Locus 3547

Sequence ID 3R_DroMel_CAF1
Location 9,597,487 – 9,597,632
Length 145
Max. P 0.987301
window5700 window5701 window5702

overview

Window 0

Location 9,597,487 – 9,597,606
Length 119
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.28
Mean single sequence MFE -28.25
Consensus MFE -25.71
Energy contribution -25.44
Covariance contribution -0.28
Combinations/Pair 1.14
Mean z-score -2.39
Structure conservation index 0.91
SVM decision value 1.59
SVM RNA-class probability 0.966378
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9597487 119 + 27905053
CACAGACGACCCAAACGAAAAGAAAAGACGACCACGACGGCCAGAAAUAAGCAA-AUUAUUUGGCUAACAAUCGUCGAAAGGGACACUAAGGAUUACCCAGCCGACGAUUGUUGGUUAAA
.............................((((.....((((((((((......-))).)))))))(((((((((((...(((.............)))...)))))))))))))))... ( -30.22)
>DroPse_CAF1 5117 119 + 1
CACAGACGACGAAUACGACGACU-UCGAACACGACAACGGCCACAAAUAAGCAAAAUUAUUUGGCUAACAAUCGUCGAAAGGGACACUAAGGAUUACCCAGCCGAUGAUUGUUGGUUUAA
..................((...-(((....)))...))....(((((((......)))))))((((((((((((((...(((.............)))...)))))))))))))).... ( -28.22)
>DroWil_CAF1 4790 96 + 1
CACAGACGACG----------------ACGA--------GCCAAAAAUAAGCAAAAUUAUUUAGCUGACAAUCGUCGAAAGGGACACUAAGGAUUACCCAGCCGACGAUUGUUGGUUAAA
...........----------------....--------....................((((((..((((((((((...(((.............)))...))))))))))..)))))) ( -26.52)
>DroYak_CAF1 4956 114 + 1
CACAGACGACCAA-----AACGAAAAGACGACCACGACGGCCAGAAAUAAGCAA-AUUAUUUAGCUAACAAUCGUCGAAAGGGACACUAAGGAUUACCCAGCCGACGAUUGUUGGUUAAA
.............-----...........(.((.....)).)............-....((((((((((((((((((...(((.............)))...)))))))))))))))))) ( -27.82)
>DroAna_CAF1 4844 97 + 1
CACAGAC----------------------GACCACGACGGCCAGAAAUAAGCAA-AUUAUUUAGCUAACAAUCGUCGAAAGGGACACUAAGGAUUACCCAGCCGACGAUUGUUGGUUAAA
.......----------------------(.((.....)).)............-....((((((((((((((((((...(((.............)))...)))))))))))))))))) ( -27.82)
>DroPer_CAF1 5047 119 + 1
CACAGACGACGAAUACGACGACU-UCGACCACGACAACGGCCAGAAAUAAGCAAAAUUAUUUGGCUAACAAUCGUCGAAAGGGACACUAAGGAUUACCCAGCCGAUGAUUGUUGGUUUAA
......((.((....)).))...-..((((........(((((..(((((......))))))))))(((((((((((...(((.............)))...)))))))))))))))... ( -28.92)
>consensus
CACAGACGACGAA_______A_____GACGACCACGACGGCCAGAAAUAAGCAA_AUUAUUUAGCUAACAAUCGUCGAAAGGGACACUAAGGAUUACCCAGCCGACGAUUGUUGGUUAAA
...........................................................((((((((((((((((((...(((.............)))...)))))))))))))))))) (-25.71 = -25.44 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,597,527 – 9,597,632
Length 105
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 82.68
Mean single sequence MFE -32.15
Consensus MFE -29.00
Energy contribution -28.64
Covariance contribution -0.36
Combinations/Pair 1.16
Mean z-score -4.09
Structure conservation index 0.90
SVM decision value 2.07
SVM RNA-class probability 0.987301
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9597527 105 + 27905053
CCAGAAAUAAGCAA-AUUAUUUGGCUAACAAUCGUCGAAAGGGACACUAAGGAUUACCCAGCCGACGAUUGUUGGUUAAAUUUUGCCAACGGC-----AGCGCGAA----AACUU
..........((..-...(((((((((((((((((((...(((.............)))...))))))))))))))))))).(((((...)))-----)).))...----..... ( -34.32)
>DroVir_CAF1 4110 98 + 1
CCACAAAUAAGCAA-AUUAUUUAGCUGACAAUCGUCGAAAGGGACACUAAGGAUUACCCAGCCGACGAUUGUCCGUUAAAGUUUGCGAGCGGCUAGCUA----------------
..........((((-((..((((((.(((((((((((...(((.............)))...))))))))))).)))))))))))).(((.....))).---------------- ( -34.72)
>DroPse_CAF1 5156 101 + 1
CCACAAAUAAGCAAAAUUAUUUGGCUAACAAUCGUCGAAAGGGACACUAAGGAUUACCCAGCCGAUGAUUGUUGGUUUAAAUUUGCUAACGGC-----ACCGCGAA---------
.........((((((.(((...(((((((((((((((...(((.............)))...)))))))))))))))))).))))))..((..-----..))....--------- ( -29.02)
>DroWil_CAF1 4806 92 + 1
CCAAAAAUAAGCAAAAUUAUUUAGCUGACAAUCGUCGAAAGGGACACUAAGGAUUACCCAGCCGACGAUUGUUGGUUAAAAAUUGCAAAA--------------AA---------
..........((((.....((((((..((((((((((...(((.............)))...))))))))))..))))))..))))....--------------..--------- ( -29.92)
>DroMoj_CAF1 3944 114 + 1
CCAGAAAUAAGCAA-AUUAUUUAGCUGACAAUCGUCGAAAGGGACACUAAGGAUUACCCAGCCGACGAUUGUUGGUUAAAAUUUGCGAAAGGCUAGCUAACGCGAACUACAAAUU
..((......((((-(((..(((((..((((((((((...(((.............)))...))))))))))..))))))))))))......)).((....))............ ( -36.52)
>DroPer_CAF1 5086 101 + 1
CCAGAAAUAAGCAAAAUUAUUUGGCUAACAAUCGUCGAAAGGGACACUAAGGAUUACCCAGCCGAUGAUUGUUGGUUUAAAUUUGCUAACGGC-----AGCGCGAA---------
.........((((((.(((...(((((((((((((((...(((.............)))...)))))))))))))))))).))))))......-----........--------- ( -28.42)
>consensus
CCAGAAAUAAGCAA_AUUAUUUAGCUAACAAUCGUCGAAAGGGACACUAAGGAUUACCCAGCCGACGAUUGUUGGUUAAAAUUUGCGAACGGC_____A_CGCGAA_________
..........((((.....((((((((((((((((((...(((.............)))...))))))))))))))))))..))))............................. (-29.00 = -28.64 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,597,527 – 9,597,632
Length 105
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 82.68
Mean single sequence MFE -26.04
Consensus MFE -21.10
Energy contribution -21.60
Covariance contribution 0.50
Combinations/Pair 1.05
Mean z-score -1.82
Structure conservation index 0.81
SVM decision value 0.54
SVM RNA-class probability 0.775397
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9597527 105 - 27905053
AAGUU----UUCGCGCU-----GCCGUUGGCAAAAUUUAACCAACAAUCGUCGGCUGGGUAAUCCUUAGUGUCCCUUUCGACGAUUGUUAGCCAAAUAAU-UUGCUUAUUUCUGG
.....----...(((..-----....(((((...........((((((((((((..(((.............)))..)))))))))))).))))).....-.))).......... ( -27.52)
>DroVir_CAF1 4110 98 - 1
----------------UAGCUAGCCGCUCGCAAACUUUAACGGACAAUCGUCGGCUGGGUAAUCCUUAGUGUCCCUUUCGACGAUUGUCAGCUAAAUAAU-UUGCUUAUUUGUGG
----------------.(((.....)))((((((........((((((((((((..(((.............)))..))))))))))))(((........-..)))..)))))). ( -31.02)
>DroPse_CAF1 5156 101 - 1
---------UUCGCGGU-----GCCGUUAGCAAAUUUAAACCAACAAUCAUCGGCUGGGUAAUCCUUAGUGUCCCUUUCGACGAUUGUUAGCCAAAUAAUUUUGCUUAUUUGUGG
---------..(((((.-----......((((((.(((..(.(((((((.((((..(((.............)))..)))).))))))).).....))).))))))...))))). ( -22.82)
>DroWil_CAF1 4806 92 - 1
---------UU--------------UUUUGCAAUUUUUAACCAACAAUCGUCGGCUGGGUAAUCCUUAGUGUCCCUUUCGACGAUUGUCAGCUAAAUAAUUUUGCUUAUUUUUGG
---------..--------------....((((..((((.(..(((((((((((..(((.............)))..)))))))))))..).)))).....)))).......... ( -24.42)
>DroMoj_CAF1 3944 114 - 1
AAUUUGUAGUUCGCGUUAGCUAGCCUUUCGCAAAUUUUAACCAACAAUCGUCGGCUGGGUAAUCCUUAGUGUCCCUUUCGACGAUUGUCAGCUAAAUAAU-UUGCUUAUUUCUGG
........(((.((....)).))).....((((((((((.(..(((((((((((..(((.............)))..)))))))))))..).)))..)))-)))).......... ( -29.62)
>DroPer_CAF1 5086 101 - 1
---------UUCGCGCU-----GCCGUUAGCAAAUUUAAACCAACAAUCAUCGGCUGGGUAAUCCUUAGUGUCCCUUUCGACGAUUGUUAGCCAAAUAAUUUUGCUUAUUUCUGG
---------...(((((-----(....))))...........(((((((.((((..(((.............)))..)))).)))))))..............)).......... ( -20.82)
>consensus
_________UUCGCG_U_____GCCGUUAGCAAAUUUUAACCAACAAUCGUCGGCUGGGUAAUCCUUAGUGUCCCUUUCGACGAUUGUCAGCCAAAUAAU_UUGCUUAUUUCUGG
.............................((((.........((((((((((((..(((.............)))..))))))))))))............)))).......... (-21.10 = -21.60 +   0.50)

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 11:03:56 2006