Locus 5023

Sequence ID	3L_DroMel_CAF1
Location	13,775,508 – 13,775,725
Length	217
Max. P	0.866534

overview

Window 8

Location	13,775,508 – 13,775,619
Length	111
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	94.43
Mean single sequence MFE	-29.26
Consensus MFE	-29.48
Energy contribution	-28.44
Covariance contribution	-1.04
Combinations/Pair	1.15
Mean z-score	-1.05
Structure conservation index	1.01
SVM decision value	0.34
SVM RNA-class probability	0.694948
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13775508 111 + 23771897
AAGGUUGGAAAUAAUCAAUAAUGAAAUGAAGGAGUUUGCCGAAACUUUGGCAAUAAGUGGUUUUGGGCUUGGCUUCCCUCG-GGCAGACUCCGUAGGUUUUGCUUAAUUUUG
..(((((....)))))......(((((...((((((((((((((((...((.....))))))))(((........)))...-)))))))))).((((.....))))))))). ( -28.10)
>DroSec_CAF1 22129 108 + 1
AAGGUUGGAAA---UCAAUAAUGAAAUGAAGGAGUUUGCCGAAACUUUGGCAAUAAGUGGUUUUGGGCUUGGCUUCCCUCG-GGCAGACUCCGUAGGUUUUGCUUAAUUUUG
...((((....---.))))...(((((...((((((((((((((((...((.....))))))))(((........)))...-)))))))))).((((.....))))))))). ( -26.70)
>DroSim_CAF1 17797 111 + 1
AAGGUUGGAAAUAAUCAAUAAUGAAAUGAAGGAGUUUGCCGAAACUUUGGCAAUAAGUGGUUUUGGGCUUGACUUCCCUCG-GGCAGACUCCGUAGGUUUUGCUUAAUUUUG
..(((((....)))))......(((((...((((((((((((((((...((.....))))))))(((........)))...-)))))))))).((((.....))))))))). ( -28.10)
>DroEre_CAF1 21567 111 + 1
AAGGUUGAAAAUAAUCAAUAAUGGAAUGAAGGAGUUUGCCGAAACUUUGGCAAUAAGUGGUUUCGGGCUUGGUUUCCCUCG-GGCAGACUCUGAAGGUUUCGCUUAAUUUGG
((((((((......)))))...(((((...((((((((((((((((...((.....))))))))(((........)))...-))))))))))....))))).)))....... ( -30.50)
>DroYak_CAF1 20302 112 + 1
AAGGUUGAAAAUAAUCAAUAAUGAAAUGAAGGAGUUUGCCGAAACUUUGGCAAUAAGUGGUUUCGGGCUUGGUUUCCCUCGGGGCAGACUCCGAAGGUUUCGCUUAAUUUUG
((((((((......)))))...(((((...((((((((((((((((...((.....))))))))(((........)))....))))))))))....))))).)))....... ( -32.90)
>consensus
AAGGUUGGAAAUAAUCAAUAAUGAAAUGAAGGAGUUUGCCGAAACUUUGGCAAUAAGUGGUUUUGGGCUUGGCUUCCCUCG_GGCAGACUCCGUAGGUUUUGCUUAAUUUUG
((((((((......)))))...(((((...((((((((((((((((...((.....))))))))(((........)))....))))))))))....))))).)))....... (-29.48 = -28.44 +  -1.04)

alignment

secondary structure

dotplot

Window 9

Location	13,775,508 – 13,775,619
Length	111
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	94.43
Mean single sequence MFE	-21.20
Consensus MFE	-17.10
Energy contribution	-17.30
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.64
Structure conservation index	0.81
SVM decision value	0.44
SVM RNA-class probability	0.739089
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13775508 111 - 23771897
CAAAAUUAAGCAAAACCUACGGAGUCUGCC-CGAGGGAAGCCAAGCCCAAAACCACUUAUUGCCAAAGUUUCGGCAAACUCCUUCAUUUCAUUAUUGAUUAUUUCCAACCUU
...((((((...........(((((.((((-.(((((........)))......((((.......)))).)))))).)))))............))))))............ ( -20.10)
>DroSec_CAF1 22129 108 - 1
CAAAAUUAAGCAAAACCUACGGAGUCUGCC-CGAGGGAAGCCAAGCCCAAAACCACUUAUUGCCAAAGUUUCGGCAAACUCCUUCAUUUCAUUAUUGA---UUUCCAACCUU
..(((((((...........(((((.((((-.(((((........)))......((((.......)))).)))))).)))))............))))---)))........ ( -20.40)
>DroSim_CAF1 17797 111 - 1
CAAAAUUAAGCAAAACCUACGGAGUCUGCC-CGAGGGAAGUCAAGCCCAAAACCACUUAUUGCCAAAGUUUCGGCAAACUCCUUCAUUUCAUUAUUGAUUAUUUCCAACCUU
...((((((...........(((((.((((-.(((((........)))......((((.......)))).)))))).)))))............))))))............ ( -20.10)
>DroEre_CAF1 21567 111 - 1
CCAAAUUAAGCGAAACCUUCAGAGUCUGCC-CGAGGGAAACCAAGCCCGAAACCACUUAUUGCCAAAGUUUCGGCAAACUCCUUCAUUCCAUUAUUGAUUAUUUUCAACCUU
.....................((((.((((-...((....))......(((((..............))))))))).)))).............((((......)))).... ( -20.24)
>DroYak_CAF1 20302 112 - 1
CAAAAUUAAGCGAAACCUUCGGAGUCUGCCCCGAGGGAAACCAAGCCCGAAACCACUUAUUGCCAAAGUUUCGGCAAACUCCUUCAUUUCAUUAUUGAUUAUUUUCAACCUU
...........((((.....(((((.((((....((....))......(((((..............))))))))).)))))....))))....((((......)))).... ( -25.14)
>consensus
CAAAAUUAAGCAAAACCUACGGAGUCUGCC_CGAGGGAAGCCAAGCCCAAAACCACUUAUUGCCAAAGUUUCGGCAAACUCCUUCAUUUCAUUAUUGAUUAUUUCCAACCUU
....................(((((.((((....(((........)))......((((.......))))...)))).))))).............................. (-17.10 = -17.30 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	13,775,619 – 13,775,725
Length	106
Sequences	4
Columns	106
Reading direction	reverse
Mean pairwise identity	97.64
Mean single sequence MFE	-25.77
Consensus MFE	-24.65
Energy contribution	-24.27
Covariance contribution	-0.37
Combinations/Pair	1.06
Mean z-score	-2.03
Structure conservation index	0.96
SVM decision value	0.85
SVM RNA-class probability	0.866534
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13775619 106 - 23771897
GACUAAUGUAAUAUUUAAGCGACAGAAAUAUUCACAAAAAGUUCAGCUUAAUCGCAAGCUGCAUCUGUUGCUAUACCAACUUUUGCCUGGUAUUUAAGUAAGGCAU
.....((((..(((((((((((((((.......((.....)).((((((......))))))..)))))))))((((((.........)))))).))))))..)))) ( -26.60)
>DroSim_CAF1 17908 106 - 1
GGAUAAUGUAAUAUUUAAGCGACAGAAAUAUUCACAAAAAGUUGAGCUUAAUCGCAGGCUGCAUCUGUUGCUAUACCAACUUUUGCCUGGUAUUUAAGUAAGGCAU
.....((((..(((((((((((((((........(((....)))(((((......)))))...)))))))))((((((.........)))))).))))))..)))) ( -25.60)
>DroEre_CAF1 21678 106 - 1
GGAUAAUGUAAUAUUUAAGCGACAGAAAUAUUCACAAAAAGUUGAGCUUAAUCGCAGGCUGCAUCUGUUGCUAUACCAACUUUUGCCUGGUAUUUAAGUGAGGCAU
.....((((..(((((((((((((((........(((....)))(((((......)))))...)))))))))((((((.........)))))).))))))..)))) ( -25.30)
>DroYak_CAF1 20414 106 - 1
GGAUAAUGUAAUAUUUAAGCGACAGAAAUAUUCACAAAAAGUUGAGCUUAAUCGCAGGCUGCAUCUGUUGCUAUACCAACUUUUGCCUGGUAUUUAAGUAAGGCAU
.....((((..(((((((((((((((........(((....)))(((((......)))))...)))))))))((((((.........)))))).))))))..)))) ( -25.60)
>consensus
GGAUAAUGUAAUAUUUAAGCGACAGAAAUAUUCACAAAAAGUUGAGCUUAAUCGCAGGCUGCAUCUGUUGCUAUACCAACUUUUGCCUGGUAUUUAAGUAAGGCAU
.....((((..(((((((((((((((.......((.....))..(((((......)))))...)))))))))((((((.........)))))).))))))..)))) (-24.65 = -24.27 +  -0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:54 2006