Locus 3038

Sequence ID 3R_DroMel_CAF1
Location 8,085,670 – 8,086,164
Length 494
Max. P 0.999978
window4895 window4896 window4897 window4898 window4899 window4900 window4901 window4902

overview

Window 5

Location 8,085,670 – 8,085,782
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.49
Mean single sequence MFE -40.96
Consensus MFE -38.02
Energy contribution -39.18
Covariance contribution 1.16
Combinations/Pair 1.03
Mean z-score -3.19
Structure conservation index 0.93
SVM decision value 5.20
SVM RNA-class probability 0.999978
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8085670 112 - 27905053
CCAUUCGUAUCUCACAGUUGCAUCUUGUUAUCUCGUCAAGAGAUUCGAGUGCGAGUGUGAGUGUGCGUGGGUAAACUCUCUGCUUGGCGACAAUUUUGCGUCAUUUGCGGUU--------
(((..(((((((((((.(((((.((((..(((((.....))))).))))))))).)))))).)))))))).........((((.(((((.((....)))))))...))))..-------- ( -44.20)
>DroSec_CAF1 10592 112 - 1
CCAUUCGUAUCUCACAGUUGCAUCUUGUUAUCUCGUCAAGAGAUUCGAGUGCGAGUGUGAGUGUGCGUGGGUAAACUCUCUGCUUGGCGACAAUUUUGCGUCAUUUGCGGUU--------
(((..(((((((((((.(((((.((((..(((((.....))))).))))))))).)))))).)))))))).........((((.(((((.((....)))))))...))))..-------- ( -44.20)
>DroSim_CAF1 9428 112 - 1
CCAUUCGUAUCUCACAGUUGCAUCUUGUUAUCUCGUCAAGAGAUUCGAGUGCGAGUGUGAGUGUGCGUGGGUAAACUCUCUGCUUGGCGACAAUUUUGCGUCAUUUGCGGUU--------
(((..(((((((((((.(((((.((((..(((((.....))))).))))))))).)))))).)))))))).........((((.(((((.((....)))))))...))))..-------- ( -44.20)
>DroEre_CAF1 12349 106 - 1
CCAGUCGUAUCUCACAGUUGCAUCUUGUUAUCUCGUCAAGAGAUUCGAGUGUGAGUGU------GCGUGGGUAAACUCUCUGCUUGGCGACAAUUUUGCGUCAUUUGCGGUU--------
(((..(((((((((((.(((..(((((.........)))))....))).)))))).))------)))))).........((((.(((((.((....)))))))...))))..-------- ( -32.90)
>DroYak_CAF1 5702 120 - 1
CCAGUCGUAUCUCACAGUUGCAUCUUUUUAUCUCGUCAAGAGAUUCGAGUGUGAGUGUGCGUGUGCGUGGGUAAACUCUCUGCUUGGCGACAAUUUUGCGUCAUUUGCGGUUGGUUGUCU
(((..((((((.((((.(..((.(((...(((((.....)))))..)))))..).)))).).))))))))...((((..((((.(((((.((....)))))))...))))..)))).... ( -39.30)
>consensus
CCAUUCGUAUCUCACAGUUGCAUCUUGUUAUCUCGUCAAGAGAUUCGAGUGCGAGUGUGAGUGUGCGUGGGUAAACUCUCUGCUUGGCGACAAUUUUGCGUCAUUUGCGGUU________
(((..(((((((((((.(((((.((((..(((((.....))))).))))))))).)))))).)))))))).........((((.(((((.((....)))))))...)))).......... (-38.02 = -39.18 +   1.16)

alignment

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secondary structure

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Window 6

Location 8,085,702 – 8,085,822
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.75
Mean single sequence MFE -42.32
Consensus MFE -38.60
Energy contribution -39.76
Covariance contribution 1.16
Combinations/Pair 1.03
Mean z-score -2.55
Structure conservation index 0.91
SVM decision value 3.89
SVM RNA-class probability 0.999685
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8085702 120 - 27905053
AAGCUGUGUGCGAGGGCCUCAUUAAACGGUAUUUUUGUGGCCAUUCGUAUCUCACAGUUGCAUCUUGUUAUCUCGUCAAGAGAUUCGAGUGCGAGUGUGAGUGUGCGUGGGUAAACUCUC
..((.....))(((((((.((..((......))..)).))))...(((((((((((.(((((.((((..(((((.....))))).))))))))).)))))).)))))........))).. ( -45.00)
>DroSec_CAF1 10624 120 - 1
AAGCUGUGUGCGAGGGCCUCAUUAAACGGUAUUUUUGUGGCCAUUCGUAUCUCACAGUUGCAUCUUGUUAUCUCGUCAAGAGAUUCGAGUGCGAGUGUGAGUGUGCGUGGGUAAACUCUC
..((.....))(((((((.((..((......))..)).))))...(((((((((((.(((((.((((..(((((.....))))).))))))))).)))))).)))))........))).. ( -45.00)
>DroSim_CAF1 9460 120 - 1
AAGCUGUGUGCGAGGGCCUCAUUAAACGGUAUUUUUGUGGCCAUUCGUAUCUCACAGUUGCAUCUUGUUAUCUCGUCAAGAGAUUCGAGUGCGAGUGUGAGUGUGCGUGGGUAAACUCUC
..((.....))(((((((.((..((......))..)).))))...(((((((((((.(((((.((((..(((((.....))))).))))))))).)))))).)))))........))).. ( -45.00)
>DroEre_CAF1 12381 114 - 1
AAGCUGUGUGCGAGGGCCUCAUUAAACGGUAUUUUUGUGGCCAGUCGUAUCUCACAGUUGCAUCUUGUUAUCUCGUCAAGAGAUUCGAGUGUGAGUGU------GCGUGGGUAAACUCUC
.((((((((((((.((((.((..((......))..)).))))..)))))...)))))))(((.((((..(((((.....))))).)))))))((((.(------((....))).)))).. ( -39.00)
>DroYak_CAF1 5742 120 - 1
AAGCUGUGAGCGAGGGCCUCAUUAAACGGUAUUUCUGUGGCCAGUCGUAUCUCACAGUUGCAUCUUUUUAUCUCGUCAAGAGAUUCGAGUGUGAGUGUGCGUGUGCGUGGGUAAACUCUC
.((((((((((((.((((.((..((......))..)).))))..)))...)))))))))(((.(((...(((((.....)))))..))))))((((.(((.(......).))).)))).. ( -37.60)
>consensus
AAGCUGUGUGCGAGGGCCUCAUUAAACGGUAUUUUUGUGGCCAUUCGUAUCUCACAGUUGCAUCUUGUUAUCUCGUCAAGAGAUUCGAGUGCGAGUGUGAGUGUGCGUGGGUAAACUCUC
..((.....))(((((((.((..((......))..)).))))...(((((((((((.(((((.((((..(((((.....))))).))))))))).)))))).)))))........))).. (-38.60 = -39.76 +   1.16)

alignment

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secondary structure

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Window 7

Location 8,085,742 – 8,085,857
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.59
Mean single sequence MFE -29.70
Consensus MFE -24.82
Energy contribution -24.82
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.34
Structure conservation index 0.84
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8085742 115 + 27905053
CUUGACGAGAUAACAAGAUGCAACUGUGAGAUACGAAUGGCCACAAAAAUACCGUUUAAUGAGGCCCUCGCACACAGCUUGACUAUUUCUUAGAUCUUAU-----CCGUAGGGAAGUCAC
..(((((((((...((((.(((((((((.(...(((..((((.((..((......))..)).)))).)))).))))).))).)....))))..))))).(-----((....))).)))). ( -27.30)
>DroSec_CAF1 10664 119 + 1
CUUGACGAGAUAACAAGAUGCAACUGUGAGAUACGAAUGGCCACAAAAAUACCGUUUAAUGAGGCCCUCGCACACAGCUUGACUAUUUCUUAGAUCUUAUCCCAUCCGUAGGG-AGUCAC
..(((((((((...((((.(((((((((.(...(((..((((.((..((......))..)).)))).)))).))))).))).)....))))..))))).((((.......)))-))))). ( -30.20)
>DroSim_CAF1 9500 119 + 1
CUUGACGAGAUAACAAGAUGCAACUGUGAGAUACGAAUGGCCACAAAAAUACCGUUUAAUGAGGCCCUCGCACACAGCUUGACUAUUUCUUAGAUCUUAUCCCAUCCGUAGGG-AGUCAC
..(((((((((...((((.(((((((((.(...(((..((((.((..((......))..)).)))).)))).))))).))).)....))))..))))).((((.......)))-))))). ( -30.20)
>DroEre_CAF1 12415 114 + 1
CUUGACGAGAUAACAAGAUGCAACUGUGAGAUACGACUGGCCACAAAAAUACCGUUUAAUGAGGCCCUCGCACACAGCUUGACUAUUUCUUAGAUCUUAU-----CCGUAGGG-AGUCAC
..(((((((((...((((.(((((((((.(...(((..((((.((..((......))..)).)))).)))).))))).))).)....))))..))))).(-----((....))-))))). ( -27.30)
>DroYak_CAF1 5782 114 + 1
CUUGACGAGAUAAAAAGAUGCAACUGUGAGAUACGACUGGCCACAGAAAUACCGUUUAAUGAGGCCCUCGCUCACAGCUUGACUAUUUCUUAGAUCUUAU-----CCGUAGGG-AGUCAC
..(((((((((...((((.(((((((((((...(((..((((.((..((......))..)).)))).)))))))))).))).)....))))..))))).(-----((....))-))))). ( -33.50)
>consensus
CUUGACGAGAUAACAAGAUGCAACUGUGAGAUACGAAUGGCCACAAAAAUACCGUUUAAUGAGGCCCUCGCACACAGCUUGACUAUUUCUUAGAUCUUAU_____CCGUAGGG_AGUCAC
..(((((((((...((((.(((((((((.(...(((..((((.((..((......))..)).)))).)))).))))).))).)....))))..))))).......((....))..)))). (-24.82 = -24.82 +   0.00)

alignment

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secondary structure

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Window 8

Location 8,085,857 – 8,085,968
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.29
Mean single sequence MFE -30.41
Consensus MFE -23.76
Energy contribution -24.16
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.78
SVM decision value 1.03
SVM RNA-class probability 0.903392
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8085857 111 + 27905053
UCAAAGGAUAUUGGC-CGGCUGCCUAUUCUCUAUGAAAUCGAUUCUAUUCAUCCCGCU--------UUUUCGGGUUUCCGAGGCCCAUAACUCGUGUUACUUUAUGCAGCCGGCUUUGUU
......((((..(((-(((((((...........((((..((......))..((((..--------....))))))))((((........))))...........)))))))))).)))) ( -32.80)
>DroSec_CAF1 10783 112 + 1
UCAAAGGAUAUUGGCCCGGCUGCCUAUUCUCAUUGAAAUCGAUUCUAUUCAUCCCGCU--------UUUUCGGGUUUCCGAGGCCCAUAACUCGUGUUACUUUAUGCAGCCGGCUUUGUU
......((((..((((.((((((...........((((..((......))..((((..--------....))))))))((((........))))...........)))))))))).)))) ( -29.00)
>DroSim_CAF1 9619 111 + 1
UCAAAGGAUAUUGGCCCGGCUGCCUAUUCUCAUUGAAAUCGAUUCUAUUCAUC-CGCU--------UUUUCGGGUUUCCGAGGCCCAUAACUCGUGUUGCUUUAUGCAGCCGGCUUUGUU
.(((((..(((.(((((((..((((.(((.....)))...((......))...-....--------.....))))..))).)))).)))..(((.(((((.....))))))))))))).. ( -32.30)
>DroEre_CAF1 12529 118 + 1
UCAAAGGAUAUUGGC-CGGCUGCCUAUUCUCAUUGAAAUCGAAUCUAUUCAUCC-ACUAUCCACACUAUUCGGGUUUCCGAGGCCCAUAACUCCUGGUACUUUAUGCAGCCGGCUUUGUU
......((((..(((-(((((((...........((((((((((..........-............)))).)))))).(((..(((.......)))..)))...)))))))))).)))) ( -30.05)
>DroYak_CAF1 5896 116 + 1
UCAAAGGAUAUUGGC-CGGCUGCCUAUUCUCAUUGAAAUCGAUUCUAUUCAGCCUACUA---CUACUAUUCGUGUUUCCGAUGCCCAUAACUCCUGGUACUUUAUGCAGCCGGCUUUGUU
......((((..(((-(((((((.......((((((((((((........((....)).---.......))).)))).))))).(((.......)))........)))))))))).)))) ( -27.89)
>consensus
UCAAAGGAUAUUGGC_CGGCUGCCUAUUCUCAUUGAAAUCGAUUCUAUUCAUCCCGCU________UUUUCGGGUUUCCGAGGCCCAUAACUCGUGUUACUUUAUGCAGCCGGCUUUGUU
......((((..(((.(((((((...(((.....)))..................................(((((.....)))))...................)))))))))).)))) (-23.76 = -24.16 +   0.40)

alignment

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secondary structure

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Window 9

Location 8,085,968 – 8,086,088
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.42
Mean single sequence MFE -28.24
Consensus MFE -27.50
Energy contribution -27.18
Covariance contribution -0.32
Combinations/Pair 1.06
Mean z-score -1.23
Structure conservation index 0.97
SVM decision value 0.77
SVM RNA-class probability 0.846194
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8085968 120 + 27905053
UGACCACAAAGUGUCGCUGACCAAGUCCCCAUAAUCGAUUGAAUUACUUGCUCCCUAGCAGCUUCCUUCCGCAAUUCAUGUCAGGCUCUAAAUUCAAAGGUUUAGAGCCCCAAAAUGUGC
....((((..(((..(((.....)))...)))....(((((((((...((((....))))((........)))))))).))).((((((((((......))))))))))......)))). ( -27.60)
>DroSec_CAF1 10895 120 + 1
UGACCACAAAGUGUCGCUGACCAAGUCCCCAUAAUCGAUUGAAUUACCCGCUCCCUAGCAGCUUCCUUCCGCAAUUCUUGUCAGGCUCUAAAUUCAAGGGUUUAGAGCCCCAAAAUGUGC
....((((..(((..(((.....)))...)))....(((.(((((....(((....))).((........)))))))..))).(((((((((((....)))))))))))......)))). ( -27.50)
>DroSim_CAF1 9730 120 + 1
UGACCACAAAGUGUCGCUGACCAAGUCUCCAUAAUCGAUUGAAUUACCCGCUCCCUAGCAGCUUCCUUCCGCAAUUCAUGUCAGGCUCUAAAUUCAAGGGUUUAGAGCCCCAAAAUGUGC
....((((..(((..(((.....)))...)))....(((((((((....(((....))).((........)))))))).))).(((((((((((....)))))))))))......)))). ( -28.40)
>DroEre_CAF1 12647 120 + 1
UGACCACAAAGUGUCGCUGACCAAGUCCCUAUAAUCGAUUGAAUUACCCGCUCCCAAGCAGCUUCCUUCCGCAAUUCCUGUCAGGCUCUAAAUUCAAGGGUUUAGAGCCCCAAAAUGUGC
....((((....(..(((.....)))..).......(((.(((((....(((....))).((........)))))))..))).(((((((((((....)))))))))))......)))). ( -26.90)
>DroYak_CAF1 6012 120 + 1
UGACCACAAAGUGUCGCUGACCAAGUCCCCAUAAUCGAUUGAAUUACCCGCUCUCUGGCAGCUUCCUUCCGCAAUUCAUGUCAGGCUCUAAACUCAAGGGUUUAGAGCCCCAAAAUGUGC
....((((..(((..(((.....)))...)))....(((((((((....(((....))).((........)))))))).))).(((((((((((....)))))))))))......)))). ( -30.80)
>consensus
UGACCACAAAGUGUCGCUGACCAAGUCCCCAUAAUCGAUUGAAUUACCCGCUCCCUAGCAGCUUCCUUCCGCAAUUCAUGUCAGGCUCUAAAUUCAAGGGUUUAGAGCCCCAAAAUGUGC
....((((...((....((((..((((.........))))(((((....(((....))).((........)))))))..))))(((((((((((....))))))))))).))...)))). (-27.50 = -27.18 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,086,008 – 8,086,128
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.42
Mean single sequence MFE -33.44
Consensus MFE -27.56
Energy contribution -28.24
Covariance contribution 0.68
Combinations/Pair 1.06
Mean z-score -1.41
Structure conservation index 0.82
SVM decision value 0.22
SVM RNA-class probability 0.641365
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8086008 120 + 27905053
GAAUUACUUGCUCCCUAGCAGCUUCCUUCCGCAAUUCAUGUCAGGCUCUAAAUUCAAAGGUUUAGAGCCCCAAAAUGUGCAGCGUCAACUGUCGAGAAUGGAUUUAGUGGCAGUGCAUCU
........((((....))))((...((.(((((((((((.((.((((((((((......)))))))))).........((((......)))).))..)))))))..)))).)).)).... ( -32.40)
>DroSec_CAF1 10935 120 + 1
GAAUUACCCGCUCCCUAGCAGCUUCCUUCCGCAAUUCUUGUCAGGCUCUAAAUUCAAGGGUUUAGAGCCCCAAAAUGUGCAGCGUCAACUGUCGAGAAAGGAUUUAGUGGCAGUGCAUCU
.........(((....))).((...((.(((((((((((.((.(((((((((((....))))))))))).........((((......)))).))..)))))))..)))).)).)).... ( -33.00)
>DroSim_CAF1 9770 120 + 1
GAAUUACCCGCUCCCUAGCAGCUUCCUUCCGCAAUUCAUGUCAGGCUCUAAAUUCAAGGGUUUAGAGCCCCAAAAUGUGCAGCGUCAACUGUCGAGAAAGGAUUUAGUGGCAGUGCAUCU
........((((((((((.....(((((.((((...(((....(((((((((((....))))))))))).....))))))..((.(....).)).).))))).)))).)).))))..... ( -31.80)
>DroEre_CAF1 12687 120 + 1
GAAUUACCCGCUCCCAAGCAGCUUCCUUCCGCAAUUCCUGUCAGGCUCUAAAUUCAAGGGUUUAGAGCCCCAAAAUGUGCAGCGUCAACUGUCGAUAAAGGAUUUAAAGGAACUGCAUCC
.................((((.((((((.......(((((((.(((((((((((....))))))))))).........((((......)))).)))..))))....)))))))))).... ( -35.50)
>DroYak_CAF1 6052 120 + 1
GAAUUACCCGCUCUCUGGCAGCUUCCUUCCGCAAUUCAUGUCAGGCUCUAAACUCAAGGGUUUAGAGCCCCAAAAUGUGCAGCGUCAACUGUCGAGAAAGGAUUUUAAAGAACUGCAUCU
.......((..((((.(((((........(((....(((....(((((((((((....))))))))))).....)))....)))....)))))))))..))................... ( -34.50)
>consensus
GAAUUACCCGCUCCCUAGCAGCUUCCUUCCGCAAUUCAUGUCAGGCUCUAAAUUCAAGGGUUUAGAGCCCCAAAAUGUGCAGCGUCAACUGUCGAGAAAGGAUUUAGUGGCAGUGCAUCU
(((((....(((....))).((........)))))))......(((((((((((....))))))))))).......(((((..((((...(((.......)))....))))..))))).. (-27.56 = -28.24 +   0.68)

alignment

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secondary structure

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Window 1

Location 8,086,008 – 8,086,128
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.42
Mean single sequence MFE -36.38
Consensus MFE -33.92
Energy contribution -34.36
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.24
Structure conservation index 0.93
SVM decision value 0.66
SVM RNA-class probability 0.813346
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8086008 120 - 27905053
AGAUGCACUGCCACUAAAUCCAUUCUCGACAGUUGACGCUGCACAUUUUGGGGCUCUAAACCUUUGAAUUUAGAGCCUGACAUGAAUUGCGGAAGGAAGCUGCUAGGGAGCAAGUAAUUC
...(((..(((............((((..(((((..(.(((((.(((((.((((((((((........)))))))))).)...)))))))))..)..)))))...))))))).))).... ( -30.90)
>DroSec_CAF1 10935 120 - 1
AGAUGCACUGCCACUAAAUCCUUUCUCGACAGUUGACGCUGCACAUUUUGGGGCUCUAAACCCUUGAAUUUAGAGCCUGACAAGAAUUGCGGAAGGAAGCUGCUAGGGAGCGGGUAAUUC
.................((((.(((((..(((((..(.(((((..(((((((((((((((........))))))))))..)))))..)))))..)..)))))...))))).))))..... ( -38.00)
>DroSim_CAF1 9770 120 - 1
AGAUGCACUGCCACUAAAUCCUUUCUCGACAGUUGACGCUGCACAUUUUGGGGCUCUAAACCCUUGAAUUUAGAGCCUGACAUGAAUUGCGGAAGGAAGCUGCUAGGGAGCGGGUAAUUC
.................((((.(((((..(((((..(.(((((.(((((.((((((((((........)))))))))).)...)))))))))..)..)))))...))))).))))..... ( -36.10)
>DroEre_CAF1 12687 120 - 1
GGAUGCAGUUCCUUUAAAUCCUUUAUCGACAGUUGACGCUGCACAUUUUGGGGCUCUAAACCCUUGAAUUUAGAGCCUGACAGGAAUUGCGGAAGGAAGCUGCUUGGGAGCGGGUAAUUC
(((......))).....((((....(((((((((..(.(((((..(((((((((((((((........))))))))))..)))))..)))))..)..))))).))))....))))..... ( -36.60)
>DroYak_CAF1 6052 120 - 1
AGAUGCAGUUCUUUAAAAUCCUUUCUCGACAGUUGACGCUGCACAUUUUGGGGCUCUAAACCCUUGAGUUUAGAGCCUGACAUGAAUUGCGGAAGGAAGCUGCCAGAGAGCGGGUAAUUC
.................((((.(((((..(((((..(.(((((.(((((.(((((((((((......))))))))))).)...)))))))))..)..)))))...))))).))))..... ( -40.30)
>consensus
AGAUGCACUGCCACUAAAUCCUUUCUCGACAGUUGACGCUGCACAUUUUGGGGCUCUAAACCCUUGAAUUUAGAGCCUGACAUGAAUUGCGGAAGGAAGCUGCUAGGGAGCGGGUAAUUC
.................((((.(((((..(((((..(.(((((.(((((.((((((((((........)))))))))).)...)))))))))..)..)))))...))))).))))..... (-33.92 = -34.36 +   0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,086,048 – 8,086,164
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.18
Mean single sequence MFE -38.00
Consensus MFE -28.00
Energy contribution -28.04
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -2.35
Structure conservation index 0.74
SVM decision value 0.65
SVM RNA-class probability 0.812554
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8086048 116 + 27905053
UCAGGCUCUAAAUUCAAAGGUUUAGAGCCCCAAAAUGUGCAGCGUCAACUGUCGAGAAUGGAUUUAGUGGCAGUGCAUCUUAGCAGGAA---ACUACUACGGAUUGGUUGG-AUGCUGGC
...((((((((((......))))))))))..........(((((((.(((((((..((.....))..)))))))..(((((((.((...---.)).))).))))......)-)))))).. ( -40.10)
>DroSec_CAF1 10975 116 + 1
UCAGGCUCUAAAUUCAAGGGUUUAGAGCCCCAAAAUGUGCAGCGUCAACUGUCGAGAAAGGAUUUAGUGGCAGUGCAUCUUAGCAGGAA---ACUAGUACCGAUUGGUUGG-AUGCUGGC
...(((((((((((....)))))))))))..........(((((((.(((((((..((.....))..)))))))((......))....(---((((((....))))))).)-)))))).. ( -38.70)
>DroSim_CAF1 9810 116 + 1
UCAGGCUCUAAAUUCAAGGGUUUAGAGCCCCAAAAUGUGCAGCGUCAACUGUCGAGAAAGGAUUUAGUGGCAGUGCAUCUUAGCAGGAA---ACUACUACCAAUUGGUUGG-AUGCUGGC
...(((((((((((....)))))))))))..........(((((((.(((((((..((.....))..)))))))((......))((...---.)).(.(((....))).))-)))))).. ( -39.40)
>DroEre_CAF1 12727 116 + 1
UCAGGCUCUAAAUUCAAGGGUUUAGAGCCCCAAAAUGUGCAGCGUCAACUGUCGAUAAAGGAUUUAAAGGAACUGCAUCCUAGCUGGAA---ACUACUACUGAUUGGUUGG-AUGCUGGC
...(((((((((((....)))))))))))..........(((((((((((((((....(((((.((.......)).)))))((..(...---.)..))..))).))))).)-)))))).. ( -35.40)
>DroYak_CAF1 6092 120 + 1
UCAGGCUCUAAACUCAAGGGUUUAGAGCCCCAAAAUGUGCAGCGUCAACUGUCGAGAAAGGAUUUUAAAGAACUGCAUCUUAGCAGGAUGCUACUACUACUGAUUGGUUGGAAUGCUGGC
...(((((((((((....)))))))))))..........((((((((((((((.((..((............))((((((.....))))))........)))).))))))..)))))).. ( -36.40)
>consensus
UCAGGCUCUAAAUUCAAGGGUUUAGAGCCCCAAAAUGUGCAGCGUCAACUGUCGAGAAAGGAUUUAGUGGCAGUGCAUCUUAGCAGGAA___ACUACUACCGAUUGGUUGG_AUGCUGGC
...(((((((((((....)))))))))))..........((((((((((((((.......)))..........(((......)))....................)))))..)))))).. (-28.00 = -28.04 +   0.04)

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 10:51:02 2006