Locus 4779

Sequence ID 2L_DroMel_CAF1
Location 13,651,161 – 13,651,462
Length 301
Max. P 0.995362
window7561 window7562 window7563 window7564 window7565 window7566

overview

Window 1

Location 13,651,161 – 13,651,263
Length 102
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 70.19
Mean single sequence MFE -24.93
Consensus MFE -15.34
Energy contribution -15.40
Covariance contribution 0.06
Combinations/Pair 1.40
Mean z-score -2.01
Structure conservation index 0.62
SVM decision value 2.21
SVM RNA-class probability 0.990411
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13651161 102 + 22407834
------UUUUGACAUUCUAUCCGAGUAUUCAUUGUGCAGCAGCAUACAACCACAUUUGCUGU------------GGUAGCUCUGGUUUAUGAAUGUUGAUAAAUAUUUACAAUUUUAAUA
------..(..((((((...((((((......(((((....)))))..((((((.....)))------------))).)))).)).....))))))..)..................... ( -25.90)
>DroPse_CAF1 19738 119 + 1
UCGAGCCUUUUAUAUUUAUUACGAAAUUCCAUUAUGCGCAUUCAUGCAUCUAAAUUUUUUUCCUUCAGGAGGGGAGGGGCUUUGGCUCAUGAAUGUUGAUAAAUAUUUCCAAU-UUAAUA
...........((((((((((.(......).......(((((((((...(((((.((((((((((....)))))))))).)))))..))))))))))))))))))).......-...... ( -25.10)
>DroSim_CAF1 16392 102 + 1
------CUUUGACAUUCUAUCCGAGUAUUCAUUGUGCAGCACCACACAACCACAUUUGCUGC------------GGUAGCUCUGGUUUAUGAAUGUUGAUAAAUAUUUACAAUUUUAAUA
------..(..((((((...(((.((((.....))))((((((.(((((......))).)).------------))).))).))).....))))))..)..................... ( -20.40)
>DroPer_CAF1 20063 119 + 1
UCAAGCCUUUUAUAUUUAUUACGAAAUUCCAUUAUGCGCAUUCAUGCAUCUAAAUUUUUUCCCUUCAGGAAGGGAGGGGCUUUGGCUCAUGAAUGUUGAUAAAUAUUUCCAAU-UUAAUA
...........((((((((((.(......).......(((((((((...(((((.((((((((((....)))))))))).)))))..))))))))))))))))))).......-...... ( -28.30)
>consensus
______CUUUGACAUUCAAUACGAAAAUCCAUUAUGCACAAUCAUACAACCAAAUUUGCUGC____________AGGAGCUCUGGCUCAUGAAUGUUGAUAAAUAUUUACAAU_UUAAUA
........(((((((((...............((((......)))).(((((((.((((((((((....)))))))))).)))))))...)))))))))..................... (-15.34 = -15.40 +   0.06)

alignment

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secondary structure

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Window 2

Location 13,651,263 – 13,651,382
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 79.94
Mean single sequence MFE -23.38
Consensus MFE -16.10
Energy contribution -16.85
Covariance contribution 0.75
Combinations/Pair 1.14
Mean z-score -2.42
Structure conservation index 0.69
SVM decision value 1.91
SVM RNA-class probability 0.982407
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13651263 119 - 22407834
AACAAAACUUUUGCGUUAA-AAACAGAAAAGUGUUUUGAGCUACUCGACACUAGGCAAAAAACGCCAGGAAAAGUGCAAAAAAAAAGUAAACACAGUCUGAAAGUAGCCAACUAAACUUU
......((((((..((...-..))..))))))...(((.((((((.(((.((.(((.......))).))....(((...............))).)))....)))))))))......... ( -19.66)
>DroPse_CAF1 19857 99 - 1
AACAAAACUUUCGCGUUAAAAAACAGAAAAGUGUUUUGUGCUCCUCGACACAA------------CAAGAGGAGUGCAGAAAAA---------UGGUCGGAGAGUGGCCAACUAAACUUU
........((((..(((....))).))))(((.(((((..((((((.......------------...))))))..)))))...---------((((((.....)))))))))....... ( -27.10)
>DroSim_CAF1 16494 119 - 1
AACAAAACUUUUGCGUUAA-AAACAGAAAAGUGUUUUGAGCUACUCGACACUAGGCAAAAAACGCCAGGAAAAGUGCAAAAAAAAAGUAAACACAGUCUGAAAGUAGCCAACUAAACUUU
......((((((..((...-..))..))))))...(((.((((((.(((.((.(((.......))).))....(((...............))).)))....)))))))))......... ( -19.66)
>DroPer_CAF1 20182 99 - 1
AACAAAACUUUCGCGUUAAAAAACAGAAAAGUGUUUUGUGCUCCUCGACACAA------------CAAGAGGAGUGCAGAAAAA---------UGGUCGGAGAGUGGCCAACUAAACUUU
........((((..(((....))).))))(((.(((((..((((((.......------------...))))))..)))))...---------((((((.....)))))))))....... ( -27.10)
>consensus
AACAAAACUUUCGCGUUAA_AAACAGAAAAGUGUUUUGAGCUACUCGACACAA____________CAAGAAAAGUGCAAAAAAA_________CAGUCGGAAAGUAGCCAACUAAACUUU
......((((((..(((....))).........(((((((((((((......................)))))))))))))..................))))))............... (-16.10 = -16.85 +   0.75)

alignment

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secondary structure

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Window 3

Location 13,651,303 – 13,651,422
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.29
Mean single sequence MFE -25.60
Consensus MFE -18.90
Energy contribution -18.90
Covariance contribution 0.00
Combinations/Pair 1.12
Mean z-score -1.96
Structure conservation index 0.74
SVM decision value 0.74
SVM RNA-class probability 0.837329
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13651303 119 + 22407834
UUUGCACUUUUCCUGGCGUUUUUUGCCUAGUGUCGAGUAGCUCAAAACACUUUUCUGUUU-UUAACGCAAAAGUUUUGUUAUGGAAAUGCAGCAAGUUCUUGGUACUUUUUCAUAUUUUU
...((((((..(((((((.....)))).)).)..)))).)).((((..((((((.(((..-...))).)))))))))).((((((((.(.(.(((....))).).).))))))))..... ( -22.10)
>DroPse_CAF1 19888 108 + 1
UCUGCACUCCUCUUG------------UUGUGUCGAGGAGCACAAAACACUUUUCUGUUUUUUAACGCGAAAGUUUUGUUAUGGAAAUGCGGCAAGUUUUUGCUACUUUUCCAUAUUUCU
......((((((...------------.......)))))).(((((((...((((((((....)))).)))))))))))((((((((.(..((((....))))..).))))))))..... ( -29.10)
>DroSim_CAF1 16534 119 + 1
UUUGCACUUUUCCUGGCGUUUUUUGCCUAGUGUCGAGUAGCUCAAAACACUUUUCUGUUU-UUAACGCAAAAGUUUUGUUAUGGAAAUGCAGCAAGUUCUUGGUACUUUUUCAUAUUUUU
...((((((..(((((((.....)))).)).)..)))).)).((((..((((((.(((..-...))).)))))))))).((((((((.(.(.(((....))).).).))))))))..... ( -22.10)
>DroPer_CAF1 20213 108 + 1
UCUGCACUCCUCUUG------------UUGUGUCGAGGAGCACAAAACACUUUUCUGUUUUUUAACGCGAAAGUUUUGUUAUGGAAAUGCGGCAAGUUUUUGCUACUUUUCCAUAUUUCU
......((((((...------------.......)))))).(((((((...((((((((....)))).)))))))))))((((((((.(..((((....))))..).))))))))..... ( -29.10)
>consensus
UCUGCACUCCUCCUG____________UAGUGUCGAGGAGCACAAAACACUUUUCUGUUU_UUAACGCAAAAGUUUUGUUAUGGAAAUGCAGCAAGUUCUUGCUACUUUUCCAUAUUUCU
......((((((......................))))))..((((..((((((.((((....)))).)))))))))).((((((((.(.(((((....))))).).))))))))..... (-18.90 = -18.90 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,651,303 – 13,651,422
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.29
Mean single sequence MFE -27.75
Consensus MFE -21.05
Energy contribution -24.30
Covariance contribution 3.25
Combinations/Pair 1.03
Mean z-score -3.72
Structure conservation index 0.76
SVM decision value 2.57
SVM RNA-class probability 0.995362
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13651303 119 - 22407834
AAAAAUAUGAAAAAGUACCAAGAACUUGCUGCAUUUCCAUAACAAAACUUUUGCGUUAA-AAACAGAAAAGUGUUUUGAGCUACUCGACACUAGGCAAAAAACGCCAGGAAAAGUGCAAA
.....((((.(((.(((.(((....))).))).))).)))).....((((((.(.....-.........((((((..(((...))))))))).(((.......))).).))))))..... ( -21.60)
>DroPse_CAF1 19888 108 - 1
AGAAAUAUGGAAAAGUAGCAAAAACUUGCCGCAUUUCCAUAACAAAACUUUCGCGUUAAAAAACAGAAAAGUGUUUUGUGCUCCUCGACACAA------------CAAGAGGAGUGCAGA
.....((((((((.(..((((....))))..).)))))))).....((((((..(((....))).).)))))..((((..((((((.......------------...))))))..)))) ( -33.90)
>DroSim_CAF1 16534 119 - 1
AAAAAUAUGAAAAAGUACCAAGAACUUGCUGCAUUUCCAUAACAAAACUUUUGCGUUAA-AAACAGAAAAGUGUUUUGAGCUACUCGACACUAGGCAAAAAACGCCAGGAAAAGUGCAAA
.....((((.(((.(((.(((....))).))).))).)))).....((((((.(.....-.........((((((..(((...))))))))).(((.......))).).))))))..... ( -21.60)
>DroPer_CAF1 20213 108 - 1
AGAAAUAUGGAAAAGUAGCAAAAACUUGCCGCAUUUCCAUAACAAAACUUUCGCGUUAAAAAACAGAAAAGUGUUUUGUGCUCCUCGACACAA------------CAAGAGGAGUGCAGA
.....((((((((.(..((((....))))..).)))))))).....((((((..(((....))).).)))))..((((..((((((.......------------...))))))..)))) ( -33.90)
>consensus
AAAAAUAUGAAAAAGUACCAAAAACUUGCCGCAUUUCCAUAACAAAACUUUCGCGUUAA_AAACAGAAAAGUGUUUUGAGCUACUCGACACAA____________CAAGAAAAGUGCAAA
.....((((((((.(((((((....))))))).)))))))).....((((((..(((....)))..))))))..((((((((((((......................)))))))))))) (-21.05 = -24.30 +   3.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,651,343 – 13,651,462
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.69
Mean single sequence MFE -17.64
Consensus MFE -15.85
Energy contribution -15.60
Covariance contribution -0.25
Combinations/Pair 1.10
Mean z-score -1.27
Structure conservation index 0.90
SVM decision value 0.10
SVM RNA-class probability 0.584749
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13651343 119 + 22407834
CUCAAAACACUUUUCUGUUU-UUAACGCAAAAGUUUUGUUAUGGAAAUGCAGCAAGUUCUUGGUACUUUUUCAUAUUUUUCUUCGUUCCAUGUCGCUACUUUUUUUGUAUCUAUUUCAUU
...((((((......)))))-)..(((.((((((..((.(((((((.((.((.(((....(((.......)))....))))).))))))))).))..))))))..)))............ ( -15.20)
>DroPse_CAF1 19916 111 + 1
CACAAAACACUUUUCUGUUUUUUAACGCGAAAGUUUUGUUAUGGAAAUGCGGCAAGUUUUUGCUACUUUUCCAUAUUUCUGCUAGAUUCCUUUUUU--UUUUUUUUGCCACCA-------
.(((((((...((((((((....)))).)))))))))))((((((((.(..((((....))))..).)))))))).....................--...............------- ( -21.00)
>DroSim_CAF1 16574 119 + 1
CUCAAAACACUUUUCUGUUU-UUAACGCAAAAGUUUUGUUAUGGAAAUGCAGCAAGUUCUUGGUACUUUUUCAUAUUUUUCUUCGCUUCAUGUCGCUACUUUUUUUGUAUCUAUUUCAUU
...((((((......)))))-)....(((((((......((((((((.(.(.(((....))).).).)))))))).........((........)).....)))))))............ ( -13.30)
>DroPer_CAF1 20241 111 + 1
CACAAAACACUUUUCUGUUUUUUAACGCGAAAGUUUUGUUAUGGAAAUGCGGCAAGUUUUUGCUACUUUUCCAUAUUUCUGCUGGAUUCCUUUUAU--UUUUUUUUGCCACCA-------
.(((((((...((((((((....)))).)))))))))))((((((((.(..((((....))))..).)))))))).....(.(((...........--.........))).).------- ( -21.05)
>consensus
CACAAAACACUUUUCUGUUU_UUAACGCAAAAGUUUUGUUAUGGAAAUGCAGCAAGUUCUUGCUACUUUUCCAUAUUUCUCCUCGAUUCAUGUCGC__CUUUUUUUGCAACCA_______
..(((((.((((((.((((....)))).)))))).....((((((((.(.(((((....))))).).))))))))...........................)))))............. (-15.85 = -15.60 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,651,343 – 13,651,462
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.69
Mean single sequence MFE -18.88
Consensus MFE -15.65
Energy contribution -16.90
Covariance contribution 1.25
Combinations/Pair 1.04
Mean z-score -1.70
Structure conservation index 0.83
SVM decision value 0.58
SVM RNA-class probability 0.789544
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13651343 119 - 22407834
AAUGAAAUAGAUACAAAAAAAGUAGCGACAUGGAACGAAGAAAAAUAUGAAAAAGUACCAAGAACUUGCUGCAUUUCCAUAACAAAACUUUUGCGUUAA-AAACAGAAAAGUGUUUUGAG
.............(((((...((((((((.(((.((..................)).))).)...)))))))..............((((((..((...-..))..)))))).))))).. ( -15.37)
>DroPse_CAF1 19916 111 - 1
-------UGGUGGCAAAAAAAA--AAAAAAGGAAUCUAGCAGAAAUAUGGAAAAGUAGCAAAAACUUGCCGCAUUUCCAUAACAAAACUUUCGCGUUAAAAAACAGAAAAGUGUUUUGUG
-------...............--.....................((((((((.(..((((....))))..).))))))))(((((((((((..(((....))).))))...))))))). ( -22.30)
>DroSim_CAF1 16574 119 - 1
AAUGAAAUAGAUACAAAAAAAGUAGCGACAUGAAGCGAAGAAAAAUAUGAAAAAGUACCAAGAACUUGCUGCAUUUCCAUAACAAAACUUUUGCGUUAA-AAACAGAAAAGUGUUUUGAG
........((((((...((((((.((........)).........((((.(((.(((.(((....))).))).))).)))).....))))))..((...-..))......)))))).... ( -13.50)
>DroPer_CAF1 20241 111 - 1
-------UGGUGGCAAAAAAAA--AUAAAAGGAAUCCAGCAGAAAUAUGGAAAAGUAGCAAAAACUUGCCGCAUUUCCAUAACAAAACUUUCGCGUUAAAAAACAGAAAAGUGUUUUGUG
-------((.(((.........--...........))).))....((((((((.(..((((....))))..).))))))))(((((((((((..(((....))).))))...))))))). ( -24.35)
>consensus
_______UAGAGACAAAAAAAA__ACAAAAGGAAUCGAACAAAAAUAUGAAAAAGUACCAAAAACUUGCCGCAUUUCCAUAACAAAACUUUCGCGUUAA_AAACAGAAAAGUGUUUUGAG
.............................................((((((((.(((((((....))))))).)))))))).((((((((((..(((....))).))))...)))))).. (-15.65 = -16.90 +   1.25)

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 11:27:10 2006