Locus 5168

Sequence ID 3R_DroMel_CAF1
Location 13,566,104 – 13,566,258
Length 154
Max. P 0.995526
window8444 window8445 window8446

overview

Window 4

Location 13,566,104 – 13,566,218
Length 114
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 89.58
Mean single sequence MFE -40.42
Consensus MFE -31.28
Energy contribution -32.12
Covariance contribution 0.84
Combinations/Pair 1.14
Mean z-score -2.18
Structure conservation index 0.77
SVM decision value 1.22
SVM RNA-class probability 0.932129
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13566104 114 + 27905053
GAUGGCCAAAGAUUUAUGGCUCUGUGGGGGCUUUACACUUCCGGGGA---AGGUGGAAUCGGGGCAAGUGUUUACUAUUCGAAGCCCUCCGGUGGAAGUUCGGGUAGUAAACAUUUG
....(((...(((((..(((((.....))))).(((.((((....))---))))))))))..)))((((((((((((((((((..((......))...)))))))))))))))))). ( -43.40)
>DroSec_CAF1 8099 114 + 1
GAUGGCCAAAGAUUUAUGGCUCUGUGGGGGCUUUACACUUCCGGGGA---AGGUGGAAUCUGGGCAAGUGUUUACUAUUCGCAGCCCUCCGGUGGAAGUUCGGGUAGUAAACAUUUG
....(((..((((((..(((((.....))))).(((.((((....))---))))))))))).)))((((((((((((((((.(((..(((...))).))))))))))))))))))). ( -42.10)
>DroSim_CAF1 6168 114 + 1
GAUGGCCAAAGAUUUAUGGCUCUGUGGGGGCUUUACACUUCCGGGGA---AGGUGGAAUCGGGGCAAGUGUUUACUAUUCGCAGCCCUCCGGUGGAAGUUCGGGUAGUAAACAUUUG
....(((...(((((..(((((.....))))).(((.((((....))---))))))))))..)))((((((((((((((((.(((..(((...))).))))))))))))))))))). ( -42.40)
>DroEre_CAF1 6903 114 + 1
GAUGGCUAAAGAUUUAUGGCUCUGUGGGGGCAUUACACUGCCCGGGA---GGAAGGAAUCGGGGCAAGUGUUUACUACUUGGCGCUCUCCGGUGGAAGUUCGGAUAGUAAACAUUUG
....(((...(((((....((((....(((((......))))).)))---)....)))))..)))((((((((((((.((.(.(((.(((...)))))).).)))))))))))))). ( -36.40)
>DroYak_CAF1 6589 117 + 1
GAUGGCUGAAGAUUUAUGGCUCUGUGGGGGAAUUACACUUGCCGCGAAGAAGAAGGAAUCGAAGCCAGUGUUUACUAUUUGGCGCUCUCCGGUGGAAGUUCGGGUAGUAAACAUUUA
..(((((...(((((....((.(((((.((........)).))))).))......)))))..)))))(((((((((((((((.(((.(((...)))))))))))))))))))))... ( -37.80)
>consensus
GAUGGCCAAAGAUUUAUGGCUCUGUGGGGGCUUUACACUUCCGGGGA___AGGUGGAAUCGGGGCAAGUGUUUACUAUUCGCAGCCCUCCGGUGGAAGUUCGGGUAGUAAACAUUUG
....(((...(((((.....(((.((((((.......)))))).)))........)))))..)))(((((((((((((((((...((......))....))))))))))))))))). (-31.28 = -32.12 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 13,566,144 – 13,566,258
Length 114
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 85.33
Mean single sequence MFE -45.46
Consensus MFE -33.34
Energy contribution -36.14
Covariance contribution 2.80
Combinations/Pair 1.10
Mean z-score -3.48
Structure conservation index 0.73
SVM decision value 2.59
SVM RNA-class probability 0.995526
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13566144 114 + 27905053
CCGGGGA---AGGUGGAAUCGGGGCAAGUGUUUACUAUUCGAAGCCCUCCGGUGGAAGUUCGGGUAGUAAACAUUUGCCCAAAUCGAUGGGGGAGCACAUUUGGUCGAUUUCGAUUU
((.....---.))..((((((((((((((((((((((((((((..((......))...))))))))))))))))))))))((((((((.(((.......))).)))))))))))))) ( -49.00)
>DroSec_CAF1 8139 114 + 1
CCGGGGA---AGGUGGAAUCUGGGCAAGUGUUUACUAUUCGCAGCCCUCCGGUGGAAGUUCGGGUAGUAAACAUUUGCCCAAAUCGAUGGGGGAGCACAUUUGGUCGAUUCCGAUUU
((.....---.))((((((((((((((((((((((((((((.(((..(((...))).))))))))))))))))))))))))....(((.(((.......))).)))))))))).... ( -47.30)
>DroSim_CAF1 6208 114 + 1
CCGGGGA---AGGUGGAAUCGGGGCAAGUGUUUACUAUUCGCAGCCCUCCGGUGGAAGUUCGGGUAGUAAACAUUUGCCCAAAUCGAUGGGGGAGCACAUUUGGUCGAUUCCGAUUU
((.....---.))((((((((((((((((((((((((((((.(((..(((...))).)))))))))))))))))))))))..(((((((.(....).)).))))))))))))).... ( -48.40)
>DroEre_CAF1 6943 100 + 1
CCCGGGA---GGAAGGAAUCGGGGCAAGUGUUUACUACUUGGCGCUCUCCGGUGGAAGUUCGGAUAGUAAACAUUUGCCCAAAUCGAUGGGGGAGCA--------------CGAUUC
.((....---))...((((((((((((((((((((((.((.(.(((.(((...)))))).).))))))))))))))))))..........(....).--------------)))))) ( -38.10)
>DroYak_CAF1 6629 117 + 1
GCCGCGAAGAAGAAGGAAUCGAAGCCAGUGUUUACUAUUUGGCGCUCUCCGGUGGAAGUUCGGGUAGUAAACAUUUACCCAAAUCGAUUGGGGAGCCCAUUUGGUCGAUUCCGAUUC
........(((...(((((((((((....))))((((..(((.((((((((((.((..((.((((((.......)))))))).)).)))))))))))))..)))))))))))..))) ( -44.50)
>consensus
CCGGGGA___AGGUGGAAUCGGGGCAAGUGUUUACUAUUCGCAGCCCUCCGGUGGAAGUUCGGGUAGUAAACAUUUGCCCAAAUCGAUGGGGGAGCACAUUUGGUCGAUUCCGAUUU
...............(((((((((((((((((((((((((((...((......))....))))))))))))))))))))).(((((((.(((.......))).))))))).)))))) (-33.34 = -36.14 +   2.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 13,566,144 – 13,566,258
Length 114
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 85.33
Mean single sequence MFE -35.03
Consensus MFE -24.87
Energy contribution -26.87
Covariance contribution 2.00
Combinations/Pair 1.12
Mean z-score -3.03
Structure conservation index 0.71
SVM decision value 1.90
SVM RNA-class probability 0.981945
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13566144 114 - 27905053
AAAUCGAAAUCGACCAAAUGUGCUCCCCCAUCGAUUUGGGCAAAUGUUUACUACCCGAACUUCCACCGGAGGGCUUCGAAUAGUAAACACUUGCCCCGAUUCCACCU---UCCCCGG
.((((((((((((.................)))))))((((((.(((((((((..(((.(((((...)))))...)))..))))))))).)))))))))))......---....... ( -35.93)
>DroSec_CAF1 8139 114 - 1
AAAUCGGAAUCGACCAAAUGUGCUCCCCCAUCGAUUUGGGCAAAUGUUUACUACCCGAACUUCCACCGGAGGGCUGCGAAUAGUAAACACUUGCCCAGAUUCCACCU---UCCCCGG
.....((((((((.((....)).))...........(((((((.(((((((((..((..(((((...)))))....))..))))))))).)))))))))))))....---....... ( -38.20)
>DroSim_CAF1 6208 114 - 1
AAAUCGGAAUCGACCAAAUGUGCUCCCCCAUCGAUUUGGGCAAAUGUUUACUACCCGAACUUCCACCGGAGGGCUGCGAAUAGUAAACACUUGCCCCGAUUCCACCU---UCCCCGG
.....(((((((.......(((......)))......((((((.(((((((((..((..(((((...)))))....))..))))))))).)))))))))))))....---....... ( -37.70)
>DroEre_CAF1 6943 100 - 1
GAAUCG--------------UGCUCCCCCAUCGAUUUGGGCAAAUGUUUACUAUCCGAACUUCCACCGGAGAGCGCCAAGUAGUAAACACUUGCCCCGAUUCCUUCC---UCCCGGG
((((((--------------((......)).))))))((((((.((((((((((.((..((((....))))..))....)))))))))).)))))).........((---....)). ( -29.60)
>DroYak_CAF1 6629 117 - 1
GAAUCGGAAUCGACCAAAUGGGCUCCCCAAUCGAUUUGGGUAAAUGUUUACUACCCGAACUUCCACCGGAGAGCGCCAAAUAGUAAACACUGGCUUCGAUUCCUUCUUCUUCGCGGC
.....((((((((((....))((((.((....((((((((((.........))))))))..))....)).))))((((............)))).)))))))).............. ( -33.70)
>consensus
AAAUCGGAAUCGACCAAAUGUGCUCCCCCAUCGAUUUGGGCAAAUGUUUACUACCCGAACUUCCACCGGAGGGCUCCGAAUAGUAAACACUUGCCCCGAUUCCACCU___UCCCCGG
.((((((((((((.................)))))))((((((.(((((((((..((..(((((...)))))....))..))))))))).)))))))))))................ (-24.87 = -26.87 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:14 2006