Locus 3881

Sequence ID 2L_DroMel_CAF1
Location 11,363,642 – 11,363,776
Length 134
Max. P 0.893128
window6103 window6104 window6105

overview

Window 3

Location 11,363,642 – 11,363,737
Length 95
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 76.83
Mean single sequence MFE -19.59
Consensus MFE -10.70
Energy contribution -13.03
Covariance contribution 2.33
Combinations/Pair 1.00
Mean z-score -2.06
Structure conservation index 0.55
SVM decision value 0.97
SVM RNA-class probability 0.893128
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11363642 95 + 22407834
UUCCCACUUUU---------UUUUUCGCUGCCUC----CUCAACCGUUUUUAUUUCCCAUAUUUUCUUUGGCUUUUUUCGGGAAAGUCAAUUCGGUGGGAGGAAA---AAA
...........---------..........((((----((..((((..((..((((((.....................))))))...))..))))))))))...---... ( -21.90)
>DroSec_CAF1 80904 95 + 1
UUCCCACUUUU---------UUUUUCGCUGCCUC----CUCAACCGUUUUUAUUUCCCAUAUUUUCUUUGGCUUUUUUCGGGAAAGUCAAUUCGGUGGGAGGAAA---AAA
...........---------..........((((----((..((((..((..((((((.....................))))))...))..))))))))))...---... ( -21.90)
>DroSim_CAF1 85615 95 + 1
UUCCCACUUUU---------UUUUUCGCUGCCUC----CUCAACCGUUUUUAUUUCCCAUAUUUUCUUUGGCUUUUUUCGGGAAAGUCAAUUCGGUGGGAGGAAA---AAA
...........---------..........((((----((..((((..((..((((((.....................))))))...))..))))))))))...---... ( -21.90)
>DroEre_CAF1 84430 92 + 1
UUCCCACUUU------------UUUCGCUACCUC----CGCAGCCGUUUUUAUUUCCCAUAUUUUCCUUGGCUUUUUUCGGGAAAGUCAUUUCGGUGGGAGGAAA---AAA
..........------------........((((----(...((((......((((((.....................)))))).......)))).)))))...---... ( -21.42)
>DroWil_CAF1 88041 98 + 1
UC-CUACAUUUCGGUUUCUUUCUUUCAUUUUCUUCUAUUUGCACCCUUUCCUUCUCCCAGGGUUUCUUA-UCUCUUGUUGGCAUAUUUAU-------GGAUC-AA---AAA
..-........................((((..(((((.((((((((...........)))))......-...(.....)))).....))-------)))..-))---)). (  -8.90)
>DroYak_CAF1 82644 98 + 1
UUCCCACUUUU-----------UUUCGCUGCCUC-AACCUCAACCGUUUUUAUUUCCCAUAUUUUCUUUGGCUU-UUUCGGGAAAGUCAAUGCGGUGGGAGGAAAAAAAAA
.......((((-----------((((.((.((..-.......(((((.....((((((................-....))))))......))))))).)))))))))).. ( -21.55)
>consensus
UUCCCACUUUU_________UUUUUCGCUGCCUC____CUCAACCGUUUUUAUUUCCCAUAUUUUCUUUGGCUUUUUUCGGGAAAGUCAAUUCGGUGGGAGGAAA___AAA
....................................................((((((((.......(((((((((.....)))))))))....))))))))......... (-10.70 = -13.03 +   2.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,363,642 – 11,363,737
Length 95
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 76.83
Mean single sequence MFE -18.06
Consensus MFE -12.11
Energy contribution -12.64
Covariance contribution 0.53
Combinations/Pair 1.35
Mean z-score -1.21
Structure conservation index 0.67
SVM decision value 0.24
SVM RNA-class probability 0.650238
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11363642 95 - 22407834
UUU---UUUCCUCCCACCGAAUUGACUUUCCCGAAAAAAGCCAAAGAAAAUAUGGGAAAUAAAAACGGUUGAG----GAGGCAGCGAAAAA---------AAAAGUGGGAA
(((---(((((((((((((..((...(((((((...................)))))))..))..))).)).)----))))....))))))---------........... ( -18.91)
>DroSec_CAF1 80904 95 - 1
UUU---UUUCCUCCCACCGAAUUGACUUUCCCGAAAAAAGCCAAAGAAAAUAUGGGAAAUAAAAACGGUUGAG----GAGGCAGCGAAAAA---------AAAAGUGGGAA
(((---(((((((((((((..((...(((((((...................)))))))..))..))).)).)----))))....))))))---------........... ( -18.91)
>DroSim_CAF1 85615 95 - 1
UUU---UUUCCUCCCACCGAAUUGACUUUCCCGAAAAAAGCCAAAGAAAAUAUGGGAAAUAAAAACGGUUGAG----GAGGCAGCGAAAAA---------AAAAGUGGGAA
(((---(((((((((((((..((...(((((((...................)))))))..))..))).)).)----))))....))))))---------........... ( -18.91)
>DroEre_CAF1 84430 92 - 1
UUU---UUUCCUCCCACCGAAAUGACUUUCCCGAAAAAAGCCAAGGAAAAUAUGGGAAAUAAAAACGGCUGCG----GAGGUAGCGAAA------------AAAGUGGGAA
...---.....((((((.........(((((((.......(....)......)))))))........(((((.----...)))))....------------...)))))). ( -23.62)
>DroWil_CAF1 88041 98 - 1
UUU---UU-GAUCC-------AUAAAUAUGCCAACAAGAGA-UAAGAAACCCUGGGAGAAGGAAAGGGUGCAAAUAGAAGAAAAUGAAAGAAAGAAACCGAAAUGUAG-GA
(((---((-(...(-------((....)))....)))))).-......(((((...........)))))............................((........)-). (  -8.90)
>DroYak_CAF1 82644 98 - 1
UUUUUUUUUCCUCCCACCGCAUUGACUUUCCCGAAA-AAGCCAAAGAAAAUAUGGGAAAUAAAAACGGUUGAGGUU-GAGGCAGCGAAA-----------AAAAGUGGGAA
.((((((((((((..((((..((...(((((((...-...(....)......)))))))..))..)))).)))(((-(...))))))))-----------)))))...... ( -19.10)
>consensus
UUU___UUUCCUCCCACCGAAUUGACUUUCCCGAAAAAAGCCAAAGAAAAUAUGGGAAAUAAAAACGGUUGAG____GAGGCAGCGAAAAA_________AAAAGUGGGAA
...........((((((.........(((((((...................)))))))........((((..........))))...................)))))). (-12.11 = -12.64 +   0.53)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,363,667 – 11,363,776
Length 109
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 94.03
Mean single sequence MFE -34.36
Consensus MFE -26.84
Energy contribution -28.08
Covariance contribution 1.24
Combinations/Pair 1.03
Mean z-score -2.05
Structure conservation index 0.78
SVM decision value 0.82
SVM RNA-class probability 0.858277
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11363667 109 + 22407834
CUCAACCGUUUUUAUUUCCCAUAUUUUCUUUGGCUUUUUUCGGGAAAGUCAAUUCGGUGGGAGGAAA---AAAGCGUGGGGCUGAGGUUCACCUUUGCCG-GAGUUUUUCCAU
(((..((((((((.((((((((.......(((((((((.....)))))))))....))))))))..)---)))))).).(((.((((....)))).))).-)))......... ( -35.20)
>DroSec_CAF1 80929 109 + 1
CUCAACCGUUUUUAUUUCCCAUAUUUUCUUUGGCUUUUUUCGGGAAAGUCAAUUCGGUGGGAGGAAA---AAAGCGUGGGGCUGAGGUUCACCUUUGCCG-GAGUUUUUCCAU
(((..((((((((.((((((((.......(((((((((.....)))))))))....))))))))..)---)))))).).(((.((((....)))).))).-)))......... ( -35.20)
>DroSim_CAF1 85640 109 + 1
CUCAACCGUUUUUAUUUCCCAUAUUUUCUUUGGCUUUUUUCGGGAAAGUCAAUUCGGUGGGAGGAAA---AAAGCGUGGGGCUGAGGUUCACCUUUGCCG-GAGUUUUUCCAU
(((..((((((((.((((((((.......(((((((((.....)))))))))....))))))))..)---)))))).).(((.((((....)))).))).-)))......... ( -35.20)
>DroEre_CAF1 84452 109 + 1
CGCAGCCGUUUUUAUUUCCCAUAUUUUCCUUGGCUUUUUUCGGGAAAGUCAUUUCGGUGGGAGGAAA---AAAGCGUGGGGCUCGGGCUCACCUUCGGCG-GAGUUUUUCCAU
....(((((((((.((((((((........((((((((.....)))))))).....))))))))..)---)))))(((((.(...).)))))....)))(-(((...)))).. ( -33.42)
>DroYak_CAF1 82670 112 + 1
CUCAACCGUUUUUAUUUCCCAUAUUUUCUUUGGCUU-UUUCGGGAAAGUCAAUGCGGUGGGAGGAAAAAAAAAGCGUGGGGCUGAGGUUCACCUUUUGCGGGAGUUUUUCCAU
................((((((.......(((((((-((....)))))))))....))))))(((((((....(((..(((.((.....)))))..))).....))))))).. ( -32.80)
>consensus
CUCAACCGUUUUUAUUUCCCAUAUUUUCUUUGGCUUUUUUCGGGAAAGUCAAUUCGGUGGGAGGAAA___AAAGCGUGGGGCUGAGGUUCACCUUUGCCG_GAGUUUUUCCAU
(((..(((((((..((((((((.......(((((((((.....)))))))))....))))))))......)))))).).(((.((((....)))).)))..)))......... (-26.84 = -28.08 +   1.24)

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 11:03:36 2006