Locus 3199

Sequence ID 3L_DroMel_CAF1
Location 9,334,136 – 9,334,295
Length 159
Max. P 0.948860
window4981 window4982 window4983

overview

Window 1

Location 9,334,136 – 9,334,255
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.38
Mean single sequence MFE -32.14
Consensus MFE -19.72
Energy contribution -19.92
Covariance contribution 0.20
Combinations/Pair 1.19
Mean z-score -1.85
Structure conservation index 0.61
SVM decision value 0.01
SVM RNA-class probability 0.539321
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9334136 119 + 23771897
UUUUGAUUUGAAAAGGAAUCGAUUUUUGGUGACGGCUUCAGAUCCA-UUUUCUCUAGCUACGUCGAUAGCAUGAACAGAUGAUUAUCCACAUCUGGUGGUUGCCUGUAUGGCCACCUGGU
....((((((((..(..(((((...)))))..)...))))))))..-.........((((......)))).....((((((........))))))..(((.(((.....))).))).... ( -29.20)
>DroSec_CAF1 31608 115 + 1
U-UUGAUUUCAAAAGAAAUCGAUUCUUAGUGACGGAUCCAGAU-CA-UUUU--UUGGCUACGUCGAUAGCAUGAACAGAUGAAUAUCCACAUCUGGUGGUGGCCUGUAUGGCCACCUGGC
.-((((((((....)))))))).......(((((...(((((.-..-...)--))))...)))))...((.....((((((........))))))..(((((((.....)))))))..)) ( -40.60)
>DroSim_CAF1 31903 105 + 1
UUUUGAUUUCAAAAGAAAUCGAUUCUUAGUGACGGAUCCAGAUCCA-UUUU--UUGGCUACGUCGAUAGCAUGAACAGAUGAUUAUCCACAUCUG------------AUGGCCACCUGGU
..((((((((....))))))))..((...(((((...(((((....-...)--))))...)))))..))......((((((........))))))------------...(((....))) ( -26.10)
>DroEre_CAF1 26232 105 + 1
UUUUAAUUUGAAAAGAAAUCGAUUUUAAGUGACGGAUCCAGAUCCA-UUUU--CUGGCUAUGUCGAUAGCUCGAACAGAUGAUUAUCCACAUCUGAUG------------GCCACCUGGU
.....((((((((.(....)..))))))))...((((....)))).-....--.(((((((.((((....)))).((((((........)))))))))------------))))...... ( -25.00)
>DroYak_CAF1 37835 118 + 1
CUUUGAUUUCAAAAGAAAUCGAUUUCCAGUGACGGAUCCAGAUCCGCUUUU--GUGGCUACGUCGAUAGCUCGAACAGAUGAUUAUCCACAUCUGGUGGCUGCCUGUUUGGCCACCUGGU
..((((((((....))))))))...((((...(((((....))))).....--(((((((..(.(.(((((....((((((........))))))..))))).).)..))))))))))). ( -39.80)
>consensus
UUUUGAUUUCAAAAGAAAUCGAUUUUUAGUGACGGAUCCAGAUCCA_UUUU__CUGGCUACGUCGAUAGCAUGAACAGAUGAUUAUCCACAUCUGGUGG__GCCUGUAUGGCCACCUGGU
..((((((((....)))))))).......(((((...((((............))))...)))))..........((((((........))))))...............(((....))) (-19.72 = -19.92 +   0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,334,136 – 9,334,255
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.38
Mean single sequence MFE -31.25
Consensus MFE -22.58
Energy contribution -23.10
Covariance contribution 0.52
Combinations/Pair 1.11
Mean z-score -2.40
Structure conservation index 0.72
SVM decision value 1.39
SVM RNA-class probability 0.948860
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9334136 119 - 23771897
ACCAGGUGGCCAUACAGGCAACCACCAGAUGUGGAUAAUCAUCUGUUCAUGCUAUCGACGUAGCUAGAGAAAA-UGGAUCUGAAGCCGUCACCAAAAAUCGAUUCCUUUUCAAAUCAAAA
..(((((((((.....)))..((((.....)))).....)))))).((..(((((....)))))..))(((((-.(((..(((...............)))..))))))))......... ( -26.46)
>DroSec_CAF1 31608 115 - 1
GCCAGGUGGCCAUACAGGCCACCACCAGAUGUGGAUAUUCAUCUGUUCAUGCUAUCGACGUAGCCAA--AAAA-UG-AUCUGGAUCCGUCACUAAGAAUCGAUUUCUUUUGAAAUCAA-A
....(((((((.....))))))).(((((((((((((......)))))))(((((....)))))...--....-..-)))))).................((((((....))))))..-. ( -37.60)
>DroSim_CAF1 31903 105 - 1
ACCAGGUGGCCAU------------CAGAUGUGGAUAAUCAUCUGUUCAUGCUAUCGACGUAGCCAA--AAAA-UGGAUCUGGAUCCGUCACUAAGAAUCGAUUUCUUUUGAAAUCAAAA
....((((((...------------((((((........)))))).....))))))((((...(((.--....-......)))...))))..........((((((....)))))).... ( -27.90)
>DroEre_CAF1 26232 105 - 1
ACCAGGUGGC------------CAUCAGAUGUGGAUAAUCAUCUGUUCGAGCUAUCGACAUAGCCAG--AAAA-UGGAUCUGGAUCCGUCACUUAAAAUCGAUUUCUUUUCAAAUUAAAA
....((((((------------(..((((((........))))))...).))))))(((....((((--(...-....)))))....))).............................. ( -24.60)
>DroYak_CAF1 37835 118 - 1
ACCAGGUGGCCAAACAGGCAGCCACCAGAUGUGGAUAAUCAUCUGUUCGAGCUAUCGACGUAGCCAC--AAAAGCGGAUCUGGAUCCGUCACUGGAAAUCGAUUUCUUUUGAAAUCAAAG
.(((((((((......(..((((..((((((........))))))...).)))..)......)))))--....((((((....))))))..)))).....((((((....)))))).... ( -39.70)
>consensus
ACCAGGUGGCCAUACAGGC__CCACCAGAUGUGGAUAAUCAUCUGUUCAUGCUAUCGACGUAGCCAA__AAAA_UGGAUCUGGAUCCGUCACUAAAAAUCGAUUUCUUUUGAAAUCAAAA
....((((((...............((((((........)))))).....(((((....)))))...........((((....)))))))))).......((((((....)))))).... (-22.58 = -23.10 +   0.52)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,334,176 – 9,334,295
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.53
Mean single sequence MFE -39.84
Consensus MFE -26.80
Energy contribution -27.76
Covariance contribution 0.96
Combinations/Pair 1.03
Mean z-score -2.03
Structure conservation index 0.67
SVM decision value 0.22
SVM RNA-class probability 0.641085
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9334176 119 + 23771897
GAUCCA-UUUUCUCUAGCUACGUCGAUAGCAUGAACAGAUGAUUAUCCACAUCUGGUGGUUGCCUGUAUGGCCACCUGGUAACACUGCACCAUGGGGGUGGUGAUAAAAGGGGGUGUUGU
.((((.-.......(((((((((.....)).....((((((........)))))))))))))(((.(((.((((((((((........)))....))))))).)))..)))))))..... ( -34.80)
>DroSec_CAF1 31647 116 + 1
GAU-CA-UUUU--UUGGCUACGUCGAUAGCAUGAACAGAUGAAUAUCCACAUCUGGUGGUGGCCUGUAUGGCCACCUGGCAACACUGCACCAUGGUGGUGGUGAUAAAAGGGGGUGUUGU
..(-((-(((.--(((((...))))).)).)))).((((((........))))))..(((((((.....)))))))..((((((((.((((((....)))))).........)))))))) ( -40.80)
>DroSim_CAF1 31943 105 + 1
GAUCCA-UUUU--UUGGCUACGUCGAUAGCAUGAACAGAUGAUUAUCCACAUCUG------------AUGGCCACCUGGUAACACUGCACCAUGGGGGUGGUGAUAAAAGGGGGUGUUGU
.((((.-....--.((((((((((....).)))..((((((........))))))------------.))))))(((..((.(((..(.((....)))..))).))..)))))))..... ( -32.40)
>DroEre_CAF1 26272 105 + 1
GAUCCA-UUUU--CUGGCUAUGUCGAUAGCUCGAACAGAUGAUUAUCCACAUCUGAUG------------GCCACCUGGUAACACUGCCCCAUGGGGGUGGUGAUACAAGGGGGUGUUGU
.((((.-....--.(((((((.((((....)))).((((((........)))))))))------------))))(((.(((.(((..((((...))))..))).))).)))))))..... ( -43.70)
>DroYak_CAF1 37875 118 + 1
GAUCCGCUUUU--GUGGCUACGUCGAUAGCUCGAACAGAUGAUUAUCCACAUCUGGUGGCUGCCUGUUUGGCCACCUGGUAACACUGCCCCAUGGGGGUGGUGAUAAAAGGGGGUGUUGU
.((((.(((((--((((((((.((((....)))).((((((........))))))))))))(((.....)))..........(((..((((...))))..)))))))))).))))..... ( -47.50)
>consensus
GAUCCA_UUUU__CUGGCUACGUCGAUAGCAUGAACAGAUGAUUAUCCACAUCUGGUGG__GCCUGUAUGGCCACCUGGUAACACUGCACCAUGGGGGUGGUGAUAAAAGGGGGUGUUGU
.((((.........((((((..(((......))).((((((........)))))).............))))))(((..((.(((..(.((....)))..))).))..)))))))..... (-26.80 = -27.76 +   0.96)

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 10:51:53 2006