Locus 7371

Sequence ID 2L_DroMel_CAF1
Location 20,528,424 – 20,528,623
Length 199
Max. P 0.978969
window11839 window11840 window11841 window11842

overview

Window 9

Location 20,528,424 – 20,528,544
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.33
Mean single sequence MFE -22.44
Consensus MFE -18.39
Energy contribution -19.59
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -1.40
Structure conservation index 0.82
SVM decision value 0.19
SVM RNA-class probability 0.626076
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20528424 120 + 22407834
AAAUUUGAAGGCAAUGAAGGCCGAUCAUAAAAAGCAGUAAUAAAAAUGGCGGCCAUAUUUUAAAUGGAAUGUACAAUCCCACAUAUUUUAUAAUGCCAGUGCCCGUGAAAAAUGCACCUC
.........((((.....(((((.((((.................))))))))).........(((((((((..........)))))))))..)))).((((...(....)..))))... ( -24.53)
>DroSec_CAF1 49709 120 + 1
AAAUUUGAAGGCAAUGAAGGCCGAUCAUAAAAAGCAGUAAUAAAAAUGGCGGCCAUAUUUUAAAUGGAAUGUACAAUGCCACAUAUUUUAUAAUGCCAGUGCACGAAAAAAAUGCACCUC
.........((((.((..(((((.((((.................)))))))))(((((((....))))))).)).))))..................(((((.........)))))... ( -25.33)
>DroSim_CAF1 51012 120 + 1
AAAUUUGAAGGCAAUGAAGGCCAAUCAUAAAAAGCAGUAAUAAAAAUGGCGGCCAUAUUUUAAAUGGAAUGUACAAUGCCACAUAUUUUAUAAUGCCAGUGCACGUAAAAAAUGCACCUC
.........((((.((..((((..((((.................)))).))))(((((((....))))))).)).)))).(((.((((((..(((....))).)))))).)))...... ( -21.33)
>DroEre_CAF1 42833 120 + 1
AAAUUUGAAGGCAAAUAAGGCCGAUCACAAAAAGCAGUAAUAAUAAUGGCGGCCAUAAUUUAAAUGGAAUGUACAAUCCCACAUAUUUUAUAAUGCCAGCGCACGUAAAAAACGCACCUC
.........((((.....(((((.(((...................))))))))((((..((..(((.((.....)).)))..))..))))..)))).(((...........)))..... ( -21.61)
>DroYak_CAF1 45108 120 + 1
AAAUUGGAAGGCAAAUAAGAGCGAUCACAAAAAGAGGUUAUACAAAUGGCGGCCAUAUAUUAAAUGGAAUGUACAAUCCAACAUAUUUUAUAAUGCCAGUGCACGUAAAAAAUGCACCUC
...(((((..((........))..)).)))...(((((........(((((.((((.......)))).((((........)))).........)))))..(((.........)))))))) ( -19.40)
>consensus
AAAUUUGAAGGCAAUGAAGGCCGAUCAUAAAAAGCAGUAAUAAAAAUGGCGGCCAUAUUUUAAAUGGAAUGUACAAUCCCACAUAUUUUAUAAUGCCAGUGCACGUAAAAAAUGCACCUC
.........((((.....(((((.((((.................))))))))).........(((((((((..........)))))))))..)))).((((...........))))... (-18.39 = -19.59 +   1.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,528,424 – 20,528,544
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.33
Mean single sequence MFE -25.76
Consensus MFE -21.67
Energy contribution -21.83
Covariance contribution 0.16
Combinations/Pair 1.18
Mean z-score -1.46
Structure conservation index 0.84
SVM decision value 0.56
SVM RNA-class probability 0.782999
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20528424 120 - 22407834
GAGGUGCAUUUUUCACGGGCACUGGCAUUAUAAAAUAUGUGGGAUUGUACAUUCCAUUUAAAAUAUGGCCGCCAUUUUUAUUACUGCUUUUUAUGAUCGGCCUUCAUUGCCUUCAAAUUU
..(((((...........)))))((((........((.(((((((.....))))))).))......(((((.(((.................)))..))))).....))))......... ( -24.53)
>DroSec_CAF1 49709 120 - 1
GAGGUGCAUUUUUUUCGUGCACUGGCAUUAUAAAAUAUGUGGCAUUGUACAUUCCAUUUAAAAUAUGGCCGCCAUUUUUAUUACUGCUUUUUAUGAUCGGCCUUCAUUGCCUUCAAAUUU
((((.(((........(((((.((.(((..........))).)).)))))................(((((.(((.................)))..))))).....)))))))...... ( -25.93)
>DroSim_CAF1 51012 120 - 1
GAGGUGCAUUUUUUACGUGCACUGGCAUUAUAAAAUAUGUGGCAUUGUACAUUCCAUUUAAAAUAUGGCCGCCAUUUUUAUUACUGCUUUUUAUGAUUGGCCUUCAUUGCCUUCAAAUUU
..(((((((.......)))))))((((..((((((...(((((..(((..............)))..)))))...))))))...)))).....(((..(((.......))).)))..... ( -25.04)
>DroEre_CAF1 42833 120 - 1
GAGGUGCGUUUUUUACGUGCGCUGGCAUUAUAAAAUAUGUGGGAUUGUACAUUCCAUUUAAAUUAUGGCCGCCAUUAUUAUUACUGCUUUUUGUGAUCGGCCUUAUUUGCCUUCAAAUUU
.(((..(((.....)))..).))((((..((((..((.(((((((.....))))))).))......(((((........(((((........)))))))))))))).))))......... ( -29.10)
>DroYak_CAF1 45108 120 - 1
GAGGUGCAUUUUUUACGUGCACUGGCAUUAUAAAAUAUGUUGGAUUGUACAUUCCAUUUAAUAUAUGGCCGCCAUUUGUAUAACCUCUUUUUGUGAUCGCUCUUAUUUGCCUUCCAAUUU
(((((((((.......))))..((((........(((((((((((.(......).)))))))))))....))))........)))))...(((.((..((........))..)))))... ( -24.20)
>consensus
GAGGUGCAUUUUUUACGUGCACUGGCAUUAUAAAAUAUGUGGGAUUGUACAUUCCAUUUAAAAUAUGGCCGCCAUUUUUAUUACUGCUUUUUAUGAUCGGCCUUCAUUGCCUUCAAAUUU
..(((((((.......)))))))((((........((.(((((((.....))))))).))......(((((.(((.................)))..))))).....))))......... (-21.67 = -21.83 +   0.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,528,464 – 20,528,583
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 92.86
Mean single sequence MFE -26.49
Consensus MFE -20.64
Energy contribution -21.32
Covariance contribution 0.68
Combinations/Pair 1.03
Mean z-score -2.04
Structure conservation index 0.78
SVM decision value 0.91
SVM RNA-class probability 0.880415
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20528464 119 - 22407834
GCGAAAAAAAACACAUACUUCUGUUGAUUUAAUUAAACAGAGGUGCAUUUUUCACGGGCACUGGCAUUAUAAAAUAUGUGGGAUUGUACAUUCCAUUUAAAAUAUGGCCGCCAUUUUUA
(.((((((.......((((((((((..........))))))))))..)))))).).(((...(((............(((((((.....)))))))..........))))))....... ( -26.15)
>DroSec_CAF1 49749 116 - 1
CUGAA---AAACACAUACUUCUGUUGAUUUAAUUAAACAGAGGUGCAUUUUUUUCGUGCACUGGCAUUAUAAAAUAUGUGGCAUUGUACAUUCCAUUUAAAAUAUGGCCGCCAUUUUUA
..(((---(((....((((((((((..........))))))))))....))))))(((((.((.(((..........))).)).)))))...((((.......))))............ ( -26.50)
>DroSim_CAF1 51052 116 - 1
CUGAA---AAACACAUACUUCUGUUGAUUUAAUUAAACAGAGGUGCAUUUUUUACGUGCACUGGCAUUAUAAAAUAUGUGGCAUUGUACAUUCCAUUUAAAAUAUGGCCGCCAUUUUUA
.((((---(((....((((((((((..........))))))))))..))))))).(((((.((.(((..........))).)).)))))...((((.......))))............ ( -24.10)
>DroEre_CAF1 42873 117 - 1
CUGGAA--AAACACAUACUUCUGUUGAUUUAAUUAAACAGAGGUGCGUUUUUUACGUGCGCUGGCAUUAUAAAAUAUGUGGGAUUGUACAUUCCAUUUAAAUUAUGGCCGCCAUUAUUA
...(((--((((...((((((((((..........)))))))))).)))))))..(((.((.(((..(((((..((.(((((((.....))))))).))..)))))))))))))..... ( -29.40)
>DroYak_CAF1 45148 116 - 1
CUAAAA---AAAACAUACUUCUGUUGAUUUAAUUAAACAGAGGUGCAUUUUUUACGUGCACUGGCAUUAUAAAAUAUGUUGGAUUGUACAUUCCAUUUAAUAUAUGGCCGCCAUUUGUA
....((---((((..((((((((((..........))))))))))..))))))..((((((..((((........))))..)..)))))..........(((.((((...)))).))). ( -26.30)
>consensus
CUGAAA__AAACACAUACUUCUGUUGAUUUAAUUAAACAGAGGUGCAUUUUUUACGUGCACUGGCAUUAUAAAAUAUGUGGGAUUGUACAUUCCAUUUAAAAUAUGGCCGCCAUUUUUA
................(((((((((..........)))))))))((((.......))))..((((.(((((......(((((((.....)))))))......)))))..))))...... (-20.64 = -21.32 +   0.68)

alignment

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secondary structure

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Window 2

Location 20,528,504 – 20,528,623
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 93.03
Mean single sequence MFE -27.60
Consensus MFE -22.78
Energy contribution -23.66
Covariance contribution 0.88
Combinations/Pair 1.06
Mean z-score -2.12
Structure conservation index 0.83
SVM decision value 1.83
SVM RNA-class probability 0.978969
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20528504 119 - 22407834
AUAUUUAUUGGGUAAAAUAUGUUGUCGCAUUAUGAAUGCGGCGAAAAAAAACACAUACUUCUGUUGAUUUAAUUAAACAGAGGUGCAUUUUUCACGGGCACUGGCAUUAUAAAAUAUGU
((((((.....((.(((.((((((((((((.....)))))))))...........((((((((((..........))))))))))))).))).))..((....))......)))))).. ( -25.90)
>DroSec_CAF1 49789 116 - 1
AUAUUUAUUGGGUAAAAUAUGCUGUCGCAUUAUGAAUGCGCUGAA---AAACACAUACUUCUGUUGAUUUAAUUAAACAGAGGUGCAUUUUUUUCGUGCACUGGCAUUAUAAAAUAUGU
.................((((.((((((((.....))))((((((---(((....((((((((((..........))))))))))....))))))).))...)))).))))........ ( -26.70)
>DroSim_CAF1 51092 116 - 1
AUAUUUAUUGGGUAAAAUAUGCUGUCGCAUUAUGAAUGCGCUGAA---AAACACAUACUUCUGUUGAUUUAAUUAAACAGAGGUGCAUUUUUUACGUGCACUGGCAUUAUAAAAUAUGU
((((((.....((((((.((((.(.(((((.....))))))....---........(((((((((..........))))))))))))).))))))((((....))))....)))))).. ( -28.00)
>DroEre_CAF1 42913 117 - 1
AUAUUUAUUGGUUCAAAUAUGCUGUCGCAUUAUGAAUGCGCUGGAA--AAACACAUACUUCUGUUGAUUUAAUUAAACAGAGGUGCGUUUUUUACGUGCGCUGGCAUUAUAAAAUAUGU
((((((....(((((...((((....))))..)))))((((..(((--((((...((((((((((..........)))))))))).)))))))....))))..........)))))).. ( -30.90)
>DroYak_CAF1 45188 116 - 1
AAAUUUAUCGGGUAAAAUAUGCCGUCGCAUUAUGAAUGCGCUAAAA---AAAACAUACUUCUGUUGAUUUAAUUAAACAGAGGUGCAUUUUUUACGUGCACUGGCAUUAUAAAAUAUGU
...........((((((.((((.(.(((((.....)))))).....---.......(((((((((..........))))))))))))).))))))((((....))))............ ( -26.50)
>consensus
AUAUUUAUUGGGUAAAAUAUGCUGUCGCAUUAUGAAUGCGCUGAAA__AAACACAUACUUCUGUUGAUUUAAUUAAACAGAGGUGCAUUUUUUACGUGCACUGGCAUUAUAAAAUAUGU
((((((.....((((((.((((...(((((.....)))))................(((((((((..........))))))))))))).))))))((((....))))....)))))).. (-22.78 = -23.66 +   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 12:35:06 2006