Locus 4663

Sequence ID 3L_DroMel_CAF1
Location 13,205,006 – 13,205,174
Length 168
Max. P 0.999831
window7334 window7335 window7336 window7337 window7338

overview

Window 4

Location 13,205,006 – 13,205,106
Length 100
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 77.42
Mean single sequence MFE -33.87
Consensus MFE -23.73
Energy contribution -22.85
Covariance contribution -0.88
Combinations/Pair 1.12
Mean z-score -3.41
Structure conservation index 0.70
SVM decision value 4.19
SVM RNA-class probability 0.999831
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13205006 100 + 23771897
------GGAUGCUGCACUU--UGGCUGU------------UGCUGGUGUUUUGGUUCUUCCUUUUUAGCUACUUAAAGCUUUUAGAGCGGCAGCUAGAUGUAAUAUAAAUUACAUUAGCU
------...((((((.((.--.((((((------------.(((((......((.....))...))))).))....))))...)).))))))(((.((((((((....))))))))))). ( -29.00)
>DroSim_CAF1 3627 101 + 1
------AGAUGCUGCACUU--UGGCUGUU-----------UGCUGGUUUUUUGGUUCUUCCUUUUCAGCUACUUAAAGCUUUUAGAGCGGCAGCUAGAUGUAAUAUAAAUUACAUUAGCU
------...((((((.((.--.((((...-----------.(((((......((.....))...))))).......))))...)).))))))(((.((((((((....))))))))))). ( -31.10)
>DroAna_CAF1 88802 116 + 1
GGGCCAAGAAGCUGCACUUCGUGGCUGCCACUUCCACUGCCACUGCCGCUGUUGUU----CUUUUCAGCUACUUAGAGCUUUUAGAGCGGCAGCAAGAUGUAAUAUAAAUUACAUUAGCU
.(((...((((.....))))(((((.............))))).)))(((((((((----((....((((......))))...)))))))))))..((((((((....)))))))).... ( -41.52)
>consensus
______AGAUGCUGCACUU__UGGCUGU____________UGCUGGUGUUUUGGUUCUUCCUUUUCAGCUACUUAAAGCUUUUAGAGCGGCAGCUAGAUGUAAUAUAAAUUACAUUAGCU
..........(((((......((((((..............((..(....)..))..........))))))......((((...)))).)))))..((((((((....)))))))).... (-23.73 = -22.85 +  -0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 13,205,006 – 13,205,106
Length 100
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 77.42
Mean single sequence MFE -27.07
Consensus MFE -16.68
Energy contribution -16.79
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.55
Structure conservation index 0.62
SVM decision value 2.15
SVM RNA-class probability 0.989122
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13205006 100 - 23771897
AGCUAAUGUAAUUUAUAUUACAUCUAGCUGCCGCUCUAAAAGCUUUAAGUAGCUAAAAAGGAAGAACCAAAACACCAGCA------------ACAGCCA--AAGUGCAGCAUCC------
((((((((((((....))))))).)))))((.((.((...((((......)))).....((.....))............------------.......--.)).)).))....------ ( -20.70)
>DroSim_CAF1 3627 101 - 1
AGCUAAUGUAAUUUAUAUUACAUCUAGCUGCCGCUCUAAAAGCUUUAAGUAGCUGAAAAGGAAGAACCAAAAAACCAGCA-----------AACAGCCA--AAGUGCAGCAUCU------
((((((((((((....))))))).)))))((.((.((...((((......)))).....((.....))............-----------........--.)).)).))....------ ( -20.70)
>DroAna_CAF1 88802 116 - 1
AGCUAAUGUAAUUUAUAUUACAUCUUGCUGCCGCUCUAAAAGCUCUAAGUAGCUGAAAAG----AACAACAGCGGCAGUGGCAGUGGAAGUGGCAGCCACGAAGUGCAGCUUCUUGGCCC
.(((((((((((....))))))).(..((((((((((....((.....)).((((.....----.....)))))).))))))))..)...)))).((((.((((.....)))).)))).. ( -39.80)
>consensus
AGCUAAUGUAAUUUAUAUUACAUCUAGCUGCCGCUCUAAAAGCUUUAAGUAGCUGAAAAGGAAGAACCAAAACACCAGCA____________ACAGCCA__AAGUGCAGCAUCU______
((((((((((((....))))))).)))))((.((.((...((((......)))).......................((................)).....)).)).)).......... (-16.68 = -16.79 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 13,205,026 – 13,205,146
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.00
Mean single sequence MFE -30.67
Consensus MFE -21.90
Energy contribution -21.57
Covariance contribution -0.33
Combinations/Pair 1.07
Mean z-score -2.40
Structure conservation index 0.71
SVM decision value 0.00
SVM RNA-class probability 0.534896
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13205026 120 + 23771897
UGCUGGUGUUUUGGUUCUUCCUUUUUAGCUACUUAAAGCUUUUAGAGCGGCAGCUAGAUGUAAUAUAAAUUACAUUAGCUAAGUGCCAGGCGGCAAUUAAAAACAAAAAAUACUCGUGAA
.((.((((((((((.....))......((..(((...((((...))))(((((((.((((((((....)))))))))))....)))))))..))............)))))))).))... ( -29.80)
>DroSim_CAF1 3648 120 + 1
UGCUGGUUUUUUGGUUCUUCCUUUUCAGCUACUUAAAGCUUUUAGAGCGGCAGCUAGAUGUAAUAUAAAUUACAUUAGCUAAGUGCCAGGCGGCAAUUAAAAACAAAAAAUACUCGUGAA
.....(((((((((((((........((((......))))...)))))...((((.((((((((....))))))))))))...((((....))))........))))))))......... ( -27.00)
>DroAna_CAF1 88842 115 + 1
CACUGCCGCUGUUGUU----CUUUUCAGCUACUUAGAGCUUUUAGAGCGGCAGCAAGAUGUAAUAUAAAUUACAUUAGCUAAGUGCCAGGCGGCAAUUAA-AACAAAAAAUACUCGACAA
..((((((((((((((----((....((((......))))...)))))))))))..((((((((....)))))))).((.....))..))))).......-................... ( -35.20)
>consensus
UGCUGGUGUUUUGGUUCUUCCUUUUCAGCUACUUAAAGCUUUUAGAGCGGCAGCUAGAUGUAAUAUAAAUUACAUUAGCUAAGUGCCAGGCGGCAAUUAAAAACAAAAAAUACUCGUGAA
.((..(....)..))............((..(((...((((...))))(((((((.((((((((....)))))))))))....)))))))..)).......................... (-21.90 = -21.57 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 13,205,066 – 13,205,174
Length 108
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.36
Mean single sequence MFE -28.03
Consensus MFE -22.38
Energy contribution -22.50
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.76
Structure conservation index 0.80
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13205066 108 + 23771897
UUUAGAGCGGCAGCUAGAUGUAAUAUAAAUUACAUUAGCUAAGUGCCAGGCGGCAAUUAAAAACAAAAAAUACUCGUGAAGUUUUC------------CUCCGCCUUUGUUGUUGCUGAU
.....(((((((((..((((((((....)))))))).((.....)).((((((......(((((................))))).------------..))))))..)))))))))... ( -27.29)
>DroSim_CAF1 3688 108 + 1
UUUAGAGCGGCAGCUAGAUGUAAUAUAAAUUACAUUAGCUAAGUGCCAGGCGGCAAUUAAAAACAAAAAAUACUCGUGAAGUUUUC------------CUCCGCCUUUGUUGUUGCUGAU
.....(((((((((..((((((((....)))))))).((.....)).((((((......(((((................))))).------------..))))))..)))))))))... ( -27.29)
>DroAna_CAF1 88878 119 + 1
UUUAGAGCGGCAGCAAGAUGUAAUAUAAAUUACAUUAGCUAAGUGCCAGGCGGCAAUUAA-AACAAAAAAUACUCGACAACUUCUUCCUUCGGUGCCUCUCCGCCGUUGUUGUUCUUGAU
...(((((((((((..((((((((....))))))))...(((.((((....)))).))).-..............................((((......))))))))))))))).... ( -29.50)
>consensus
UUUAGAGCGGCAGCUAGAUGUAAUAUAAAUUACAUUAGCUAAGUGCCAGGCGGCAAUUAAAAACAAAAAAUACUCGUGAAGUUUUC____________CUCCGCCUUUGUUGUUGCUGAU
.((((((((((((((.((((((((....))))))))))))........(((((...............................................)))))...)))))).)))). (-22.38 = -22.50 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 13,205,066 – 13,205,174
Length 108
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 87.36
Mean single sequence MFE -30.03
Consensus MFE -22.16
Energy contribution -22.39
Covariance contribution 0.23
Combinations/Pair 1.07
Mean z-score -2.62
Structure conservation index 0.74
SVM decision value 0.64
SVM RNA-class probability 0.809460
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13205066 108 - 23771897
AUCAGCAACAACAAAGGCGGAG------------GAAAACUUCACGAGUAUUUUUUGUUUUUAAUUGCCGCCUGGCACUUAGCUAAUGUAAUUUAUAUUACAUCUAGCUGCCGCUCUAAA
...(((........((((((..------------((((((................)))))).....))))))((((....(((((((((((....))))))).)))))))))))..... ( -30.99)
>DroSim_CAF1 3688 108 - 1
AUCAGCAACAACAAAGGCGGAG------------GAAAACUUCACGAGUAUUUUUUGUUUUUAAUUGCCGCCUGGCACUUAGCUAAUGUAAUUUAUAUUACAUCUAGCUGCCGCUCUAAA
...(((........((((((..------------((((((................)))))).....))))))((((....(((((((((((....))))))).)))))))))))..... ( -30.99)
>DroAna_CAF1 88878 119 - 1
AUCAAGAACAACAACGGCGGAGAGGCACCGAAGGAAGAAGUUGUCGAGUAUUUUUUGUU-UUAAUUGCCGCCUGGCACUUAGCUAAUGUAAUUUAUAUUACAUCUUGCUGCCGCUCUAAA
..............((((((...((((..((((.(((((((........))))))).))-))...)))).))........(((..(((((((....)))))))...)))))))....... ( -28.10)
>consensus
AUCAGCAACAACAAAGGCGGAG____________GAAAACUUCACGAGUAUUUUUUGUUUUUAAUUGCCGCCUGGCACUUAGCUAAUGUAAUUUAUAUUACAUCUAGCUGCCGCUCUAAA
...............(((((..............(((.((((...)))).)))..............))))).((((....(((((((((((....))))))).))))))))........ (-22.16 = -22.39 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:03 2006