Locus 9715

Sequence ID 3R_DroMel_CAF1
Location 25,691,570 – 25,691,704
Length 134
Max. P 0.995337
window15516 window15517 window15518 window15519

overview

Window 6

Location 25,691,570 – 25,691,668
Length 98
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 90.70
Mean single sequence MFE -21.31
Consensus MFE -18.12
Energy contribution -18.04
Covariance contribution -0.08
Combinations/Pair 1.11
Mean z-score -1.81
Structure conservation index 0.85
SVM decision value 1.46
SVM RNA-class probability 0.955689
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25691570 98 + 27905053
GUAGACUUUAUCUAAAAUGCAGGUACUUAAAUGAUAAAUAUAUAUUUGCCAAUAUGGCUUGUUCGAGUUCGAGCAAUAAUUAAUUGGCUUUUUCCAUA
(((...((((((....................))))))..)))....((((((.....(((((((....)))))))......)))))).......... ( -16.55)
>DroSec_CAF1 7374 98 + 1
CUAGACUUUAUCUAAAAUGCAGGUACUUAAAUGAUAAAUAUAUCUUUGCCAAUUUGGCUUGCUCGAGUUCGAGCAGUAAUUAAUUGGCUUUUUCCAUA
.((((.....)))).......((.........((((....))))...(((((((..(((.(((((....))))))))....))))))).....))... ( -22.70)
>DroSim_CAF1 7388 98 + 1
GUAGACUUUAUCUAGAAUGCAGGUACUUAAAUGAUAAAUAUAUCUUUGCCAAUUUGGCUUGCUCGAGUUCGAGCAGUAAUUAAUUGGCUUUUUCCAUA
(((..((......))..))).((.........((((....))))...(((((((..(((.(((((....))))))))....))))))).....))... ( -23.80)
>DroEre_CAF1 7898 96 + 1
GUGGACUUUAUCUAAAAUGCAGGUACUUAAAUGAUUA--AUAUCUUUGCCAAUUUCGAUUGUUCGAGUUCGAGCAAUAAUUAAUUGGCUUUUUCUAUA
(((((...............(((((.((((....)))--))))))..(((((((...((((((((....))))))))....)))))))....))))). ( -23.10)
>DroYak_CAF1 7891 96 + 1
AUGGGCUUUAUCGAAAAUGCAGGUACUUAAAUGAUUU--AUAUCUUUGCCAAUUUUGUUUGCUCGCGUUCGAGCAAUAAUUAAUUGGCUUUUUCUAUA
............(((((...............(((..--..)))...(((((((....(((((((....))))))).....))))))).))))).... ( -20.40)
>consensus
GUAGACUUUAUCUAAAAUGCAGGUACUUAAAUGAUAAAUAUAUCUUUGCCAAUUUGGCUUGCUCGAGUUCGAGCAAUAAUUAAUUGGCUUUUUCCAUA
........(((((.......)))))......................(((((((....(((((((....))))))).....))))))).......... (-18.12 = -18.04 +  -0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 25,691,570 – 25,691,668
Length 98
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 90.70
Mean single sequence MFE -20.06
Consensus MFE -16.14
Energy contribution -17.54
Covariance contribution 1.40
Combinations/Pair 1.09
Mean z-score -2.50
Structure conservation index 0.80
SVM decision value 2.16
SVM RNA-class probability 0.989330
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25691570 98 - 27905053
UAUGGAAAAAGCCAAUUAAUUAUUGCUCGAACUCGAACAAGCCAUAUUGGCAAAUAUAUAUUUAUCAUUUAAGUACCUGCAUUUUAGAUAAAGUCUAC
...((.....((((((......(((.(((....))).))).....)))))).......((((((.....)))))))).......(((((...))))). ( -17.20)
>DroSec_CAF1 7374 98 - 1
UAUGGAAAAAGCCAAUUAAUUACUGCUCGAACUCGAGCAAGCCAAAUUGGCAAAGAUAUAUUUAUCAUUUAAGUACCUGCAUUUUAGAUAAAGUCUAG
...((.....(((((((......((((((....)))))).....)))))))...((((....)))).........)).......(((((...))))). ( -23.20)
>DroSim_CAF1 7388 98 - 1
UAUGGAAAAAGCCAAUUAAUUACUGCUCGAACUCGAGCAAGCCAAAUUGGCAAAGAUAUAUUUAUCAUUUAAGUACCUGCAUUCUAGAUAAAGUCUAC
..(((((...(((((((......((((((....)))))).....)))))))...((((....))))...............)))))............ ( -23.20)
>DroEre_CAF1 7898 96 - 1
UAUAGAAAAAGCCAAUUAAUUAUUGCUCGAACUCGAACAAUCGAAAUUGGCAAAGAUAU--UAAUCAUUUAAGUACCUGCAUUUUAGAUAAAGUCCAC
..........(((((((....((((.(((....))).))))...)))))))...(((..--..)))(((((((.........)))))))......... ( -15.10)
>DroYak_CAF1 7891 96 - 1
UAUAGAAAAAGCCAAUUAAUUAUUGCUCGAACGCGAGCAAACAAAAUUGGCAAAGAUAU--AAAUCAUUUAAGUACCUGCAUUUUCGAUAAAGCCCAU
....(((((.(((((((.....(((((((....)))))))....)))))))...(((..--..)))...............)))))............ ( -21.60)
>consensus
UAUGGAAAAAGCCAAUUAAUUAUUGCUCGAACUCGAGCAAGCCAAAUUGGCAAAGAUAUAUUUAUCAUUUAAGUACCUGCAUUUUAGAUAAAGUCUAC
..(((((...(((((((.....(((((((....)))))))....)))))))...((((....))))...............)))))............ (-16.14 = -17.54 +   1.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 25,691,600 – 25,691,704
Length 104
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 88.58
Mean single sequence MFE -24.48
Consensus MFE -18.88
Energy contribution -19.00
Covariance contribution 0.12
Combinations/Pair 1.17
Mean z-score -2.30
Structure conservation index 0.77
SVM decision value 1.37
SVM RNA-class probability 0.947406
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25691600 104 + 27905053
AUGAUAAAUAUAUAUUUGCCAAUAUGGCUUGUUCGAGUUCGAGCAAUAAUUAAUUGGCUUUUUCCAUAAUUAAUAAGCAAUUUAGAUGCAGUUA----GUUAGUUUGA
....(((((........((((((.....(((((((....)))))))......))))))........((((((((..(((.......))).))))----))))))))). ( -20.70)
>DroSec_CAF1 7404 108 + 1
AUGAUAAAUAUAUCUUUGCCAAUUUGGCUUGCUCGAGUUCGAGCAGUAAUUAAUUGGCUUUUUCCAUAAUUUAUAAGCAAUUAAGAUGAAGUCAUGUGCUUAGUUUGA
..((((....))))...(((((((..(((.(((((....))))))))....)))))))...............((((((.....(((...)))...))))))...... ( -25.80)
>DroSim_CAF1 7418 107 + 1
AUGAUAAAUAUAUCUUUGCCAAUUUGGCUUGCUCGAGUUCGAGCAGUAAUUAAUUGGCUUUUUCCAUAAUUUAUAAGCAAUUAAGAUGAAGUCAUG-GCUUAGUUUGA
....(((((.(((((..(((((((..(((.(((((....))))))))....)))))))...............(((....))))))))((((....-)))).))))). ( -25.20)
>DroEre_CAF1 7928 106 + 1
AUGAUUA--AUAUCUUUGCCAAUUUCGAUUGUUCGAGUUCGAGCAAUAAUUAAUUGGCUUUUUCUAUAAUUUAUAAGCAAUUUAGAUGUAGUUAUAUGCUUAGUUUGA
..(((((--........(((((((...((((((((....))))))))....)))))))........)))))..((((((...(((......)))..))))))...... ( -23.49)
>DroYak_CAF1 7921 106 + 1
AUGAUUU--AUAUCUUUGCCAAUUUUGUUUGCUCGCGUUCGAGCAAUAAUUAAUUGGCUUUUUCUAUAAUUCAUAAGCAAUUUAGACGCAGUUAUAUGCUUAGUUUGA
((((.((--(((.....(((((((....(((((((....))))))).....)))))))......))))).)))).......(((((((((......)))...)))))) ( -27.20)
>consensus
AUGAUAAAUAUAUCUUUGCCAAUUUGGCUUGCUCGAGUUCGAGCAAUAAUUAAUUGGCUUUUUCCAUAAUUUAUAAGCAAUUUAGAUGAAGUUAUAUGCUUAGUUUGA
.................(((((((....(((((((....))))))).....)))))))...............((((((.....(((...)))...))))))...... (-18.88 = -19.00 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 25,691,600 – 25,691,704
Length 104
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 88.58
Mean single sequence MFE -21.14
Consensus MFE -16.41
Energy contribution -18.21
Covariance contribution 1.80
Combinations/Pair 1.00
Mean z-score -3.20
Structure conservation index 0.78
SVM decision value 2.57
SVM RNA-class probability 0.995337
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25691600 104 - 27905053
UCAAACUAAC----UAACUGCAUCUAAAUUGCUUAUUAAUUAUGGAAAAAGCCAAUUAAUUAUUGCUCGAACUCGAACAAGCCAUAUUGGCAAAUAUAUAUUUAUCAU
..........----.....(((.......)))....(((.((((......((((((......(((.(((....))).))).....)))))).....)))).))).... ( -15.20)
>DroSec_CAF1 7404 108 - 1
UCAAACUAAGCACAUGACUUCAUCUUAAUUGCUUAUAAAUUAUGGAAAAAGCCAAUUAAUUACUGCUCGAACUCGAGCAAGCCAAAUUGGCAAAGAUAUAUUUAUCAU
......((((((.(((....)))......))))))...............(((((((......((((((....)))))).....)))))))...((((....)))).. ( -23.80)
>DroSim_CAF1 7418 107 - 1
UCAAACUAAGC-CAUGACUUCAUCUUAAUUGCUUAUAAAUUAUGGAAAAAGCCAAUUAAUUACUGCUCGAACUCGAGCAAGCCAAAUUGGCAAAGAUAUAUUUAUCAU
..........(-(((((......................)))))).....(((((((......((((((....)))))).....)))))))...((((....)))).. ( -23.05)
>DroEre_CAF1 7928 106 - 1
UCAAACUAAGCAUAUAACUACAUCUAAAUUGCUUAUAAAUUAUAGAAAAAGCCAAUUAAUUAUUGCUCGAACUCGAACAAUCGAAAUUGGCAAAGAUAU--UAAUCAU
......((((((.................))))))...............(((((((....((((.(((....))).))))...)))))))...(((..--..))).. ( -18.13)
>DroYak_CAF1 7921 106 - 1
UCAAACUAAGCAUAUAACUGCGUCUAAAUUGCUUAUGAAUUAUAGAAAAAGCCAAUUAAUUAUUGCUCGAACGCGAGCAAACAAAAUUGGCAAAGAUAU--AAAUCAU
......((((((.................))))))(((.(((((......(((((((.....(((((((....)))))))....))))))).....)))--)).))). ( -25.53)
>consensus
UCAAACUAAGCACAUAACUGCAUCUAAAUUGCUUAUAAAUUAUGGAAAAAGCCAAUUAAUUAUUGCUCGAACUCGAGCAAGCCAAAUUGGCAAAGAUAUAUUUAUCAU
......((((((.................))))))...............(((((((.....(((((((....)))))))....)))))))................. (-16.41 = -18.21 +   1.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:40:29 2006