Locus 6550

Sequence ID 3L_DroMel_CAF1
Location 17,300,306 – 17,300,718
Length 412
Max. P 0.959463
window10657 window10658 window10659 window10660 window10661 window10662 window10663 window10664 window10665 window10666

overview

Window 7

Location 17,300,306 – 17,300,419
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.68
Mean single sequence MFE -25.55
Consensus MFE -22.75
Energy contribution -22.75
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.41
Structure conservation index 0.89
SVM decision value 1.50
SVM RNA-class probability 0.959463
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17300306 113 + 23771897
GCAUAUUCCUGCUCCACAUCCCCGUUUGG-------CAAAAGGAAAAUAAAAGAGCCACUUCCGUUUUAUUUGCGCAAAAUUAAAUAAACCGAAAUAUGGCUGACCAUAUUGGCGCAUAA
((...((((((((..((......))..))-------)...))))).........(((.....((.((((((((........)))))))).)).(((((((....)))))))))))).... ( -25.20)
>DroSim_CAF1 807 111 + 1
GCAUAUUCCUGCUCCACAUCCUC--UUGG-------AAAAAGGAAAAUAAAAGAGCCACUUCCGUUUUAUUUGCGCAAAAUUAAAUAAACCGAAAUAUGGCUGACCAUAUUGGCGCAUAA
((...(((((..((((.......--.)))-------)...))))).........(((.....((.((((((((........)))))))).)).(((((((....)))))))))))).... ( -27.40)
>DroEre_CAF1 4509 112 + 1
GCAUAUUCCUGCGCCACAUCCCC--UUGG------AAAAAAGGAAAAUAAAAGAGCCACUUCCGUUUUAUUUGCGCAAAAUUAAAUAAACCGAAAUAUGGCUGACCAUAUUGGCGCAUAA
.........(((((((.....((--((..------....))))..........(((((....((.((((((((........)))))))).)).....)))))........)))))))... ( -27.00)
>DroYak_CAF1 4829 118 + 1
GCAUAUUCCUGCUCCACAUCCCC--UUGGCAAGAAAAAAAAGGAAAAUAAAAGAGCCACUUCCGUUUUAUUUGCGCAAAAUUAAAUAAACCGAAAUAUGGCUGACCAUAUUGGCGCAUAA
((...(((((.(((((.......--.)))..)).......))))).........(((.....((.((((((((........)))))))).)).(((((((....)))))))))))).... ( -22.60)
>consensus
GCAUAUUCCUGCUCCACAUCCCC__UUGG_______AAAAAGGAAAAUAAAAGAGCCACUUCCGUUUUAUUUGCGCAAAAUUAAAUAAACCGAAAUAUGGCUGACCAUAUUGGCGCAUAA
((...(((((.........((......))...........))))).........(((.....((.((((((((........)))))))).)).(((((((....)))))))))))).... (-22.75 = -22.75 +   0.00)

alignment

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secondary structure

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Window 8

Location 17,300,339 – 17,300,458
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 98.61
Mean single sequence MFE -26.34
Consensus MFE -25.31
Energy contribution -25.31
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.35
Structure conservation index 0.96
SVM decision value 1.00
SVM RNA-class probability 0.897069
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17300339 119 + 23771897
AGGAAAAUAAAAGAGCCACUUCCGUUUUAUUUGCGCAAAAUUAAAUAAACCGAAAUAUGGCUGACCAUAUUGGCGCAUAAUGGGCAAAAAUAUUUUUUUCAUUAAUGCCCCAUGCCCCA-
.((...........(((.....((.((((((((........)))))))).)).(((((((....))))))))))((((...(((((...................))))).)))).)).- ( -27.31)
>DroSim_CAF1 838 120 + 1
AGGAAAAUAAAAGAGCCACUUCCGUUUUAUUUGCGCAAAAUUAAAUAAACCGAAAUAUGGCUGACCAUAUUGGCGCAUAAUGGGCAAAAAUAUUUUUUUCAUUAAUGCCCCAUGCCCCAC
.((...........(((.....((.((((((((........)))))))).)).(((((((....))))))))))((((...(((((...................))))).)))).)).. ( -27.31)
>DroEre_CAF1 4541 120 + 1
AGGAAAAUAAAAGAGCCACUUCCGUUUUAUUUGCGCAAAAUUAAAUAAACCGAAAUAUGGCUGACCAUAUUGGCGCAUAAUGGGCAAAAAUAUUUUUUUCAUUAAUGCCCCAUGCCUCAU
............(((((.....((.((((((((........)))))))).)).(((((((....))))))))))((((...(((((...................))))).)))).)).. ( -25.41)
>DroYak_CAF1 4867 120 + 1
AGGAAAAUAAAAGAGCCACUUCCGUUUUAUUUGCGCAAAAUUAAAUAAACCGAAAUAUGGCUGACCAUAUUGGCGCAUAAUGGGCAAAAAUAUUUUUUUCAUUAAUGCCCCAUGCCACAU
..............(((.....((.((((((((........)))))))).)).(((((((....))))))))))((((...(((((...................))))).))))..... ( -25.31)
>consensus
AGGAAAAUAAAAGAGCCACUUCCGUUUUAUUUGCGCAAAAUUAAAUAAACCGAAAUAUGGCUGACCAUAUUGGCGCAUAAUGGGCAAAAAUAUUUUUUUCAUUAAUGCCCCAUGCCCCAU
..............(((.....((.((((((((........)))))))).)).(((((((....))))))))))((((...(((((...................))))).))))..... (-25.31 = -25.31 +   0.00)

alignment

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secondary structure

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Window 9

Location 17,300,339 – 17,300,458
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 98.61
Mean single sequence MFE -32.20
Consensus MFE -30.60
Energy contribution -30.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.53
Structure conservation index 0.95
SVM decision value 1.09
SVM RNA-class probability 0.913779
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17300339 119 - 23771897
-UGGGGCAUGGGGCAUUAAUGAAAAAAAUAUUUUUGCCCAUUAUGCGCCAAUAUGGUCAGCCAUAUUUCGGUUUAUUUAAUUUUGCGCAAAUAAAACGGAAGUGGCUCUUUUAUUUUCCU
-(((.((((((((((..((((.......))))..)))))..))))).)))........((((((.(((((.(((((((..........))))))).)))))))))))............. ( -33.70)
>DroSim_CAF1 838 120 - 1
GUGGGGCAUGGGGCAUUAAUGAAAAAAAUAUUUUUGCCCAUUAUGCGCCAAUAUGGUCAGCCAUAUUUCGGUUUAUUUAAUUUUGCGCAAAUAAAACGGAAGUGGCUCUUUUAUUUUCCU
.(((.((((((((((..((((.......))))..)))))..))))).)))........((((((.(((((.(((((((..........))))))).)))))))))))............. ( -33.90)
>DroEre_CAF1 4541 120 - 1
AUGAGGCAUGGGGCAUUAAUGAAAAAAAUAUUUUUGCCCAUUAUGCGCCAAUAUGGUCAGCCAUAUUUCGGUUUAUUUAAUUUUGCGCAAAUAAAACGGAAGUGGCUCUUUUAUUUUCCU
.....((((((((((..((((.......))))..)))))..)))))((((.(((((....)))))(((((.(((((((..........))))))).))))).)))).............. ( -30.60)
>DroYak_CAF1 4867 120 - 1
AUGUGGCAUGGGGCAUUAAUGAAAAAAAUAUUUUUGCCCAUUAUGCGCCAAUAUGGUCAGCCAUAUUUCGGUUUAUUUAAUUUUGCGCAAAUAAAACGGAAGUGGCUCUUUUAUUUUCCU
.....((((((((((..((((.......))))..)))))..)))))((((.(((((....)))))(((((.(((((((..........))))))).))))).)))).............. ( -30.60)
>consensus
AUGGGGCAUGGGGCAUUAAUGAAAAAAAUAUUUUUGCCCAUUAUGCGCCAAUAUGGUCAGCCAUAUUUCGGUUUAUUUAAUUUUGCGCAAAUAAAACGGAAGUGGCUCUUUUAUUUUCCU
.....((((((((((..((((.......))))..)))))..)))))((((.(((((....)))))(((((.(((((((..........))))))).))))).)))).............. (-30.60 = -30.60 +  -0.00)

alignment

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secondary structure

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Window 0

Location 17,300,379 – 17,300,485
Length 106
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.37
Mean single sequence MFE -27.55
Consensus MFE -21.01
Energy contribution -21.14
Covariance contribution 0.12
Combinations/Pair 1.05
Mean z-score -2.27
Structure conservation index 0.76
SVM decision value 0.81
SVM RNA-class probability 0.856839
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17300379 106 + 23771897
UUAAAUAAACCGAAAUAUGGCUGACCAUAUUGGCGCAUAAUGGGCAAAAAUAUUUUUUUCAUUAAUGCCCCAUGCCCCA--------------UACCCCAGCGGAGUAGAUGGCAAAAUA
.............(((((((....)))))))((.((((((((((.((((....)))))))))).)))).)).((((...--------------(((((....)).)))...))))..... ( -24.80)
>DroSim_CAF1 878 120 + 1
UUAAAUAAACCGAAAUAUGGCUGACCAUAUUGGCGCAUAAUGGGCAAAAAUAUUUUUUUCAUUAAUGCCCCAUGCCCCACGCCCCAUACCCCGUGCCCCAGCGGAGUAGAUGGCAAAAUA
.............(((((((....)))))))((.((((...(((((...................))))).)))).))..(((...(((.((((......)))).)))...)))...... ( -32.61)
>DroEre_CAF1 4581 106 + 1
UUAAAUAAACCGAAAUAUGGCUGACCAUAUUGGCGCAUAAUGGGCAAAAAUAUUUUUUUCAUUAAUGCCCCAUGCCUCAUGCC--------------CCAGCGGAGUAGAUGGCAAAAUA
.............(((((((....)))))))((.((((((((((.((((....)))))))))).)))).)).((((...((((--------------(....)).)))...))))..... ( -25.50)
>DroYak_CAF1 4907 113 + 1
UUAAAUAAACCGAAAUAUGGCUGACCAUAUUGGCGCAUAAUGGGCAAAAAUAUUUUUUUCAUUAAUGCCCCAUGCCACAUGCCCCA-------UUCCCCAGCGGAGUAGAUGGCAAAAUA
.............(((((((....)))))))((.((((((((((.((((....)))))))))).)))).)).(((((..((((((.-------.......).)).)))..)))))..... ( -27.30)
>consensus
UUAAAUAAACCGAAAUAUGGCUGACCAUAUUGGCGCAUAAUGGGCAAAAAUAUUUUUUUCAUUAAUGCCCCAUGCCCCAUGCC__________U_CCCCAGCGGAGUAGAUGGCAAAAUA
.........(((.(((((((....)))))))((.((((...(((((...................))))).)))).)).......................)))................ (-21.01 = -21.14 +   0.12)

alignment

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secondary structure

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Window 1

Location 17,300,379 – 17,300,485
Length 106
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.37
Mean single sequence MFE -34.00
Consensus MFE -25.12
Energy contribution -25.88
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.55
Structure conservation index 0.74
SVM decision value 0.82
SVM RNA-class probability 0.857958
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17300379 106 - 23771897
UAUUUUGCCAUCUACUCCGCUGGGGUA--------------UGGGGCAUGGGGCAUUAAUGAAAAAAAUAUUUUUGCCCAUUAUGCGCCAAUAUGGUCAGCCAUAUUUCGGUUUAUUUAA
......(((...((((((...))))))--------------(((.((((((((((..((((.......))))..)))))..))))).)))((((((....))))))...)))........ ( -33.10)
>DroSim_CAF1 878 120 - 1
UAUUUUGCCAUCUACUCCGCUGGGGCACGGGGUAUGGGGCGUGGGGCAUGGGGCAUUAAUGAAAAAAAUAUUUUUGCCCAUUAUGCGCCAAUAUGGUCAGCCAUAUUUCGGUUUAUUUAA
......(((...(((((((........)))))))...))).(((.((((((((((..((((.......))))..)))))..))))).)))((((((....)))))).............. ( -40.60)
>DroEre_CAF1 4581 106 - 1
UAUUUUGCCAUCUACUCCGCUGG--------------GGCAUGAGGCAUGGGGCAUUAAUGAAAAAAAUAUUUUUGCCCAUUAUGCGCCAAUAUGGUCAGCCAUAUUUCGGUUUAUUUAA
......(((............((--------------.((((((......(((((..((((.......))))..))))).)))))).))(((((((....)))))))..)))........ ( -29.90)
>DroYak_CAF1 4907 113 - 1
UAUUUUGCCAUCUACUCCGCUGGGGAA-------UGGGGCAUGUGGCAUGGGGCAUUAAUGAAAAAAAUAUUUUUGCCCAUUAUGCGCCAAUAUGGUCAGCCAUAUUUCGGUUUAUUUAA
.....((((..(((.(((.....))).-------)))))))....((((((((((..((((.......))))..)))))..)))))((((((((((....)))))))..)))........ ( -32.40)
>consensus
UAUUUUGCCAUCUACUCCGCUGGGG_A__________GGCAUGGGGCAUGGGGCAUUAAUGAAAAAAAUAUUUUUGCCCAUUAUGCGCCAAUAUGGUCAGCCAUAUUUCGGUUUAUUUAA
..................((((((.................(((.((((((((((..((((.......))))..)))))..))))).)))((((((....))))))))))))........ (-25.12 = -25.88 +   0.75)

alignment

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secondary structure

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Window 2

Location 17,300,485 – 17,300,602
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.78
Mean single sequence MFE -31.79
Consensus MFE -28.10
Energy contribution -28.61
Covariance contribution 0.50
Combinations/Pair 1.09
Mean z-score -1.98
Structure conservation index 0.88
SVM decision value 1.02
SVM RNA-class probability 0.901183
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17300485 117 + 23771897
AAUAAAUAAAUAAGCGGAGCCAAAAAGGAAAGCCGAAAAGUAAAAGCUCCGACUGCGACCAGCUUAUUGUGUGUCAAUAUUUGGUUGACCAGGCCAACGAAUCCA---GUUUGGUGGCUA
............((((((((......((....))...........)))))).)).(((((((..(((((.....))))).)))))))....(((((.(((((...---))))).))))). ( -30.13)
>DroSim_CAF1 998 117 + 1
AAUAAAUAAAUAAGCGGAGCCAAAAAGGAAAGCCGAAAAGUAAAAGCUCCGACUGCGACCAGCUUAUUGUGUGUCAAUAUUUGGUUGACCAGGCCAACGGAUCCA---GUUUGGUGGCUA
............(((...((((((..(((...(((...(((....)))....((((((((((..(((((.....))))).)))))))..))).....))).))).---.)))))).))). ( -30.70)
>DroEre_CAF1 4687 112 + 1
AA----UAAAUAAGCGGAGCCAAAAAGGAAAGCCGAAAAGUAAAAGCCCCGACUGCGACCAGCUUAUUGUGUGUCAAUAUUUGGUUGACCAGGCCAACGGAUCCA----GUUGGUGGCUA
..----........(((..((.....))....))).........((((((((((((((((((..(((((.....))))).))))))).((........))...))----))))).)))). ( -34.20)
>DroYak_CAF1 5020 116 + 1
AA----UAAAUAAGCGGAGCCAAAAAGGAAAGCCGAAAAGUAAAAGCUCCGACUGCGACCAGCUUAUUGUGUGUCAAUAUUUGGUUGACCAGGCCAACGGAUCCACCAAACUGGUGGCUA
..----......((((((((......((....))...........)))))).))((.(((((..(((((.....)))))((((((.((((........)).)).))))))))))).)).. ( -32.13)
>consensus
AA____UAAAUAAGCGGAGCCAAAAAGGAAAGCCGAAAAGUAAAAGCUCCGACUGCGACCAGCUUAUUGUGUGUCAAUAUUUGGUUGACCAGGCCAACGGAUCCA___GUUUGGUGGCUA
............((((((((......((....))...........)))))).)).(((((((..(((((.....))))).)))))))....(((((.(((((......))))).))))). (-28.10 = -28.61 +   0.50)

alignment

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secondary structure

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Window 3

Location 17,300,525 – 17,300,638
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.42
Mean single sequence MFE -39.90
Consensus MFE -34.06
Energy contribution -34.81
Covariance contribution 0.75
Combinations/Pair 1.08
Mean z-score -1.48
Structure conservation index 0.85
SVM decision value 0.02
SVM RNA-class probability 0.542386
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17300525 113 + 23771897
UAAAAGCUCCGACUGCGACCAGCUUAUUGUGUGUCAAUAUUUGGUUGACCAGGCCAACGAAUCCA---GUUUGGUGGCUAAGUGAGUGC----CUGGCCAGCGGGCGGAGGUGGAAUAAU
......(((((.((((..((((((((((.((.((((((.....))))))))(((((.(((((...---))))).))))).))))))...----))))...)))).))))).......... ( -38.80)
>DroSim_CAF1 1038 113 + 1
UAAAAGCUCCGACUGCGACCAGCUUAUUGUGUGUCAAUAUUUGGUUGACCAGGCCAACGGAUCCA---GUUUGGUGGCUAAGUGAGUGG----CUGGCCAGCGGGCGGAGGUGGAAUAAU
......(((((.((((..((((((.(((.((.((((((.....))))))))(((((.(((((...---))))).))))).....)))))----))))...)))).))))).......... ( -40.00)
>DroEre_CAF1 4723 112 + 1
UAAAAGCCCCGACUGCGACCAGCUUAUUGUGUGUCAAUAUUUGGUUGACCAGGCCAACGGAUCCA----GUUGGUGGCUAAGUGAGUGC----CUGGCCAACGGGCGGAGGUGGAAUAAU
....((((((((((((((((((..(((((.....))))).))))))).((........))...))----))))).)))).......(((----(((.....))))))............. ( -37.70)
>DroYak_CAF1 5056 120 + 1
UAAAAGCUCCGACUGCGACCAGCUUAUUGUGUGUCAAUAUUUGGUUGACCAGGCCAACGGAUCCACCAAACUGGUGGCUAAGUGAGUGCCUGCCUGGCCAGCGGGCGGAGGUGGAAUAAU
......(((((.((((((((((..(((((.....))))).))))))(.((((((..((..(((((((.....)))))....))..))....)))))).).)))).))))).......... ( -43.10)
>consensus
UAAAAGCUCCGACUGCGACCAGCUUAUUGUGUGUCAAUAUUUGGUUGACCAGGCCAACGGAUCCA___GUUUGGUGGCUAAGUGAGUGC____CUGGCCAGCGGGCGGAGGUGGAAUAAU
......(((((.((((..((((((((((.((.((((((.....))))))))(((((.(((((......))))).))))).)))))).......))))...)))).))))).......... (-34.06 = -34.81 +   0.75)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,300,525 – 17,300,638
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.42
Mean single sequence MFE -35.67
Consensus MFE -27.75
Energy contribution -27.38
Covariance contribution -0.38
Combinations/Pair 1.07
Mean z-score -2.42
Structure conservation index 0.78
SVM decision value 0.57
SVM RNA-class probability 0.783648
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17300525 113 - 23771897
AUUAUUCCACCUCCGCCCGCUGGCCAG----GCACUCACUUAGCCACCAAAC---UGGAUUCGUUGGCCUGGUCAACCAAAUAUUGACACACAAUAAGCUGGUCGCAGUCGGAGCUUUUA
..........(((((.(.(((((((((----((....((....(((......---)))....))..)))))))))((((..(((((.....)))))...)))).)).).)))))...... ( -34.40)
>DroSim_CAF1 1038 113 - 1
AUUAUUCCACCUCCGCCCGCUGGCCAG----CCACUCACUUAGCCACCAAAC---UGGAUCCGUUGGCCUGGUCAACCAAAUAUUGACACACAAUAAGCUGGUCGCAGUCGGAGCUUUUA
..........(((((.(.((.((((((----(.....(((..((((((....---.))......))))..)))........(((((.....))))).))))))))).).)))))...... ( -31.40)
>DroEre_CAF1 4723 112 - 1
AUUAUUCCACCUCCGCCCGUUGGCCAG----GCACUCACUUAGCCACCAAC----UGGAUCCGUUGGCCUGGUCAACCAAAUAUUGACACACAAUAAGCUGGUCGCAGUCGGGGCUUUUA
..............(((((((((((((----((....((....(((.....----)))....))..)))))))))))....(((((.....))))).((((....))))..))))..... ( -35.00)
>DroYak_CAF1 5056 120 - 1
AUUAUUCCACCUCCGCCCGCUGGCCAGGCAGGCACUCACUUAGCCACCAGUUUGGUGGAUCCGUUGGCCUGGUCAACCAAAUAUUGACACACAAUAAGCUGGUCGCAGUCGGAGCUUUUA
..........(((((.(.((.((((((.(((((....((....(((((.....)))))....))..)))))(((((.......)))))..........)))))))).).)))))...... ( -41.90)
>consensus
AUUAUUCCACCUCCGCCCGCUGGCCAG____GCACUCACUUAGCCACCAAAC___UGGAUCCGUUGGCCUGGUCAACCAAAUAUUGACACACAAUAAGCUGGUCGCAGUCGGAGCUUUUA
..........(((((.(.((.((((((..........(((..(((((((......)))......))))..)))........(((((.....)))))..)))))))).).)))))...... (-27.75 = -27.38 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,300,565 – 17,300,678
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.28
Mean single sequence MFE -39.15
Consensus MFE -32.65
Energy contribution -32.65
Covariance contribution -0.00
Combinations/Pair 1.03
Mean z-score -1.50
Structure conservation index 0.83
SVM decision value -0.04
SVM RNA-class probability 0.515317
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17300565 113 + 23771897
UUGGUUGACCAGGCCAACGAAUCCA---GUUUGGUGGCUAAGUGAGUGC----CUGGCCAGCGGGCGGAGGUGGAAUAAUAAAAUCAUUUUAAUAGUUUCGCUGCCUGCAGUUUUACCGG
.((((.((((((((.......(((.---(((((.((((((.((....))----.)))))).))))))))((((((((.((.(((....))).)).)))))))))))))..)))..)))). ( -38.30)
>DroSim_CAF1 1078 113 + 1
UUGGUUGACCAGGCCAACGGAUCCA---GUUUGGUGGCUAAGUGAGUGG----CUGGCCAGCGGGCGGAGGUGGAAUAAUAAAAUCAUUUUAAUAGUUUCGCUGCCUGCAGUUUUACCGG
.((((.((((((((.......(((.---(((((.((((((.((.....)----))))))).))))))))((((((((.((.(((....))).)).)))))))))))))..)))..)))). ( -37.30)
>DroEre_CAF1 4763 112 + 1
UUGGUUGACCAGGCCAACGGAUCCA----GUUGGUGGCUAAGUGAGUGC----CUGGCCAACGGGCGGAGGUGGAAUAAUAAAAUCAUUUUAAUAGUUUCGCCGCCUGCAGUUUUACCGG
.((((.((((((((.......(((.----(((.(((((((.((....))----.))))).)).))))))((((((((.((.(((....))).)).)))))))))))))..)))..)))). ( -37.70)
>DroYak_CAF1 5096 120 + 1
UUGGUUGACCAGGCCAACGGAUCCACCAAACUGGUGGCUAAGUGAGUGCCUGCCUGGCCAGCGGGCGGAGGUGGAAUAAUAAAAUCAUUUUAAUAGUUUCGCCGCCUGCAGUUUUACCGG
.((((((..((((((.((..(.(((((.....))))).)..))..).)))))..))))))((((((...((((((((.((.(((....))).)).))))))))))))))........... ( -43.30)
>consensus
UUGGUUGACCAGGCCAACGGAUCCA___GUUUGGUGGCUAAGUGAGUGC____CUGGCCAGCGGGCGGAGGUGGAAUAAUAAAAUCAUUUUAAUAGUUUCGCCGCCUGCAGUUUUACCGG
.((((.(((..(((((......(((......)))..(((.....))).......))))).((((((...((((((((.((.(((....))).)).)))))))))))))).)))..)))). (-32.65 = -32.65 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,300,602 – 17,300,718
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.90
Mean single sequence MFE -34.25
Consensus MFE -28.96
Energy contribution -28.96
Covariance contribution 0.00
Combinations/Pair 1.03
Mean z-score -1.76
Structure conservation index 0.85
SVM decision value 0.04
SVM RNA-class probability 0.556104
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17300602 116 + 23771897
AGUGAGUGC----CUGGCCAGCGGGCGGAGGUGGAAUAAUAAAAUCAUUUUAAUAGUUUCGCUGCCUGCAGUUUUACCGGGCUUUAUGCAGCUCAAUGAAAUUAAAAUGAACUGUCAUUA
.(((((.((----((((...((((((...((((((((.((.(((....))).)).)))))))))))))).......)))))))))))((((.(((.(........).))).))))..... ( -32.10)
>DroSim_CAF1 1115 116 + 1
AGUGAGUGG----CUGGCCAGCGGGCGGAGGUGGAAUAAUAAAAUCAUUUUAAUAGUUUCGCUGCCUGCAGUUUUACCGGGCUUUAUGCAGCUCAAUGAAAUUAAAAUGAACUGUCAUUA
....(((((----(.(..((((((((...((((((((.((.(((....))).)).))))))))))))))(((((((..(((((......)))))..)))))))....))..).)))))). ( -33.40)
>DroEre_CAF1 4799 116 + 1
AGUGAGUGC----CUGGCCAACGGGCGGAGGUGGAAUAAUAAAAUCAUUUUAAUAGUUUCGCCGCCUGCAGUUUUACCGGGCUUUACGGAGCUCAAUGAAAUUAAAAUGAACUGUCAUUA
.(((((.((----((((..(((..((((.((((((((.((.(((....))).)).))))))))..)))).)))...)))))))))))..................(((((....))))). ( -33.80)
>DroYak_CAF1 5136 120 + 1
AGUGAGUGCCUGCCUGGCCAGCGGGCGGAGGUGGAAUAAUAAAAUCAUUUUAAUAGUUUCGCCGCCUGCAGUUUUACCGGGCUUUAUGGAGCUCAAUGAAAUUAAAAUGAACUGUCAUUA
..(((((.((.((((((..(((..((((.((((((((.((.(((....))).)).))))))))..)))).)))...)))))).....)).)))))..........(((((....))))). ( -37.70)
>consensus
AGUGAGUGC____CUGGCCAGCGGGCGGAGGUGGAAUAAUAAAAUCAUUUUAAUAGUUUCGCCGCCUGCAGUUUUACCGGGCUUUAUGCAGCUCAAUGAAAUUAAAAUGAACUGUCAUUA
..(((((........((((.((((((...((((((((.((.(((....))).)).)))))))))))))).(......).)))).......)))))..........(((((....))))). (-28.96 = -28.96 +   0.00)

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 12:24:08 2006