Locus 484

Sequence ID 2R_DroMel_CAF1
Location 2,697,151 – 2,697,317
Length 166
Max. P 0.998569
window914 window915 window916 window917 window918 window919

overview

Window 4

Location 2,697,151 – 2,697,243
Length 92
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.52
Mean single sequence MFE -30.57
Consensus MFE -19.66
Energy contribution -21.66
Covariance contribution 2.00
Combinations/Pair 1.14
Mean z-score -2.77
Structure conservation index 0.64
SVM decision value 2.85
SVM RNA-class probability 0.997398
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2697151 92 + 20766785
--------------------------GGGAACUAUUUCCCUGCCUGGGGACACACCUGUGCCCCCG--AUGUGGCGCCAACUUUUCCCAUUACGAUAGCCCUUUAUGGGCCAACAAAAUU
--------------------------(((((.........(((((((((.(((....))).)))))--....)))).......))))).........((((.....)))).......... ( -28.99)
>DroSec_CAF1 11997 92 + 1
--------------------------GGGAACUAUUUCCCUGCCUUGGGACACACCUGUGCCCCCG--AUGUGGCGCCAACUUUUCCCAUUACGAUGGCCCUUUAUGGGCCAACAAAAUU
--------------------------(((((.....((((......)))).......(((((....--....)))))......))))).....(.((((((.....)))))).)...... ( -32.30)
>DroEre_CAF1 9517 92 + 1
--------------------------GGGAACUAUUUCCCUGCCUGG-GACACACCUGUGCCCCCGGCAUGUGGCGCCAACUUUUCGCAUAACGAUGGCCCU-UAUGGGCCAACAAAAUU
--------------------------(((((....)))))((((.((-(.(((....))).))).))))(((.(((.........)))...))).((((((.-...))))))........ ( -36.30)
>DroWil_CAF1 12405 116 + 1
GUCGAGGGAGGGCAAGAAAAGAAAAAGAAAACUAUUUC-AUGCAUAAGGACACACCUGCGAACU-U--CUGGAACUCUAACUUUUCCCAUUAUUAUGGCCUUUAAUGGGCCAACAAAAUU
...(.(((((((..(((..((((...((((....))))-.((((...((.....))))))...)-)--)).....)))..)))))))).......((((((.....))))))........ ( -24.00)
>DroYak_CAF1 9330 92 + 1
--------------------------GGAAACUAUUUCCCUGCCUGGGGACACACCUGUGCCCCCA--AUGUGGCGCCAACUUUUCCCAUUACGAUGGCCCUUUAUGGGCCAACAAAAUU
--------------------------(((((.........(((((((((.(((....))).)))))--....))))......)))))......(.((((((.....)))))).)...... ( -31.26)
>consensus
__________________________GGGAACUAUUUCCCUGCCUGGGGACACACCUGUGCCCCCG__AUGUGGCGCCAACUUUUCCCAUUACGAUGGCCCUUUAUGGGCCAACAAAAUU
..........................(((((....))))).((((((((.(((....))).)))))......)))....................((((((.....))))))........ (-19.66 = -21.66 +   2.00) 

alignment

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secondary structure

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dotplot

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Window 5

Location 2,697,151 – 2,697,243
Length 92
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.52
Mean single sequence MFE -34.32
Consensus MFE -25.26
Energy contribution -25.94
Covariance contribution 0.68
Combinations/Pair 1.24
Mean z-score -2.52
Structure conservation index 0.74
SVM decision value 2.55
SVM RNA-class probability 0.995163
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2697151 92 - 20766785
AAUUUUGUUGGCCCAUAAAGGGCUAUCGUAAUGGGAAAAGUUGGCGCCACAU--CGGGGGCACAGGUGUGUCCCCAGGCAGGGAAAUAGUUCCC--------------------------
.(((.((.((((((.....)))))).)).)))(((((..(((....((...(--(((((((((....)))))))).))...)).)))..)))))-------------------------- ( -35.30)
>DroSec_CAF1 11997 92 - 1
AAUUUUGUUGGCCCAUAAAGGGCCAUCGUAAUGGGAAAAGUUGGCGCCACAU--CGGGGGCACAGGUGUGUCCCAAGGCAGGGAAAUAGUUCCC--------------------------
......(.((((((.....)))))).)((..(((((..(.(((((.((....--..)).)).))).)...)))))..)).(((((....)))))-------------------------- ( -36.20)
>DroEre_CAF1 9517 92 - 1
AAUUUUGUUGGCCCAUA-AGGGCCAUCGUUAUGCGAAAAGUUGGCGCCACAUGCCGGGGGCACAGGUGUGUC-CCAGGCAGGGAAAUAGUUCCC--------------------------
((((((..((((((...-.))))))(((.....))))))))).........((((.(((((((....)))))-)).))))(((((....)))))-------------------------- ( -39.30)
>DroWil_CAF1 12405 116 - 1
AAUUUUGUUGGCCCAUUAAAGGCCAUAAUAAUGGGAAAAGUUAGAGUUCCAG--A-AGUUCGCAGGUGUGUCCUUAUGCAU-GAAAUAGUUUUCUUUUUCUUUUCUUGCCCUCCCUCGAC
........(((((.......))))).......((((...((.((((...((.--(-((..(((....)))..))).))...-((((.((....)).))))..)))).))..))))..... ( -23.10)
>DroYak_CAF1 9330 92 - 1
AAUUUUGUUGGCCCAUAAAGGGCCAUCGUAAUGGGAAAAGUUGGCGCCACAU--UGGGGGCACAGGUGUGUCCCCAGGCAGGGAAAUAGUUUCC--------------------------
.(((.((.((((((.....)))))).)).)))(((((..(((....((...(--(((((((((....))))))))))....)).)))..)))))-------------------------- ( -37.70)
>consensus
AAUUUUGUUGGCCCAUAAAGGGCCAUCGUAAUGGGAAAAGUUGGCGCCACAU__CGGGGGCACAGGUGUGUCCCCAGGCAGGGAAAUAGUUCCC__________________________
.(((.((.((((((.....)))))).)).)))(((((..(((....((.......((((((((....))))))))......)).)))..))))).......................... (-25.26 = -25.94 +   0.68) 

alignment

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secondary structure

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Window 6

Location 2,697,165 – 2,697,280
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 69.89
Mean single sequence MFE -37.80
Consensus MFE -17.61
Energy contribution -20.95
Covariance contribution 3.34
Combinations/Pair 1.12
Mean z-score -2.81
Structure conservation index 0.47
SVM decision value 2.94
SVM RNA-class probability 0.997828
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2697165 115 + 20766785
UGCCUGGGGACACACCUGUGCCCCCG--AUGUGGCGCCAACUUUUCCCAUUACGAUAGCCCUUUAUGGGCCAACAAAAUUGCCCAUUUCACGAGAGGAAUGCG-GGCCCACACCC--CGC
....(((((.(((....))).)))))--.(((((.(((...................((((.....))))............(((((((......)))))).)-))))))))...--... ( -36.60)
>DroSec_CAF1 12011 115 + 1
UGCCUUGGGACACACCUGUGCCCCCG--AUGUGGCGCCAACUUUUCCCAUUACGAUGGCCCUUUAUGGGCCAACAAAAUUGCCCAUUUCACGGGAGGAAUGUG-GGCCCACAUCC--CGC
......(((.(((....))))))..(--((((((.(((.((..((((......(.((((((.....)))))).).......(((.......))).)))).)).-)))))))))).--... ( -46.30)
>DroSim_CAF1 9469 115 + 1
NNNNNNNNNNNNNNNNNNNNNNNNNN--NNNNNNNNNNNNNNNNNNNNNNNNNGAUGGCCCUUUAUGGGCCAACAAAAUUGCCCAUUUCACGGGAGGAAUGUG-GGCCCACACCC--CGC
..........................--...........................((((((.....))))))........(((((((((.(....)))).)))-)))........--... ( -24.40)
>DroEre_CAF1 9531 115 + 1
UGCCUGG-GACACACCUGUGCCCCCGGCAUGUGGCGCCAACUUUUCGCAUAACGAUGGCCCU-UAUGGGCCAACAAAAUUGCCCAUUUCAUGGCAGGAAUGUG-GGCCCACACCC--CGC
((((.((-(.(((....))).))).))))(((((.(((.((.((((.......(.((((((.-...)))))).).....((((........)))))))).)).-))))))))...--... ( -49.60)
>DroWil_CAF1 12444 102 + 1
UGCAUAAGGACACACCUGCGAACU-U--CUGGAACUCUAACUUUUCCCAUUAUUAUGGCCUUUAAUGGGCCAACAAAAUUGCCCAUUCCUGGC-------------CCUACCCUU--GGG
.(((...((.....))))).....-.--.................((((....((.((((...(((((((..........)))))))...)))-------------).))....)--))) ( -24.70)
>DroYak_CAF1 9344 118 + 1
UGCCUGGGGACACACCUGUGCCCCCA--AUGUGGCGCCAACUUUUCCCAUUACGAUGGCCCUUUAUGGGCCAACAAAAUUGUCCAUUUCAGGCGAGGAAUGUGAGGCCCACACCCAACGC
....(((((.(((....))).)))))--.(((((.(((.((..((((......(.((((((.....)))))).)....(((((.......))))))))).))..))))))))........ ( -45.20)
>consensus
UGCCUGGGGACACACCUGUGCCCCCG__AUGUGGCGCCAACUUUUCCCAUUACGAUGGCCCUUUAUGGGCCAACAAAAUUGCCCAUUUCACGGGAGGAAUGUG_GGCCCACACCC__CGC
......(((.(((....))).)))......((((.(((.................((((((.....))))))...........((((((......))))))...)))))))......... (-17.61 = -20.95 +   3.34) 

alignment

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secondary structure

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Window 7

Location 2,697,165 – 2,697,280
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 69.89
Mean single sequence MFE -45.23
Consensus MFE -20.23
Energy contribution -22.67
Covariance contribution 2.44
Combinations/Pair 1.26
Mean z-score -2.99
Structure conservation index 0.45
SVM decision value 3.14
SVM RNA-class probability 0.998569
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2697165 115 - 20766785
GCG--GGGUGUGGGCC-CGCAUUCCUCUCGUGAAAUGGGCAAUUUUGUUGGCCCAUAAAGGGCUAUCGUAAUGGGAAAAGUUGGCGCCACAU--CGGGGGCACAGGUGUGUCCCCAGGCA
((.--.((((((((((-.((.(((((.(..(((....((((....))))(((((.....))))).)))..).)))))..)).))).))))))--)((((((((....))))))))..)). ( -53.00)
>DroSec_CAF1 12011 115 - 1
GCG--GGAUGUGGGCC-CACAUUCCUCCCGUGAAAUGGGCAAUUUUGUUGGCCCAUAAAGGGCCAUCGUAAUGGGAAAAGUUGGCGCCACAU--CGGGGGCACAGGUGUGUCCCAAGGCA
((.--.((((((((((-.((.((((((((((...)))))..(((.((.((((((.....)))))).)).))))))))..)).))).))))))--).(((((((....)))))))...)). ( -54.10)
>DroSim_CAF1 9469 115 - 1
GCG--GGGUGUGGGCC-CACAUUCCUCCCGUGAAAUGGGCAAUUUUGUUGGCCCAUAAAGGGCCAUCNNNNNNNNNNNNNNNNNNNNNNNNN--NNNNNNNNNNNNNNNNNNNNNNNNNN
..(--(((((((....-)))))))).(((((...))))).........((((((.....))))))...........................--.......................... ( -27.20)
>DroEre_CAF1 9531 115 - 1
GCG--GGGUGUGGGCC-CACAUUCCUGCCAUGAAAUGGGCAAUUUUGUUGGCCCAUA-AGGGCCAUCGUUAUGCGAAAAGUUGGCGCCACAUGCCGGGGGCACAGGUGUGUC-CCAGGCA
(((--(.(((((((((-.((.....((((........)))).((((((((((((...-.)))))).......)))))).)).))).)))))).)).(((((((....)))))-))..)). ( -55.31)
>DroWil_CAF1 12444 102 - 1
CCC--AAGGGUAGG-------------GCCAGGAAUGGGCAAUUUUGUUGGCCCAUUAAAGGCCAUAAUAAUGGGAAAAGUUAGAGUUCCAG--A-AGUUCGCAGGUGUGUCCUUAUGCA
(((--(....((.(-------------(((...(((((((..........)))))))...)))).))....))))..............((.--(-((..(((....)))..))).)).. ( -29.70)
>DroYak_CAF1 9344 118 - 1
GCGUUGGGUGUGGGCCUCACAUUCCUCGCCUGAAAUGGACAAUUUUGUUGGCCCAUAAAGGGCCAUCGUAAUGGGAAAAGUUGGCGCCACAU--UGGGGGCACAGGUGUGUCCCCAGGCA
((....((((((((((.....(((((.(((......)).).(((.((.((((((.....)))))).)).)))))))).....))).))))))--)((((((((....))))))))..)). ( -52.10)
>consensus
GCG__GGGUGUGGGCC_CACAUUCCUCCCGUGAAAUGGGCAAUUUUGUUGGCCCAUAAAGGGCCAUCGUAAUGGGAAAAGUUGGCGCCACAU__CGGGGGCACAGGUGUGUCCCCAGGCA
.......(((((((((...............(((((.....)))))..((((((.....)))))).................))).))))))....(((((((....)))))))...... (-20.23 = -22.67 +   2.44) 

alignment

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secondary structure

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dotplot

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Window 8

Location 2,697,203 – 2,697,317
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.84
Mean single sequence MFE -33.62
Consensus MFE -16.80
Energy contribution -18.61
Covariance contribution 1.81
Combinations/Pair 1.14
Mean z-score -2.32
Structure conservation index 0.50
SVM decision value 1.18
SVM RNA-class probability 0.926942
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2697203 114 + 20766785
CUUUUCCCAUUACGAUAGCCCUUUAUGGGCCAACAAAAUUGCCCAUUUCACGAGAGGAAUGCG-GGCCCACACCC--CGCA---ACCCCCAUAAUGCUUAAUGGCGCGCAAAUGUGGGCC
.................((((.....))))..........((((((....((.(.((..((((-((.......))--))))---..)).).....(((....))).)).....)))))). ( -32.70)
>DroSec_CAF1 12049 114 + 1
CUUUUCCCAUUACGAUGGCCCUUUAUGGGCCAACAAAAUUGCCCAUUUCACGGGAGGAAUGUG-GGCCCACAUCC--CGCA---ACCCUCAUAAUGCUUAAUGGCGCGCAAAUGUUGGCC
......((((....)))).........((((((((....((((((((...((.((((..((((-((.......))--))))---..))))....))...))))).)))....)))))))) ( -38.20)
>DroSim_CAF1 9507 114 + 1
NNNNNNNNNNNNNGAUGGCCCUUUAUGGGCCAACAAAAUUGCCCAUUUCACGGGAGGAAUGUG-GGCCCACACCC--CGCA---ACCCCCAUAAUGCUUAAUGGCGCGCAAAUGCUGGCC
...............((((((.....))))))........(((((((((.((((.((..((((-((.......))--))))---.))))).....(((....)))).).)))))..))). ( -36.50)
>DroEre_CAF1 9570 113 + 1
CUUUUCGCAUAACGAUGGCCCU-UAUGGGCCAACAAAAUUGCCCAUUUCAUGGCAGGAAUGUG-GGCCCACACCC--CGCA---ACCCCCAUAAUGCUUAAUGGCGCGCAAAUGUUGGUC
......((.....(.((((((.-...)))))).)......(((((((....((((((..((((-((.......))--))))---..))......)))).))))).))))........... ( -35.80)
>DroWil_CAF1 12481 95 + 1
CUUUUCCCAUUAUUAUGGCCUUUAAUGGGCCAACAAAAUUGCCCAUUCCUGGC-------------CCUACCCUU--GGGGAGGACAUCU-AAAUGUU---------CCAAAUGUUGCUU
...((((((....((.((((...(((((((..........)))))))...)))-------------).))....)--)))))((((((..-..)))))---------)............ ( -29.40)
>DroYak_CAF1 9382 117 + 1
CUUUUCCCAUUACGAUGGCCCUUUAUGGGCCAACAAAAUUGUCCAUUUCAGGCGAGGAAUGUGAGGCCCACACCCAACGCA---ACUUCUAUAAUGUUUAAUGGCGCGCAAAUGUUGGCC
...((((......(.((((((.....)))))).)....(((((.......))))))))).....((((.(((.....(((.---....((((........)))).)))....))).)))) ( -29.10)
>consensus
CUUUUCCCAUUACGAUGGCCCUUUAUGGGCCAACAAAAUUGCCCAUUUCACGGGAGGAAUGUG_GGCCCACACCC__CGCA___ACCCCCAUAAUGCUUAAUGGCGCGCAAAUGUUGGCC
...............((((((.....))))))...........((((((......))))))...((((.(((.....(((.........................)))....))).)))) (-16.80 = -18.61 +   1.81) 

alignment

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secondary structure

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dotplot

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Window 9

Location 2,697,203 – 2,697,317
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.84
Mean single sequence MFE -39.18
Consensus MFE -19.08
Energy contribution -19.97
Covariance contribution 0.88
Combinations/Pair 1.30
Mean z-score -2.18
Structure conservation index 0.49
SVM decision value 0.81
SVM RNA-class probability 0.856683
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2697203 114 - 20766785
GGCCCACAUUUGCGCGCCAUUAAGCAUUAUGGGGGU---UGCG--GGGUGUGGGCC-CGCAUUCCUCUCGUGAAAUGGGCAAUUUUGUUGGCCCAUAAAGGGCUAUCGUAAUGGGAAAAG
..((((...((((((.(((((...(((...((((..---((((--((.......))-))))..))))..))).)))))))......(.((((((.....)))))).)))))))))..... ( -45.30)
>DroSec_CAF1 12049 114 - 1
GGCCAACAUUUGCGCGCCAUUAAGCAUUAUGAGGGU---UGCG--GGAUGUGGGCC-CACAUUCCUCCCGUGAAAUGGGCAAUUUUGUUGGCCCAUAAAGGGCCAUCGUAAUGGGAAAAG
((((.........).)))......((((((((((((---((((--(((((((....-))))))))..((((...)))))))))))...((((((.....))))))))))))))....... ( -42.40)
>DroSim_CAF1 9507 114 - 1
GGCCAGCAUUUGCGCGCCAUUAAGCAUUAUGGGGGU---UGCG--GGGUGUGGGCC-CACAUUCCUCCCGUGAAAUGGGCAAUUUUGUUGGCCCAUAAAGGGCCAUCNNNNNNNNNNNNN
.(((..(((((.(((.((((........))))(((.---...(--(((((((....-)))))))).))))))))))))))........((((((.....))))))............... ( -41.40)
>DroEre_CAF1 9570 113 - 1
GACCAACAUUUGCGCGCCAUUAAGCAUUAUGGGGGU---UGCG--GGGUGUGGGCC-CACAUUCCUGCCAUGAAAUGGGCAAUUUUGUUGGCCCAUA-AGGGCCAUCGUUAUGCGAAAAG
((((..(((.(((..........)))..)))..)))---)(((--(((((((....-))))))))((((........))))((..((.((((((...-.)))))).))..))))...... ( -41.50)
>DroWil_CAF1 12481 95 - 1
AAGCAACAUUUGG---------AACAUUU-AGAUGUCCUCCCC--AAGGGUAGG-------------GCCAGGAAUGGGCAAUUUUGUUGGCCCAUUAAAGGCCAUAAUAAUGGGAAAAG
.....((((((((---------(...)))-))))))....(((--(....((.(-------------(((...(((((((..........)))))))...)))).))....))))..... ( -28.90)
>DroYak_CAF1 9382 117 - 1
GGCCAACAUUUGCGCGCCAUUAAACAUUAUAGAAGU---UGCGUUGGGUGUGGGCCUCACAUUCCUCGCCUGAAAUGGACAAUUUUGUUGGCCCAUAAAGGGCCAUCGUAAUGGGAAAAG
((((.((((..(.((((.(((............)))---.)))))..)))).)))).....(((((.(((......)).).(((.((.((((((.....)))))).)).))))))))... ( -35.60)
>consensus
GGCCAACAUUUGCGCGCCAUUAAGCAUUAUGGGGGU___UGCG__GGGUGUGGGCC_CACAUUCCUCCCGUGAAAUGGGCAAUUUUGUUGGCCCAUAAAGGGCCAUCGUAAUGGGAAAAG
((((.(((((((((.(((.(((.......))).)))...)))...)))))).))))...............(((((.....)))))..((((((.....))))))............... (-19.08 = -19.97 +   0.88) 

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 09:39:48 2006