Locus 8644

Sequence ID	3L_DroMel_CAF1
Location	22,443,290 – 22,443,609
Length	319
Max. P	0.963137

overview

Window 4

Location	22,443,290 – 22,443,410
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	98.75
Mean single sequence MFE	-35.52
Consensus MFE	-34.45
Energy contribution	-34.70
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.90
Structure conservation index	0.97
SVM decision value	0.41
SVM RNA-class probability	0.725345
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22443290 120 - 23771897
UAAAAAUAAUGAGUUUGCCGCUUCCUCUUUGGCAGCGGCUCCUGCGGAAGCGGCUUGAAAACCCGAUUAAAAAUUGAGCAGCGAGCAAGGACGUUAAGUAGAAAUGUCAAUAUGACAGCU
......(((((.....((((((.((.....)).))))))((((((....)).(((((....(.((((.....)))).)...))))).)))))))))........((((.....))))... ( -35.50)
>DroSec_CAF1 14990 120 - 1
UAAAAAUAAUGAGUUUGCCGCUUCCUCUUUGGCAGCGGCUCCUGCGGAAGCGGCUUGAAAACCCGAUUAAAAAUUGAGCAGCGAGCAAGGACGUUAAGUAGAAAUGUCAAUAUGACAGCU
......(((((.....((((((.((.....)).))))))((((((....)).(((((....(.((((.....)))).)...))))).)))))))))........((((.....))))... ( -35.50)
>DroSim_CAF1 19571 120 - 1
UAAAAAUAAUGAGUUUGCCGCUUCCUCUUUGGCAGCGGCUCCUGCGGAAGCGGCUUGAAAACCCGAUUAAAAAUUGAGCAGCGAGCAAGGACGUUAAGUAGAAAUGUCAAUAUGACAGCU
......(((((.....((((((.((.....)).))))))((((((....)).(((((....(.((((.....)))).)...))))).)))))))))........((((.....))))... ( -35.50)
>DroEre_CAF1 21849 120 - 1
UAAAAAUAAUGAGUUUGCCGCUUCCUCUUUGGACGCGGCUCCUGCGGAAGCGGCUUGGAAACCCGAUUAAAAAUUGAGCAGCGAGCAAGGACGUUAAGUAGAAAUGUCAAUAUGACAGCU
............(((((((((.(((.....))).)))((((((((....)))).((((....)))).........)))).))))))...((((((.......))))))............ ( -35.60)
>consensus
UAAAAAUAAUGAGUUUGCCGCUUCCUCUUUGGCAGCGGCUCCUGCGGAAGCGGCUUGAAAACCCGAUUAAAAAUUGAGCAGCGAGCAAGGACGUUAAGUAGAAAUGUCAAUAUGACAGCU
......(((((.....((((((.((.....)).))))))((((((....)).(((((....(.((((.....)))).)...))))).)))))))))........((((.....))))... (-34.45 = -34.70 +   0.25)

alignment

secondary structure

dotplot

Window 5

Location	22,443,370 – 22,443,490
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	97.64
Mean single sequence MFE	-27.97
Consensus MFE	-26.35
Energy contribution	-26.60
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.04
Structure conservation index	0.94
SVM decision value	0.78
SVM RNA-class probability	0.849695
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22443370 120 - 23771897
UAAAUAUGAAAAUUAAAAUUACAAAAUGCACAAAUUGCAGCGACGUGGAGCGAGGUGAAGUGCAGCGAAAAUCAUAUUAAUAAAAAUAAUGAGUUUGCCGCUUCCUCUUUGGCAGCGGCU
..(((((((.(((....)))......(((((...(..(.((........))...)..).))))).......)))))))..................((((((.((.....)).)))))). ( -27.40)
>DroSec_CAF1 15070 120 - 1
UAAAUAUGAAAAUUAAAAUUACAAAAUGCACAAAUUGCAGCGACGUGAAGCGAGGUGAAGUGCAGUGAAAAUCAUAUUAAUAAAAAUAAUGAGUUUGCCGCUUCCUCUUUGGCAGCGGCU
..(((((((.(((....))).((...(((((...(..(.((........))...)..).))))).))....)))))))..................((((((.((.....)).)))))). ( -28.60)
>DroSim_CAF1 19651 120 - 1
UAAAUAUGAAAAUUAAAAUUACAAAAUGCACAAAUUGCAGCGACGUGAAGCGAGGUGAAGUGCAGUGAAAAUCAUAUUAAUAAAAAUAAUGAGUUUGCCGCUUCCUCUUUGGCAGCGGCU
..(((((((.(((....))).((...(((((...(..(.((........))...)..).))))).))....)))))))..................((((((.((.....)).)))))). ( -28.60)
>DroEre_CAF1 21929 120 - 1
UAAAUAUGAAAAUUAAAAUUACAAAAUGCACAAAUUGCAGCGACGUGGAGCGAAGUGAAGUGCAGCGAAAAUCAUAUUAAUAAAAAUAAUGAGUUUGCCGCUUCCUCUUUGGACGCGGCU
..(((((((.................((((.....))))....(((...((........))...)))....)))))))..................(((((.(((.....))).))))). ( -27.30)
>consensus
UAAAUAUGAAAAUUAAAAUUACAAAAUGCACAAAUUGCAGCGACGUGAAGCGAGGUGAAGUGCAGCGAAAAUCAUAUUAAUAAAAAUAAUGAGUUUGCCGCUUCCUCUUUGGCAGCGGCU
..(((((((.(((....)))......(((((...(..(.((........))...)..).))))).......)))))))..................((((((.((.....)).)))))). (-26.35 = -26.60 +   0.25)

alignment

secondary structure

dotplot

Window 6

Location	22,443,490 – 22,443,609
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	97.08
Mean single sequence MFE	-35.63
Consensus MFE	-34.00
Energy contribution	-34.25
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.48
Structure conservation index	0.95
SVM decision value	1.55
SVM RNA-class probability	0.963137
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22443490 119 - 23771897
AGGCUUAAAACAAAUAAUUGCAAAUAAAUGAUGUUCAUUGGAGGGAACAAUGAGAUGCAUUGACACUGGCGCAUACUGUCAGCUUCAUCGCAUCAGCAUCAGGAGCCC-GGCAAUGCCCU
.(((((....(((....)))........((((((((((((.......))))))(((((..(((..((((((.....))))))..)))..))))).)))))).))))).-(((...))).. ( -36.20)
>DroSec_CAF1 15190 120 - 1
AGGCUUAAAACAAAUAAUUGCAAAUAAAUGAUGUUCAUUGGAGGGAACAAUGAGAUGCAUUGACACUGGCGCGCACUGUCAGCUUCAUCGCAUCAGCAUCAGCAGCCCAGGCAAUGCCCU
.(((..............(((.......((((((((((((.......))))))(((((..(((..((((((.....))))))..)))..))))).)))))))))((....))...))).. ( -35.61)
>DroSim_CAF1 19771 120 - 1
AGGCUUAAAACAAAUAAUUGCAAAUAAAUGAUGUUCAUUGGAGAGAACAAUGAGAUGCAUUGACACUGGCGCGCACUGUCAGCUUCAUCGCAUCAGCAUCAGCAGCCCAGGCAAUGCCCU
.(((..............(((.......((((((((((((.......))))))(((((..(((..((((((.....))))))..)))..))))).)))))))))((....))...))).. ( -35.61)
>DroEre_CAF1 22049 120 - 1
AGGCUUAAAACAAAUAAUUGCAAAUAAAUGAUGUUCAUUGGAGGGAACAAUGAGAUGCAUUGACACUGGCGCGCACUGUCAGCCGCAUCGCAUCAGCAUCAGCAGCCCAGGCAAUGCCCU
.(((..............(((.......((((((((((((.......))))))(((((.((((((.((.....)).))))))..)))))))))))......)))((....))...))).. ( -35.12)
>consensus
AGGCUUAAAACAAAUAAUUGCAAAUAAAUGAUGUUCAUUGGAGGGAACAAUGAGAUGCAUUGACACUGGCGCGCACUGUCAGCUUCAUCGCAUCAGCAUCAGCAGCCCAGGCAAUGCCCU
.(((........................((((((((((((.......))))))(((((..(((..((((((.....))))))..)))..))))).))))))...((....))...))).. (-34.00 = -34.25 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:21:13 2006