Locus 7265

Sequence ID 2L_DroMel_CAF1
Location 20,342,203 – 20,342,357
Length 154
Max. P 0.983376
window11624 window11625 window11626

overview

Window 4

Location 20,342,203 – 20,342,318
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.53
Mean single sequence MFE -22.43
Consensus MFE -18.20
Energy contribution -17.95
Covariance contribution -0.25
Combinations/Pair 1.32
Mean z-score -2.56
Structure conservation index 0.81
SVM decision value 1.94
SVM RNA-class probability 0.983376
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20342203 115 - 22407834
AAGUAAAAUCGCA---AUAUUUUCGAAUGCCUCGAAAAUUAUAUUACGACAUUGUUACUCACAAA-AACCCCCAAUAUUCCAAAGCUUAAUUGAAAUGGUCUCUUGUAUGAGUGGCACU-
........(((.(---((((((((((.....))))))...))))).)))...((((((((((((.-.(((..((((.............))))....)))...))))..))))))))..- ( -19.62)
>DroSec_CAF1 89191 117 - 1
AAGCAAAAUCGCAA--AUAUUUUCGAAUGCCUCGAAAAUUAUAUUGCGACAUUGUUACCCACAAA-AAACCUCAAUAUUCCAAAGAUAAAUCCAACUGGUCUCUCGUAUGAGUGACACCU
.(((((..((((((--..((((((((.....))))))))....))))))..))))).........-................................(((.(((....))).))).... ( -24.10)
>DroSim_CAF1 85178 117 - 1
AAGCAAAAUCGCAA--AUAUUUUCGAAUGCCUCGAAAAUUAUAUUGCGACAUUGUUACCCACAAA-AAACAUUAAUAUUCCAAAGCUAAAUCGAAAUGGUCUCAUGUAUGAGUGACACCU
.(((((..((((((--..((((((((.....))))))))....))))))..))))).........-...............................(((.((((......)))).))). ( -23.80)
>DroEre_CAF1 71872 117 - 1
AAGCAAAAUUGCAAAAAUAUUUUCGAAAAACUCGAGAGUUAUAUUGCGACAUUGCUACCCACAAUCAAACCUAAAUAUUCCAAAGCAAAAUCCAAA---UCUUGUGUAUGAGUGACUCCU
.(((((..((((((....((((((((.....))))))))....))))))..)))))...................(((((....((((........---..))))....)))))...... ( -22.20)
>consensus
AAGCAAAAUCGCAA__AUAUUUUCGAAUGCCUCGAAAAUUAUAUUGCGACAUUGUUACCCACAAA_AAACCUCAAUAUUCCAAAGCUAAAUCCAAAUGGUCUCUUGUAUGAGUGACACCU
.(((((..((((((....((((((((.....))))))))....))))))..)))))..........................................(((.(((....))).))).... (-18.20 = -17.95 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,342,242 – 20,342,357
Length 115
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 84.05
Mean single sequence MFE -26.77
Consensus MFE -17.06
Energy contribution -17.38
Covariance contribution 0.31
Combinations/Pair 1.16
Mean z-score -1.67
Structure conservation index 0.64
SVM decision value 0.01
SVM RNA-class probability 0.537868
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20342242 115 + 22407834
GAAUAUUGGGGGUU-UUUGUGAGUAACAAUGUCGUAAUAUAAUUUUCGAGGCAUUCGAAAAUAU---UGCGAUUUUACUUCUUUCUAUAGAUAUCUGAUGUAUAGAGUGCACUUGCCUU
........(((((.-..(((((((((....((((((((((...(((((((...)))))))))))---)))))).))))))..(((((((.((.....)).))))))).)))...))))) ( -28.50)
>DroSec_CAF1 89231 113 + 1
GAAUAUUGAGGUUU-UUUGUGGGUAACAAUGUCGCAAUAUAAUUUUCGAGGCAUUCGAAAAUAU--UUGCGAUUUUGCUUCUUUCUAUAGAUAUCUC---GAUCGAGUGCACUUGCCUU
....((((((((..-((((((((...(((.(((((((....(((((((((...)))))))))..--))))))).)))......)))))))).)))))---))).(((.((....))))) ( -31.20)
>DroSim_CAF1 85218 113 + 1
GAAUAUUAAUGUUU-UUUGUGGGUAACAAUGUCGCAAUAUAAUUUUCGAGGCAUUCGAAAAUAU--UUGCGAUUUUGCUUCUUUCUAUAGAUAUCUC---GAUCGAGUGCACUUGCCUU
..............-.....((((((....(((((((....(((((((((...)))))))))..--)))))))..(((.(((......)))...(((---....))).))).)))))). ( -23.30)
>DroEre_CAF1 71909 115 + 1
GAAUAUUUAGGUUUGAUUGUGGGUAGCAAUGUCGCAAUAUAACUCUCGAGUUUUUCGAAAAUAUUUUUGCAAUUUUGCUUUUUACGUGCAAUGU-UG---GAUCUAGUGCACUUGCUUU
......(((((((..((((((.(((((((.((.((((........(((((...)))))........)))).)).)))))....)).))))..))-..---))))))).((....))... ( -24.09)
>consensus
GAAUAUUGAGGUUU_UUUGUGGGUAACAAUGUCGCAAUAUAAUUUUCGAGGCAUUCGAAAAUAU__UUGCGAUUUUGCUUCUUUCUAUAGAUAUCUC___GAUCGAGUGCACUUGCCUU
..................(..(((.((...(((((((....(((((((((...)))))))))....)))))))......(((......)))...............))..)))..)... (-17.06 = -17.38 +   0.31)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,342,242 – 20,342,357
Length 115
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 84.05
Mean single sequence MFE -20.75
Consensus MFE -17.76
Energy contribution -17.20
Covariance contribution -0.56
Combinations/Pair 1.24
Mean z-score -2.28
Structure conservation index 0.86
SVM decision value 1.67
SVM RNA-class probability 0.971420
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20342242 115 - 22407834
AAGGCAAGUGCACUCUAUACAUCAGAUAUCUAUAGAAAGAAGUAAAAUCGCA---AUAUUUUCGAAUGCCUCGAAAAUUAUAUUACGACAUUGUUACUCACAAA-AACCCCCAAUAUUC
.......(((...((((((.((.....)).))))))....(((((..(((.(---((((((((((.....))))))...))))).))).....))))))))...-.............. ( -14.70)
>DroSec_CAF1 89231 113 - 1
AAGGCAAGUGCACUCGAUC---GAGAUAUCUAUAGAAAGAAGCAAAAUCGCAA--AUAUUUUCGAAUGCCUCGAAAAUUAUAUUGCGACAUUGUUACCCACAAA-AAACCUCAAUAUUC
.......(((..(((....---)))...............(((((..((((((--..((((((((.....))))))))....))))))..)))))...)))...-.............. ( -22.30)
>DroSim_CAF1 85218 113 - 1
AAGGCAAGUGCACUCGAUC---GAGAUAUCUAUAGAAAGAAGCAAAAUCGCAA--AUAUUUUCGAAUGCCUCGAAAAUUAUAUUGCGACAUUGUUACCCACAAA-AAACAUUAAUAUUC
.......(((..(((....---)))...............(((((..((((((--..((((((((.....))))))))....))))))..)))))...)))...-.............. ( -22.30)
>DroEre_CAF1 71909 115 - 1
AAAGCAAGUGCACUAGAUC---CA-ACAUUGCACGUAAAAAGCAAAAUUGCAAAAAUAUUUUCGAAAAACUCGAGAGUUAUAUUGCGACAUUGCUACCCACAAUCAAACCUAAAUAUUC
.......(((((.......---..-....)))))......(((((..((((((....((((((((.....))))))))....))))))..)))))........................ ( -23.72)
>consensus
AAGGCAAGUGCACUCGAUC___CAGAUAUCUAUAGAAAGAAGCAAAAUCGCAA__AUAUUUUCGAAUGCCUCGAAAAUUAUAUUGCGACAUUGUUACCCACAAA_AAACCUCAAUAUUC
.......(((..................(((......)))(((((..((((((....((((((((.....))))))))....))))))..)))))...))).................. (-17.76 = -17.20 +  -0.56)

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 12:31:51 2006