Locus 2043

Sequence ID X_DroMel_CAF1
Location 5,609,484 – 5,609,632
Length 148
Max. P 0.968477
window3324 window3325 window3326 window3327

overview

Window 4

Location 5,609,484 – 5,609,603
Length 119
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 81.37
Mean single sequence MFE -29.68
Consensus MFE -20.70
Energy contribution -24.20
Covariance contribution 3.50
Combinations/Pair 1.16
Mean z-score -1.95
Structure conservation index 0.70
SVM decision value 0.78
SVM RNA-class probability 0.847792
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5609484 119 + 22224390
GUUAAUCGAUUUGCGGGUUAUCGGCUUGUUCGAAAGCUAAAAAUCGAUUAAAUUGAUCGAAUACAGGAUAACGGUACGUUUUUGUAUUAGAUCUAACUGAAACUACGUUUUCCAAUUAG
.(((((((((((...((((.((((.....)))).))))..)))))))))))...((((.(((((((((..(((...)))))))))))).)))).......................... ( -28.80)
>DroSec_CAF1 11158 119 + 1
GUCAAUCGAUUAGCGGGUUAUCGGCUUGUACGAUAGCUAAACAUCGAUUGGAUUAAUCGAAUAAAGGAUAACGGUAUGUUUUUGUAUUCGAUCUAACUGAAAUUGCGUGUUCCAAUUAG
.(((((((((.....((((((((.......))))))))....)))))))))....(((((((((((((((......))))))).))))))))((((.((.(((.....))).)).)))) ( -30.50)
>DroSim_CAF1 12876 119 + 1
GUCAAUCGAUUAGCGGGUUAUCGGCUUGUACGAUAGCUAAACAUCGAUUGGAUUGAUCGAAUACAGGAUAACGGUAUGUUUUUGUAUUCGAUCUAACUGAAAUUGCGUUUUCCAAUAAG
.(((((((((.....((((((((.......))))))))....)))))))))...((((((((((((((...........)))))))))))))).....((((......))))....... ( -37.20)
>DroYak_CAF1 11736 104 + 1
GUCA-------------UAA--GGCUUGUUCGAUAUUUAAAAAUCGAUUAGAUUGAUCGAGUGCACAAUAACGGUAAGGUUUUGUAUUCGAUCUUACUCAAAUAGAGUUUUCCAAUUGG
....-------------...--((((...(((((........)))))..))...(((((((((((....(((......))).)))))))))))..((((.....))))...))...... ( -22.20)
>consensus
GUCAAUCGAUUAGCGGGUUAUCGGCUUGUACGAUAGCUAAAAAUCGAUUAGAUUGAUCGAAUACAGGAUAACGGUAUGUUUUUGUAUUCGAUCUAACUGAAAUUGCGUUUUCCAAUUAG
.(((((((((.....((((((((.......))))))))....)))))))))...((((((((((((((...........)))))))))))))).......................... (-20.70 = -24.20 +   3.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 5,609,484 – 5,609,603
Length 119
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 81.37
Mean single sequence MFE -26.40
Consensus MFE -14.56
Energy contribution -18.69
Covariance contribution 4.12
Combinations/Pair 1.08
Mean z-score -3.13
Structure conservation index 0.55
SVM decision value 1.63
SVM RNA-class probability 0.968477
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5609484 119 - 22224390
CUAAUUGGAAAACGUAGUUUCAGUUAGAUCUAAUACAAAAACGUACCGUUAUCCUGUAUUCGAUCAAUUUAAUCGAUUUUUAGCUUUCGAACAAGCCGAUAACCCGCAAAUCGAUUAAC
.(((((((((.......)))))))))((((.((((((..((((...))))....)))))).))))...(((((((((((...((((......))))((......)).))))))))))). ( -25.60)
>DroSec_CAF1 11158 119 - 1
CUAAUUGGAACACGCAAUUUCAGUUAGAUCGAAUACAAAAACAUACCGUUAUCCUUUAUUCGAUUAAUCCAAUCGAUGUUUAGCUAUCGUACAAGCCGAUAACCCGCUAAUCGAUUGAC
((((((((((.......))))))))))((((((((....(((.....)))......)))))))).....((((((((...(((((((((.......)))))....)))))))))))).. ( -27.70)
>DroSim_CAF1 12876 119 - 1
CUUAUUGGAAAACGCAAUUUCAGUUAGAUCGAAUACAAAAACAUACCGUUAUCCUGUAUUCGAUCAAUCCAAUCGAUGUUUAGCUAUCGUACAAGCCGAUAACCCGCUAAUCGAUUGAC
...(((((((.......)))))))..(((((((((((..(((.....)))....)))))))))))....((((((((...(((((((((.......)))))....)))))))))))).. ( -31.40)
>DroYak_CAF1 11736 104 - 1
CCAAUUGGAAAACUCUAUUUGAGUAAGAUCGAAUACAAAACCUUACCGUUAUUGUGCACUCGAUCAAUCUAAUCGAUUUUUAAAUAUCGAACAAGCC--UUA-------------UGAC
....(((((..((((.....))))..((((((.((((((((......))).)))))...))))))..)))))(((((........))))).......--...-------------.... ( -20.90)
>consensus
CUAAUUGGAAAACGCAAUUUCAGUUAGAUCGAAUACAAAAACAUACCGUUAUCCUGUAUUCGAUCAAUCCAAUCGAUGUUUAGCUAUCGAACAAGCCGAUAACCCGCUAAUCGAUUGAC
.(((((((((.......)))))))))(((((((((((..(((.....)))....)))))))))))....((((((((.......(((((.......)))))........)))))))).. (-14.56 = -18.69 +   4.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 5,609,524 – 5,609,632
Length 108
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 77.09
Mean single sequence MFE -26.23
Consensus MFE -19.07
Energy contribution -18.01
Covariance contribution -1.06
Combinations/Pair 1.40
Mean z-score -2.02
Structure conservation index 0.73
SVM decision value 1.55
SVM RNA-class probability 0.963468
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5609524 108 + 22224390
AAAUCGAUUAAAUUGAUCGAAUACAGGAUAACGGUACGUUUUUGUAUUAGAUCUAACUGAAACUACGUUUUCCAAUUAGA---------UUUCGUAUUAAUUGA-UUCUUGUUAAAAA-
.((((((((((...((((.(((((((((..(((...)))))))))))).))))..........((((...((......))---------...))))))))))))-))...........- ( -21.10)
>DroSec_CAF1 11198 108 + 1
ACAUCGAUUGGAUUAAUCGAAUAAAGGAUAACGGUAUGUUUUUGUAUUCGAUCUAACUGAAAUUGCGUGUUCCAAUUAGA---------UUUCGCAUUAAUCGA-UUCGUGUUAAGAA-
(((.(((.(.((((((((((((((((((((......))))))).)))))))............((((...((......))---------...)))))))))).)-.))))))......- ( -22.80)
>DroSim_CAF1 12916 108 + 1
ACAUCGAUUGGAUUGAUCGAAUACAGGAUAACGGUAUGUUUUUGUAUUCGAUCUAACUGAAAUUGCGUUUUCCAAUAAGA---------UUUCGCAUUAAUCGA-UUCGUGUUAAGAA-
..(((((((((...((((((((((((((...........))))))))))))))..........((((...((......))---------...))))))))))))-)............- ( -29.00)
>DroYak_CAF1 11761 119 + 1
AAAUCGAUUAGAUUGAUCGAGUGCACAAUAACGGUAAGGUUUUGUAUUCGAUCUUACUCAAAUAGAGUUUUCCAAUUGGAACAUUGGAACCUUUCAGUAAUUGGAAGACUGAGAGCAUC
.((((.....))))(((((((((((....(((......))).)))))))))))..((((.....)))).(((((((......))))))).((((((((.........)))))))).... ( -32.00)
>consensus
AAAUCGAUUAGAUUGAUCGAAUACAGGAUAACGGUAUGUUUUUGUAUUCGAUCUAACUGAAAUUGCGUUUUCCAAUUAGA_________UUUCGCAUUAAUCGA_UUCGUGUUAAGAA_
...((((((((...((((((((((((((...........))))))))))))))...........(((.........................))).))))))))............... (-19.07 = -18.01 +  -1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 5,609,524 – 5,609,632
Length 108
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 77.09
Mean single sequence MFE -23.40
Consensus MFE -11.84
Energy contribution -14.65
Covariance contribution 2.81
Combinations/Pair 1.03
Mean z-score -2.71
Structure conservation index 0.51
SVM decision value 1.50
SVM RNA-class probability 0.959035
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5609524 108 - 22224390
-UUUUUAACAAGAA-UCAAUUAAUACGAAA---------UCUAAUUGGAAAACGUAGUUUCAGUUAGAUCUAAUACAAAAACGUACCGUUAUCCUGUAUUCGAUCAAUUUAAUCGAUUU
-..........(((-((.(((((...((..---------(((((((((((.......)))))))))))((.((((((..((((...))))....)))))).))))...))))).))))) ( -19.00)
>DroSec_CAF1 11198 108 - 1
-UUCUUAACACGAA-UCGAUUAAUGCGAAA---------UCUAAUUGGAACACGCAAUUUCAGUUAGAUCGAAUACAAAAACAUACCGUUAUCCUUUAUUCGAUUAAUCCAAUCGAUGU
-......((((((.-..(((((((.(((((---------(((((((((((.......))))))))))))..........(((.....)))........)))))))))))...))).))) ( -21.80)
>DroSim_CAF1 12916 108 - 1
-UUCUUAACACGAA-UCGAUUAAUGCGAAA---------UCUUAUUGGAAAACGCAAUUUCAGUUAGAUCGAAUACAAAAACAUACCGUUAUCCUGUAUUCGAUCAAUCCAAUCGAUGU
-............(-((((((..((((...---------(((....)))...))))..........(((((((((((..(((.....)))....))))))))))).....))))))).. ( -27.00)
>DroYak_CAF1 11761 119 - 1
GAUGCUCUCAGUCUUCCAAUUACUGAAAGGUUCCAAUGUUCCAAUUGGAAAACUCUAUUUGAGUAAGAUCGAAUACAAAACCUUACCGUUAUUGUGCACUCGAUCAAUCUAAUCGAUUU
(((.((.(((((.........))))).)).(((((((......))))))).((((.....))))..((((((.((((((((......))).)))))...))))))......)))..... ( -25.80)
>consensus
_UUCUUAACACGAA_UCAAUUAAUGCGAAA_________UCUAAUUGGAAAACGCAAUUUCAGUUAGAUCGAAUACAAAAACAUACCGUUAUCCUGUAUUCGAUCAAUCCAAUCGAUGU
...............((((((....................(((((((((.......)))))))))(((((((((((..(((.....)))....))))))))))).....))))))... (-11.84 = -14.65 +   2.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:55 2006