Locus 4098

Sequence ID	2L_DroMel_CAF1
Location	11,785,932 – 11,786,132
Length	200
Max. P	0.998562

overview

Window 9

Location	11,785,932 – 11,786,052
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.00
Mean single sequence MFE	-27.84
Consensus MFE	-24.88
Energy contribution	-24.88
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.40
Structure conservation index	0.89
SVM decision value	0.30
SVM RNA-class probability	0.678601
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11785932 120 + 22407834
AUCUGUAAAAUAUUCGAACCAUUUUGCUGCCGCUUCUUUGCCAUUUGUAAACAGACCGCCCAAUUCCUCCCUGGAAUCGAGUGGGUCCCUUAGUCAUGUUUGAUUUGCAAUUUUGCACAA
....(((((((.........)))))))....((....((((......(((((((((.((((((((((.....)))))....)))))......))).))))))....))))....)).... ( -24.80)
>DroSec_CAF1 43678 120 + 1
AUCUGUAAAAUAUUCGAACCAUUUUGCUGGCGCUUCUUUGCCAUUUGUAAACAGACCGCCCAAUUCCUCCCUGGAAUCGAGUGGGUGCCUUAGUCAUGUUUGAUUUGCAAUUUUGCACAA
...((((((((..((((((...((((((((((......)))))...)))))..((((((((((((((.....)))))....)))))).....)))..))))))......))))))))... ( -30.30)
>DroSim_CAF1 42887 120 + 1
AUCUGUAAAAUAUUCGAACCAUUUUGCUGGCGCUUCUUUGCCAUUUGUAAACAGACCGCCCAAUUCCUCCCUGGAAUCGAGUGGGUCCCUUAGUCAUGUUUGAUUUGCAAUUUUGCACAA
...((((((((..((((((...((((((((((......)))))...)))))..(((.((((((((((.....)))))....)))))......)))..))))))......))))))))... ( -27.50)
>DroEre_CAF1 54089 120 + 1
AUCAGUAAAAUAUUCGAACCAUUUUGCUGCCGCUUCUUUGCCAUUUGUAAACAGACCGCCCAAUUCCUAUCUGGAAUCGAGUGGGUCCCUUAGUCAUGUUUGAUUUGCAAUUUUGCACAA
..(((((((((.........)))))))))..((....((((......(((((((((.((((((((((.....)))))....)))))......))).))))))....))))....)).... ( -28.30)
>DroYak_CAF1 45715 120 + 1
AUCAGUAAAAUAUUCGAACCAUUUUGCUGCCGCUUCUUUGCCAUUUGUAAACAGACCGCCCAAUUCCUCCCUGGAAUCGAGUGGGUCCCUUAGUCAUGUUUGAUUUGCAAUUUUGCACAA
..(((((((((.........)))))))))..((....((((......(((((((((.((((((((((.....)))))....)))))......))).))))))....))))....)).... ( -28.30)
>consensus
AUCUGUAAAAUAUUCGAACCAUUUUGCUGCCGCUUCUUUGCCAUUUGUAAACAGACCGCCCAAUUCCUCCCUGGAAUCGAGUGGGUCCCUUAGUCAUGUUUGAUUUGCAAUUUUGCACAA
....(((((((.........)))))))....((....((((......(((((((((.((((((((((.....)))))....)))))......))).))))))....))))....)).... (-24.88 = -24.88 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	11,785,972 – 11,786,092
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.50
Mean single sequence MFE	-37.90
Consensus MFE	-31.72
Energy contribution	-31.56
Covariance contribution	-0.16
Combinations/Pair	1.09
Mean z-score	-2.19
Structure conservation index	0.84
SVM decision value	1.90
SVM RNA-class probability	0.981761
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11785972 120 + 22407834
CCAUUUGUAAACAGACCGCCCAAUUCCUCCCUGGAAUCGAGUGGGUCCCUUAGUCAUGUUUGAUUUGCAAUUUUGCACAAUCGUUUGAUUGCCAAGGCUCGAAUGGGAUGGAAUCGGAGU
((.((((....))))(((((((.((((.....))))((((((.(((.....(((((....(((((((((....)))).)))))..))))))))...)))))).)))).)))....))... ( -35.10)
>DroSec_CAF1 43718 120 + 1
CCAUUUGUAAACAGACCGCCCAAUUCCUCCCUGGAAUCGAGUGGGUGCCUUAGUCAUGUUUGAUUUGCAAUUUUGCACAAUCAAACUCUUGCCAAGGCUCGAAUUGGAUGGAAGCGGAGU
((((((.........((((.(.(((((.....))))).).))))(.(((((.((...((((((((((((....)))).))))))))....)).))))).).....))))))......... ( -37.20)
>DroSim_CAF1 42927 120 + 1
CCAUUUGUAAACAGACCGCCCAAUUCCUCCCUGGAAUCGAGUGGGUCCCUUAGUCAUGUUUGAUUUGCAAUUUUGCACAAUCAAACUCUUGCCAAGGCUCGAAUUGGAUGGAAGCGGAGU
...((((....))))(((((((.((((.....))))((((((.(((.....((....((((((((((((....)))).)))))))).)).)))...))))))......)))..))))... ( -34.60)
>DroEre_CAF1 54129 120 + 1
CCAUUUGUAAACAGACCGCCCAAUUCCUAUCUGGAAUCGAGUGGGUCCCUUAGUCAUGUUUGAUUUGCAAUUUUGCACAAUCAAACUCUUGCCAAGGCUCGAAUUGGGUGGAACCGGAGU
((.((((....))))((((((((((((.....))))((((((.(((.....((....((((((((((((....)))).)))))))).)).)))...)))))).))))))))....))... ( -41.30)
>DroYak_CAF1 45755 120 + 1
CCAUUUGUAAACAGACCGCCCAAUUCCUCCCUGGAAUCGAGUGGGUCCCUUAGUCAUGUUUGAUUUGCAAUUUUGCACAAUCAAACUCUUGCCAAGGCUCGAAUUGGGUGGAACCGGAGU
((.((((....))))((((((((((((.....))))((((((.(((.....((....((((((((((((....)))).)))))))).)).)))...)))))).))))))))....))... ( -41.30)
>consensus
CCAUUUGUAAACAGACCGCCCAAUUCCUCCCUGGAAUCGAGUGGGUCCCUUAGUCAUGUUUGAUUUGCAAUUUUGCACAAUCAAACUCUUGCCAAGGCUCGAAUUGGAUGGAACCGGAGU
((((((.........((((.(.(((((.....))))).).))))(..((((.((...((((((((((((....)))).))))))))....)).))))..).....))))))......... (-31.72 = -31.56 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	11,785,972 – 11,786,092
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.50
Mean single sequence MFE	-38.16
Consensus MFE	-33.78
Energy contribution	-35.18
Covariance contribution	1.40
Combinations/Pair	1.05
Mean z-score	-2.37
Structure conservation index	0.89
SVM decision value	3.14
SVM RNA-class probability	0.998562
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11785972 120 - 22407834
ACUCCGAUUCCAUCCCAUUCGAGCCUUGGCAAUCAAACGAUUGUGCAAAAUUGCAAAUCAAACAUGACUAAGGGACCCACUCGAUUCCAGGGAGGAAUUGGGCGGUCUGUUUACAAAUGG
..(((((((((.((((..((((((((((((((((....)))))((((....))))............))))))......))))).....))))))))))))).................. ( -35.50)
>DroSec_CAF1 43718 120 - 1
ACUCCGCUUCCAUCCAAUUCGAGCCUUGGCAAGAGUUUGAUUGUGCAAAAUUGCAAAUCAAACAUGACUAAGGCACCCACUCGAUUCCAGGGAGGAAUUGGGCGGUCUGUUUACAAAUGG
.........((((.........(((((((((...((((((((.((((....)))))))))))).)).)))))))..((.(((((((((.....))))))))).))...........)))) ( -39.30)
>DroSim_CAF1 42927 120 - 1
ACUCCGCUUCCAUCCAAUUCGAGCCUUGGCAAGAGUUUGAUUGUGCAAAAUUGCAAAUCAAACAUGACUAAGGGACCCACUCGAUUCCAGGGAGGAAUUGGGCGGUCUGUUUACAAAUGG
.........((((..........((((((((...((((((((.((((....)))))))))))).)).))))))((((..(((((((((.....))))))))).)))).........)))) ( -37.80)
>DroEre_CAF1 54129 120 - 1
ACUCCGGUUCCACCCAAUUCGAGCCUUGGCAAGAGUUUGAUUGUGCAAAAUUGCAAAUCAAACAUGACUAAGGGACCCACUCGAUUCCAGAUAGGAAUUGGGCGGUCUGUUUACAAAUGG
....(((..((.(((((.(((((((((((((...((((((((.((((....)))))))))))).)).))))))......)))))((((.....))))))))).)).)))........... ( -38.00)
>DroYak_CAF1 45755 120 - 1
ACUCCGGUUCCACCCAAUUCGAGCCUUGGCAAGAGUUUGAUUGUGCAAAAUUGCAAAUCAAACAUGACUAAGGGACCCACUCGAUUCCAGGGAGGAAUUGGGCGGUCUGUUUACAAAUGG
..(((((((((.(((...(((((((((((((...((((((((.((((....)))))))))))).)).))))))......))))).....))).))))))))).................. ( -40.20)
>consensus
ACUCCGCUUCCAUCCAAUUCGAGCCUUGGCAAGAGUUUGAUUGUGCAAAAUUGCAAAUCAAACAUGACUAAGGGACCCACUCGAUUCCAGGGAGGAAUUGGGCGGUCUGUUUACAAAUGG
..(((((((((.(((...(((((((((((((...((((((((.((((....)))))))))))).)).))))))......))))).....))).))))))))).................. (-33.78 = -35.18 +   1.40)

alignment

secondary structure

dotplot

Window 2

Location	11,786,012 – 11,786,132
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.54
Mean single sequence MFE	-36.08
Consensus MFE	-26.50
Energy contribution	-27.62
Covariance contribution	1.12
Combinations/Pair	1.08
Mean z-score	-2.79
Structure conservation index	0.73
SVM decision value	0.79
SVM RNA-class probability	0.852046
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11786012 120 - 22407834
CAAUUUUUGGGAUUUAGCCUGCUGGCUGGCUGCUCCCGAAACUCCGAUUCCAUCCCAUUCGAGCCUUGGCAAUCAAACGAUUGUGCAAAAUUGCAAAUCAAACAUGACUAAGGGACCCAC
....((((((((..(((((........))))).))))))))...........((((......((....))........((((.((((....))))))))............))))..... ( -31.20)
>DroSec_CAF1 43758 116 - 1
CAAUUUUUGGGAUUUAGCCUGCUG----GCUGCUCCCGAAACUCCGCUUCCAUCCAAUUCGAGCCUUGGCAAGAGUUUGAUUGUGCAAAAUUGCAAAUCAAACAUGACUAAGGCACCCAC
....((((((((..(((((....)----)))).)))))))).....................(((((((((...((((((((.((((....)))))))))))).)).)))))))...... ( -39.10)
>DroSim_CAF1 42967 116 - 1
CAAUUUUUGGGAUUUAGCCUGCUG----GCUGCUCCCGAAACUCCGCUUCCAUCCAAUUCGAGCCUUGGCAAGAGUUUGAUUGUGCAAAAUUGCAAAUCAAACAUGACUAAGGGACCCAC
....((((((((..(((((....)----)))).)))))))).(((((((...........))))(((((((...((((((((.((((....)))))))))))).)).))))))))..... ( -36.40)
>DroEre_CAF1 54169 116 - 1
CAAUUUUUGGGAUUUAGCCUGCUG----GCUGCUCCUGAAACUCCGGUUCCACCCAAUUCGAGCCUUGGCAAGAGUUUGAUUGUGCAAAAUUGCAAAUCAAACAUGACUAAGGGACCCAC
....(((..(((..(((((....)----)))).)))..)))....((((((.......((..((....))..))((((((((.((((....))))))))))))........))))))... ( -38.80)
>DroYak_CAF1 45795 116 - 1
CAAUUUUUGGGAUUUAGUCUGCUG----GCAGCUCCUGAAACUCCGGUUCCACCCAAUUCGAGCCUUGGCAAGAGUUUGAUUGUGCAAAAUUGCAAAUCAAACAUGACUAAGGGACCCAC
.......((((.((((((((((..----(..((((..(((.....((.....))...))))))).)..)))...((((((((.((((....))))))))))))..)))))))...)))). ( -34.90)
>consensus
CAAUUUUUGGGAUUUAGCCUGCUG____GCUGCUCCCGAAACUCCGCUUCCAUCCAAUUCGAGCCUUGGCAAGAGUUUGAUUGUGCAAAAUUGCAAAUCAAACAUGACUAAGGGACCCAC
....((((((((..((((..........)))).))))))))(((.((((......)))).)))((((((((...((((((((.((((....)))))))))))).)).))))))....... (-26.50 = -27.62 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:22 2006