Locus 1916

Sequence ID 3R_DroMel_CAF1
Location 5,439,267 – 5,439,392
Length 125
Max. P 0.985472
window3148 window3149 window3150

overview

Window 8

Location 5,439,267 – 5,439,365
Length 98
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.85
Mean single sequence MFE -34.76
Consensus MFE -26.82
Energy contribution -27.70
Covariance contribution 0.88
Combinations/Pair 1.09
Mean z-score -1.87
Structure conservation index 0.77
SVM decision value 0.69
SVM RNA-class probability 0.824062
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5439267 98 + 27905053
UUC------------------GCAAACUACAGCCUUGGCUAAUGGCCAGUCAACGGCAACUGACAUGGGCGAUAUCGGCCGGCUCUCUUGGCC-AAAAGCCGAGCU---UUUUUAAUGGC
...------------------((.......(((.((((((..((((((((((..(....))))).(((.((....)).))).......)))))-)..)))))))))---.........)) ( -33.59)
>DroSec_CAF1 25822 99 + 1
UUG------------------GCAAACUACAGCCUUGGCUAAUGGCCAGUCAACGGCAACUGACAUGGGCGAUAUCGGCCGGCUCUCUUGGCCGAAAAGCCGAGCU---UUUUUAAUGGC
(((------------------((........((((((((.....))))((((..(....)))))..))))....((((((((.....))))))))...)))))(((---........))) ( -35.80)
>DroSim_CAF1 20992 98 + 1
UUG------------------GCAAACUACAGCCUUGGCUAAUGGCCAGUCAACGGCAACUGACAUGGGCGAUAUCGGCCGUCUCUCUUGGCCGAAAAGCCGAGCU---UUUUUAAUGG-
(((------------------((........((((((((.....))))((((..(....)))))..))))....(((((((.......)))))))...)))))...---..........- ( -35.00)
>DroEre_CAF1 26411 115 + 1
UUCAGAAACUUCAGAAACUACACAAACUACAGCCUUGGCUAAUGGCCAGUCAACGGCAACUGACAUGGGCGAUAUCGGUCGGCUCUCUUGGCCAAAAAGAA-----GUGCUUUUAAUGGC
.......(((((..................(((....)))..((((((((((..(....)))))..(((((((....))).))))...))))))....)))-----))(((......))) ( -30.50)
>DroYak_CAF1 26836 120 + 1
UUCAGAAACUUCACAAGCUACACAAACUACAGCCUUGGCUAAUGGCCAGUCAACGGCAACUGACAUGGGCGAUAUCGGCCGGCUCUCUUGGCCAAAAAGCCGAGCUGAGCUUUUAAUGGC
................((((...(((((.((((.((((((..((((((((((..(....))))).(((.((....)).))).......))))))...)))))))))))).)))...)))) ( -38.90)
>consensus
UUC__________________GCAAACUACAGCCUUGGCUAAUGGCCAGUCAACGGCAACUGACAUGGGCGAUAUCGGCCGGCUCUCUUGGCCAAAAAGCCGAGCU___UUUUUAAUGGC
.................................(((((((..((((((((((..(....))))).(((.((....)).))).......))))))...)))))))................ (-26.82 = -27.70 +   0.88)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,439,289 – 5,439,392
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.13
Mean single sequence MFE -44.28
Consensus MFE -26.70
Energy contribution -27.64
Covariance contribution 0.94
Combinations/Pair 1.05
Mean z-score -2.86
Structure conservation index 0.60
SVM decision value 2.01
SVM RNA-class probability 0.985472
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5439289 103 + 27905053
AAUGGCCAGUCAACGGCAACUGACAUGGGCGAUAUCGGCCGGCUCUCUUGGCC-AAAAGCCGAGCU---UUUUUAAUGGCUCA--------GCGGCUCAGCGGCU-----GAGUGGCCUU
...((((.((((..(....)))))..((.((....)).)))))).....((((-(..(((((((((---........))))).--------((......))))))-----...))))).. ( -43.90)
>DroSec_CAF1 25844 112 + 1
AAUGGCCAGUCAACGGCAACUGACAUGGGCGAUAUCGGCCGGCUCUCUUGGCCGAAAAGCCGAGCU---UUUUUAAUGGCUCAGUGGCUCGGCGGCUCAGCGGCU-----GAGUGGCCUU
...((((.((((..(....)))))...(((....((((((((.....))))))))...)))(((((---........)))))....(((((((.((...)).)))-----)))))))).. ( -50.30)
>DroSim_CAF1 21014 88 + 1
AAUGGCCAGUCAACGGCAACUGACAUGGGCGAUAUCGGCCGUCUCUCUUGGCCGAAAAGCCGAGCU---UUUUUAAUGG------------------------CU-----GAGUGGCCUU
...(((((.((..((((..((.....))......(((((((.......)))))))...))))((((---........))------------------------))-----)).))))).. ( -35.60)
>DroEre_CAF1 26451 102 + 1
AAUGGCCAGUCAACGGCAACUGACAUGGGCGAUAUCGGUCGGCUCUCUUGGCCAAAAAGAA-----GUGCUUUUAAUGGCUCAGUG--------GCUCAGUGGCU-----GAGUGGCCUU
...(((((.(((...((.(((((..(((.((....)).)))(((..((.((((((((((..-----...)))))..))))).)).)--------))))))).)))-----)).))))).. ( -37.10)
>DroYak_CAF1 26876 116 + 1
AAUGGCCAGUCAACGGCAACUGACAUGGGCGAUAUCGGCCGGCUCUCUUGGCCAAAAAGCCGAGCUGAGCUUUUAAUGGCUCAGUGGU----GAGCUCGGUGGCUGAGCUGAGUGGCCUU
...(((((.(((.((((.(((((..(((.((....)).)))((((.((((((......)))))((((((((......)))))))).).----))))))))).))))...))).))))).. ( -54.50)
>consensus
AAUGGCCAGUCAACGGCAACUGACAUGGGCGAUAUCGGCCGGCUCUCUUGGCCAAAAAGCCGAGCU___UUUUUAAUGGCUCAGUG________GCUCAGCGGCU_____GAGUGGCCUU
...(((((.((..((((.........((.((....)).))((((.....)))).....))))................................(((....)))......)).))))).. (-26.70 = -27.64 +   0.94)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,439,289 – 5,439,392
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.13
Mean single sequence MFE -39.03
Consensus MFE -22.56
Energy contribution -23.20
Covariance contribution 0.64
Combinations/Pair 1.05
Mean z-score -2.66
Structure conservation index 0.58
SVM decision value 1.55
SVM RNA-class probability 0.963308
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5439289 103 - 27905053
AAGGCCACUC-----AGCCGCUGAGCCGC--------UGAGCCAUUAAAAA---AGCUCGGCUUUU-GGCCAAGAGAGCCGGCCGAUAUCGCCCAUGUCAGUUGCCGUUGACUGGCCAUU
..(((((.((-----(((.((.(.(((((--------(((((.........---.)))))))....-((((....).)))))))(((((.....)))))....)).))))).)))))... ( -41.80)
>DroSec_CAF1 25844 112 - 1
AAGGCCACUC-----AGCCGCUGAGCCGCCGAGCCACUGAGCCAUUAAAAA---AGCUCGGCUUUUCGGCCAAGAGAGCCGGCCGAUAUCGCCCAUGUCAGUUGCCGUUGACUGGCCAUU
..(((((.((-----(((.((.(.((((((((((.................---.))))))).....((((....).)))))))(((((.....)))))....)).))))).)))))... ( -43.67)
>DroSim_CAF1 21014 88 - 1
AAGGCCACUC-----AG------------------------CCAUUAAAAA---AGCUCGGCUUUUCGGCCAAGAGAGACGGCCGAUAUCGCCCAUGUCAGUUGCCGUUGACUGGCCAUU
..(((((.((-----((------------------------(...(((...---.((..(((...((((((.........))))))....)))...))...)))..))))).)))))... ( -30.60)
>DroEre_CAF1 26451 102 - 1
AAGGCCACUC-----AGCCACUGAGC--------CACUGAGCCAUUAAAAGCAC-----UUCUUUUUGGCCAAGAGAGCCGACCGAUAUCGCCCAUGUCAGUUGCCGUUGACUGGCCAUU
..(((((.((-----(((......((--------(.((..((((..(((((...-----..)))))))))..)).).))((((.(((((.....))))).))))..))))).)))))... ( -31.40)
>DroYak_CAF1 26876 116 - 1
AAGGCCACUCAGCUCAGCCACCGAGCUC----ACCACUGAGCCAUUAAAAGCUCAGCUCGGCUUUUUGGCCAAGAGAGCCGGCCGAUAUCGCCCAUGUCAGUUGCCGUUGACUGGCCAUU
..(((((.(((((.((((..(((.((((----....((((((........))))))((.((((....)))).)).)))))))..(((((.....))))).))))..))))).)))))... ( -47.70)
>consensus
AAGGCCACUC_____AGCCACUGAGC________CACUGAGCCAUUAAAAA___AGCUCGGCUUUUCGGCCAAGAGAGCCGGCCGAUAUCGCCCAUGUCAGUUGCCGUUGACUGGCCAUU
..(((((....................................................(((...((((((.........))))))....)))...(((((......))))))))))... (-22.56 = -23.20 +   0.64)

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 10:22:46 2006