Locus 5311

Sequence ID	2R_DroMel_CAF1
Location	17,229,089 – 17,229,237
Length	148
Max. P	0.994530

overview

Window 4

Location	17,229,089 – 17,229,197
Length	108
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	77.33
Mean single sequence MFE	-24.02
Consensus MFE	-19.83
Energy contribution	-18.99
Covariance contribution	-0.84
Combinations/Pair	1.40
Mean z-score	-2.41
Structure conservation index	0.83
SVM decision value	2.49
SVM RNA-class probability	0.994530
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17229089 108 + 20766785
AACUGUAACUGUCCUACCUUUAUUACAAAUUUCGAGCUUCUGUUUCUGUGUGUUUUAUGAAGCUGAUAAGCAGC------ACCCACCGCCCUGCUUAUCAGCUUAGAGUUCUGC
...(((((..(........)..)))))......((((((........(((.....))).((((((((((((((.------.(.....)..)))))))))))))).))))))... ( -25.60)
>DroSec_CAF1 28894 101 + 1
AACUUUUA-------ACCUUUAUUACAAAUUUCGAACUUCUUUUUCUGUGUGUUUUAUGGAGCUAAUAAGCAGC------ACCCACCGCCCUGCUUAUCAGUUUAGAGUUCUGC
........-------..................((((((.....((((((.....))))))(((.((((((((.------.(.....)..)))))))).)))...))))))... ( -18.40)
>DroSim_CAF1 31313 98 + 1
----------------CCUUUAUUACAACUUUCGAGCUUCUGUUUCUGUGUGUUUUAUGGAACUGAUAAGCGGUUCCAUAACCCACCGCCCUGCUUAUCAGUUUAGAGUUCUGC
----------------.................(((((.(((...(((.(((..(((((((((((.....)))))))))))..))).((...))....)))..))))))))... ( -26.60)
>DroEre_CAF1 29472 104 + 1
AGCUUUAAUUUUCCUACCUUUAUUACAAAUGUCGAGGUUUUUCUUUGG---UUUGUUUGGUGCUGAUAAGUAGC------ACCC-CCGCCCUGCUUAUCAGUUUAGAGUUCUGC
((((((((.......(((......((((((..(((((.....))))))---)))))..)))((((((((((((.------.(..-..)..)))))))))))))))))))).... ( -26.60)
>DroYak_CAF1 29451 103 + 1
AGCUUUAACCUUCCUACCUUUAUUACAAAUUUCGAGCUUCUUUUUU-----UUUUUAUGAAGCUGAUAAGUAGC------ACCCCCCGCCCUGCUUAUCAGUUUAGGGCUCUGC
((((((((.((.......................((((((......-----.......))))))(((((((((.------.(.....)..))))))))))).)))))))).... ( -22.92)
>consensus
AACUUUAA___UCCUACCUUUAUUACAAAUUUCGAGCUUCUUUUUCUGUGUGUUUUAUGGAGCUGAUAAGCAGC______ACCCACCGCCCUGCUUAUCAGUUUAGAGUUCUGC
.................................((((((....................((((((((((((((.................)))))))))))))).))))))... (-19.83 = -18.99 +  -0.84)

alignment

secondary structure

dotplot

Window 5

Location	17,229,127 – 17,229,237
Length	110
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	78.50
Mean single sequence MFE	-27.48
Consensus MFE	-19.13
Energy contribution	-18.97
Covariance contribution	-0.16
Combinations/Pair	1.29
Mean z-score	-1.58
Structure conservation index	0.70
SVM decision value	0.33
SVM RNA-class probability	0.692371
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17229127 110 + 20766785
UCUGUUUCUGUGUGUUUUAUGAAGCUGAUAAGCAGC------ACCCACCGCCCUGCUUAUCAGCUUAGAGUUCUGCCCUCAUAUGCUACCAUAAGGAAAUUCCGGGCUAAGAUAAC
............(((((((..((((((((((((((.------.(.....)..))))))))))))))........((((...((((....)))).((.....))))))))))))).. ( -33.50)
>DroSec_CAF1 28925 110 + 1
UCUUUUUCUGUGUGUUUUAUGGAGCUAAUAAGCAGC------ACCCACCGCCCUGCUUAUCAGUUUAGAGUUCUGCCUUCAUAUGCUACCAUUAGGAAAUUCCGGGUUAAGAUAAG
((((..((((...........(((((.((((((((.------.(.....)..)))))))).))))).(((((...(((....(((....))).))).)))))))))..)))).... ( -23.10)
>DroSim_CAF1 31335 116 + 1
UCUGUUUCUGUGUGUUUUAUGGAACUGAUAAGCGGUUCCAUAACCCACCGCCCUGCUUAUCAGUUUAGAGUUCUGCCUUCAUAUGCUACCAUUAGGAAAUUCCGGGUUAAGAUAAC
......((((.(((..(((((((((((.....)))))))))))..))))((((.((.(((.((..(((....)))..)).))).))........((.....))))))..))).... ( -28.80)
>DroEre_CAF1 29510 93 + 1
UUUUCUUUGG---UUUGUUUGGUGCUGAUAAGUAGC------ACCC-CCGCCCUGCUUAUCAGUUUAGAGUUCUGCCCUCAUGUGUUAUCAUAAGGAAA-------------UUAC
.(((((((((---(...(((...((((((((((((.------.(..-..)..))))))))))))...)))....))).....(((....))))))))))-------------.... ( -21.60)
>DroYak_CAF1 29489 105 + 1
UCUUUUUU-----UUUUUAUGAAGCUGAUAAGUAGC------ACCCCCCGCCCUGCUUAUCAGUUUAGGGCUCUGCCCUCAUGUGUCAGCAUAAGGAAAUUCCGGGUGAAGAUUAC
(((((.((-----((((((((((((((((((((((.------.(.....)..))))))))))))))(((((...)))))..........))))))))))........))))).... ( -30.40)
>consensus
UCUUUUUCUGUGUGUUUUAUGGAGCUGAUAAGCAGC______ACCCACCGCCCUGCUUAUCAGUUUAGAGUUCUGCCCUCAUAUGCUACCAUAAGGAAAUUCCGGGUUAAGAUAAC
..............(((((((((((((((((((((.................)))))))))))))).(((.......))).........))))))).................... (-19.13 = -18.97 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:47 2006