUGCGCAACAUAUGUGAAUGUUGCAUUAGCAGUUUGCAGUUG------CAGUUGCACUC-UUAAUUUGCAAGUGCAGCU
(((((.-(((.....)))(((((((......)))))))....)))))....(((((------((.(((((...-......))))).))))))) ( -33.20)
>DroSim_CAF1 71248 91 - 1
GCUGCA-GCGGCACAUGCGCAACAUAUGUGAAUGUUGCAUUAGCAGUUUGCAGUUGCAGUUGCAGUUGCACUC-UUAAUUUGCAAAUGCAGCU
..((((-((.(((..((((((((((......)))))))....)))...))).))))))((((((.(((((...-......))))).)))))). ( -35.10)
>DroEre_CAF1 77571 90 - 1
GCUGCA-GCGGCACAUGCGCAGCAUAUGUGAAUGUUGCAUUAGCAGUU-GCACUUGCAGUUGCAGUUGCACUC-UUAAUUUGCAAAUGCUGCU
.....(-((((((..((((((((((......)))))))(((((.(((.-(((.((((....)))).)))))).-)))))..)))..))))))) ( -34.10)
>DroYak_CAF1 72563 92 - 1
GCUGCAAGCGGCACAUGCGCAACAUAUGUGAAUGUUGCAUUAGCAGUU-GCACUUCCACUUGCAGUUGCACUUUUUAAUUUGCAAAUGCUGCC
.......((((((..((((((((((......)))))))....(((..(-(((........))))..)))............)))..)))))). ( -32.10)
>DroAna_CAF1 71661 86 - 1
GAUGCU-GCCGCACAUGCGCAACAUAUGUGAAUGUUGCAGAUGCAAUG-AAUGUUGCAGUUGCCAUUGU-----CGGAGCUGCAAUUGCAGCU
...(((-((.(((.....(((((((......)))))))...)))....-...(((((((((.((.....-----.))))))))))).))))). ( -31.70)
>consensus
GCUGCA_GCGGCACAUGCGCAACAUAUGUGAAUGUUGCAUUAGCAGUU_GCAGUUGCAGUUGCAGUUGCACUC_UUAAUUUGCAAAUGCAGCU
((((((....(((..((((((((((......)))))))....)))....((((((((....))))))))...........)))...)))))). (-24.44 = -25.52 +   1.07)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:12:20 2006