Locus 1006

Sequence ID 2L_DroMel_CAF1
Location 2,892,553 – 2,892,810
Length 257
Max. P 0.999393
window1610 window1611 window1612 window1613 window1614

overview

Window 0

Location 2,892,553 – 2,892,650
Length 97
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 91.18
Mean single sequence MFE -25.42
Consensus MFE -21.06
Energy contribution -21.26
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -3.38
Structure conservation index 0.83
SVM decision value 3.57
SVM RNA-class probability 0.999393
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2892553 97 + 22407834
ACGUGUGCGACACUCUCAACAAACUGAUAAAAUUUUAAUUUCUCCAAAAUUGAAAUUUUAAUGUGUGUCUAGAUCGCGGUUUACCCCCGUUCAG-------CAC
....(((((((((.((((......)))((((((((((((((.....))))))))))))))..).)))))..((.((.((......)))).)).)-------))) ( -24.40)
>DroSec_CAF1 11243 97 + 1
ACGUGUGCGACACUCUCAACAAACUGAUAAAAUUUUAAUUUCUCCAAAAUUGAAAUUUUAAUGUGUGUCUAGAGCGCGGUUUACCCCCGUUCAG-------CAC
....(((((((((.((((......)))((((((((((((((.....))))))))))))))..).)))))..(((((.((......))))))).)-------))) ( -28.50)
>DroSim_CAF1 11551 97 + 1
ACGUGUGCGACACUCUCAACAAACUGAUAAAAUUUUAAUUUCUCCAAAAUUGAAAUUUUAAUGUGUGUCUAGAGCGCGGUUUACCCCCGUUCAG-------CAC
....(((((((((.((((......)))((((((((((((((.....))))))))))))))..).)))))..(((((.((......))))))).)-------))) ( -28.50)
>DroEre_CAF1 11490 87 + 1
ACGUGUGCGACACUCUCAACAAACUGAUAAAAUUUUAAUUUCUCCAAAAUUGAAAUUUUAAUGUGUGUCUAGAGCGCGGUUUACCU-----------------C
.(((((..(((((.((((......)))((((((((((((((.....))))))))))))))..).)))))....)))))........-----------------. ( -21.80)
>DroYak_CAF1 11589 104 + 1
ACGUGUGCGACACUCUCAACAAACUGAUAAAAUUUUAAUUUCUCCAAAAUUGAAAUUUUAAUGUGUGUCUAGAGCGCGGUUUACCCCUGUUCCAAGGCUCCCCC
.(((((..(((((.((((......)))((((((((((((((.....))))))))))))))..).)))))....))))).......(((......)))....... ( -23.90)
>consensus
ACGUGUGCGACACUCUCAACAAACUGAUAAAAUUUUAAUUUCUCCAAAAUUGAAAUUUUAAUGUGUGUCUAGAGCGCGGUUUACCCCCGUUCAG_______CAC
.(((((..(((((.((((......)))((((((((((((((.....))))))))))))))..).)))))....))))).......................... (-21.06 = -21.26 +   0.20)

alignment

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secondary structure

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Window 1

Location 2,892,553 – 2,892,650
Length 97
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 91.18
Mean single sequence MFE -25.68
Consensus MFE -19.32
Energy contribution -19.52
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.08
Structure conservation index 0.75
SVM decision value 0.70
SVM RNA-class probability 0.827062
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2892553 97 - 22407834
GUG-------CUGAACGGGGGUAAACCGCGAUCUAGACACACAUUAAAAUUUCAAUUUUGGAGAAAUUAAAAUUUUAUCAGUUUGUUGAGAGUGUCGCACACGU
(((-------(.((.((.((.....)).)).))..(((((....((((((((.((((((...)))))).))))))))((((....))))..))))))))).... ( -26.00)
>DroSec_CAF1 11243 97 - 1
GUG-------CUGAACGGGGGUAAACCGCGCUCUAGACACACAUUAAAAUUUCAAUUUUGGAGAAAUUAAAAUUUUAUCAGUUUGUUGAGAGUGUCGCACACGU
(((-------(......((......))(((((((.((((.((..((((((((.((((((...)))))).))))))))...)).)))).))))))).)))).... ( -27.40)
>DroSim_CAF1 11551 97 - 1
GUG-------CUGAACGGGGGUAAACCGCGCUCUAGACACACAUUAAAAUUUCAAUUUUGGAGAAAUUAAAAUUUUAUCAGUUUGUUGAGAGUGUCGCACACGU
(((-------(......((......))(((((((.((((.((..((((((((.((((((...)))))).))))))))...)).)))).))))))).)))).... ( -27.40)
>DroEre_CAF1 11490 87 - 1
G-----------------AGGUAAACCGCGCUCUAGACACACAUUAAAAUUUCAAUUUUGGAGAAAUUAAAAUUUUAUCAGUUUGUUGAGAGUGUCGCACACGU
.-----------------.((....))(((((((.((((.((..((((((((.((((((...)))))).))))))))...)).)))).)))))))......... ( -20.60)
>DroYak_CAF1 11589 104 - 1
GGGGGAGCCUUGGAACAGGGGUAAACCGCGCUCUAGACACACAUUAAAAUUUCAAUUUUGGAGAAAUUAAAAUUUUAUCAGUUUGUUGAGAGUGUCGCACACGU
((...(.(((((...))))).)...))(((((((.((((.((..((((((((.((((((...)))))).))))))))...)).)))).)))))))......... ( -27.00)
>consensus
GUG_______CUGAACGGGGGUAAACCGCGCUCUAGACACACAUUAAAAUUUCAAUUUUGGAGAAAUUAAAAUUUUAUCAGUUUGUUGAGAGUGUCGCACACGU
...................((....))(((((((.((((.((..((((((((.((((((...)))))).))))))))...)).)))).)))))))......... (-19.32 = -19.52 +   0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,892,650 – 2,892,770
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.61
Mean single sequence MFE -26.04
Consensus MFE -19.40
Energy contribution -19.28
Covariance contribution -0.12
Combinations/Pair 1.09
Mean z-score -2.11
Structure conservation index 0.75
SVM decision value 0.93
SVM RNA-class probability 0.884136
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2892650 120 + 22407834
CCCUUUUAUCCACCAACUCGACUGCACUUUGUGUUCUCCUCCUCCUCCUCCUGCUGCCUGGUUUUCCCACCUUGCCGGGAAAAUGUGCUGCUACACCCUAUGUGUGGCACUUCGCCAUAC
...................((..((((...))))..))..............((.((...((((((((........))))))))..)).))..........(((((((.....))))))) ( -25.90)
>DroSec_CAF1 11340 111 + 1
CCCUUUUACCCACCAACUCGACUGCACUUUGUGUCCGCCUCCUCCU---G------CCUGGUUUUCCCACCUUGCCGGGAAAAUGUGCUGCUACACCCUAUGUGUGGCACUCCGCCAUAC
.......................((((.........((........---)------)...((((((((........))))))))))))((((((((.....))))))))........... ( -25.20)
>DroSim_CAF1 11648 115 + 1
CCCUUUUACCCACCAACUCGACUGCACUUUGUGUCCGCCUCCUCCU---CCUGC--CCUGGUUUUCCCACCUUGCCGGGAAAAUGUGCUGCUACACCCUAUGUGUGGCACUCCGCCAUAC
.......................((((...((....))........---.....--....((((((((........))))))))))))((((((((.....))))))))........... ( -24.40)
>DroEre_CAF1 11577 103 + 1
CCUACUUUCCCUCCAUUUCGACUGCACUUUGUGUCCACC-----CU---G------CCAGGUUUUCCCACCUUGCCGAGAAAAUGUG---CUACACCCUAUGUGUGGCACUCCGCCAUGC
...............(((((...((((...)))).....-----..---(------(.((((......)))).)))))))....(((---((((((.....))))))))).......... ( -24.10)
>DroYak_CAF1 11693 103 + 1
CCCUUUUUCCCUGCAUUUCGACUGCACUUUGUGUCCUCC-----CU---G------CCCGGUUUUCCCACCUUGCCGGGAAAAUGUG---CUACACCCAAUGUGUGGCACUCCGCCAUAC
....(((((((.(((....((..((((...))))..)).-----..---.------...(((......))).))).))))))).(((---((((((.....))))))))).......... ( -30.60)
>consensus
CCCUUUUACCCACCAACUCGACUGCACUUUGUGUCCGCCUCCUCCU___G______CCUGGUUUUCCCACCUUGCCGGGAAAAUGUGCUGCUACACCCUAUGUGUGGCACUCCGCCAUAC
...................(((.((.....))))).........................((((((((........))))))))(((......))).....(((((((.....))))))) (-19.40 = -19.28 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,892,690 – 2,892,810
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.66
Mean single sequence MFE -35.46
Consensus MFE -28.84
Energy contribution -28.88
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -2.12
Structure conservation index 0.81
SVM decision value 1.61
SVM RNA-class probability 0.967671
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2892690 120 + 22407834
CCUCCUCCUCCUGCUGCCUGGUUUUCCCACCUUGCCGGGAAAAUGUGCUGCUACACCCUAUGUGUGGCACUUCGCCAUACACGCGCACAAGUUUUGGGUUUUUGCGGGUUUCCCCAACCC
.........(((((.(((..((((((((........)))))))(((((((((((((.....))))))))....((.......)))))))....)..)))....)))))............ ( -39.30)
>DroSec_CAF1 11380 111 + 1
CCUCCU---G------CCUGGUUUUCCCACCUUGCCGGGAAAAUGUGCUGCUACACCCUAUGUGUGGCACUCCGCCAUACACGCGCACAAGUUUUGGGUUUUUGCGGGUUUCCCCAACCC
......---(------((..((((((((........)))))))(((((((((((((.....))))))))....((.......)))))))....)..)))......(((((.....))))) ( -35.30)
>DroSim_CAF1 11688 115 + 1
CCUCCU---CCUGC--CCUGGUUUUCCCACCUUGCCGGGAAAAUGUGCUGCUACACCCUAUGUGUGGCACUCCGCCAUACACGCGCACAAGUUUUGGGUUUUUGCGGGUUUCCCCAACCC
......---...((--((..((((((((........))))))))((((((((((((.....))))))))....((.......)))))).......))))......(((((.....))))) ( -36.70)
>DroEre_CAF1 11616 104 + 1
----CU---G------CCAGGUUUUCCCACCUUGCCGAGAAAAUGUG---CUACACCCUAUGUGUGGCACUCCGCCAUGCACGCGCACAAGUUUUGGGUUUUUGCGGGUUUCCCCAACCC
----..---(------(.((((......)))).(((.((((..((((---(.........((((((((.....))))))))...)))))..)))).)))....))(((((.....))))) ( -29.70)
>DroYak_CAF1 11732 104 + 1
----CU---G------CCCGGUUUUCCCACCUUGCCGGGAAAAUGUG---CUACACCCAAUGUGUGGCACUCCGCCAUACACGCGCACAAGUUCUGGGUUUUUGCGGGUUUCCCCAACCC
----..---(------((((((((((((........)))))))((((---(.........((((((((.....))))))))...)))))....))))))......(((((.....))))) ( -36.30)
>consensus
CCUCCU___G______CCUGGUUUUCCCACCUUGCCGGGAAAAUGUGCUGCUACACCCUAUGUGUGGCACUCCGCCAUACACGCGCACAAGUUUUGGGUUUUUGCGGGUUUCCCCAACCC
....................((((((((........))))))))..........((((..((((((((.....)))))))).((......))...))))......(((((.....))))) (-28.84 = -28.88 +   0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,892,690 – 2,892,810
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.66
Mean single sequence MFE -43.14
Consensus MFE -35.64
Energy contribution -35.68
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -2.69
Structure conservation index 0.83
SVM decision value 2.78
SVM RNA-class probability 0.996963
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2892690 120 - 22407834
GGGUUGGGGAAACCCGCAAAAACCCAAAACUUGUGCGCGUGUAUGGCGAAGUGCCACACAUAGGGUGUAGCAGCACAUUUUCCCGGCAAGGUGGGAAAACCAGGCAGCAGGAGGAGGAGG
((((((((....))).....)))))....(((.(((((((((.((((.....)))).)))).((((((....)))).((((((((......))))))))))..)).))).)))....... ( -46.40)
>DroSec_CAF1 11380 111 - 1
GGGUUGGGGAAACCCGCAAAAACCCAAAACUUGUGCGCGUGUAUGGCGGAGUGCCACACAUAGGGUGUAGCAGCACAUUUUCCCGGCAAGGUGGGAAAACCAGG------C---AGGAGG
((((((((....))).....)))))....(((.(((..((((.((((.....)))).)))).((((((....)))).((((((((......))))))))))..)------)---).))). ( -44.40)
>DroSim_CAF1 11688 115 - 1
GGGUUGGGGAAACCCGCAAAAACCCAAAACUUGUGCGCGUGUAUGGCGGAGUGCCACACAUAGGGUGUAGCAGCACAUUUUCCCGGCAAGGUGGGAAAACCAGG--GCAGG---AGGAGG
((((((((....))).....)))))....(((.(((.(((((.((((.....)))).)))).((((((....)))).((((((((......)))))))))).).--))).)---)).... ( -46.30)
>DroEre_CAF1 11616 104 - 1
GGGUUGGGGAAACCCGCAAAAACCCAAAACUUGUGCGCGUGCAUGGCGGAGUGCCACACAUAGGGUGUAG---CACAUUUUCUCGGCAAGGUGGGAAAACCUGG------C---AG----
((((((((....))).......((((...(((((.(((.......)))..((((.((((.....)))).)---))).........))))).))))..)))))..------.---..---- ( -39.20)
>DroYak_CAF1 11732 104 - 1
GGGUUGGGGAAACCCGCAAAAACCCAGAACUUGUGCGCGUGUAUGGCGGAGUGCCACACAUUGGGUGUAG---CACAUUUUCCCGGCAAGGUGGGAAAACCGGG------C---AG----
((((((((....))).....)))))........(((.((.((........((((.((((.....)))).)---)))..(((((((......))))))))))).)------)---).---- ( -39.40)
>consensus
GGGUUGGGGAAACCCGCAAAAACCCAAAACUUGUGCGCGUGUAUGGCGGAGUGCCACACAUAGGGUGUAGCAGCACAUUUUCCCGGCAAGGUGGGAAAACCAGG______C___AGGAGG
.(((((((....))).......((((...(((((....((((.((((.....)))).)))).((((((......)))....))).))))).))))..))))................... (-35.64 = -35.68 +   0.04)

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 09:50:51 2006