Locus 4635

Sequence ID 2L_DroMel_CAF1
Location 13,256,092 – 13,256,219
Length 127
Max. P 0.969470
window7320 window7321 window7322

overview

Window 0

Location 13,256,092 – 13,256,201
Length 109
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 77.22
Mean single sequence MFE -43.60
Consensus MFE -22.62
Energy contribution -22.96
Covariance contribution 0.34
Combinations/Pair 1.35
Mean z-score -2.57
Structure conservation index 0.52
SVM decision value 1.64
SVM RNA-class probability 0.969470
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13256092 109 + 22407834
AGUGGCCUUUCGGUUCCUUUGCUGGCGG---------CCAGUGGCCACCAGCGCUACCGACUCACCCACCCACAACGGGUGGUUGGCCACCACCGCUGCCCACCCAUCCGCCGAACCA
.((((((..(((((.....((((((.((---------((...)))).))))))..))))).....((((((.....))))))..))))))............................ ( -46.00)
>DroPse_CAF1 40829 118 + 1
AGUGGCCAUUCGGCUCCUUUGCCGGAGGCCCAGUAGCCCAAUGGCCGCCACCGCUGCCCACCCAUCCGCCUACAACUGGAGGCUGGCCCCCACCGCUUCCAACCCAUCCGCCCAACCA
.(((((((((.((((.((..(((...)))..)).)))).)))))))))............................(((((((.((......)))))))))................. ( -38.50)
>DroGri_CAF1 31481 115 + 1
AAUGGCCUUUUGGCACCUUUGCUGGUGGC---UUGCCACAGUGGCCGCCACCGGUGCCCACACACCCACCCACCGUUGGCGGUUGGCCACCUCCAAUUCCGACCCAUCCGCCGAGUCA
..((((.....((((((......((((((---..(((.....))).)))))))))))).................(((((((.(((.................))).))))))))))) ( -41.63)
>DroYak_CAF1 31139 109 + 1
AGUGGCCCUUUGGCUCCUUUGCGGGCGG---------CCAGUGGCCACCAGCGCUGCCAACCCACCCACCCACAACUGGGGGUUGGCCACCACCGCUGCCCACCCAUCCGCCAAACCA
.((((((..(((((((((....))).))---------)))).))))))(((((..((((((((..(((........)))))))))))......))))).................... ( -44.40)
>DroMoj_CAF1 38365 115 + 1
AAUGGCCCUUCGGCAACUUUGCCGGUGGC---UUUCCACAGUGGCCGCCGCCAUUGCCCACCCAUCCGCCCAGCGUUGGGGGUUGGCCACCACCGAUACCGACACACCCACCGAACCA
..(((...(((((((....))))((((((---(..((.(((((((....)))))))....((((..(((...))).))))))..))))))).....................)))))) ( -43.40)
>DroAna_CAF1 38603 115 + 1
AAUGGCCAUUUGGCACCUUUGCGGGAGGC---GUGGCCCAGUGGCCGCCUCCGCUGCCCACGCACCCGCCCACAACGGGUGGCUGGCCACCACCACUGCCCACCCAUCCCCCCAACCA
....(((....)))......(((((..((---((((..((((((......)))))).)))))).))))).......((((((((((......)))..).))))))............. ( -47.70)
>consensus
AAUGGCCAUUCGGCACCUUUGCCGGAGGC____U__CCCAGUGGCCGCCACCGCUGCCCACCCACCCACCCACAACUGGGGGUUGGCCACCACCGCUGCCCACCCAUCCGCCGAACCA
....(((....)))........((((((............(((((((((.((.........................)).))).)))))).................))))))..... (-22.62 = -22.96 +   0.34)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,256,092 – 13,256,201
Length 109
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 77.22
Mean single sequence MFE -54.77
Consensus MFE -30.27
Energy contribution -31.05
Covariance contribution 0.78
Combinations/Pair 1.36
Mean z-score -2.08
Structure conservation index 0.55
SVM decision value 0.99
SVM RNA-class probability 0.895226
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13256092 109 - 22407834
UGGUUCGGCGGAUGGGUGGGCAGCGGUGGUGGCCAACCACCCGUUGUGGGUGGGUGAGUCGGUAGCGCUGGUGGCCACUGG---------CCGCCAGCAAAGGAACCGAAAGGCCACU
..(((.(((((..((((.(.(((((.((.((((((.((((((.....)))))).)).)))).)).))))).).))).)...---------))))))))...((..((....))))... ( -55.00)
>DroPse_CAF1 40829 118 - 1
UGGUUGGGCGGAUGGGUUGGAAGCGGUGGGGGCCAGCCUCCAGUUGUAGGCGGAUGGGUGGGCAGCGGUGGCGGCCAUUGGGCUACUGGGCCUCCGGCAAAGGAGCCGAAUGGCCACU
((((((..(((....((.....))(.((((((((.(((.((.(((((..((......))..))))))).)))((((....))))....)))))))).).......)))..)))))).. ( -49.80)
>DroGri_CAF1 31481 115 - 1
UGACUCGGCGGAUGGGUCGGAAUUGGAGGUGGCCAACCGCCAACGGUGGGUGGGUGUGUGGGCACCGGUGGCGGCCACUGUGGCAA---GCCACCAGCAAAGGUGCCAAAAGGCCAUU
.((((((.....)))))).........(((((((..(((((.......))))).......((((((((((((.(((.....)))..---))))))......))))))....))))))) ( -52.60)
>DroYak_CAF1 31139 109 - 1
UGGUUUGGCGGAUGGGUGGGCAGCGGUGGUGGCCAACCCCCAGUUGUGGGUGGGUGGGUUGGCAGCGCUGGUGGCCACUGG---------CCGCCCGCAAAGGAGCCAAAGGGCCACU
..((..(((((.(.(((((.((.(((((.((.((((((((((.(....).)))..))))))))).))))).)).))))).)---------))))).))..((..(((....)))..)) ( -55.90)
>DroMoj_CAF1 38365 115 - 1
UGGUUCGGUGGGUGUGUCGGUAUCGGUGGUGGCCAACCCCCAACGCUGGGCGGAUGGGUGGGCAAUGGCGGCGGCCACUGUGGAAA---GCCACCGGCAAAGUUGCCGAAGGGCCAUU
((((((((..(.(.(((((((..(((((((.(((..((((((.(((...)))..)))).))((....))))).))))))).((...---.))))))))).).)..))))...)))).. ( -57.00)
>DroAna_CAF1 38603 115 - 1
UGGUUGGGGGGAUGGGUGGGCAGUGGUGGUGGCCAGCCACCCGUUGUGGGCGGGUGCGUGGGCAGCGGAGGCGGCCACUGGGCCAC---GCCUCCCGCAAAGGUGCCAAAUGGCCAUU
((((((..((.(((((.((((.((((((((((((.(((..(((((((..(((....)))..))))))).))))))))))..)))))---)))))))......)).))...)))))).. ( -58.30)
>consensus
UGGUUCGGCGGAUGGGUGGGCAGCGGUGGUGGCCAACCACCAGUUGUGGGCGGGUGGGUGGGCAGCGGUGGCGGCCACUGGG__A____GCCACCAGCAAAGGAGCCAAAAGGCCACU
(((((((((......((((((..(((((((.(((..((.((.......)).)).((......)).....))).)))))))((........))))))))......)))...)))))).. (-30.27 = -31.05 +   0.78)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,256,123 – 13,256,219
Length 96
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 81.81
Mean single sequence MFE -40.33
Consensus MFE -28.56
Energy contribution -28.20
Covariance contribution -0.36
Combinations/Pair 1.45
Mean z-score -1.79
Structure conservation index 0.71
SVM decision value 0.42
SVM RNA-class probability 0.728181
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13256123 96 - 22407834
GGGUGCGUGGGAUAAUGGUGGUUCGGCGGAUGGGUGGGCAGCGGUGGUGGCCAACCACCCGUUGUGGGUGGGUGAGUCGGUAGCGCUGGUGGCCAC
..((.(((.((((.......)))).))).)).(((.(.(((((.((.((((((.((((((.....)))))).)).)))).)).))))).).))).. ( -44.70)
>DroVir_CAF1 35705 96 - 1
GGAUGCGUUGGAUACUGAUGACUCGGAGGAUGAGUCGGUAUCGGAGGUGGCCAACCGCCAACGGUGGGCGGAUGCGUCGGUAUUGGUGGCGGCCAC
....((.((.((((((...((((((.....)))))))))))).)).))((((..(((((((...(.((((....)))).)..))))))).)))).. ( -39.80)
>DroGri_CAF1 31518 96 - 1
GGAUGCGUGGGAUACUGAUGACUCGGCGGAUGGGUCGGAAUUGGAGGUGGCCAACCGCCAACGGUGGGUGGGUGUGUGGGCACCGGUGGCGGCCAC
......((((..((((..(((((((.....)))))))........((((.(((..((((.((.....)).))))..))).))))))))....)))) ( -34.00)
>DroEre_CAF1 30885 96 - 1
GGAUGCGUGGGAUAAUGGUGGUUCGGCGGAUGGGUGGGCAGCGGUGGUGGCCAACCGCCCGUGGUGGGUGGGUGCGUCGGUAGCGCUGGUGGCCAC
..((.(((.((((.......)))).))).)).(((.(.(((((.((.((((((.((((((.....)))))).)).)))).)).))))).).))).. ( -44.00)
>DroYak_CAF1 31170 96 - 1
GGAUGCGUAGGAUAAUGGUGGUUUGGCGGAUGGGUGGGCAGCGGUGGUGGCCAACCCCCAGUUGUGGGUGGGUGGGUUGGCAGCGCUGGUGGCCAC
..((.(((..(((.......)))..))).))..((((.((.(((((.((.((((((((((.(....).)))..))))))))).))))).)).)))) ( -40.30)
>DroMoj_CAF1 38402 96 - 1
GGAUGCGUUGGAUACUGAUGGUUCGGUGGGUGUGUCGGUAUCGGUGGUGGCCAACCCCCAACGCUGGGCGGAUGGGUGGGCAAUGGCGGCGGCCAC
..........((((((((((..((....))..))))))))))(((.((.((((.((((((.(((...)))..)))).))....)))).)).))).. ( -39.20)
>consensus
GGAUGCGUGGGAUAAUGAUGGUUCGGCGGAUGGGUCGGCAGCGGUGGUGGCCAACCGCCAACGGUGGGUGGGUGCGUCGGCAGCGCUGGCGGCCAC
..((.(((.((((.......)))).))).)).(((.(.(((((.((.((((((.(((((.......))))).)).)))).)).))))).).))).. (-28.56 = -28.20 +  -0.36)

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 11:23:13 2006