Locus 2262

Sequence ID 2L_DroMel_CAF1
Location 6,155,942 – 6,156,066
Length 124
Max. P 0.996654
window3627 window3628 window3629

overview

Window 7

Location 6,155,942 – 6,156,037
Length 95
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.63
Mean single sequence MFE -39.86
Consensus MFE -21.60
Energy contribution -22.16
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -3.42
Structure conservation index 0.54
SVM decision value 2.73
SVM RNA-class probability 0.996654
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6155942 95 + 22407834
----CGGGG-------------------CUUGUGGGG-GUUGGCUUGUUAUUAUUUUGACACUUGCCAAACAAUUGGCAUGCGAAAUG-AAAACCCAGCUGCCUCCAAGGAGCAACAAAA
----.(..(-------------------(((.(((((-((.((((.(((.((((((((.((..((((((....)))))))))))))))-).)))..)))))))))))..))))..).... ( -37.10)
>DroPse_CAF1 1989 118 + 1
GGGCUGGGGCUGCGGGGUCAGGAUUGGACUU-CUGGG-GGUGGCUUGUUAUUAUUUUGACACUUGCCAAACAAUUGGCAUGCGAAAUGGAAAACCCAGCUGCCUUAAAGGAGCAGCCAGC
..(((((.(((.(((((((.......)))))-)..((-((..(((.(((.((((((((.((..((((((....))))))))))))))))..)))..)))..))))...).)))..))))) ( -43.70)
>DroSim_CAF1 1802 95 + 1
----CGGGG-------------------CUUGUGGGG-GGUGGCUUGUUAUUAUUUUGACACUUGCCAAACAAUUGGCAUGCGAAAUG-AAAACCCAGCUGCCUCCAAGGAGCAACAAAA
----.(..(-------------------(((.(.(((-((..(((.(((.((((((((.((..((((((....)))))))))))))))-).)))..)))..))))).).))))..).... ( -40.50)
>DroYak_CAF1 1760 95 + 1
----U-UGG-------------------CUUGCGGGGGGUUGGCUUGUUAUUAUUUUGACACUUGCCAAACAAUUGGCAUGCGAAAUG-AAAACCCAGCUGCCUCCAAGGAGCAACAAAA
----.-..(-------------------(((...((((((.((((.(((.((((((((.((..((((((....)))))))))))))))-).)))..))))))))))...))))....... ( -33.80)
>DroPer_CAF1 1973 115 + 1
----UGGGGCUGCGGGGUCAGGAUUGGACUUCCUGGG-GGUGGCUUGUUAUUAUUUUGACACUUGCCAAACAAUUGGCAUGCGAAAUGGAAAACCCAGCUGCCUUAAAGGAGCAGCCAGC
----...((((((..((((.......))))((((..(-((..(((.(((.((((((((.((..((((((....))))))))))))))))..)))..)))..)))...))))))))))... ( -44.20)
>consensus
____UGGGG___________________CUUGCGGGG_GGUGGCUUGUUAUUAUUUUGACACUUGCCAAACAAUUGGCAUGCGAAAUG_AAAACCCAGCUGCCUCCAAGGAGCAACAAAA
............................(((...(((.(((((((.(((..(((((((.((..((((((....)))))))))))))))...)))..))))))))))...)))........ (-21.60 = -22.16 +   0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,155,958 – 6,156,066
Length 108
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 86.18
Mean single sequence MFE -30.52
Consensus MFE -19.10
Energy contribution -20.35
Covariance contribution 1.25
Combinations/Pair 1.04
Mean z-score -2.12
Structure conservation index 0.63
SVM decision value 0.23
SVM RNA-class probability 0.644060
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6155958 108 + 22407834
UGGCUUGUUAUUAUUUUGACACUUGCCAAACAAUUGGCAUGCGAAAUG-AAAACCCAGCUGCCUCCAAGGAGCAACAAAAAGAACAGAACGACGUCGGACUGAGGGAAA
..........((((((((.((..((((((....)))))))))))))))-)...(((.(((.((.....)))))...........(((..((....))..))).)))... ( -29.00)
>DroPse_CAF1 2027 107 + 1
UGGCUUGUUAUUAUUUUGACACUUGCCAAACAAUUGGCAUGCGAAAUGGAAAACCCAGCUGCCUUAAAGGAGCAGCCAGCGGCAGCCAGCAGCAGCCGA--AAAGGAAA
((((.(((((......)))))...)))).....(((((.(((....(((....(((.(((((((....)).)))))..).))...)))...))))))))--........ ( -33.40)
>DroSim_CAF1 1818 108 + 1
UGGCUUGUUAUUAUUUUGACACUUGCCAAACAAUUGGCAUGCGAAAUG-AAAACCCAGCUGCCUCCAAGGAGCAACAAAAAGAACAGAACGUCGUCGGACUGAGGGAAA
..........((((((((.((..((((((....)))))))))))))))-)...(((.(((.((.....)))))...........(((..((....))..))).)))... ( -28.40)
>DroPer_CAF1 2008 107 + 1
UGGCUUGUUAUUAUUUUGACACUUGCCAAACAAUUGGCAUGCGAAAUGGAAAACCCAGCUGCCUUAAAGGAGCAGCCAGCGGCAGCCAGCAGCAACCGA--AAAGGAAA
((((.(((((......)))))...)))).....(((((.(((....(((.....)))(((((((....)).))))).....))))))))......((..--...))... ( -31.30)
>consensus
UGGCUUGUUAUUAUUUUGACACUUGCCAAACAAUUGGCAUGCGAAAUG_AAAACCCAGCUGCCUCAAAGGAGCAACAAAAAGAACACAACAGCAUCCGA__AAAGGAAA
..(((((((..(((((((.((..((((((....))))))))))))))).........(((.((.....))))))))))))............................. (-19.10 = -20.35 +   1.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,155,958 – 6,156,066
Length 108
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 86.18
Mean single sequence MFE -30.09
Consensus MFE -22.27
Energy contribution -21.52
Covariance contribution -0.75
Combinations/Pair 1.14
Mean z-score -1.48
Structure conservation index 0.74
SVM decision value 0.08
SVM RNA-class probability 0.571345
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6155958 108 - 22407834
UUUCCCUCAGUCCGACGUCGUUCUGUUCUUUUUGUUGCUCCUUGGAGGCAGCUGGGUUUU-CAUUUCGCAUGCCAAUUGUUUGGCAAGUGUCAAAAUAAUAACAAGCCA
...(((.(((..((....))..)))........(((((((....)).))))).)))....-.....(((.((((((....)))))).)))................... ( -27.00)
>DroPse_CAF1 2027 107 - 1
UUUCCUUU--UCGGCUGCUGCUGGCUGCCGCUGGCUGCUCCUUUAAGGCAGCUGGGUUUUCCAUUUCGCAUGCCAAUUGUUUGGCAAGUGUCAAAAUAAUAACAAGCCA
........--..((((....(..((((((...((.....)).....))))))..)(((........(((.((((((....)))))).)))..........))).)))). ( -34.87)
>DroSim_CAF1 1818 108 - 1
UUUCCCUCAGUCCGACGACGUUCUGUUCUUUUUGUUGCUCCUUGGAGGCAGCUGGGUUUU-CAUUUCGCAUGCCAAUUGUUUGGCAAGUGUCAAAAUAAUAACAAGCCA
...(((.(((..((....))..)))........(((((((....)).))))).)))....-.....(((.((((((....)))))).)))................... ( -26.00)
>DroPer_CAF1 2008 107 - 1
UUUCCUUU--UCGGUUGCUGCUGGCUGCCGCUGGCUGCUCCUUUAAGGCAGCUGGGUUUUCCAUUUCGCAUGCCAAUUGUUUGGCAAGUGUCAAAAUAAUAACAAGCCA
........--..((((....(..((((((...((.....)).....))))))..)(((........(((.((((((....)))))).)))..........))).)))). ( -32.47)
>consensus
UUUCCCUC__UCCGACGCCGCUCGCUGCCGCUGGCUGCUCCUUGAAGGCAGCUGGGUUUU_CAUUUCGCAUGCCAAUUGUUUGGCAAGUGUCAAAAUAAUAACAAGCCA
...................(((........(..((((((.......))))))..)(((........(((.((((((....)))))).)))..........))).))).. (-22.27 = -21.52 +  -0.75)

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 10:23:25 2006