Locus 2382

Sequence ID 2L_DroMel_CAF1
Location 6,480,928 – 6,481,073
Length 145
Max. P 0.999828
window3837 window3838 window3839 window3840

overview

Window 7

Location 6,480,928 – 6,481,040
Length 112
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 79.76
Mean single sequence MFE -29.50
Consensus MFE -19.68
Energy contribution -21.43
Covariance contribution 1.75
Combinations/Pair 1.23
Mean z-score -2.74
Structure conservation index 0.67
SVM decision value 1.51
SVM RNA-class probability 0.960154
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6480928 112 + 22407834
UUGACAAUUCUGAGGCAUGAGUACAAACAAACACUCACGCAGUGCACUCUGUUGGCGAGCGUAAUAAAUAUGUGGGAAAAUUCCCACAUA-UAUACAGUAUUCAGUGCUAGUG
.............(((((((((((......((.(((.(((((......))))..).))).)).....((((((((((....)))))))))-).....))))))).)))).... ( -34.30)
>DroPse_CAF1 9424 93 + 1
AAAACAAAUGCAAAGCAACAAUACAAACACACGCACAGGCAAUUC-------AAGCAGGCGUAAUAUAUAUGG------AUCGUCAUAUAAUAGAGAGCGUUCAGU-------
......(((((...................((((....((.....-------..))..))))....(((((((------....))))))).......)))))....------- ( -14.70)
>DroSec_CAF1 3341 112 + 1
UUGACAAUUCUGAGGCAUGAGCACAAACAAACACUCACGCAGUGCAUUCAGUUGGCGAGCGUAAUAAAUAUGUGGGAAAAUUCCCACAUA-UAUACAGUAUUCAGUGCUAGUG
...............(((.(((((............((((..(((.........))).)))).....((((((((((....)))))))))-)............))))).))) ( -29.10)
>DroSim_CAF1 3636 112 + 1
UUGACAAUUCUGAGACAUGAGCACAAACAAACACUCACGCAGUGCAUUCAGUUGGCGAGCGUAAUAAAUAUGUGGGAAAAUUCCCACAUA-UAUACAGUAUUCAGUGCUAGUG
...............(((.(((((............((((..(((.........))).)))).....((((((((((....)))))))))-)............))))).))) ( -29.40)
>DroEre_CAF1 3373 112 + 1
UUGACAAUUGUGAGGCAUGAAUACAAACAAACACUCACGCAGUGCAUUCAGUAGGCGAGCGUAAUAAAUAUGUGGGAGAAUUCCCACAUA-UAUAUAGUAUUCAGUGCCAGUG
.............(((((((((((......((.(((..((..(((.....))).))))).)).(((.(((((((((......))))))))-).))).))))))).)))).... ( -35.70)
>DroYak_CAF1 3326 108 + 1
UUGACAAUUGUGAGGAAUGAAUACA----AACACUCACGUAGUGCAUUCAGUAGGCGAGCGUAAUAAAUAUGUGGGAGAAUUCCCACAUA-UAUAUAGUAUUCAGUGCCAGUG
.............((..(((((((.----.((.(((.(.((.((....)).)).).))).)).(((.(((((((((......))))))))-).))).)))))))...)).... ( -33.80)
>consensus
UUGACAAUUCUGAGGCAUGAAUACAAACAAACACUCACGCAGUGCAUUCAGUAGGCGAGCGUAAUAAAUAUGUGGGAAAAUUCCCACAUA_UAUACAGUAUUCAGUGCUAGUG
.............(((((((((((............((((..(((.........))).))))......((((((((......)))))))).......))))))).)))).... (-19.68 = -21.43 +   1.75)

alignment

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secondary structure

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Window 8

Location 6,480,928 – 6,481,040
Length 112
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 79.76
Mean single sequence MFE -31.25
Consensus MFE -18.47
Energy contribution -20.11
Covariance contribution 1.64
Combinations/Pair 1.19
Mean z-score -3.37
Structure conservation index 0.59
SVM decision value 1.85
SVM RNA-class probability 0.979937
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6480928 112 - 22407834
CACUAGCACUGAAUACUGUAUA-UAUGUGGGAAUUUUCCCACAUAUUUAUUACGCUCGCCAACAGAGUGCACUGCGUGAGUGUUUGUUUGUACUCAUGCCUCAGAAUUGUCAA
........((((.....(((.(-(((((((((....)))))))))).)))..(((((.......)))))....(((((((((........))))))))).))))......... ( -35.40)
>DroPse_CAF1 9424 93 - 1
-------ACUGAACGCUCUCUAUUAUAUGACGAU------CCAUAUAUAUUACGCCUGCUU-------GAAUUGCCUGUGCGUGUGUUUGUAUUGUUGCUUUGCAUUUGUUUU
-------...((((((.......((((((.....------.))))))....(((((.((..-------.....))..).))))))))))....(((......)))........ ( -15.00)
>DroSec_CAF1 3341 112 - 1
CACUAGCACUGAAUACUGUAUA-UAUGUGGGAAUUUUCCCACAUAUUUAUUACGCUCGCCAACUGAAUGCACUGCGUGAGUGUUUGUUUGUGCUCAUGCCUCAGAAUUGUCAA
((..(((((.(((((..(((.(-(((((((((....)))))))))).))).((((((((((..((....)).)).)))))))).))))))))))..))............... ( -32.50)
>DroSim_CAF1 3636 112 - 1
CACUAGCACUGAAUACUGUAUA-UAUGUGGGAAUUUUCCCACAUAUUUAUUACGCUCGCCAACUGAAUGCACUGCGUGAGUGUUUGUUUGUGCUCAUGUCUCAGAAUUGUCAA
((..(((((.(((((..(((.(-(((((((((....)))))))))).))).((((((((((..((....)).)).)))))))).))))))))))..))............... ( -32.70)
>DroEre_CAF1 3373 112 - 1
CACUGGCACUGAAUACUAUAUA-UAUGUGGGAAUUCUCCCACAUAUUUAUUACGCUCGCCUACUGAAUGCACUGCGUGAGUGUUUGUUUGUAUUCAUGCCUCACAAUUGUCAA
....((((.(((((((.(((.(-(((((((((....)))))))))).))).((((((((.((.((....)).)).))))))))......)))))))))))............. ( -38.70)
>DroYak_CAF1 3326 108 - 1
CACUGGCACUGAAUACUAUAUA-UAUGUGGGAAUUCUCCCACAUAUUUAUUACGCUCGCCUACUGAAUGCACUACGUGAGUGUU----UGUAUUCAUUCCUCACAAUUGUCAA
....((...(((((((.(((.(-(((((((((....)))))))))).))).((((((((.((.((....)).)).)))))))).----.)))))))..))............. ( -33.20)
>consensus
CACUAGCACUGAAUACUGUAUA_UAUGUGGGAAUUUUCCCACAUAUUUAUUACGCUCGCCAACUGAAUGCACUGCGUGAGUGUUUGUUUGUACUCAUGCCUCACAAUUGUCAA
.....(((.(((.(((.......(((((((((....)))))))))......((((((((................))))))))......))).)))))).............. (-18.47 = -20.11 +   1.64)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,480,964 – 6,481,073
Length 109
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 93.49
Mean single sequence MFE -34.16
Consensus MFE -29.04
Energy contribution -29.52
Covariance contribution 0.48
Combinations/Pair 1.07
Mean z-score -1.86
Structure conservation index 0.85
SVM decision value 1.67
SVM RNA-class probability 0.970964
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6480964 109 + 22407834
ACGCAGUGCACUCUGUUGGCGAGCGUAAUAAAUAUGUGGGAAAAUUCCCACAUAUAUACAGUAUUCAGUGCUAGUGCCGAGAACUCGCAACGAACCCGGUCGCGUCGUU
..((((......))))..((((.((......((((((((((....))))))))))........(((..(((.(((.......))).)))..)))..)).))))...... ( -33.10)
>DroSec_CAF1 3377 109 + 1
ACGCAGUGCAUUCAGUUGGCGAGCGUAAUAAAUAUGUGGGAAAAUUCCCACAUAUAUACAGUAUUCAGUGCUAGUGCCGAGAACUCGCAACGAACGCGGACGCGUCGUU
((((..(((.(((.((((.((((........((((((((((....)))))))))).((((((((...))))).))).......))))))))))).)))...)))).... ( -34.90)
>DroSim_CAF1 3672 109 + 1
ACGCAGUGCAUUCAGUUGGCGAGCGUAAUAAAUAUGUGGGAAAAUUCCCACAUAUAUACAGUAUUCAGUGCUAGUGCCGAGAACUCGCAACGAACGCGGACGCGUCGUU
((((..(((.(((.((((.((((........((((((((((....)))))))))).((((((((...))))).))).......))))))))))).)))...)))).... ( -34.90)
>DroEre_CAF1 3409 109 + 1
ACGCAGUGCAUUCAGUAGGCGAGCGUAAUAAAUAUGUGGGAGAAUUCCCACAUAUAUAUAGUAUUCAGUGCCAGUGCCGAGAACUCGGACCGAAAACGGACGCGUCGUG
.(((..(((........((((((..(.(((.(((((((((......))))))))).))).)..)))...))).((.((((....)))).(((....))))))))..))) ( -35.00)
>DroYak_CAF1 3358 109 + 1
ACGUAGUGCAUUCAGUAGGCGAGCGUAAUAAAUAUGUGGGAGAAUUCCCACAUAUAUAUAGUAUUCAGUGCCAGUGCCGAGAACUCGGAUCGAACACGGACGCGUCGUG
..................((((((((.(((.(((((((((......))))))))).)))........(((......((((....))))......)))..)))).)))). ( -32.90)
>consensus
ACGCAGUGCAUUCAGUUGGCGAGCGUAAUAAAUAUGUGGGAAAAUUCCCACAUAUAUACAGUAUUCAGUGCUAGUGCCGAGAACUCGCAACGAACACGGACGCGUCGUU
.(((...((.....))..))).((((.....((((((((((....)))))))))).....((.(((..(((.(((.......))).)))..))).))..))))...... (-29.04 = -29.52 +   0.48)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,480,964 – 6,481,073
Length 109
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 93.49
Mean single sequence MFE -36.62
Consensus MFE -31.96
Energy contribution -33.20
Covariance contribution 1.24
Combinations/Pair 1.08
Mean z-score -3.17
Structure conservation index 0.87
SVM decision value 4.18
SVM RNA-class probability 0.999828
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6480964 109 - 22407834
AACGACGCGACCGGGUUCGUUGCGAGUUCUCGGCACUAGCACUGAAUACUGUAUAUAUGUGGGAAUUUUCCCACAUAUUUAUUACGCUCGCCAACAGAGUGCACUGCGU
....(((((...(.(((((((((((((((...((....))...)).....(((.((((((((((....))))))))))....)))))))).)))).)))).)..))))) ( -34.60)
>DroSec_CAF1 3377 109 - 1
AACGACGCGUCCGCGUUCGUUGCGAGUUCUCGGCACUAGCACUGAAUACUGUAUAUAUGUGGGAAUUUUCCCACAUAUUUAUUACGCUCGCCAACUGAAUGCACUGCGU
....(((((...(((((((((((((((((...((....))...)).....(((.((((((((((....))))))))))....)))))))).)))).))))))..))))) ( -41.40)
>DroSim_CAF1 3672 109 - 1
AACGACGCGUCCGCGUUCGUUGCGAGUUCUCGGCACUAGCACUGAAUACUGUAUAUAUGUGGGAAUUUUCCCACAUAUUUAUUACGCUCGCCAACUGAAUGCACUGCGU
....(((((...(((((((((((((((((...((....))...)).....(((.((((((((((....))))))))))....)))))))).)))).))))))..))))) ( -41.40)
>DroEre_CAF1 3409 109 - 1
CACGACGCGUCCGUUUUCGGUCCGAGUUCUCGGCACUGGCACUGAAUACUAUAUAUAUGUGGGAAUUCUCCCACAUAUUUAUUACGCUCGCCUACUGAAUGCACUGCGU
....(((((...((.((((((((((....))))....(((...((.....(((.((((((((((....)))))))))).))).....))))).)))))).))..))))) ( -34.10)
>DroYak_CAF1 3358 109 - 1
CACGACGCGUCCGUGUUCGAUCCGAGUUCUCGGCACUGGCACUGAAUACUAUAUAUAUGUGGGAAUUCUCCCACAUAUUUAUUACGCUCGCCUACUGAAUGCACUACGU
..(((.(((((.((((..(..((((....))))..)..)))).)).....(((.((((((((((....)))))))))).)))..))))))................... ( -31.60)
>consensus
AACGACGCGUCCGCGUUCGUUGCGAGUUCUCGGCACUAGCACUGAAUACUGUAUAUAUGUGGGAAUUUUCCCACAUAUUUAUUACGCUCGCCAACUGAAUGCACUGCGU
....(((((...(((((((((((((((((...((....))...)).....(((.((((((((((....)))))))))).)))...))))).)))).))))))..))))) (-31.96 = -33.20 +   1.24)

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 10:26:45 2006