Locus 4451

Sequence ID 2R_DroMel_CAF1
Location 14,638,746 – 14,638,928
Length 182
Max. P 0.930357
window7110 window7111 window7112

overview

Window 0

Location 14,638,746 – 14,638,866
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 72.78
Mean single sequence MFE -43.75
Consensus MFE -20.94
Energy contribution -18.78
Covariance contribution -2.16
Combinations/Pair 1.67
Mean z-score -1.73
Structure conservation index 0.48
SVM decision value 0.26
SVM RNA-class probability 0.655361
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14638746 120 - 20766785
GCAGCGCUGCCAACGAGGCAGAUAAUGUCUUGCAAAUCCAGGCCAAUUUGUACGAUAAGGAUGGCAUAUUGGUGGCGAAUGCCACGUCGGACCAAAAACUUGGCGGCAAGCUGCAAGUGA
((((((((((((((((((((.....)))))))....(((..((((.(((........))).))))......(((((....)))))...)))........))))))))..)))))...... ( -46.60)
>DroVir_CAF1 1531 120 - 1
GCACAGCCGCUAAUGAAGCGGACAAUACCCUGUACGCACGGCUGCAGCUGUACAGCAGGGAGGGCAUACUAGUGGCCAAUGCCACCUCGGACAGCAAGCUCUUGGGUUCAUUGAAAGUUG
((...((((((.....))))).)....((((((..(.(((((....))))).).))))))...))......(((((....)))))...((((..(((....))).))))........... ( -37.80)
>DroPse_CAF1 1511 120 - 1
GAAGCGCCGUCAAUGAAGCAGACAAUUCCCUGUACGUACGAGCCCAGCUGUACGACCGGGAGGGCAAGUUGGUGGCCAAUGGCACCUCGGAUGAGGAACUUUGUGGAAGUCUGCAGGUGG
....((((.((...)).((((((..(((((.((.(((((.(((...)))))))))).))))).(((((((....(((...))).((((....))))))).))))....)))))).)))). ( -42.50)
>DroEre_CAF1 1439 120 - 1
GCAGCGCUGCCAACGAGGCAGAUAAUGUGCUGCACGUUCAGGCCAACUUGUACGAUAAGGAAGGCAAAUUGGUAGCGAAUGCCACGUCGGACGGAAAACUAGGCGGCAAGUUGCAAGUGA
(((((.(((((.....)))))......((((((.(((((..(((..(((........)))..)))....(((((.....)))))....))))).........)))))).)))))...... ( -41.10)
>DroYak_CAF1 1405 120 - 1
GCAGCGCUGCCAAUGAGGCGGAUAAUGUGCUGCACAUUCAGGCCAACUUGUACGAUAAGGAAGGCGUCCUGGUGGCGAAUGCCACAUCGGACGGCAAACUAGGCGGCAAGUUGCAGGUGA
(((((((((((.....))))......))))))).((((...((.(((((((.((...((...(.(((((..(((((....)))))...))))).)...))...))))))))))).)))). ( -48.80)
>DroPer_CAF1 1511 120 - 1
GAAGCGCCGUCAACGAAGCAGACAAUUCCCUGUACGUACGAGCCCAGCUGUACGACCGGGAGGGCAAGUUGGUGGCCAAUGGCACCUCGGAUGAGGAGCUUUGUGGAAGUCUGCAGGUGG
....(((((....)...((((((..(((((.((.(((((.(((...)))))))))).))))).............(((..(((.((((....)))).)))...)))..)))))).)))). ( -45.70)
>consensus
GCAGCGCCGCCAACGAAGCAGACAAUGCCCUGCACGUACAGGCCAAGCUGUACGACAAGGAGGGCAAAUUGGUGGCCAAUGCCACCUCGGACGAAAAACUUGGCGGCAAGCUGCAAGUGA
.....(((((((.....((((........))))........((((..((........))..))))....)))))))..........................((((....))))...... (-20.94 = -18.78 +  -2.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,638,786 – 14,638,902
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.92
Mean single sequence MFE -38.37
Consensus MFE -21.41
Energy contribution -20.83
Covariance contribution -0.58
Combinations/Pair 1.37
Mean z-score -1.71
Structure conservation index 0.56
SVM decision value 0.03
SVM RNA-class probability 0.546740
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14638786 116 - 20766785
----CAGUUGGCGAAGUGUUCUAUAGCGUAAGCGUGAAUGGCAGCGCUGCCAACGAGGCAGAUAAUGUCUUGCAAAUCCAGGCCAAUUUGUACGAUAAGGAUGGCAUAUUGGUGGCGAAU
----..((((((..((((((((((.((....))....)))).))))))))))))((((((.....))))))((....(((.((((.(((........))).))))....)))..)).... ( -37.40)
>DroPse_CAF1 1551 116 - 1
----UAGGUGGGGAAGUCAUCUAUAGCGUCAAAUUUAAUGGAAGCGCCGUCAAUGAAGCAGACAAUUCCCUGUACGUACGAGCCCAGCUGUACGACCGGGAGGGCAAGUUGGUGGCCAAU
----(((((((.....)))))))..((.((..........)).))(((..((((...((......(((((.((.(((((.(((...)))))))))).))))).))..))))..))).... ( -35.30)
>DroSim_CAF1 1481 116 - 1
----UAGUUGGCGAAGUGUUCUAUAGCGUAAGUGUGAAUGGCAGCGCUGCCAAUGAGGCAGAUAACGUCCUGCACAUUCAGGCCAAUUUGUACGAUAAGGAAGGCAUUUUGGUGGCGAAU
----..((((.(((((((((((.((.((((.((.(((((((((((((((((.....)))))....))..)))).)))))).)).......)))).)).)))..)))))))).)))).... ( -37.40)
>DroEre_CAF1 1479 120 - 1
AAAACAGUUGGCGAGGUGUUCUACAGCGUAAGCGUGAAUGGCAGCGCUGCCAACGAGGCAGAUAAUGUGCUGCACGUUCAGGCCAACUUGUACGAUAAGGAAGGCAAAUUGGUAGCGAAU
......((((.(((.((.((((....((((.((.(((((((((((((((((.....))))......))))))).)))))).)).......))))....)))).))...))).)))).... ( -42.70)
>DroYak_CAF1 1445 116 - 1
----CAGUUGGUGAGGUAUUCUACAGCGUAAGCGUGAAUGGCAGCGCUGCCAAUGAGGCGGAUAAUGUGCUGCACAUUCAGGCCAACUUGUACGAUAAGGAAGGCGUCCUGGUGGCGAAU
----..((((((.............((....)).(((((((((((((((((.....))))......))))))).)))))).))))))((((.((...((((.....))))..)))))).. ( -40.60)
>DroPer_CAF1 1551 116 - 1
----UAGGUGGGGAAGUCAUCUAUAGCGUCAAAUUUAAUGGAAGCGCCGUCAACGAAGCAGACAAUUCCCUGUACGUACGAGCCCAGCUGUACGACCGGGAGGGCAAGUUGGUGGCCAAU
----(((((((.....)))))))..((.((..........)).))(((..((((...((......(((((.((.(((((.(((...)))))))))).))))).))..))))..))).... ( -36.80)
>consensus
____CAGUUGGCGAAGUGUUCUAUAGCGUAAGCGUGAAUGGCAGCGCUGCCAACGAGGCAGAUAAUGUCCUGCACAUUCAGGCCAACUUGUACGAUAAGGAAGGCAAAUUGGUGGCGAAU
......((((..((.....))..)))).................(((((((((....((((........))))........(((..(((((...)))))...)))...)))))))))... (-21.41 = -20.83 +  -0.58)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,638,826 – 14,638,928
Length 102
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 74.76
Mean single sequence MFE -29.27
Consensus MFE -18.29
Energy contribution -16.94
Covariance contribution -1.35
Combinations/Pair 1.65
Mean z-score -1.76
Structure conservation index 0.62
SVM decision value 1.20
SVM RNA-class probability 0.930357
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14638826 102 - 20766785
UAACUUAUUUAAUA-CUGU--AAUACUUU----------CAGUUGGCGAAGUGUUCUAUAGCGUAAGCGUGAAUGGCAGCGCUGCCAACGAGGCAGAUAAUGUCUUGCAAAUCCA
..............-.(((--........----------..((((((..((((((((((.((....))....)))).))))))))))))((((((.....)))))))))...... ( -27.80)
>DroVir_CAF1 1611 102 - 1
GAGCUAU---AAUAUCUGCAGUUCAUUUU----------CAGUGGGCACUGUGAAUUACAGCAUUGCGGUGAAUGGCACAGCCGCUAAUGAAGCGGACAAUACCCUGUACGCACG
..(((((---.....(((((((((((...----------..)))))).(((((...)))))...)))))...)))))(((((((((.....)))))........))))....... ( -26.40)
>DroSec_CAF1 1638 102 - 1
UAACUUAUUUAAAA-CUGU--AAUGCUUU----------UAGUUGGCGAAGUGUUCUAUAGCGUAAGCGUGAAUGGCAGCGCUGCCAAUGAGGCAGAUAAUGUCCUCCACAUCCA
..............-.(((--........----------..((((((..((((((((((.((....))....)))).))))))))))))((((((.....)).)))).))).... ( -25.50)
>DroSim_CAF1 1521 102 - 1
UAACUUAAUUAAAA-CUGU--AAUACUUU----------UAGUUGGCGAAGUGUUCUAUAGCGUAAGUGUGAAUGGCAGCGCUGCCAAUGAGGCAGAUAACGUCCUGCACAUUCA
..(((((.......-((((--((((((((----------........)))))))..)))))..))))).(((((((((((((((((.....)))))....))..)))).)))))) ( -26.10)
>DroEre_CAF1 1519 109 - 1
UAAUUU---UAAUA-CUGG--AAUACUUGCCCUUAAAAACAGUUGGCGAGGUGUUCUACAGCGUAAGCGUGAAUGGCAGCGCUGCCAACGAGGCAGAUAAUGUGCUGCACGUUCA
......---.....-.(((--((((((((((.............))).))))))))))..((....)).(((((((((((((((((.....))))......))))))).)))))) ( -38.82)
>DroYak_CAF1 1485 102 - 1
UAAUAAUAAUAAUA-UUGU--AAUACUUU----------CAGUUGGUGAGGUAUUCUACAGCGUAAGCGUGAAUGGCAGCGCUGCCAAUGAGGCGGAUAAUGUGCUGCACAUUCA
..............-.(((--((((((((----------........)))))))..))))((....)).(((((((((((((((((.....))))......))))))).)))))) ( -31.00)
>consensus
UAACUUA_UUAAUA_CUGU__AAUACUUU__________CAGUUGGCGAAGUGUUCUACAGCGUAAGCGUGAAUGGCAGCGCUGCCAAUGAGGCAGAUAAUGUCCUGCACAUUCA
...............(((...((((((((..................))))))))...))).......(((...((((...(((((.....)))))....))))...)))..... (-18.29 = -16.94 +  -1.35)

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 11:19:55 2006