Locus 733

Sequence ID 2L_DroMel_CAF1
Location 2,122,068 – 2,122,217
Length 149
Max. P 0.994522
window1203 window1204 window1205 window1206

overview

Window 3

Location 2,122,068 – 2,122,177
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.64
Mean single sequence MFE -30.06
Consensus MFE -20.38
Energy contribution -22.54
Covariance contribution 2.16
Combinations/Pair 1.03
Mean z-score -3.08
Structure conservation index 0.68
SVM decision value 2.49
SVM RNA-class probability 0.994522
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2122068 109 + 22407834
--------GUCCACCUUCGCCAUGUAAAAGUGAACAAUUGCCAACUAUUUCUCAUUGAAAUACUUGUGCGGUAAUAAGGGAGUGAA-UUCCGACUCAUUCCCC--UCUUUUUCUCGCAGU
--------..........((...(.(((((.(....((((((((.((((((.....)))))).))).))))).....((((((((.-.......)))))))))--.))))).)..))... ( -27.00)
>DroSec_CAF1 122358 117 + 1
CACUGCCAGUCCACCUUCGCCAGGUAAAAGUGAACAAUUGCCAACUAUUUCUCAUUGAAAUACUUGUGCGGUAAUAAGGGAGUGAA-UUCCGAUUCAUUCCCC--UCUUUUUCUCGCAGU
.(((((.((...((((.....))))(((((.(....((((((((.((((((.....)))))).))).))))).....(((((((((-(....)))))))))))--.))))).)).))))) ( -35.40)
>DroSim_CAF1 122146 111 + 1
CACUGCCAGU------UCGCCUGGUAAAAGUGAACAAUUGCCAACUAUUUCUCAUUGAAAUACUUGUGCGGUAAUAAGGGAGUGAA-UUCCGACUCAUUCCCC--UCUUUUUCUCGCAGU
.(((((..((------((((.(.....).)))))).((((((((.((((((.....)))))).))).))))).....((((((((.-.......)))))))).--..........))))) ( -34.10)
>DroEre_CAF1 125087 101 + 1
CAGUGCCAGUCCACCC----------------AACAAUUGCCAACUAUUUCUUAUCGAAAUACUUGUGCGCUAAUAAGCGAGUGGA-UGCCACUUCAUUCCCC--CCUUUUUCUCGCAGU
.((((...((((((.(----------------.......(((((.((((((.....)))))).))).))(((....)))).)))))-)..)))).........--............... ( -23.60)
>DroYak_CAF1 127399 120 + 1
CACUGCCAGUCCACCCUUACCAUGUAAAAGUGAACAAUUCCCAACUAUUUCUCAUUGAAAUACUUGUGCGGUAAUAAGGGAGUGGAAUCCGACUUCAUUCCCCUCCUUUUUUCUCGCAGU
........((.(((..((((...))))..))).))......(((.((((((.....)))))).)))((((..((.(((((((.(((((........))))).))))))).))..)))).. ( -30.20)
>consensus
CACUGCCAGUCCACCCUCGCCAGGUAAAAGUGAACAAUUGCCAACUAUUUCUCAUUGAAAUACUUGUGCGGUAAUAAGGGAGUGAA_UUCCGAUUCAUUCCCC__UCUUUUUCUCGCAGU
.(((((.((...........................((((((((.((((((.....)))))).))).))))).....(((((((((.......)))))))))..........)).))))) (-20.38 = -22.54 +   2.16) 

alignment

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secondary structure

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dotplot

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Window 4

Location 2,122,068 – 2,122,177
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.64
Mean single sequence MFE -35.64
Consensus MFE -20.06
Energy contribution -23.92
Covariance contribution 3.86
Combinations/Pair 1.09
Mean z-score -2.98
Structure conservation index 0.56
SVM decision value 1.85
SVM RNA-class probability 0.980068
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2122068 109 - 22407834
ACUGCGAGAAAAAGA--GGGGAAUGAGUCGGAA-UUCACUCCCUUAUUACCGCACAAGUAUUUCAAUGAGAAAUAGUUGGCAAUUGUUCACUUUUACAUGGCGAAGGUGGAC--------
..((((..((....(--(((((.(((((....)-)))).)))))).))..))))(((.((((((.....)))))).)))......((((((((((.......))))))))))-------- ( -31.90)
>DroSec_CAF1 122358 117 - 1
ACUGCGAGAAAAAGA--GGGGAAUGAAUCGGAA-UUCACUCCCUUAUUACCGCACAAGUAUUUCAAUGAGAAAUAGUUGGCAAUUGUUCACUUUUACCUGGCGAAGGUGGACUGGCAGUG
(((((.........(--(((((.(((((....)-)))).))))))......((.(((.((((((.....)))))).)))))....((((((((((.......))))))))))..))))). ( -39.00)
>DroSim_CAF1 122146 111 - 1
ACUGCGAGAAAAAGA--GGGGAAUGAGUCGGAA-UUCACUCCCUUAUUACCGCACAAGUAUUUCAAUGAGAAAUAGUUGGCAAUUGUUCACUUUUACCAGGCGA------ACUGGCAGUG
(((((....((((((--(((((.(((((....)-)))).))))))......((.(((.((((((.....)))))).))))).........)))))..(((....------.)))))))). ( -34.50)
>DroEre_CAF1 125087 101 - 1
ACUGCGAGAAAAAGG--GGGGAAUGAAGUGGCA-UCCACUCGCUUAUUAGCGCACAAGUAUUUCGAUAAGAAAUAGUUGGCAAUUGUU----------------GGGUGGACUGGCACUG
.((.(........).--)).......((((.((-((((((((((....)))((.(((.((((((.....)))))).))))).......----------------))))))).)).)))). ( -34.80)
>DroYak_CAF1 127399 120 - 1
ACUGCGAGAAAAAAGGAGGGGAAUGAAGUCGGAUUCCACUCCCUUAUUACCGCACAAGUAUUUCAAUGAGAAAUAGUUGGGAAUUGUUCACUUUUACAUGGUAAGGGUGGACUGGCAGUG
(((((.........((((.(((((........))))).))))............(((.((((((.....)))))).)))......((((((((((((...))))))))))))..))))). ( -38.00)
>consensus
ACUGCGAGAAAAAGA__GGGGAAUGAAUCGGAA_UUCACUCCCUUAUUACCGCACAAGUAUUUCAAUGAGAAAUAGUUGGCAAUUGUUCACUUUUACAUGGCGAAGGUGGACUGGCAGUG
(((((............(((((.((((.......)))).))))).......((.(((.((((((.....)))))).)))))....((((((((((.......))))))))))..))))). (-20.06 = -23.92 +   3.86) 

alignment

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secondary structure

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dotplot

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Window 5

Location 2,122,100 – 2,122,217
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.30
Mean single sequence MFE -24.83
Consensus MFE -19.84
Energy contribution -20.20
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -1.73
Structure conservation index 0.80
SVM decision value 0.70
SVM RNA-class probability 0.826061
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2122100 117 + 22407834
CCAACUAUUUCUCAUUGAAAUACUUGUGCGGUAAUAAGGGAGUGAA-UUCCGACUCAUUCCCC--UCUUUUUCUCGCAGUUCACUUGGCCAACUUUGUGCUUACCUUAAACGCUUGCUUU
.(((.((((((.....)))))).))).(((....((((((((((((-((.(((..........--........))).)))))))))(((((....)).)))..)))))..)))....... ( -26.37)
>DroSec_CAF1 122398 117 + 1
CCAACUAUUUCUCAUUGAAAUACUUGUGCGGUAAUAAGGGAGUGAA-UUCCGAUUCAUUCCCC--UCUUUUUCUCGCAGUUCACCUGGCAAACUUUGUGCUUACCUUUAACGCUUGCUUU
.(((.((((((.....)))))).)))((((..((...(((((((((-(....)))))))))).--.....))..))))........(((((.....(((.(((....))))))))))).. ( -25.80)
>DroSim_CAF1 122180 117 + 1
CCAACUAUUUCUCAUUGAAAUACUUGUGCGGUAAUAAGGGAGUGAA-UUCCGACUCAUUCCCC--UCUUUUUCUCGCAGUUCACCUGGCCAACUUUGUGCUUACCUUUAACGCUUGCUUU
.(((.((((((.....)))))).))).(((((.....((((((((.-.......)))))))).--...........(((.....))))))......(((.(((....))))))..))... ( -23.50)
>DroEre_CAF1 125111 117 + 1
CCAACUAUUUCUUAUCGAAAUACUUGUGCGCUAAUAAGCGAGUGGA-UGCCACUUCAUUCCCC--CCUUUUUCUCGCAGUUCACCUGGCCAACUUUGUGCUUACCUUUAACGCUUGCCUU
.(((.((((((.....)))))).))).(((.(((((((((((((((-......)))))))...--...........(((.....)))...........)))))...))).)))....... ( -19.70)
>DroYak_CAF1 127439 120 + 1
CCAACUAUUUCUCAUUGAAAUACUUGUGCGGUAAUAAGGGAGUGGAAUCCGACUUCAUUCCCCUCCUUUUUUCUCGCAGUUCACCUGGCCAACUUUGUGCUUACCUUUAACGCUUGCCUU
.(((.((((((.....)))))).)))((((..((.(((((((.(((((........))))).))))))).))..))))........(((.......(((.(((....))))))..))).. ( -28.80)
>consensus
CCAACUAUUUCUCAUUGAAAUACUUGUGCGGUAAUAAGGGAGUGAA_UUCCGAUUCAUUCCCC__UCUUUUUCUCGCAGUUCACCUGGCCAACUUUGUGCUUACCUUUAACGCUUGCUUU
.(((.((((((.....)))))).))).(((.......(((((((((.......)))))))))...................(((..((....))..)))...........)))....... (-19.84 = -20.20 +   0.36) 

alignment

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secondary structure

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dotplot

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Window 6

Location 2,122,100 – 2,122,217
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.30
Mean single sequence MFE -32.26
Consensus MFE -23.82
Energy contribution -24.02
Covariance contribution 0.20
Combinations/Pair 1.07
Mean z-score -2.57
Structure conservation index 0.74
SVM decision value 0.89
SVM RNA-class probability 0.875833
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2122100 117 - 22407834
AAAGCAAGCGUUUAAGGUAAGCACAAAGUUGGCCAAGUGAACUGCGAGAAAAAGA--GGGGAAUGAGUCGGAA-UUCACUCCCUUAUUACCGCACAAGUAUUUCAAUGAGAAAUAGUUGG
...((..(((((((.(((.(((.....))).)))...))))).)).........(--(((((.(((((....)-)))).))))))......)).(((.((((((.....)))))).))). ( -32.20)
>DroSec_CAF1 122398 117 - 1
AAAGCAAGCGUUAAAGGUAAGCACAAAGUUUGCCAGGUGAACUGCGAGAAAAAGA--GGGGAAUGAAUCGGAA-UUCACUCCCUUAUUACCGCACAAGUAUUUCAAUGAGAAAUAGUUGG
.......((......(((((((.....))))))).(((((.((.........))(--(((((.(((((....)-)))).)))))).))))))).(((.((((((.....)))))).))). ( -35.10)
>DroSim_CAF1 122180 117 - 1
AAAGCAAGCGUUAAAGGUAAGCACAAAGUUGGCCAGGUGAACUGCGAGAAAAAGA--GGGGAAUGAGUCGGAA-UUCACUCCCUUAUUACCGCACAAGUAUUUCAAUGAGAAAUAGUUGG
.......((......(((.(((.....))).))).(((((.((.........))(--(((((.(((((....)-)))).)))))).))))))).(((.((((((.....)))))).))). ( -31.50)
>DroEre_CAF1 125111 117 - 1
AAGGCAAGCGUUAAAGGUAAGCACAAAGUUGGCCAGGUGAACUGCGAGAAAAAGG--GGGGAAUGAAGUGGCA-UCCACUCGCUUAUUAGCGCACAAGUAUUUCGAUAAGAAAUAGUUGG
.......(((((((.(((.(((.....))).)))((((((.((.(........).--))........((((..-.)))))))))).))))))).(((.((((((.....)))))).))). ( -32.50)
>DroYak_CAF1 127439 120 - 1
AAGGCAAGCGUUAAAGGUAAGCACAAAGUUGGCCAGGUGAACUGCGAGAAAAAAGGAGGGGAAUGAAGUCGGAUUCCACUCCCUUAUUACCGCACAAGUAUUUCAAUGAGAAAUAGUUGG
.......((......(((.(((.....))).))).(((((.(.....)......((((.(((((........))))).))))....))))))).(((.((((((.....)))))).))). ( -30.00)
>consensus
AAAGCAAGCGUUAAAGGUAAGCACAAAGUUGGCCAGGUGAACUGCGAGAAAAAGA__GGGGAAUGAAUCGGAA_UUCACUCCCUUAUUACCGCACAAGUAUUUCAAUGAGAAAUAGUUGG
...((..((......(((.(((.....))).))).((....))))............(((((.((((.......)))).))))).......)).(((.((((((.....)))))).))). (-23.82 = -24.02 +   0.20) 

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 09:44:15 2006