Locus 407

Sequence ID 2L_DroMel_CAF1
Location 1,231,083 – 1,231,265
Length 182
Max. P 0.996801
window648 window649 window650 window651

overview

Window 8

Location 1,231,083 – 1,231,191
Length 108
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.38
Mean single sequence MFE -29.83
Consensus MFE -22.49
Energy contribution -22.80
Covariance contribution 0.31
Combinations/Pair 1.05
Mean z-score -1.52
Structure conservation index 0.75
SVM decision value 0.14
SVM RNA-class probability 0.604793
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1231083 108 + 22407834
AUACGAAGUACACAA--GCACAAACAACGCCGGAAC-GGAAACCGCAGCAGCAGGAGUAGAUGUAACAACAUCAAGGGGUUUCCCAAGGUGGAGCCAACCACUUUC---------CCGGU
...............--...........(((((...-(((((((((....)).......(((((....)))))....))))))).(((((((......))))))).---------))))) ( -32.00)
>DroSec_CAF1 8433 109 + 1
AUACGAAGUACAACAACACACAAACAACGCCGGAGC-GGAAACCGCAGCAGCAGGAGUAGAUGUAACAACAUCAAGGGGUUUCCCAAGGUGGAUCCAACCACUUUC---------CCGG-
.............................((((.(.-(((((((((....)).......(((((....)))))....))))))))(((((((......))))))).---------))))- ( -30.20)
>DroSim_CAF1 4229 104 + 1
AUACGAAGUACACAA--GCACAAACAACGCCGGAGCCGGAAACCGCAGCAGCAGGAGUAGAUGUAACAACAUCAAGGGGUUUCCCAAGGUGGAGCCAACCACUUUC--------------
.(((...........--............(((....)))...((((....)).)).)))(((((....)))))..(((....)))(((((((......))))))).-------------- ( -24.00)
>DroYak_CAF1 4305 117 + 1
AUACGAAGUACACAA--GCACAAACAACGCCACUGC-GGAAACCGCAGCAGCAGGAGUAGACGUAGCAACAUCAAGGGGUUUCCCAAGGUGGAGCCAACCACCCUUCCACUCUGCCCGUU
...............--........(((((..((((-((...))))))..)).((.(((((.((...........(((....)))..(((((......))))).....)))))))))))) ( -33.10)
>consensus
AUACGAAGUACACAA__GCACAAACAACGCCGGAGC_GGAAACCGCAGCAGCAGGAGUAGAUGUAACAACAUCAAGGGGUUUCCCAAGGUGGAGCCAACCACUUUC_________CCGG_
.....................................(((((((((....)).......(((((....)))))....))))))).(((((((......)))))))............... (-22.49 = -22.80 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 1,231,120 – 1,231,225
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.49
Mean single sequence MFE -34.33
Consensus MFE -25.54
Energy contribution -27.35
Covariance contribution 1.81
Combinations/Pair 1.04
Mean z-score -3.10
Structure conservation index 0.74
SVM decision value 2.75
SVM RNA-class probability 0.996801
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1231120 105 + 22407834
AACCGCAGCAGCAGGAGUAGAUGUAACAACAUCAAGGGGUUUCCCAAGGUGGAGCCAACCACUUUC---------CCGGU------CCCCCAGCUCCAUUGCCCAUCUCCUCCAGCUCCA
.......(.(((.((((.(((((............((((..((..(((((((......))))))).---------..)).------.)))).((......)).))))).)))).))).). ( -34.30)
>DroSec_CAF1 8472 104 + 1
AACCGCAGCAGCAGGAGUAGAUGUAACAACAUCAAGGGGUUUCCCAAGGUGGAUCCAACCACUUUC---------CCGG-------CCCCCAGCUCCAUUGCCAAUCUCCUGCAGCUCCA
....(.(((.(((((((..(((((....)))))..((((((....(((((((......))))))).---------..))-------))))..((......))....))))))).))).). ( -38.70)
>DroSim_CAF1 4267 98 + 1
AACCGCAGCAGCAGGAGUAGAUGUAACAACAUCAAGGGGUUUCCCAAGGUGGAGCCAACCACUUUC----------------------CCCAGCUCCAUUGCCCAUCUCCUGCAGCUCCA
....(.(((.(((((((..(((((....)))))..((((((....(((((((......))))))).----------------------...)))))).........))))))).))).). ( -36.50)
>DroYak_CAF1 4342 114 + 1
AACCGCAGCAGCAGGAGUAGACGUAGCAACAUCAAGGGGUUUCCCAAGGUGGAGCCAACCACCCUUCCACUCUGCCCGUUCCCAAGUCACCAGCUUCAUUGCCCAUCUCCU------CCA
....((....)).((((.(((....((((......((((.....((..((((((..........))))))..)).....))))((((.....))))..))))...))).))------)). ( -27.80)
>consensus
AACCGCAGCAGCAGGAGUAGAUGUAACAACAUCAAGGGGUUUCCCAAGGUGGAGCCAACCACUUUC_________CCGG_______CCCCCAGCUCCAUUGCCCAUCUCCUGCAGCUCCA
....(.(((.(((((((..(((((....)))))..(((....)))(((((((......)))))))...........................((......))....))))))).))).). (-25.54 = -27.35 +   1.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 1,231,120 – 1,231,225
Length 105
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.49
Mean single sequence MFE -41.67
Consensus MFE -29.64
Energy contribution -30.95
Covariance contribution 1.31
Combinations/Pair 1.04
Mean z-score -1.97
Structure conservation index 0.71
SVM decision value 0.80
SVM RNA-class probability 0.853963
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1231120 105 - 22407834
UGGAGCUGGAGGAGAUGGGCAAUGGAGCUGGGGG------ACCGG---------GAAAGUGGUUGGCUCCACCUUGGGAAACCCCUUGAUGUUGUUACAUCUACUCCUGCUGCUGCGGUU
.(.(((.((((.((((((((((((...(.(((((------.((((---------(...((((......)))))))))....))))).).))))))).))))).)))).))).)....... ( -41.80)
>DroSec_CAF1 8472 104 - 1
UGGAGCUGCAGGAGAUUGGCAAUGGAGCUGGGGG-------CCGG---------GAAAGUGGUUGGAUCCACCUUGGGAAACCCCUUGAUGUUGUUACAUCUACUCCUGCUGCUGCGGUU
.(.(((.(((((((...(((......)))((((.-------((((---------(...((((......)))))))))....))))..(((((....)))))..))))))).))).).... ( -42.70)
>DroSim_CAF1 4267 98 - 1
UGGAGCUGCAGGAGAUGGGCAAUGGAGCUGGG----------------------GAAAGUGGUUGGCUCCACCUUGGGAAACCCCUUGAUGUUGUUACAUCUACUCCUGCUGCUGCGGUU
.(.(((.(((((((..((....((((((..(.----------------------........)..))))))....((....))))..(((((....)))))..))))))).))).).... ( -40.80)
>DroYak_CAF1 4342 114 - 1
UGG------AGGAGAUGGGCAAUGAAGCUGGUGACUUGGGAACGGGCAGAGUGGAAGGGUGGUUGGCUCCACCUUGGGAAACCCCUUGAUGUUGCUACGUCUACUCCUGCUGCUGCGGUU
.((------((.(((((((((((...(((.((..(...)..)).))).....((.(((((((......)))))))((....)))).....)))))).))))).))))(((....)))... ( -41.40)
>consensus
UGGAGCUGCAGGAGAUGGGCAAUGGAGCUGGGGG_______CCGG_________GAAAGUGGUUGGCUCCACCUUGGGAAACCCCUUGAUGUUGUUACAUCUACUCCUGCUGCUGCGGUU
.(.(((.(((((((...(((......)))((...........................((((......))))...((....))))..(((((....)))))..))))))).))).).... (-29.64 = -30.95 +   1.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 1,231,160 – 1,231,265
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.49
Mean single sequence MFE -22.00
Consensus MFE -18.41
Energy contribution -19.98
Covariance contribution 1.56
Combinations/Pair 1.04
Mean z-score -2.04
Structure conservation index 0.84
SVM decision value 1.24
SVM RNA-class probability 0.935203
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1231160 105 + 22407834
UUCCCAAGGUGGAGCCAACCACUUUC---------CCGGU------CCCCCAGCUCCAUUGCCCAUCUCCUCCAGCUCCAGCUCCAGUCGAACAAAAAAUGUUCCGUAAUGAAAGCAAUU
.......((.((..((..........---------..)).------.)))).(((.((((((.......((..(((....)))..))..(((((.....))))).))))))..))).... ( -21.70)
>DroSec_CAF1 8512 104 + 1
UUCCCAAGGUGGAUCCAACCACUUUC---------CCGG-------CCCCCAGCUCCAUUGCCAAUCUCCUGCAGCUCCAGCUCCAGUCGAACAAAAAAUGUUCCGUAAUGAAAGCAAUU
..((.(((((((......))))))).---------..))-------......(((.((((((.......(((.(((....))).)))..(((((.....))))).))))))..))).... ( -24.70)
>DroSim_CAF1 4307 98 + 1
UUCCCAAGGUGGAGCCAACCACUUUC----------------------CCCAGCUCCAUUGCCCAUCUCCUGCAGCUCCAGCUCCAGUCGAACAAAAAAUGUUCCGUAAUGAAAGCAAUU
.....(((((((......))))))).----------------------....(((.((((((.......(((.(((....))).)))..(((((.....))))).))))))..))).... ( -24.20)
>DroYak_CAF1 4382 114 + 1
UUCCCAAGGUGGAGCCAACCACCCUUCCACUCUGCCCGUUCCCAAGUCACCAGCUUCAUUGCCCAUCUCCU------CCAGCUCCAGUCGAACAAAAAAUGCUCAGUAAUGAAAGCAAUU
....((..((((((..........))))))..))..................((((((((((.........------...((....)).((.((.....)).)).)))))).)))).... ( -17.40)
>consensus
UUCCCAAGGUGGAGCCAACCACUUUC_________CCGG_______CCCCCAGCUCCAUUGCCCAUCUCCUGCAGCUCCAGCUCCAGUCGAACAAAAAAUGUUCCGUAAUGAAAGCAAUU
.....(((((((......)))))))...........................(((.((((((.......(((.(((....))).)))..(((((.....))))).))))))..))).... (-18.41 = -19.98 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:17 2006