Locus 1686

Sequence ID 3L_DroMel_CAF1
Location 4,939,623 – 4,939,806
Length 183
Max. P 0.999381
window2600 window2601 window2602 window2603

overview

Window 0

Location 4,939,623 – 4,939,739
Length 116
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.84
Mean single sequence MFE -28.44
Consensus MFE -15.97
Energy contribution -15.58
Covariance contribution -0.39
Combinations/Pair 1.18
Mean z-score -2.76
Structure conservation index 0.56
SVM decision value 1.61
SVM RNA-class probability 0.967080
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4939623 116 + 23771897
AUGGCCAGAAGGGAA--GGGGGUAUGGGAAAAUGGAUGAGAGAGAGCGUUACAAGCAAAUGAAAAAUCAAUUUGUUGAUUAUGCAUAAAUCAUAAGAUUUAUGCGACUCC--UCACUCAG
(((.((.........--..)).))).......((..((((.(((.((.......))........((((((....)))))).((((((((((....)))))))))).))))--)))..)). ( -27.80)
>DroSim_CAF1 170811 117 + 1
UUGGCCAGAAGGGAA--GG-GGUAUGGGAAAAUGGCUGAAAGAGAGCGUUACAAGCAAAUGAAAAAUCAAUUUGUUGAUUAUGCAUAAAUCAUAAGAUUUAUGCGACUCCUCUCACUCAG
(..((((........--..-............))))..)..(((((.(((...(((((((((....)).)))))))......(((((((((....))))))))))))..)))))...... ( -29.55)
>DroEre_CAF1 162114 118 + 1
AUGGCCAGAAGGGAAAAGGGGGAGUGGGAAAAUGGCUGAAAGAGAGCGUUACAAGCAAAUGAAAAAUCAAUUUGUUGAUUAUGCAUAAAUCAUAAGAUUUAUGCGACUCC--UCACUCAG
....((....)).........((((((((.....(((.......)))(((...(((((((((....)).)))))))......(((((((((....)))))))))))))))--.))))).. ( -29.90)
>DroYak_CAF1 166193 109 + 1
AUGGCCAGAAGAGUAG---------GGGAAAAUGGCUGAAAGAGAGCGUUACAAACAAAUGAAAAAUCAAUUUGUUGAUUAUGCAUAAAUCAUAAGAUUUAUGCGACUCC--UCACUCAG
..........((((.(---------((((.....(((.......)))(((...(((((((((....)).)))))))......(((((((((....)))))))))))))))--)))))).. ( -29.70)
>DroMoj_CAF1 225579 97 + 1
UUUACAAGGAG--UU----------GGG------CGUGACUUAGGGCGUGUC-AGCAAAUGAAAAAUCAAUUUGUUGUUUAUGCAUAAAUCAUGUGAUUUAUGUGACUUC--UAA--CAG
..........(--((----------(((------.((.((.....(((((.(-(((((((((....)).))))))))..)))))(((((((....))))))))).)).))--)))--).. ( -26.80)
>DroAna_CAF1 169786 100 + 1
AUUGCGAGGAU--------------GAGAGAAG----CAGUGUGAGCAUUACAAGAAAAUGAAAAAUCAAUUUGUUGAUUAUGCAUAAAUCAUAAGAUUUAUGCGACUCC--UCACUCGG
....((((((.--------------(((.....----.((((....)))).(((.(((.(((....))).))).)))....((((((((((....)))))))))).))).--)).)))). ( -26.90)
>consensus
AUGGCCAGAAGGGAA__________GGGAAAAUGGCUGAAAGAGAGCGUUACAAGCAAAUGAAAAAUCAAUUUGUUGAUUAUGCAUAAAUCAUAAGAUUUAUGCGACUCC__UCACUCAG
...........................................((((......(((((((((....)).)))))))......(((((((((....)))))))))).)))........... (-15.97 = -15.58 +  -0.39)

alignment

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secondary structure

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Window 1

Location 4,939,623 – 4,939,739
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.84
Mean single sequence MFE -24.71
Consensus MFE -16.46
Energy contribution -17.35
Covariance contribution 0.89
Combinations/Pair 1.04
Mean z-score -3.43
Structure conservation index 0.67
SVM decision value 2.02
SVM RNA-class probability 0.985703
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4939623 116 - 23771897
CUGAGUGA--GGAGUCGCAUAAAUCUUAUGAUUUAUGCAUAAUCAACAAAUUGAUUUUUCAUUUGCUUGUAACGCUCUCUCUCAUCCAUUUUCCCAUACCCCC--UUCCCUUCUGGCCAU
.((((.((--(.(((.(((((((((....))))))))).....((((((((.((....))))))).)))....)))))).))))...................--...((....)).... ( -25.40)
>DroSim_CAF1 170811 117 - 1
CUGAGUGAGAGGAGUCGCAUAAAUCUUAUGAUUUAUGCAUAAUCAACAAAUUGAUUUUUCAUUUGCUUGUAACGCUCUCUUUCAGCCAUUUUCCCAUACC-CC--UUCCCUUCUGGCCAA
.....((((((((((.(((((((((....))))))))).....((((((((.((....))))))).)))....)))).))))))((((............-..--........))))... ( -28.45)
>DroEre_CAF1 162114 118 - 1
CUGAGUGA--GGAGUCGCAUAAAUCUUAUGAUUUAUGCAUAAUCAACAAAUUGAUUUUUCAUUUGCUUGUAACGCUCUCUUUCAGCCAUUUUCCCACUCCCCCUUUUCCCUUCUGGCCAU
..(((((.--((((..(((((((((....))))))))).....((((((((.((....))))))).)))....(((.......)))....))))))))).........((....)).... ( -26.80)
>DroYak_CAF1 166193 109 - 1
CUGAGUGA--GGAGUCGCAUAAAUCUUAUGAUUUAUGCAUAAUCAACAAAUUGAUUUUUCAUUUGUUUGUAACGCUCUCUUUCAGCCAUUUUCCC---------CUACUCUUCUGGCCAU
.((((.((--(.(((.(((((((((....)))))))))...((.(((((((.((....))))))))).))...)))))).))))((((.......---------.........))))... ( -26.59)
>DroMoj_CAF1 225579 97 - 1
CUG--UUA--GAAGUCACAUAAAUCACAUGAUUUAUGCAUAAACAACAAAUUGAUUUUUCAUUUGCU-GACACGCCCUAAGUCACG------CCC----------AA--CUCCUUGUAAA
.((--(((--(......((((((((....)))))))).........(((((.((....)))))))))-))))..............------...----------..--........... ( -14.50)
>DroAna_CAF1 169786 100 - 1
CCGAGUGA--GGAGUCGCAUAAAUCUUAUGAUUUAUGCAUAAUCAACAAAUUGAUUUUUCAUUUUCUUGUAAUGCUCACACUG----CUUCUCUC--------------AUCCUCGCAAU
....((((--(((...(((((((((....))))))))).....(((.(((.(((....))).))).)))....((.......)----).......--------------.)))))))... ( -26.50)
>consensus
CUGAGUGA__GGAGUCGCAUAAAUCUUAUGAUUUAUGCAUAAUCAACAAAUUGAUUUUUCAUUUGCUUGUAACGCUCUCUUUCAGCCAUUUUCCC__________UUCCCUUCUGGCCAU
..(((((.........(((((((((....))))))))).....((((((((.((....))))))).)))...)))))........................................... (-16.46 = -17.35 +   0.89)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,939,701 – 4,939,806
Length 105
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 93.16
Mean single sequence MFE -19.08
Consensus MFE -17.65
Energy contribution -17.23
Covariance contribution -0.41
Combinations/Pair 1.15
Mean z-score -2.58
Structure conservation index 0.93
SVM decision value 3.56
SVM RNA-class probability 0.999381
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4939701 105 + 23771897
AUGCAUAAAUCAUAAGAUUUAUGCGACUCC--UCACUCAGCAUUCAUGAGUCAUUUAUCAAACGAGCAAACUUUUCUCUACUGCCUUCAUGUCAGUAUCACAAAAAC
..(((((((((....)))))))))(((((.--...............)))))...........(((.((....)))))(((((.(.....).))))).......... ( -19.79)
>DroSec_CAF1 160842 107 + 1
AUGCAUAAAUCAUAAGAUUUAUGCGACUCCUCUCACUCAGCAUUCAUGAGUCAUUUAUCAAACGAGCAAACUUUUCUCUACUGCCUCCAUGUCAGAAUCACAAAAAC
..(((((((((....)))))))))(((.......(((((.......)))))............(((((.............)).)))...))).............. ( -18.92)
>DroSim_CAF1 170888 107 + 1
AUGCAUAAAUCAUAAGAUUUAUGCGACUCCUCUCACUCAGCAUUCAUGAGUCAUUUAUCAAACGAGCAAACUUUUCUCUACUGCCUUCAUGUCAGAAUCACAAAAAC
..(((((((((....)))))))))(((.......(((((.......)))))............(((((.............)))..))..))).............. ( -18.22)
>DroEre_CAF1 162194 105 + 1
AUGCAUAAAUCAUAAGAUUUAUGCGACUCC--UCACUCAGCAUUUAUGAGUCAUUUAUCAAGCGAGCAAACUUUUCUCUACUGCCUUCAUGUCAGAAUCACAAAAAC
..(((((((((....)))))))))(((...--..(((((.......)))))............(((((.............)))..))..))).............. ( -18.22)
>DroYak_CAF1 166264 105 + 1
AUGCAUAAAUCAUAAGAUUUAUGCGACUCC--UCACUCAGCAUUUAUGAGUCAUUUAUCAAACGAGCAAACUUUUCUCCACUGCCUUCAUGUCAGAAUCACAAAAAC
..(((((((((....)))))))))(((...--..(((((.......)))))............(((((.............)))..))..))).............. ( -18.22)
>DroAna_CAF1 169848 103 + 1
AUGCAUAAAUCAUAAGAUUUAUGCGACUCC--UCACUCGGCAUUCAUGAGUCAUUUAUCAAACGGGCCAGCUC--CUUUUUUGCCUUCGUGUCAAAAUCACAAAAUC
.((((((((((....)))))))))).....--......((((....(((........)))...(((....)))--......))))...(((.......)))...... ( -21.10)
>consensus
AUGCAUAAAUCAUAAGAUUUAUGCGACUCC__UCACUCAGCAUUCAUGAGUCAUUUAUCAAACGAGCAAACUUUUCUCUACUGCCUUCAUGUCAGAAUCACAAAAAC
..(((((((((....)))))))))(((.......(((((.......)))))............(((.........)))............))).............. (-17.65 = -17.23 +  -0.41)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,939,701 – 4,939,806
Length 105
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 93.16
Mean single sequence MFE -28.75
Consensus MFE -26.05
Energy contribution -26.30
Covariance contribution 0.25
Combinations/Pair 1.10
Mean z-score -2.49
Structure conservation index 0.91
SVM decision value 2.96
SVM RNA-class probability 0.997927
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4939701 105 - 23771897
GUUUUUGUGAUACUGACAUGAAGGCAGUAGAGAAAAGUUUGCUCGUUUGAUAAAUGACUCAUGAAUGCUGAGUGA--GGAGUCGCAUAAAUCUUAUGAUUUAUGCAU
(((((..((.......))..)))))((((((......)))))).....(((...(.(((((.......))))).)--...)))(((((((((....))))))))).. ( -26.60)
>DroSec_CAF1 160842 107 - 1
GUUUUUGUGAUUCUGACAUGGAGGCAGUAGAGAAAAGUUUGCUCGUUUGAUAAAUGACUCAUGAAUGCUGAGUGAGAGGAGUCGCAUAAAUCUUAUGAUUUAUGCAU
........((((((..(((...((((...(((....(((((.((....)))))))..))).....))))..)))...))))))(((((((((....))))))))).. ( -28.60)
>DroSim_CAF1 170888 107 - 1
GUUUUUGUGAUUCUGACAUGAAGGCAGUAGAGAAAAGUUUGCUCGUUUGAUAAAUGACUCAUGAAUGCUGAGUGAGAGGAGUCGCAUAAAUCUUAUGAUUUAUGCAU
........((((((..(((...((((...(((....(((((.((....)))))))..))).....))))..)))...))))))(((((((((....))))))))).. ( -28.60)
>DroEre_CAF1 162194 105 - 1
GUUUUUGUGAUUCUGACAUGAAGGCAGUAGAGAAAAGUUUGCUCGCUUGAUAAAUGACUCAUAAAUGCUGAGUGA--GGAGUCGCAUAAAUCUUAUGAUUUAUGCAU
........((((((..(((..((((((((((......)))))).)))).....)))(((((.......)))))..--))))))(((((((((....))))))))).. ( -30.50)
>DroYak_CAF1 166264 105 - 1
GUUUUUGUGAUUCUGACAUGAAGGCAGUGGAGAAAAGUUUGCUCGUUUGAUAAAUGACUCAUAAAUGCUGAGUGA--GGAGUCGCAUAAAUCUUAUGAUUUAUGCAU
........((((((..(((...((((...(((....(((((.((....)))))))..))).....))))..))).--))))))(((((((((....))))))))).. ( -29.80)
>DroAna_CAF1 169848 103 - 1
GAUUUUGUGAUUUUGACACGAAGGCAAAAAAG--GAGCUGGCCCGUUUGAUAAAUGACUCAUGAAUGCCGAGUGA--GGAGUCGCAUAAAUCUUAUGAUUUAUGCAU
........((((((..(((...((((.....(--(.(....)))(((........))).......))))..))).--))))))(((((((((....))))))))).. ( -28.40)
>consensus
GUUUUUGUGAUUCUGACAUGAAGGCAGUAGAGAAAAGUUUGCUCGUUUGAUAAAUGACUCAUGAAUGCUGAGUGA__GGAGUCGCAUAAAUCUUAUGAUUUAUGCAU
........((((((..(((...((((...(((....((((((......).)))))..))).....))))..)))...))))))(((((((((....))))))))).. (-26.05 = -26.30 +   0.25)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:40 2006