Locus 4366

Sequence ID	3L_DroMel_CAF1
Location	12,808,506 – 12,808,603
Length	97
Max. P	0.793170

overview

Window 6

Location	12,808,506 – 12,808,603
Length	97
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	80.07
Mean single sequence MFE	-30.18
Consensus MFE	-16.81
Energy contribution	-18.62
Covariance contribution	1.81
Combinations/Pair	1.07
Mean z-score	-2.24
Structure conservation index	0.56
SVM decision value	0.59
SVM RNA-class probability	0.793170
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12808506 97 + 23771897
AUG----UAUCUGAUAGAUAUA----UAUAUGUAUCGCUGUUUAGAGAGGCGUGCGC------CGUGUGACGUCACGAAAGCCAAGCCCCAAAAAUCUGAACCAAUCAGAC
...----..((((((.((((((----....))))))...(((((((..(((.((.((------..((((....))))...)))).))).......)))))))..)))))). ( -27.20)
>DroPse_CAF1 76304 100 + 1
-UG----UAUCUGACAGAUACAGAU----AGUCAGGGGCAUUUAGAGGGGCGUGUGCGCUGCGCGUGUGACGUCACAGAAGCCAAGCCCCAA--AUCUCCACCAAUCAGAA
-((----((((.....))))))(((----.(...((((.((((...(((((...((.(((...(.((((....))))).))))).)))))))--))))))..).))).... ( -31.40)
>DroSec_CAF1 49966 99 + 1
AUG----UAUCUGACAGAUACAUAUAU--AUAUAUCGCUGUUUAGAGGGGCGUGCGC------CGUGUGACGUCACGGAAGCCAAGCCCCAAAAAUCUGAACCAAUCACAA
(((----((((.....)))))))....--..........((((((((((((..((.(------((((......)))))..))...))))).....)))))))......... ( -32.60)
>DroSim_CAF1 49383 101 + 1
AUG----UAUCUGACAGAUACAUAUGUAUAUGUAUCGCUGUUUAGAGGGGCGUACGC------CGUGUGACGUCACGGAAGCCAAGCCCCAAAAAUCUGAACCAAUCACAA
.((----(........((((((((....))))))))...((((((((((((.....(------((((......))))).......))))).....))))))).....))). ( -33.00)
>DroEre_CAF1 54031 89 + 1
AUG----UAUCUGUUAGAUA------------UAUCGCUUUGCAGAGGGGCGUGCGC------CGUGUGACGUCACGGAAGCCAGGCCCCAAAAAUCUGAACCAAUCAGAA
...----..(((((.((...------------.....))..)))))(((((.((..(------((((......)))))....)).))))).....(((((.....))))). ( -31.60)
>DroYak_CAF1 53094 93 + 1
AUGUAUGUAUCUGUUAGAUA------------UAUCGCUUUUUAGAGGGGCGUGCGC------CGCGUGACGUCACGGAAGCCAAGCCCCAAAAAUCGGAACCAAUCAGAA
..(((((((((.....))))------------))).))........(((((.((.((------..((((....))))...)))).)))))..................... ( -25.30)
>consensus
AUG____UAUCUGACAGAUACA_______AU_UAUCGCUGUUUAGAGGGGCGUGCGC______CGUGUGACGUCACGGAAGCCAAGCCCCAAAAAUCUGAACCAAUCAGAA
.........(((((..((((............)))).....)))))(((((.((.((......((((......))))...)))).))))).....(((((.....))))). (-16.81 = -18.62 +   1.81)

alignment

secondary structure

dotplot

Window 7

Location	12,808,506 – 12,808,603
Length	97
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	80.07
Mean single sequence MFE	-29.23
Consensus MFE	-18.10
Energy contribution	-18.30
Covariance contribution	0.20
Combinations/Pair	1.21
Mean z-score	-1.83
Structure conservation index	0.62
SVM decision value	0.45
SVM RNA-class probability	0.739562
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12808506 97 - 23771897
GUCUGAUUGGUUCAGAUUUUUGGGGCUUGGCUUUCGUGACGUCACACG------GCGCACGCCUCUCUAAACAGCGAUACAUAUA----UAUAUCUAUCAGAUA----CAU
(((((((..(((.(((.....(((((.(((((...(((....)))..)------)).)).)))))))).)))...((((......----..)))).))))))).----... ( -24.90)
>DroPse_CAF1 76304 100 - 1
UUCUGAUUGGUGGAGAU--UUGGGGCUUGGCUUCUGUGACGUCACACGCGCAGCGCACACGCCCCUCUAAAUGCCCCUGACU----AUCUGUAUCUGUCAGAUA----CA-
.((((((.((((.((((--..(((((.((((..(((((.((.....))))))).)).)).))))).................----)))).)))).))))))..----..- ( -35.41)
>DroSec_CAF1 49966 99 - 1
UUGUGAUUGGUUCAGAUUUUUGGGGCUUGGCUUCCGUGACGUCACACG------GCGCACGCCCCUCUAAACAGCGAUAUAU--AUAUAUGUAUCUGUCAGAUA----CAU
.((((.((((((.(((.....(((((...((..(((((......))))------).))..)))))))).)))...(((((((--....)))))))...))).))----)). ( -30.20)
>DroSim_CAF1 49383 101 - 1
UUGUGAUUGGUUCAGAUUUUUGGGGCUUGGCUUCCGUGACGUCACACG------GCGUACGCCCCUCUAAACAGCGAUACAUAUACAUAUGUAUCUGUCAGAUA----CAU
.((((.((((((.(((.....(((((...((..(((((......))))------).))..)))))))).)))...((((((((....))))))))...))).))----)). ( -31.60)
>DroEre_CAF1 54031 89 - 1
UUCUGAUUGGUUCAGAUUUUUGGGGCCUGGCUUCCGUGACGUCACACG------GCGCACGCCCCUCUGCAAAGCGAUA------------UAUCUAACAGAUA----CAU
.(((((.....))))).....(((((...((..(((((......))))------).))..)))))..............------------((((.....))))----... ( -26.20)
>DroYak_CAF1 53094 93 - 1
UUCUGAUUGGUUCCGAUUUUUGGGGCUUGGCUUCCGUGACGUCACGCG------GCGCACGCCCCUCUAAAAAGCGAUA------------UAUCUAACAGAUACAUACAU
.((((.((((...((.((((((((((.(((((..((((....)))).)------)).)).)))))...))))).))...------------...))))))))......... ( -27.10)
>consensus
UUCUGAUUGGUUCAGAUUUUUGGGGCUUGGCUUCCGUGACGUCACACG______GCGCACGCCCCUCUAAACAGCGAUA_AU_______UGUAUCUAUCAGAUA____CAU
.((((((.(((..........(((((.((((...((((......))))......)).)).)))))((........))...............))).))))))......... (-18.10 = -18.30 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:40 2006