Locus 1967

Sequence ID 3L_DroMel_CAF1
Location 5,446,110 – 5,446,310
Length 200
Max. P 0.974916
window3078 window3079 window3080 window3081 window3082

overview

Window 8

Location 5,446,110 – 5,446,230
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.18
Mean single sequence MFE -27.95
Consensus MFE -21.88
Energy contribution -22.12
Covariance contribution 0.25
Combinations/Pair 1.03
Mean z-score -1.55
Structure conservation index 0.78
SVM decision value 0.04
SVM RNA-class probability 0.553207
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5446110 120 + 23771897
UACUAUGUUGUGAGUGAUAUUCAGAGUUUAAUUUCCAUUAAGCAAAAUGCUUUUGCAUUUCGGCCGUUGGGUAAAUUUGCACUAACGCAUGUGCAUACCGAAUAUGUGCAUAUGUAUAUG
........((..(((..(((((((.(((((((....))))))).((((((....))))))......))))))).)))..)).....(((((((((((.......)))))))))))..... ( -30.20)
>DroSec_CAF1 7663 118 + 1
UACUAUGUUGUGAGUGAUACUCAGAGUUUAAUUUCCAUUAAGCAAAAUGCUUUUGCAUUUCGGCCGUUGGGUAAAUUUGCACUAACACAUGUGCAUACCGAAUAUUUGCACAU--AUAUG
...(((((.(..((((.(((((((.(((((((....))))))).((((((....))))))......)))))))....(((((........))))).......))))..)))))--).... ( -29.30)
>DroSim_CAF1 7703 118 + 1
UACUAUGUUGUGAGUGAUACUCAGAGUUUAAUUUCCAUUAAGCAAAAUGCUUUUGCAUUUCGGCCGUUGGGUAAAUUUGCACUAACACAUGUGCAUACCGAAUAUUUGCACAU--AUAUG
...(((((.(..((((.(((((((.(((((((....))))))).((((((....))))))......)))))))....(((((........))))).......))))..)))))--).... ( -29.30)
>DroEre_CAF1 7503 106 + 1
UACUAUGUUGUGAGUGAUAUUCAGAGUUUAAUUUCCAUUAAGCAAAAUGCUUUUGCAUUCCGGCCGUUGGGCAAAUUUGCACUAACGCAUGUGCAUACCGAAU--------------ACG
((((........)))).(((((...(((((((....)))))))..........(((((....((.((((((((....))).)))))))..)))))....))))--------------).. ( -23.00)
>consensus
UACUAUGUUGUGAGUGAUACUCAGAGUUUAAUUUCCAUUAAGCAAAAUGCUUUUGCAUUUCGGCCGUUGGGUAAAUUUGCACUAACACAUGUGCAUACCGAAUAUUUGCACAU__AUAUG
......(((((((((...)))))..(((((((....))))))).((((((....)))))))))).(((.((((....(((((........))))))))).)))................. (-21.88 = -22.12 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 5,446,110 – 5,446,230
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.18
Mean single sequence MFE -26.38
Consensus MFE -23.64
Energy contribution -23.70
Covariance contribution 0.06
Combinations/Pair 1.07
Mean z-score -2.25
Structure conservation index 0.90
SVM decision value 1.74
SVM RNA-class probability 0.974916
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5446110 120 - 23771897
CAUAUACAUAUGCACAUAUUCGGUAUGCACAUGCGUUAGUGCAAAUUUACCCAACGGCCGAAAUGCAAAAGCAUUUUGCUUAAUGGAAAUUAAACUCUGAAUAUCACUCACAACAUAGUA
...............((((((((..(((((........)))))(((((.((....(((.(((((((....))))))))))....))))))).....))))))))................ ( -24.50)
>DroSec_CAF1 7663 118 - 1
CAUAU--AUGUGCAAAUAUUCGGUAUGCACAUGUGUUAGUGCAAAUUUACCCAACGGCCGAAAUGCAAAAGCAUUUUGCUUAAUGGAAAUUAAACUCUGAGUAUCACUCACAACAUAGUA
.((((--(((((((.((.....)).))))))))))).(((...(((((.((....(((.(((((((....))))))))))....)))))))..))).((((.....)))).......... ( -28.30)
>DroSim_CAF1 7703 118 - 1
CAUAU--AUGUGCAAAUAUUCGGUAUGCACAUGUGUUAGUGCAAAUUUACCCAACGGCCGAAAUGCAAAAGCAUUUUGCUUAAUGGAAAUUAAACUCUGAGUAUCACUCACAACAUAGUA
.((((--(((((((.((.....)).))))))))))).(((...(((((.((....(((.(((((((....))))))))))....)))))))..))).((((.....)))).......... ( -28.30)
>DroEre_CAF1 7503 106 - 1
CGU--------------AUUCGGUAUGCACAUGCGUUAGUGCAAAUUUGCCCAACGGCCGGAAUGCAAAAGCAUUUUGCUUAAUGGAAAUUAAACUCUGAAUAUCACUCACAACAUAGUA
.((--------------((((((..(((((........)))))(((((.((....(((.(((((((....))))))))))....))))))).....))))))))................ ( -24.40)
>consensus
CAUAU__AUGUGCAAAUAUUCGGUAUGCACAUGCGUUAGUGCAAAUUUACCCAACGGCCGAAAUGCAAAAGCAUUUUGCUUAAUGGAAAUUAAACUCUGAAUAUCACUCACAACAUAGUA
...............((((((((..(((((........)))))(((((.((....(((.(((((((....))))))))))....))))))).....))))))))................ (-23.64 = -23.70 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 5,446,150 – 5,446,270
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.90
Mean single sequence MFE -29.82
Consensus MFE -23.70
Energy contribution -25.57
Covariance contribution 1.87
Combinations/Pair 1.03
Mean z-score -2.83
Structure conservation index 0.79
SVM decision value 1.44
SVM RNA-class probability 0.953944
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5446150 120 + 23771897
AGCAAAAUGCUUUUGCAUUUCGGCCGUUGGGUAAAUUUGCACUAACGCAUGUGCAUACCGAAUAUGUGCAUAUGUAUAUGGCCAUAUAUUUGGGCAAAAAAUUAUUAAAUUCAAUGAAUU
.((.((((((....)))))).((((((((((((....))).)))))(((((((((((.......)))))))))))....))))..........))......................... ( -34.90)
>DroSec_CAF1 7703 118 + 1
AGCAAAAUGCUUUUGCAUUUCGGCCGUUGGGUAAAUUUGCACUAACACAUGUGCAUACCGAAUAUUUGCACAU--AUAUGGUCAUAUAUUUGGGCAAAAAAUUAUUAAAUUCAAUGAAUU
.((.((((((....))))))..))((((((((.....(((((........)))))..((((((((.((..((.--...))..)).))))))))...............)))))))).... ( -29.10)
>DroSim_CAF1 7743 118 + 1
AGCAAAAUGCUUUUGCAUUUCGGCCGUUGGGUAAAUUUGCACUAACACAUGUGCAUACCGAAUAUUUGCACAU--AUAUGGCCAUAUAUUUGGGCAAAAAAUUAUUAAAUUCAAUGAAUU
.((.((((((....)))))).((((((((((((....))).)))))..(((((((...........)))))))--....))))..........))......................... ( -30.10)
>DroEre_CAF1 7543 106 + 1
AGCAAAAUGCUUUUGCAUUCCGGCCGUUGGGCAAAUUUGCACUAACGCAUGUGCAUACCGAAU--------------ACGGCCUUAUAUUUGGGCAAAAAAUUAUUAAAUUCAAUGAAUU
.((..(((((....)))))..(((((((((.......(((((........)))))..)))...--------------))))))..........))......................... ( -25.20)
>consensus
AGCAAAAUGCUUUUGCAUUUCGGCCGUUGGGUAAAUUUGCACUAACACAUGUGCAUACCGAAUAUUUGCACAU__AUAUGGCCAUAUAUUUGGGCAAAAAAUUAUUAAAUUCAAUGAAUU
.((..(((((....)))))...))((((((((.....(((((........)))))..((((((((.((..(((....)))..)).))))))))...............)))))))).... (-23.70 = -25.57 +   1.87)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 5,446,150 – 5,446,270
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.90
Mean single sequence MFE -26.17
Consensus MFE -20.98
Energy contribution -21.35
Covariance contribution 0.37
Combinations/Pair 1.10
Mean z-score -2.15
Structure conservation index 0.80
SVM decision value 0.93
SVM RNA-class probability 0.884195
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5446150 120 - 23771897
AAUUCAUUGAAUUUAAUAAUUUUUUGCCCAAAUAUAUGGCCAUAUACAUAUGCACAUAUUCGGUAUGCACAUGCGUUAGUGCAAAUUUACCCAACGGCCGAAAUGCAAAAGCAUUUUGCU
.........................(((.....(((((..((((....))))..)))))..(((((((((........)))))....))))....)))((((((((....)))))))).. ( -25.10)
>DroSec_CAF1 7703 118 - 1
AAUUCAUUGAAUUUAAUAAUUUUUUGCCCAAAUAUAUGACCAUAU--AUGUGCAAAUAUUCGGUAUGCACAUGUGUUAGUGCAAAUUUACCCAACGGCCGAAAUGCAAAAGCAUUUUGCU
........((((..........(((((....((((((....))))--))..))))).))))(((((((((........)))))....))))....(((.(((((((....)))))))))) ( -24.20)
>DroSim_CAF1 7743 118 - 1
AAUUCAUUGAAUUUAAUAAUUUUUUGCCCAAAUAUAUGGCCAUAU--AUGUGCAAAUAUUCGGUAUGCACAUGUGUUAGUGCAAAUUUACCCAACGGCCGAAAUGCAAAAGCAUUUUGCU
....((..(((((....)))))..))...........((((((((--(((((((.((.....)).)))))))))))..(((......))).....))))(((((((....)))))))... ( -27.80)
>DroEre_CAF1 7543 106 - 1
AAUUCAUUGAAUUUAAUAAUUUUUUGCCCAAAUAUAAGGCCGU--------------AUUCGGUAUGCACAUGCGUUAGUGCAAAUUUGCCCAACGGCCGGAAUGCAAAAGCAUUUUGCU
....((..(((((....)))))..))...........((((((--------------....(((((((((........)))))....))))..))))))(((((((....)))))))... ( -27.60)
>consensus
AAUUCAUUGAAUUUAAUAAUUUUUUGCCCAAAUAUAUGGCCAUAU__AUGUGCAAAUAUUCGGUAUGCACAUGCGUUAGUGCAAAUUUACCCAACGGCCGAAAUGCAAAAGCAUUUUGCU
....((..(((((....)))))..))...........((((......((((....))))..(((((((((........)))))....))))....))))(((((((....)))))))... (-20.98 = -21.35 +   0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 5,446,190 – 5,446,310
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.32
Mean single sequence MFE -24.98
Consensus MFE -19.54
Energy contribution -20.97
Covariance contribution 1.44
Combinations/Pair 1.07
Mean z-score -1.78
Structure conservation index 0.78
SVM decision value 0.32
SVM RNA-class probability 0.686420
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5446190 120 + 23771897
ACUAACGCAUGUGCAUACCGAAUAUGUGCAUAUGUAUAUGGCCAUAUAUUUGGGCAAAAAAUUAUUAAAUUCAAUGAAUUAUUUAUUUAGCAGGUGGCGCUGACUGAAUAAACCCGUAUA
......(((((((((((.......)))))))))))(((((((((......)))............................((((((((((((......))).))))))))).)))))). ( -30.00)
>DroSec_CAF1 7743 118 + 1
ACUAACACAUGUGCAUACCGAAUAUUUGCACAU--AUAUGGUCAUAUAUUUGGGCAAAAAAUUAUUAAAUUCAAUGAAUUAUUUAUUUAGCAGGUGGCGCUGACUGAAUAAACCCGCAUA
.........(((((...((((((((.((..((.--...))..)).))))))))............................((((((((((((......))).)))))))))...))))) ( -24.00)
>DroSim_CAF1 7783 118 + 1
ACUAACACAUGUGCAUACCGAAUAUUUGCACAU--AUAUGGCCAUAUAUUUGGGCAAAAAAUUAUUAAAUUCAAUGAAUUAUUUAUUUAGCAGGUGGCGCUGACUGAAUAAACCCGCAUA
........(((((((...........)))))))--...((.(((......))).)).................(((.....((((((((((((......))).)))))))))....))). ( -24.40)
>DroEre_CAF1 7583 106 + 1
ACUAACGCAUGUGCAUACCGAAU--------------ACGGCCUUAUAUUUGGGCAAAAAAUUAUUAAAUUCAAUGAAUUAUUUAUUUAGCAGGUGGCGCUGACUGAAUAAACCCGCAUA
.........(((((...(((...--------------.)))..........(((.............(((((...))))).((((((((((((......))).))))))))))))))))) ( -21.50)
>consensus
ACUAACACAUGUGCAUACCGAAUAUUUGCACAU__AUAUGGCCAUAUAUUUGGGCAAAAAAUUAUUAAAUUCAAUGAAUUAUUUAUUUAGCAGGUGGCGCUGACUGAAUAAACCCGCAUA
.........(((((...((((((((.((..(((....)))..)).))))))))............................((((((((((((......))).)))))))))...))))) (-19.54 = -20.97 +   1.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:22 2006