Locus 3443

Sequence ID X_DroMel_CAF1
Location 9,229,033 – 9,229,174
Length 141
Max. P 0.998447
window5642 window5643 window5644

overview

Window 2

Location 9,229,033 – 9,229,140
Length 107
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 92.19
Mean single sequence MFE -30.83
Consensus MFE -27.51
Energy contribution -29.11
Covariance contribution 1.60
Combinations/Pair 1.00
Mean z-score -1.52
Structure conservation index 0.89
SVM decision value 1.20
SVM RNA-class probability 0.930013
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9229033 107 + 22224390
---AAAACGGGAGCUGGGCAAAGGAAAGGCAAAGGGAAUUCUGGCUGCCGACAACAAAAGACUGUCAUAAAAUGGCAGCUGCAAGGAUGCGCCUCAACUUUUGUGGCUGC
---......(.((((..(((((((..((((............(((((((((((.........)))).......)))))))(((....)))))))...))))))))))).) ( -32.01)
>DroSec_CAF1 12309 102 + 1
--------GGGAGCUAGGCAAAGGAAAGGCAAAGGGAAUUCUGGCUGCCGACAACAAAAGACUGUCAUAAAAUGGCAGCUGCAAGGAUGCGCCUCAACUUUUGUGGCUGC
--------.(.((((..(((((((..((((............(((((((((((.........)))).......)))))))(((....)))))))...))))))))))).) ( -32.01)
>DroSim_CAF1 23177 102 + 1
--------GGGAGCUGGGCAAAGGAAAGGCAAAGGGAAUUCUGGCUGCCGACAACAAAAGACUGUCAUAAAAUGGCAGCUGCAAGGAUGCGCCUCAACUUUUGUGGCUGC
--------.(.((((..(((((((..((((............(((((((((((.........)))).......)))))))(((....)))))))...))))))))))).) ( -32.01)
>DroEre_CAF1 14739 105 + 1
AGAAAGAAGGGAGCUGGCC-A----AAGGCAAAGGGAAUUCUGGCUGCCGACAACAAAAGACUGUCAUAAAAUGGCAGCUGCAAGGAUGCGCCUCAACUUUUGUGGCUGC
........((.((((.(((-.----..)))....((....)))))).))((((.........))))........(((((..((((..(........)..))))..))))) ( -28.00)
>DroYak_CAF1 12487 104 + 1
--AAAGAAGGGAGCUGGGCAA----AAGGCAAAGGGAAUUCUGGCUGCCGACAACAAAAGACUGUCAUAAAAUGGCAGCUGCAAGGAUGCGCCUCAACUUUUGUGGCUGC
--.......(.((((..((((----(((....((((.((((((((((((((((.........)))).......)))))))...))))).).)))...))))))))))).) ( -30.11)
>consensus
___AA_A_GGGAGCUGGGCAAAGGAAAGGCAAAGGGAAUUCUGGCUGCCGACAACAAAAGACUGUCAUAAAAUGGCAGCUGCAAGGAUGCGCCUCAACUUUUGUGGCUGC
.........(.((((..(((((((..((((............(((((((((((.........)))).......)))))))(((....)))))))...))))))))))).) (-27.51 = -29.11 +   1.60)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,229,033 – 9,229,140
Length 107
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 92.19
Mean single sequence MFE -29.56
Consensus MFE -26.72
Energy contribution -27.72
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.14
Structure conservation index 0.90
SVM decision value 3.10
SVM RNA-class probability 0.998447
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9229033 107 - 22224390
GCAGCCACAAAAGUUGAGGCGCAUCCUUGCAGCUGCCAUUUUAUGACAGUCUUUUGUUGUCGGCAGCCAGAAUUCCCUUUGCCUUUCCUUUGCCCAGCUCCCGUUUU---
..(((....((((..((((((((....))).((((((.....(..((((....))))..).)))))).............)))))..)))).....)))........--- ( -30.50)
>DroSec_CAF1 12309 102 - 1
GCAGCCACAAAAGUUGAGGCGCAUCCUUGCAGCUGCCAUUUUAUGACAGUCUUUUGUUGUCGGCAGCCAGAAUUCCCUUUGCCUUUCCUUUGCCUAGCUCCC--------
..(((....((((..((((((((....))).((((((.....(..((((....))))..).)))))).............)))))..)))).....)))...-------- ( -30.50)
>DroSim_CAF1 23177 102 - 1
GCAGCCACAAAAGUUGAGGCGCAUCCUUGCAGCUGCCAUUUUAUGACAGUCUUUUGUUGUCGGCAGCCAGAAUUCCCUUUGCCUUUCCUUUGCCCAGCUCCC--------
..(((....((((..((((((((....))).((((((.....(..((((....))))..).)))))).............)))))..)))).....)))...-------- ( -30.50)
>DroEre_CAF1 14739 105 - 1
GCAGCCACAAAAGUUGAGGCGCAUCCUUGCAGCUGCCAUUUUAUGACAGUCUUUUGUUGUCGGCAGCCAGAAUUCCCUUUGCCUU----U-GGCCAGCUCCCUUCUUUCU
((.((((........((((((((....))).((((((.....(..((((....))))..).)))))).............)))))----)-)))..))............ ( -29.30)
>DroYak_CAF1 12487 104 - 1
GCAGCCACAAAAGUUGAGGCGCAUCCUUGCAGCUGCCAUUUUAUGACAGUCUUUUGUUGUCGGCAGCCAGAAUUCCCUUUGCCUU----UUGCCCAGCUCCCUUCUUU--
...........(((((.((((((....))).((((((.....(..((((....))))..).))))))..................----..)))))))).........-- ( -27.00)
>consensus
GCAGCCACAAAAGUUGAGGCGCAUCCUUGCAGCUGCCAUUUUAUGACAGUCUUUUGUUGUCGGCAGCCAGAAUUCCCUUUGCCUUUCCUUUGCCCAGCUCCC_U_UU___
..(((....((((..((((((((....))).((((((.....(..((((....))))..).)))))).............)))))..)))).....)))........... (-26.72 = -27.72 +   1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,229,070 – 9,229,174
Length 104
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 87.91
Mean single sequence MFE -37.20
Consensus MFE -29.39
Energy contribution -29.41
Covariance contribution 0.03
Combinations/Pair 1.08
Mean z-score -2.03
Structure conservation index 0.79
SVM decision value -0.05
SVM RNA-class probability 0.508101
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9229070 104 + 22224390
CU-----GGCUGCCGACAACAAAAGACUGUCAUAAAAUGGCAGCUGCAAGGA---U-GCGCC-UCAACUUUUGUGGCUGCCAAAGCCGCCGCGGCUAAUGGCCUUGUCACACAC
.(-----(((.(((((((.........))))......(((((((..((((..---(-.....-...)..))))..))))))).(((((...)))))...)))...))))..... ( -36.10)
>DroPse_CAF1 12302 113 + 1
CUGCCGGUGGGGCAGACAACAAAAGGCUGUCAUAAAAUGGCAGCUGCAAGGCGCUCGGGCCC-UCAACUUUUGUGGCUGCCAAAGCCGCCAUGGCUAAUGGCCUUGUCACACAC
.....(((..(((((...(((((((((((((((...))))))))....(((.((....))))-)...)))))))..)))))...)))(((((.....)))))............ ( -44.40)
>DroEre_CAF1 14774 104 + 1
CU-----GGCUGCCGACAACAAAAGACUGUCAUAAAAUGGCAGCUGCAAGGA---U-GCGCC-UCAACUUUUGUGGCUGCCAAAGCCGCCGCGGCUAAUGGCCUUGUCAUACAC
.(-----(((.(((((((.........))))......(((((((..((((..---(-.....-...)..))))..))))))).(((((...)))))...)))...))))..... ( -36.20)
>DroYak_CAF1 12521 104 + 1
CU-----GGCUGCCGACAACAAAAGACUGUCAUAAAAUGGCAGCUGCAAGGA---U-GCGCC-UCAACUUUUGUGGCUGCCAAAGCCGCCGCGGCUAAUGGCCUUGUCAUACAC
.(-----(((.(((((((.........))))......(((((((..((((..---(-.....-...)..))))..))))))).(((((...)))))...)))...))))..... ( -36.20)
>DroAna_CAF1 15997 105 + 1
CU-----AGGAGCCGACAACAAAAGACUGUCAUAAAAUGGCAGCUGCAAGUA---U-GCGCCUUCAACUUUUGUGGCUGCCAAAGCCGCCAUUGCUAAUGGCCUUGUCACACAC
..-----.......(((((((((((.(((((((...)))))))..(((....---)-))........)))))))((((.....))))(((((.....)))))..))))...... ( -30.80)
>DroPer_CAF1 12884 113 + 1
CUGCUCGUGGGGCAGACAACAAAAGGCUGUCAUAAAAUGUCAGCUGCAAGGCGCUCGGGCCC-UCAACUUUUGUGGCUGCCAAAGCCGCCAUGGCUAAUGGCCUUGUCACACAC
(((((.....))))).........(((((.(((...))).)))))(((((((.(...((((.-.........(((((.((....)).)))))))))...))))))))....... ( -39.50)
>consensus
CU_____GGCUGCCGACAACAAAAGACUGUCAUAAAAUGGCAGCUGCAAGGA___U_GCGCC_UCAACUUUUGUGGCUGCCAAAGCCGCCACGGCUAAUGGCCUUGUCACACAC
........................(((.(((((....(((((((..(((((.................)))))..))))))).(((((...))))).)))))...)))...... (-29.39 = -29.41 +   0.03)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:39 2006