Locus 8510

Sequence ID 3R_DroMel_CAF1
Location 22,716,152 – 22,716,294
Length 142
Max. P 0.969612
window13683 window13684 window13685

overview

Window 3

Location 22,716,152 – 22,716,254
Length 102
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 81.34
Mean single sequence MFE -45.65
Consensus MFE -28.78
Energy contribution -29.74
Covariance contribution 0.96
Combinations/Pair 1.08
Mean z-score -3.71
Structure conservation index 0.63
SVM decision value 1.54
SVM RNA-class probability 0.962772
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22716152 102 + 27905053
GCUAAUUUAUGCCAAUUUAUGGCAUGUGGCCCCACCCCU-UGGGGCGUC-----UGCCUGCCCACUUUCCCAC------CCAACUGUGGGU---CGUGAGUGGUGCAGGGCCAUAUC
((........)).....((((((.....((((((.....-))))))...-----..(((((((((((.(((((------......))))).---...)))))).))))))))))).. ( -47.50)
>DroSec_CAF1 6469 106 + 1
GCUAAUUUAUGCCAAUUUAUGGCAUGUGGCCCCACCCCUUUGGGGCGGC-----UGCCCGCCCACUUUGCCAC------CCAACUGCGGGUCGUCGUGAGUGGCGCAGGGCCAUAUC
(((....(((((((.....)))))))..((((((......)))))))))-----.((((((((((((.((.((------((......)))).))...)))))).)).))))...... ( -48.70)
>DroSim_CAF1 6393 106 + 1
GCUAAUUUAUGCCAAUUUAUGGCAUGUGGCCCCACCCCUUUGGGGCGGC-----GGCCCGCCCACUUUGCCAC------CCAACUGCGGGUCGUCGUGAGUGGCGCAGGGCCAUAUC
(((....(((((((.....)))))))..((((((......)))))))))-----(((((((((((((.((.((------((......)))).))...)))))).)).)))))..... ( -53.70)
>DroEre_CAF1 7778 101 + 1
GCUAAUUUAUGCCAAUUUAUGGCAUGUGGCCCCACCCCU-UGGGGCGGU-----UCCCCGCCCACUUUCCCAC------CCAACUCCGAGC---CGUGAGUGGUG-AGGGCCAUAUC
........((((((.....))))))(((((((((((...-..((((((.-----...))))))..........------...((((((...---)).))))))))-.)))))))... ( -43.80)
>DroYak_CAF1 6802 108 + 1
GCUAAUUUAUGCCAAUUUAUGGCAUGUGGCCCCACCCCU-UGGGGCGGU-----UCCCCGCCCACUUUCCCACCUCGGCCCACCUUUGAGC---CGUGAGUGGUGCAGGGCCAUAUC
........((((((.....))))))(((((((.......-..((((((.-----...))))))......(((((.((((.((....)).))---)).).))))....)))))))... ( -47.30)
>DroAna_CAF1 5387 95 + 1
ACUAAUUUAUGGCAAUUUACGGCAUGCAGCCCCACCCCU-UGGGGCGGUGCGAGUUCCCACCCAGU-CCCCAG------CCAACUCG------C------UG--GCAGGGCCGCAUC
...........((........))((((.((((((.....-))))))((((.(....).))))..((-((((((------(......)------)------))--)..)))).)))). ( -32.90)
>consensus
GCUAAUUUAUGCCAAUUUAUGGCAUGUGGCCCCACCCCU_UGGGGCGGC_____UGCCCGCCCACUUUCCCAC______CCAACUGCGGGU___CGUGAGUGGUGCAGGGCCAUAUC
........((((((.....))))))((((((((.((((...)))).)............((((((((..............................)))))).)).)))))))... (-28.78 = -29.74 +   0.96)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,716,152 – 22,716,254
Length 102
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 81.34
Mean single sequence MFE -50.82
Consensus MFE -35.86
Energy contribution -36.83
Covariance contribution 0.97
Combinations/Pair 1.20
Mean z-score -4.24
Structure conservation index 0.71
SVM decision value 1.64
SVM RNA-class probability 0.969612
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22716152 102 - 27905053
GAUAUGGCCCUGCACCACUCACG---ACCCACAGUUGG------GUGGGAAAGUGGGCAGGCA-----GACGCCCCA-AGGGGUGGGGCCACAUGCCAUAAAUUGGCAUAAAUUAGC
....(((((((((.(((((..(.---(((((....)))------)).)...))))))))....-----..(((((..-..))))))))))).((((((.....))))))........ ( -49.60)
>DroSec_CAF1 6469 106 - 1
GAUAUGGCCCUGCGCCACUCACGACGACCCGCAGUUGG------GUGGCAAAGUGGGCGGGCA-----GCCGCCCCAAAGGGGUGGGGCCACAUGCCAUAAAUUGGCAUAAAUUAGC
....(((((((((.((.(((((..(.(((((....)))------)).)....))))).)))))-----)(((((((...)))))))))))).((((((.....))))))........ ( -52.80)
>DroSim_CAF1 6393 106 - 1
GAUAUGGCCCUGCGCCACUCACGACGACCCGCAGUUGG------GUGGCAAAGUGGGCGGGCC-----GCCGCCCCAAAGGGGUGGGGCCACAUGCCAUAAAUUGGCAUAAAUUAGC
....((((((..((((((((((..((...))..).)))------)))))...(.((((((...-----.)))))))......)..)))))).((((((.....))))))........ ( -52.30)
>DroEre_CAF1 7778 101 - 1
GAUAUGGCCCU-CACCACUCACG---GCUCGGAGUUGG------GUGGGAAAGUGGGCGGGGA-----ACCGCCCCA-AGGGGUGGGGCCACAUGCCAUAAAUUGGCAUAAAUUAGC
....((((((.-((((.((((((---((.....)))..------)))))...(.((((((...-----.))))))).-...)))))))))).((((((.....))))))........ ( -48.60)
>DroYak_CAF1 6802 108 - 1
GAUAUGGCCCUGCACCACUCACG---GCUCAAAGGUGGGCCGAGGUGGGAAAGUGGGCGGGGA-----ACCGCCCCA-AGGGGUGGGGCCACAUGCCAUAAAUUGGCAUAAAUUAGC
....((((((..(.(((((..((---(((((....))))))).)))))....(.((((((...-----.))))))).-....)..)))))).((((((.....))))))........ ( -58.70)
>DroAna_CAF1 5387 95 - 1
GAUGCGGCCCUGC--CA------G------CGAGUUGG------CUGGGG-ACUGGGUGGGAACUCGCACCGCCCCA-AGGGGUGGGGCUGCAUGCCGUAAAUUGCCAUAAAUUAGU
.(((((((((..(--((------(------(......)------))((((-....((((.(....).)))).)))).-...))..)))))))))....................... ( -42.90)
>consensus
GAUAUGGCCCUGCACCACUCACG___ACCCGCAGUUGG______GUGGGAAAGUGGGCGGGCA_____ACCGCCCCA_AGGGGUGGGGCCACAUGCCAUAAAUUGGCAUAAAUUAGC
....(((((((((.((..((((......(((....)))......))))......((((((.........))))))....)).))))))))).((((((.....))))))........ (-35.86 = -36.83 +   0.97)

alignment

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secondary structure

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dotplot

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Window 5

Location 22,716,191 – 22,716,294
Length 103
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 85.29
Mean single sequence MFE -42.57
Consensus MFE -29.24
Energy contribution -29.92
Covariance contribution 0.68
Combinations/Pair 1.04
Mean z-score -2.33
Structure conservation index 0.69
SVM decision value 0.83
SVM RNA-class probability 0.861304
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22716191 103 - 27905053
UCCUUGUCCACUUACCAACAAUGGCCUUAUCGGCCGAUAAGAUAUGGCCCUGCACCACUCACG---ACCCACAGUUGG------GUGGGAAAGUGGGCAGGCAGACGCCCCA
..((((((..............((((.....))))))))))....((((((((.(((((..(.---(((((....)))------)).)...)))))))))).....)))... ( -37.93)
>DroSec_CAF1 6509 106 - 1
UGCUUGUCCACUUACCAACAAUGGCCUUAUCGGCCGAUAAGAUAUGGCCCUGCGCCACUCACGACGACCCGCAGUUGG------GUGGCAAAGUGGGCGGGCAGCCGCCCCA
(((((((((((((.........((((.((((.........)))).))))....(((((((((..((...))..).)))------))))).)))))))))))))......... ( -44.80)
>DroSim_CAF1 6433 106 - 1
UGCUUGUCCACUUACCAACAAAGGCCUUAUCGGCCGAUAAGAUAUGGCCCUGCGCCACUCACGACGACCCGCAGUUGG------GUGGCAAAGUGGGCGGGCCGCCGCCCCA
.((((((((((((.........((((.((((.........)))).))))....(((((((((..((...))..).)))------))))).)))))))))))).......... ( -43.40)
>DroEre_CAF1 7817 101 - 1
UCCGCGUCCAG-UACCAACAAUGGCCUUAUCGGCCGAUAAGAUAUGGCCCU-CACCACUCACG---GCUCGGAGUUGG------GUGGGAAAGUGGGCGGGGAACCGCCCCA
(((.(..((((-..((.....(((((.....))))).........((((..-..........)---))).))..))))------..))))..(.((((((....))))))). ( -39.90)
>DroYak_CAF1 6841 108 - 1
UCUGAGUCCAG-UACCAACAAUGGUCUUAUCGACCGAUAAGAUAUGGCCCUGCACCACUCACG---GCUCAAAGGUGGGCCGAGGUGGGAAAGUGGGCGGGGAACCGCCCCA
........(((-..(((......((((((((....)))))))).)))..)))..(((((..((---(((((....))))))).)))))....(.((((((....))))))). ( -46.80)
>consensus
UCCUUGUCCACUUACCAACAAUGGCCUUAUCGGCCGAUAAGAUAUGGCCCUGCACCACUCACG___ACCCGCAGUUGG______GUGGGAAAGUGGGCGGGCAGCCGCCCCA
.......((((...(((((...((((.....)))).........(((.......)))................)))))......))))....(.((((((....))))))). (-29.24 = -29.92 +   0.68)

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 13:13:00 2006