Locus 1615

Sequence ID X_DroMel_CAF1
Location 4,614,820 – 4,614,919
Length 99
Max. P 0.900078
window2641 window2642

overview

Window 1

Location 4,614,820 – 4,614,919
Length 99
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 59.42
Mean single sequence MFE -26.96
Consensus MFE -13.02
Energy contribution -14.28
Covariance contribution 1.25
Combinations/Pair 1.33
Mean z-score -1.45
Structure conservation index 0.48
SVM decision value 0.59
SVM RNA-class probability 0.790487
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4614820 99 + 22224390
---------------------GACUGUUUACCAUUAAGAUCUUCUUGCGAUUCCAUUUUUCUGUCCACAAGUGCCCAGCAGAGGAAUGUUGUCCUCUUCACCAGCACCAUAAUGGGCAGA
---------------------.............((((.....))))............((((((((...((((...(.((((((......)))))).)....)))).....)))))))) ( -23.50)
>DroSec_CAF1 463 92 + 1
----------------------------GACCACCAAGAUCUACGUCCGAUUCGAUAUUCCUGUCCACAAAUGCCCACGAGAGGAAAGUAAUCCUCUUCACCAGCACCAUGAUGGCCAGA
----------------------------.........((((.......))))........(((.(((((..(((....(((((((......))))))).....)))...)).))).))). ( -18.00)
>DroEre_CAF1 447 111 + 1
CUGCUGGAUUCCUGGUAAAGCGACUGUGU---------AUCCUCGUCCGACUCCACAUUCCUGUCGGGCAAUACCCAGUCCAGGAAACCAGUCUUCCUCACCAGCACCAUGACCGGCAGA
(((((((..((.((((...(((((((.((---------((....(((((((...........))))))).)))).))))).(((((.......))))).....)))))).))))))))). ( -41.00)
>DroYak_CAF1 431 111 + 1
GUGCUGCAUUUCUGGUAAAGCGACUCUUU---------AUACUCAUUCGCUUCCUUAUUCCUGUCUAGCAAUGCCCAGUCAAAGAAUGUGGUCCUUCGCACCAGCACCAUGACGGGCAGA
.(((((((.....((..((((((......---------........)))))))).......)))..)))).(((((.((((.....((((((.......)))).))...))))))))).. ( -25.34)
>consensus
_____________________GACUGUUU_________AUCCUCGUCCGAUUCCAUAUUCCUGUCCACAAAUGCCCAGUAGAGGAAAGUAGUCCUCCUCACCAGCACCAUGACGGGCAGA
............................................................(((((((....(((...((((((((......))))))))....)))......))))))). (-13.02 = -14.28 +   1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 4,614,820 – 4,614,919
Length 99
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 59.42
Mean single sequence MFE -34.02
Consensus MFE -16.60
Energy contribution -16.73
Covariance contribution 0.12
Combinations/Pair 1.38
Mean z-score -1.63
Structure conservation index 0.49
SVM decision value 1.01
SVM RNA-class probability 0.900078
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4614820 99 - 22224390
UCUGCCCAUUAUGGUGCUGGUGAAGAGGACAACAUUCCUCUGCUGGGCACUUGUGGACAGAAAAAUGGAAUCGCAAGAAGAUCUUAAUGGUAAACAGUC---------------------
((((.((((...((((((.(...((((((......))))))..).)))))).)))).)))).........((....)).....................--------------------- ( -30.00)
>DroSec_CAF1 463 92 - 1
UCUGGCCAUCAUGGUGCUGGUGAAGAGGAUUACUUUCCUCUCGUGGGCAUUUGUGGACAGGAAUAUCGAAUCGGACGUAGAUCUUGGUGGUC----------------------------
((((.((((...((((((..(((.(((((......))))))))..)))))).)))).))))..(((((((((.......))).))))))...---------------------------- ( -29.90)
>DroEre_CAF1 447 111 - 1
UCUGCCGGUCAUGGUGCUGGUGAGGAAGACUGGUUUCCUGGACUGGGUAUUGCCCGACAGGAAUGUGGAGUCGGACGAGGAU---------ACACAGUCGCUUUACCAGGAAUCCAGCAG
.((((.((......(.(((((((((..(((((..((((((...((((.....)))).))))))((((...((....))...)---------)))))))).))))))))).)..)).)))) ( -42.90)
>DroYak_CAF1 431 111 - 1
UCUGCCCGUCAUGGUGCUGGUGCGAAGGACCACAUUCUUUGACUGGGCAUUGCUAGACAGGAAUAAGGAAGCGAAUGAGUAU---------AAAGAGUCGCUUUACCAGAAAUGCAGCAC
..(((((((((.((((.((((.(....)))))))))...)))).))))).((((.(.((........(((((((.(......---------..)...)))))))........))))))). ( -33.29)
>consensus
UCUGCCCAUCAUGGUGCUGGUGAAGAGGACUACAUUCCUCGACUGGGCAUUGCUGGACAGGAAUAUGGAAUCGGACGAAGAU_________AAACAGUC_____________________
((((.((((...((((((.(...((((((......))))))..).)))))).)))).))))........................................................... (-16.60 = -16.73 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:43 2006