Locus 1133

Sequence ID	2L_DroMel_CAF1
Location	3,079,737 – 3,079,840
Length	103
Max. P	0.710200

overview

Window 4

Location	3,079,737 – 3,079,840
Length	103
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	79.14
Mean single sequence MFE	-25.76
Consensus MFE	-13.00
Energy contribution	-14.88
Covariance contribution	1.88
Combinations/Pair	1.10
Mean z-score	-2.02
Structure conservation index	0.50
SVM decision value	0.37
SVM RNA-class probability	0.710200
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3079737 103 + 22407834
UACGUAAAUCAAUUGUGGUUGAGAAGUCAGCAGACAAACAUCAUCAUAAAUCGAUUUAUGAUGUGCGUAGAUGAUGUCUGUAGAGAUGGUCCUUCUCCGCCAA
...............((((.((((((((.(((((((..((((((((((((....)))))))).......)))).))))))).)).......)))))).)))). ( -28.62)
>DroSec_CAF1 4828 102 + 1
UACCUAAAUCAAUUGUGGUUGAGAAGCCAGCAGACAAACAUCAUCAUAAAUCGAUUUAUGAUUUGCGUAGAUGAUGUC-GUAGAGACGGUCCUUCUCCGCCAA
...............((((.((((((......(((..((((((((.(((((((.....)))))))....))))))))(-((....)))))))))))).)))). ( -26.70)
>DroSim_CAF1 4820 103 + 1
UACCUAAAUCAAUUGUGGUUGAGAAGUCAGCAGACAAACAUCAUCAUAAAUCGAUUUAUGAUGUGUGUAGAUGAUGUCUGUAGAGGCGGUCCUUCUCCGCCAA
........(((((....)))))....((.(((((((.(((((((((((((....))))))))).))))......))))))).))(((((.......))))).. ( -31.40)
>DroEre_CAF1 4801 96 + 1
UGCCUAAAUCAAUUGUGGUUGAGAAGUCAGCAGACGAACAU---CAUAAAUCGAUUUAUGGUGUACCUGGUUGAUGUCUGGAG---CGGU-CUUCUCCGCCAA
...............((((.((((((.(.((......((((---((((((....))))))))))..(..(.......)..).)---).).-)))))).)))). ( -28.10)
>DroYak_CAF1 4828 81 + 1
UACCUAAAUCAAUUGUGGUCGAAAAGUCAGCAGACAAACAUCAUCAUAAAUCGAUUUAUGAUGUACCCA-----UACUCG-----------------UACUCG
.............(((((.......(((....)))......(((((((((....)))))))))...)))-----))....-----------------...... ( -14.00)
>consensus
UACCUAAAUCAAUUGUGGUUGAGAAGUCAGCAGACAAACAUCAUCAUAAAUCGAUUUAUGAUGUGCGUAGAUGAUGUCUGUAGAG_CGGUCCUUCUCCGCCAA
...............((((.((((((((....)))......(((((((((....))))))))).............................))))).)))). (-13.00 = -14.88 +   1.88)

alignment

secondary structure

dotplot

Window 5

Location	3,079,737 – 3,079,840
Length	103
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	79.14
Mean single sequence MFE	-24.48
Consensus MFE	-12.78
Energy contribution	-15.06
Covariance contribution	2.28
Combinations/Pair	1.19
Mean z-score	-1.88
Structure conservation index	0.52
SVM decision value	0.09
SVM RNA-class probability	0.580533
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3079737 103 - 22407834
UUGGCGGAGAAGGACCAUCUCUACAGACAUCAUCUACGCACAUCAUAAAUCGAUUUAUGAUGAUGUUUGUCUGCUGACUUCUCAACCACAAUUGAUUUACGUA
.(((..((((((...((.(...((((((((((((.......(((.......)))....))))))))))))..).)).))))))..)))............... ( -27.90)
>DroSec_CAF1 4828 102 - 1
UUGGCGGAGAAGGACCGUCUCUAC-GACAUCAUCUACGCAAAUCAUAAAUCGAUUUAUGAUGAUGUUUGUCUGCUGGCUUCUCAACCACAAUUGAUUUAGGUA
.(((..((((((..(((.(...((-(((((((((.....(((((.......)))))..))))))).))))..).)))))))))..)))............... ( -26.40)
>DroSim_CAF1 4820 103 - 1
UUGGCGGAGAAGGACCGCCUCUACAGACAUCAUCUACACACAUCAUAAAUCGAUUUAUGAUGAUGUUUGUCUGCUGACUUCUCAACCACAAUUGAUUUAGGUA
.(((..((((((..(.((....((((((((((((.......(((.......)))....))))))))))))..)).).))))))..)))............... ( -29.10)
>DroEre_CAF1 4801 96 - 1
UUGGCGGAGAAG-ACCG---CUCCAGACAUCAACCAGGUACACCAUAAAUCGAUUUAUG---AUGUUCGUCUGCUGACUUCUCAACCACAAUUGAUUUAGGCA
.(((..((((((-....---(..((((((((.....)))(((.((((((....))))))---.)))..)))))..).))))))..)))............... ( -23.20)
>DroYak_CAF1 4828 81 - 1
CGAGUA-----------------CGAGUA-----UGGGUACAUCAUAAAUCGAUUUAUGAUGAUGUUUGUCUGCUGACUUUUCGACCACAAUUGAUUUAGGUA
.((((.-----------------(((...-----(((...(((((((((....)))))))))......(((....))).......)))...)))))))..... ( -15.80)
>consensus
UUGGCGGAGAAGGACCG_CUCUACAGACAUCAUCUACGCACAUCAUAAAUCGAUUUAUGAUGAUGUUUGUCUGCUGACUUCUCAACCACAAUUGAUUUAGGUA
.(((..((((((...........((((((((..........((((((((....))))))))))))))))((....))))))))..)))............... (-12.78 = -15.06 +   2.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:32 2006