Locus 3595

Sequence ID 2L_DroMel_CAF1
Location 10,476,538 – 10,476,727
Length 189
Max. P 0.995727
window5677 window5678 window5679

overview

Window 7

Location 10,476,538 – 10,476,647
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.72
Mean single sequence MFE -26.50
Consensus MFE -23.14
Energy contribution -24.30
Covariance contribution 1.16
Combinations/Pair 1.03
Mean z-score -2.30
Structure conservation index 0.87
SVM decision value 2.61
SVM RNA-class probability 0.995727
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10476538 109 + 22407834
UUACCAACCUGUAUAUAACAUUU--------AUAUGUA---UAUAUAUAUAGAAAGGUGUGCUGGGCCUCCGAUUACACUCCCACAUGCAUGUUCGCACACAUGUAUGCAGUUACCAAAU
........(((((((((((((..--------..)))).---..)))))))))...((((.((((((...)).............(((((((((......))))))))))))))))).... ( -26.20)
>DroSec_CAF1 4922 112 + 1
UUACCAACCUGUAUAUAACAUAU--------AUAUGUAGGGUAUAUAUAUAGAAAGGUGUGCUGGGCCUCAGAUUACACUCCCACAUGCAUGUUAGCACACAUGUAUGCAGUUACCAAAU
........(((((((((...(((--------(((((((...)))))))))).....((((((((((....((......)))))(((....))).))))))).)))))))))......... ( -27.20)
>DroSim_CAF1 4683 112 + 1
UUACCAACCUGUAUAUAACAUAC--------AUAUGUAGGGUAUAUAUAUAGAAAGGUGUGCUGGGCCUCAGAUUACACUCCCACAUGCAUGUUCGCACACAUGUAUGCAGUUACCAAAU
........(((((((((((.(((--------....)))..)).)))))))))...((((.((((((....((......))))).(((((((((......))))))))).))))))).... ( -27.20)
>DroEre_CAF1 5289 116 + 1
UUACCGAGCUGUAUAUAAAGUAUACAUAUAUAUAU--GA--AGUAUAUAUAGAAAGGUGUGCUGGGCCUCAUAUUACACUCCCACAUGCAUGUUCGCACACAUGUAUGCAGUUACCAAAU
......(((((((((((.........(((((((((--..--.))))))))).....((((((.(((..............)))(((....)))..)))))).)))))))))))....... ( -27.94)
>DroYak_CAF1 5327 108 + 1
UUACCAACCUGUAUAUAAAGUAU--------AUAU--AG--AGUAUAUAUAGAAAGGUGCGCUGGGCCUCAUAUUACUCUCCCACAUGCAUGUUCGCACACAUGUAUGCAGUUACCAAAU
......(((((((((((...)))--------))))--))--.))...........((((.((((((..............))).(((((((((......))))))))).))))))).... ( -23.94)
>consensus
UUACCAACCUGUAUAUAACAUAU________AUAUGUAG__UAUAUAUAUAGAAAGGUGUGCUGGGCCUCAGAUUACACUCCCACAUGCAUGUUCGCACACAUGUAUGCAGUUACCAAAU
........((((((((((((((((......)))))))......)))))))))...((((.((((((..............))).(((((((((......))))))))).))))))).... (-23.14 = -24.30 +   1.16)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,476,568 – 10,476,687
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.95
Mean single sequence MFE -30.56
Consensus MFE -27.90
Energy contribution -28.10
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.71
Structure conservation index 0.91
SVM decision value 1.92
SVM RNA-class probability 0.982697
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10476568 119 - 22407834
UCCAGCCUUAAGGCUUAAUUACAUUAACGUGUGUUCCCAUAUUUGGUAACUGCAUACAUGUGUGCGAACAUGCAUGUGGGAGUGUAAUCGGAGGCCCAGCACACCUUUCUAUAUAUAUA-
(((((((....))))..((((((((..((((((((.(((....))).))).))))(((((((((....))))))))))..)))))))).)))...........................- ( -31.80)
>DroSec_CAF1 4954 118 - 1
UCCAGCCUUAAGGCUUAAUUACAUUAACGU--GUUCCCAUAUUUGGUAACUGCAUACAUGUGUGCUAACAUGCAUGUGGGAGUGUAAUCUGAGGCCCAGCACACCUUUCUAUAUAUAUAC
....((.....(((((.((((((((..(((--(((.(((....))).))).))..(((((((((....))))))))))..))))))))...)))))..)).................... ( -29.70)
>DroSim_CAF1 4715 118 - 1
UCCAGCCUUAAGGCUUAAUUACAUUAACGU--GUUCCCAUAUUUGGUAACUGCAUACAUGUGUGCGAACAUGCAUGUGGGAGUGUAAUCUGAGGCCCAGCACACCUUUCUAUAUAUAUAC
(((((((....))))....(((((...(((--(((((((....))).....(((((....)))))))))))).))))))))((((...(((.....))).))))................ ( -29.80)
>DroEre_CAF1 5326 117 - 1
UCCAGCCUUAAGGCUUAAUUACAUUAACGU--GUUCCCAUAUUUGGUAACUGCAUACAUGUGUGCGAACAUGCAUGUGGGAGUGUAAUAUGAGGCCCAGCACACCUUUCUAUAUAUACU-
(((((((....))))....(((((...(((--(((((((....))).....(((((....)))))))))))).))))))))((((((((.((((.........))))..))).))))).- ( -30.60)
>DroYak_CAF1 5356 117 - 1
UCCAGCCUUAAGGCUUAAUUACAUUAACGU--GUUCCCAUAUUUGGUAACUGCAUACAUGUGUGCGAACAUGCAUGUGGGAGAGUAAUAUGAGGCCCAGCGCACCUUUCUAUAUAUACU-
....((((((..((((..((((((...(((--(((((((....))).....(((((....)))))))))))).))))))..))))....))))))........................- ( -30.90)
>consensus
UCCAGCCUUAAGGCUUAAUUACAUUAACGU__GUUCCCAUAUUUGGUAACUGCAUACAUGUGUGCGAACAUGCAUGUGGGAGUGUAAUCUGAGGCCCAGCACACCUUUCUAUAUAUAUA_
....((.....(((((.((((((((..(....(((.(((....))).))).....(((((((((....))))))))))..))))))))...)))))..)).................... (-27.90 = -28.10 +   0.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,476,607 – 10,476,727
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.61
Mean single sequence MFE -29.06
Consensus MFE -24.80
Energy contribution -24.40
Covariance contribution -0.40
Combinations/Pair 1.11
Mean z-score -1.56
Structure conservation index 0.85
SVM decision value 0.86
SVM RNA-class probability 0.869732
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10476607 120 + 22407834
CCCACAUGCAUGUUCGCACACAUGUAUGCAGUUACCAAAUAUGGGAACACACGUUAAUGUAAUUAAGCCUUAAGGCUGGAUAAAUGCCAACUCGAGUCGUAUAUUAUUUGCGAUAUUGCA
......((((...(((((.....((((((.(((.(((....))).)))((.((.....((((((.((((....)))).)))...))).....)).)).))))))....)))))...)))) ( -28.00)
>DroSec_CAF1 4994 118 + 1
CCCACAUGCAUGUUAGCACACAUGUAUGCAGUUACCAAAUAUGGGAAC--ACGUUAAUGUAAUUAAGCCUUAAGGCUGGAUAAAAGCCAACUCGGGUCGUAUAUUAUUCGCGAUAUUGCA
.....((((((((......))))))))((((((.(((....))).)))--.((((((((((.....((((...((((.......)))).....))))..)))))))...)))....))). ( -27.90)
>DroSim_CAF1 4755 118 + 1
CCCACAUGCAUGUUCGCACACAUGUAUGCAGUUACCAAAUAUGGGAAC--ACGUUAAUGUAAUUAAGCCUUAAGGCUGGAUAAAAGCCAACGCGGGUCGUAUAUUAUUCGCGAUAUUGCA
....(((((((((......))))))))).((((((..((..((....)--)..))...))))))..((..((.((((.......))))..(((((((........))))))).))..)). ( -30.30)
>DroEre_CAF1 5365 118 + 1
CCCACAUGCAUGUUCGCACACAUGUAUGCAGUUACCAAAUAUGGGAAC--ACGUUAAUGUAAUUAAGCCUUAAGGCUGGAUAAAAAGUAACUCGGGUCAUAUAUUAUACGCGAUAUUGCA
(((.(((((((((......))))))))).((((((..((..((....)--)..))......(((.((((....)))).))).....)))))).))).............(((....))). ( -28.70)
>DroYak_CAF1 5395 118 + 1
CCCACAUGCAUGUUCGCACACAUGUAUGCAGUUACCAAAUAUGGGAAC--ACGUUAAUGUAAUUAAGCCUUAAGGCUGGAUAAAAAGUAACUCGGCUCGUAUAUUAUACGCGAUACUGCA
.....((((((((......))))))))(((((..(((....)))...(--.((((((((((....((((.....(((........))).....))))..))))))).))).)..))))). ( -30.40)
>consensus
CCCACAUGCAUGUUCGCACACAUGUAUGCAGUUACCAAAUAUGGGAAC__ACGUUAAUGUAAUUAAGCCUUAAGGCUGGAUAAAAGCCAACUCGGGUCGUAUAUUAUUCGCGAUAUUGCA
.....((((((((......))))))))(((((..(((....))).......(((((((((((((.((((....)))).)))....(((......)))..)))))))...)))..))))). (-24.80 = -24.40 +  -0.40)

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 10:56:28 2006