Locus 834

Sequence ID	3R_DroMel_CAF1
Location	2,869,882 – 2,870,101
Length	219
Max. P	0.871582

overview

Window 1

Location	2,869,882 – 2,869,985
Length	103
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.41
Mean single sequence MFE	-28.03
Consensus MFE	-19.17
Energy contribution	-18.80
Covariance contribution	-0.37
Combinations/Pair	1.08
Mean z-score	-1.59
Structure conservation index	0.68
SVM decision value	0.10
SVM RNA-class probability	0.582758
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2869882 103 - 27905053
ACAGUGCUUAGUUCAAGGAUAACCAAGAC-----------------AAUAAUUGGCAGGUGGAAAUAUGGUCGAAAUCGGUGACCUUGGACCGGCCAUUUACCAAUGGUAAUGACCAUUU
..((((.(..((((((((...(((.....-----------------.......(((..((....))...)))(....))))..))))))))..).))))....((((((....)))))). ( -24.80)
>DroSec_CAF1 822 113 - 1
ACAGC-CUGAGUUCAAGGAUAACCAAAUCGAAAAACAUCG------AACAAUUGGCAGGUGGAAAUAUGGUCGAAAUCUGUGACCUUGGACCGGCCAUUUACCAAUGGUAAUGACCAUUU
...((-(.(.((((((((.........((((......)))------)....(((((..((....))...))))).........))))))))))))........((((((....)))))). ( -28.60)
>DroSim_CAF1 1180 113 - 1
ACAGC-CUGAGUUCAAGGUUAACCAAAUCGAAAAACAUCG------AACAAUUGGCAGGUGGAAAUAUGGUUGAAAUCUGUGACCUUGGACCGGCCAUUUACCAAUGGUAAUGACCAUUU
...((-(.(.(((((((((((.((((.((((......)))------)....))))(((((...(((...)))...))))))))))))))))))))........((((((....)))))). ( -31.50)
>DroEre_CAF1 1724 119 - 1
ACAGC-CUUAGUUCAAGGAUAACCAAAAAUAACAACAUUGAACAGGAACAAUUGGCAGGUGUAAAUAUGGUCAAAAUCGCUGACCUUGGACCGGCCAUUCACCAAUGGUAAUGACCAUUU
....(-((..((((((.....................)))))))))......((((.(((.(((....(((((.......)))))))).))).))))......((((((....)))))). ( -27.20)
>consensus
ACAGC_CUGAGUUCAAGGAUAACCAAAACGAAAAACAUCG______AACAAUUGGCAGGUGGAAAUAUGGUCGAAAUCGGUGACCUUGGACCGGCCAUUUACCAAUGGUAAUGACCAUUU
..........((((((((.................................(((((..((....))...)))))..((...)))))))))).((.((((.(((...))))))).)).... (-19.17 = -18.80 +  -0.37)

alignment

secondary structure

dotplot

Window 2

Location	2,869,922 – 2,870,025
Length	103
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	82.26
Mean single sequence MFE	-30.17
Consensus MFE	-21.45
Energy contribution	-20.95
Covariance contribution	-0.50
Combinations/Pair	1.17
Mean z-score	-1.79
Structure conservation index	0.71
SVM decision value	0.48
SVM RNA-class probability	0.751558
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2869922 103 - 27905053
UCCAUUGUCAUAGAAAGGGCCAUGGCCCGACUGUCGAAGCACAGUGCUUAGUUCAAGGAUAACCAAGAC-----------------AAUAAUUGGCAGGUGGAAAUAUGGUCGAAAUCGG
((((((((((......((((....))))...((((.((((.....)))).......((....))..)))-----------------).....))))).)))))........((....)). ( -28.00)
>DroSec_CAF1 862 113 - 1
UCCAUUGUUACAGAAAGGGCCAUGGCCCAACUGUCCAGGCACAGC-CUGAGUUCAAGGAUAACCAAAUCGAAAAACAUCG------AACAAUUGGCAGGUGGAAAUAUGGUCGAAAUCUG
..........((((...(((((((..(((.((((((((((...))-))).((((..((....)).....((......)))------)))....))))).)))...)))))))....)))) ( -33.40)
>DroSim_CAF1 1220 113 - 1
UCCAUUGUUACAGAAAGGGCCAUGGCCCAACUGUCGAGGCACAGC-CUGAGUUCAAGGUUAACCAAAUCGAAAAACAUCG------AACAAUUGGCAGGUGGAAAUAUGGUUGAAAUCUG
.((((..((((.....((((....))))..(((((((((...(((-((.......)))))..))...((((......)))------)....)))))))))))....)))).......... ( -32.20)
>DroEre_CAF1 1764 119 - 1
UCCAUUGUCACAGAAAGGACCAUGGUCCAACUGUUGAGGCACAGC-CUUAGUUCAAGGAUAACCAAAAAUAACAACAUUGAACAGGAACAAUUGGCAGGUGUAAAUAUGGUCAAAAUCGC
.((((...(((.....((((....))))..((((..((((...))-)...((((((.....................))))))........)..))))))).....)))).......... ( -27.10)
>consensus
UCCAUUGUCACAGAAAGGGCCAUGGCCCAACUGUCGAGGCACAGC_CUGAGUUCAAGGAUAACCAAAACGAAAAACAUCG______AACAAUUGGCAGGUGGAAAUAUGGUCGAAAUCGG
.((((..((((.....((((....))))..(((((((.(.((........)).)..((....))...........................)))))))))))....)))).......... (-21.45 = -20.95 +  -0.50)

alignment

secondary structure

dotplot

Window 3

Location	2,869,985 – 2,870,101
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	83.33
Mean single sequence MFE	-31.40
Consensus MFE	-25.71
Energy contribution	-26.27
Covariance contribution	0.56
Combinations/Pair	1.12
Mean z-score	-1.90
Structure conservation index	0.82
SVM decision value	0.87
SVM RNA-class probability	0.871582
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2869985 116 + 27905053
GCUUCGACAGUCGGGCCAUGGCCCUUUCUAUGACAAUGGAAUAACUGAUCUGUCAUGGUUAUAAUUUACACAAUGGAAAUAAUAAUCAUCCAUUGCAGGCCGACACU----GGGUUCGGG
((...(((((((((((....)))).((((((....)))))).....)).)))))((((((((.((((.(.....).)))).)))))))).....))...((((....----....)))). ( -32.60)
>DroSec_CAF1 935 114 + 1
GCCUGGACAGUUGGGCCAUGGCCCUUUCUGUAACAAUGGAAUAACUGAUCUGUCAUGGUUAUAAUUUAUACAAUGGAAAUAAUAAUCAUCCAUUGCAGGCCGACAGU----C-UCAC-AU
(((((.((((..((((....))))...))))..(((((((.....(((....)))(((((((.((((.........)))).))))))))))))))))))).......----.-....-.. ( -34.60)
>DroSim_CAF1 1293 116 + 1
GCCUCGACAGUUGGGCCAUGGCCCUUUCUGUAACAAUGGAAUAACUGAUCUGUCAUGGUUAUAAUUUACACAAUGGUAAUAAUAAUCAUCCAUUGCAGGCCGACACU----GGUUACGGU
((((..((((..((((....))))...))))..(((((((.....(((....)))(((((((...((((......))))..)))))))))))))).))))....(((----(....)))) ( -35.20)
>DroEre_CAF1 1843 115 + 1
GCCUCAACAGUUGGACCAUGGUCCUUUCUGUGACAAUGGAAUUACUGAUCUGUCAUGGUUAUAAUUUACACAAGGGAAAUAAUAAUUAUCC-----AGGCUCACAUCCUACGUAUUUACG
((((..((((..((((....))))...)))).......((((((.(((((......)))))))))))......(((.(((....))).)))-----)))).................... ( -23.20)
>consensus
GCCUCGACAGUUGGGCCAUGGCCCUUUCUGUAACAAUGGAAUAACUGAUCUGUCAUGGUUAUAAUUUACACAAUGGAAAUAAUAAUCAUCCAUUGCAGGCCGACACU____GGUUACGGG
((((..((((..((((....))))...))))..(((((((.....(((....)))(((((((.((((.(.....).)))).)))))))))))))).)))).................... (-25.71 = -26.27 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:13 2006