Locus 7692

Sequence ID	3L_DroMel_CAF1
Location	20,592,550 – 20,592,686
Length	136
Max. P	0.970864

overview

Window 4

Location	20,592,550 – 20,592,650
Length	100
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.41
Mean single sequence MFE	-24.04
Consensus MFE	-19.74
Energy contribution	-19.94
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.93
Structure conservation index	0.82
SVM decision value	1.13
SVM RNA-class probability	0.919384
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20592550 100 + 23771897
GC--------------------UGCACUCAAUAUUCAAUUUUGCAUUUUACAACAAAUGCGUGCCUUACCAUAUUUAGGUGGCGUGCAAAAAUAAGCCAAACCCAAAAGGCUCAAGAGAC
..--------------------(((((...............((((((......))))))..(((..(((.......)))))))))))......((((..........))))........ ( -21.80)
>DroSec_CAF1 37229 100 + 1
GC--------------------UGCACUCAAUAUUCAAUUUUGCAUUUUACAACAAAUGCGUGCCUUACCAUAUUUAGGUGGCGUGCAAAAAUAAGCCAAACCCAAAAGGCUCAAGAGAC
..--------------------(((((...............((((((......))))))..(((..(((.......)))))))))))......((((..........))))........ ( -21.80)
>DroAna_CAF1 60301 117 + 1
CCGCUUACCGCAGCUUACUGCUUGCACUCAAUAUUCAAUUUUGCAUUUUACAACAAAUGCGUGCCUUACCAUAUUUAGUUGGCGUGCAAAAAUAAGCCAAAGCCUUGGGGCCGGAGA---
(((((((..((((....))))((((((...............((((((......))))))..(((..((........)).)))))))))...)))))....(((....))).))...--- ( -31.60)
>DroSim_CAF1 30724 100 + 1
GC--------------------UGCACUCAAUAUUCAAUUUUGCAUUUUACAACAAAUGCGUGCCUUACCAUAUUUAGGUGGCGUGCAAAAAUAAGCCAAACCCAAAAGGCUCAAGAGAC
..--------------------(((((...............((((((......))))))..(((..(((.......)))))))))))......((((..........))))........ ( -21.80)
>DroEre_CAF1 30393 100 + 1
GC--------------------UGCACUCAAUAUUCAAUUUUGCAUUUUACAACAAAUGCGUGCCUUACCAUAUUUAGGUGGCGUGCAAAAAUAAGCCAAGCCCAAAAGGCUCAAGAGAC
..--------------------....(((.............((((((......))))))(.((((((((.......)))(((..((........))...)))...))))).)..))).. ( -23.20)
>consensus
GC____________________UGCACUCAAUAUUCAAUUUUGCAUUUUACAACAAAUGCGUGCCUUACCAUAUUUAGGUGGCGUGCAAAAAUAAGCCAAACCCAAAAGGCUCAAGAGAC
......................(((((...............((((((......))))))..(((..(((.......))))))))))).......(((..........)))......... (-19.74 = -19.94 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	20,592,550 – 20,592,650
Length	100
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.41
Mean single sequence MFE	-30.38
Consensus MFE	-24.86
Energy contribution	-25.30
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-2.21
Structure conservation index	0.82
SVM decision value	1.67
SVM RNA-class probability	0.970864
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20592550 100 - 23771897
GUCUCUUGAGCCUUUUGGGUUUGGCUUAUUUUUGCACGCCACCUAAAUAUGGUAAGGCACGCAUUUGUUGUAAAAUGCAAAAUUGAAUAUUGAGUGCA--------------------GC
......((((((..........))))))...((((((((((((.......)))..)))..((((((......))))))...............)))))--------------------). ( -28.20)
>DroSec_CAF1 37229 100 - 1
GUCUCUUGAGCCUUUUGGGUUUGGCUUAUUUUUGCACGCCACCUAAAUAUGGUAAGGCACGCAUUUGUUGUAAAAUGCAAAAUUGAAUAUUGAGUGCA--------------------GC
......((((((..........))))))...((((((((((((.......)))..)))..((((((......))))))...............)))))--------------------). ( -28.20)
>DroAna_CAF1 60301 117 - 1
---UCUCCGGCCCCAAGGCUUUGGCUUAUUUUUGCACGCCAACUAAAUAUGGUAAGGCACGCAUUUGUUGUAAAAUGCAAAAUUGAAUAUUGAGUGCAAGCAGUAAGCUGCGGUAAGCGG
---...((((((....))))...(((((((.(((((((((.((((....))))..)))..((((((......))))))...............))))))((((....))))))))))))) ( -38.00)
>DroSim_CAF1 30724 100 - 1
GUCUCUUGAGCCUUUUGGGUUUGGCUUAUUUUUGCACGCCACCUAAAUAUGGUAAGGCACGCAUUUGUUGUAAAAUGCAAAAUUGAAUAUUGAGUGCA--------------------GC
......((((((..........))))))...((((((((((((.......)))..)))..((((((......))))))...............)))))--------------------). ( -28.20)
>DroEre_CAF1 30393 100 - 1
GUCUCUUGAGCCUUUUGGGCUUGGCUUAUUUUUGCACGCCACCUAAAUAUGGUAAGGCACGCAUUUGUUGUAAAAUGCAAAAUUGAAUAUUGAGUGCA--------------------GC
.....(..((((.....))))..).......((((((((((((.......)))..)))..((((((......))))))...............)))))--------------------). ( -29.30)
>consensus
GUCUCUUGAGCCUUUUGGGUUUGGCUUAUUUUUGCACGCCACCUAAAUAUGGUAAGGCACGCAUUUGUUGUAAAAUGCAAAAUUGAAUAUUGAGUGCA____________________GC
......((((((..........))))))....(((((((((((.......)))..)))..((((((......))))))...............)))))...................... (-24.86 = -25.30 +   0.44)

alignment

secondary structure

dotplot

Window 6

Location	20,592,570 – 20,592,686
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.14
Mean single sequence MFE	-31.28
Consensus MFE	-22.28
Energy contribution	-23.16
Covariance contribution	0.88
Combinations/Pair	1.07
Mean z-score	-1.79
Structure conservation index	0.71
SVM decision value	-0.04
SVM RNA-class probability	0.513727
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20592570 116 + 23771897
UUGCAUUUUACAACAAAUGCGUGCCUUACCAUAUUUAGGUGGCGUGCAAAAAUAAGCCAAACCCAAAAGGCUCAAGAGACGGGGACAAAAUGUUC--ACUUGGCCAAGAUGC--AAGAUG
(((((((((........((((((((..(((.......)))))))))))....................(((.((((......((((.....))))--.))))))))))))))--)).... ( -31.50)
>DroSec_CAF1 37249 116 + 1
UUGCAUUUUACAACAAAUGCGUGCCUUACCAUAUUUAGGUGGCGUGCAAAAAUAAGCCAAACCCAAAAGGCUCAAGAGACGGGGACAAAAUGUUC--ACUUGGCCAAGAUGC--AAGAUG
(((((((((........((((((((..(((.......)))))))))))....................(((.((((......((((.....))))--.))))))))))))))--)).... ( -31.50)
>DroAna_CAF1 60341 115 + 1
UUGCAUUUUACAACAAAUGCGUGCCUUACCAUAUUUAGUUGGCGUGCAAAAAUAAGCCAAAGCCUUGGGGCCGGAGA-----GGGCAAAAUGUUCCAAGUUGGCCAAGUUGGUUUGGGGA
..((((((......)))))).((((((.((........(((((............))))).(((....))).))..)-----))))).....(((((((..(((...)))..))))))). ( -32.60)
>DroSim_CAF1 30744 116 + 1
UUGCAUUUUACAACAAAUGCGUGCCUUACCAUAUUUAGGUGGCGUGCAAAAAUAAGCCAAACCCAAAAGGCUCAAGAGACGGGGACAAAAUGUUC--ACUUGGCCAAGAUGC--AAGAUG
(((((((((........((((((((..(((.......)))))))))))....................(((.((((......((((.....))))--.))))))))))))))--)).... ( -31.50)
>DroEre_CAF1 30413 116 + 1
UUGCAUUUUACAACAAAUGCGUGCCUUACCAUAUUUAGGUGGCGUGCAAAAAUAAGCCAAGCCCAAAAGGCUCAAGAGACGGGGACAAAAUGUUC--ACUUGGCCAAGAAGC--AAGAUG
((((.((((........((((((((..(((.......))))))))))).......((((((((.....)))...........((((.....))))--..))))).)))).))--)).... ( -29.30)
>consensus
UUGCAUUUUACAACAAAUGCGUGCCUUACCAUAUUUAGGUGGCGUGCAAAAAUAAGCCAAACCCAAAAGGCUCAAGAGACGGGGACAAAAUGUUC__ACUUGGCCAAGAUGC__AAGAUG
..(((((((........((((((((..(((.......)))))))))))....................(((.((((......((((.....))))...))))))))))))))........ (-22.28 = -23.16 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:54:03 2006