Locus 2904

Sequence ID X_DroMel_CAF1
Location 7,772,058 – 7,772,169
Length 111
Max. P 0.977786
window4758 window4759

overview

Window 8

Location 7,772,058 – 7,772,169
Length 111
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 80.34
Mean single sequence MFE -18.67
Consensus MFE -11.69
Energy contribution -12.47
Covariance contribution 0.78
Combinations/Pair 1.06
Mean z-score -2.15
Structure conservation index 0.63
SVM decision value 0.68
SVM RNA-class probability 0.821380
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7772058 111 + 22224390
AGUUGUCAA----UAUCGCAAACAAAAAAUUGCGAAUGCUUAAAUAAGCG-AAAGAGAACACAAAUGUUCUACUAAUAUUAGUAG---UGAGGUGUGAAUAAAUAUAGAAACAAA-AAGG
.(((.((..----..((((((........)))))).(((((....)))))-...)).)))(((......((((((....))))))---.....)))...................-.... ( -21.40)
>DroSec_CAF1 6174 104 + 1
GGGUGUCAA----UAUCGCAAACAAAAAAUUGCGAA--------UAAGCGGAAAGAGAACAUAAAUGUUCUACUAAUAUUAGUAG---UGAGGUGUGAAUAAAUAUAGAAACAAA-AAGG
..((.((..----..((((((........)))))).--------...............((((......((((((....))))))---.....))))..........)).))...-.... ( -16.20)
>DroYak_CAF1 6374 118 + 1
AGAUGUCAAAUUGUAUCGCAAACACA-AACUGCGAAUGCUUAAAUAAGCA-AAAGAGAACACAAAAGUACUAAUAAUAGUAGUAAGCUGGGGGUGUUGAGAAAUAUAGAAACAAAAAAGG
...(((.....(((.((...(((((.-..(.((...(((((....)))))-..............(.(((((....))))).)..)).)...)))))..)).))).....)))....... ( -18.40)
>consensus
AGAUGUCAA____UAUCGCAAACAAAAAAUUGCGAAUGCUUAAAUAAGCG_AAAGAGAACACAAAUGUUCUACUAAUAUUAGUAG___UGAGGUGUGAAUAAAUAUAGAAACAAA_AAGG
.....((........((((((........)))))).......................((((.......((((((....)))))).......))))...........))........... (-11.69 = -12.47 +   0.78)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 9

Location 7,772,058 – 7,772,169
Length 111
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.34
Mean single sequence MFE -16.23
Consensus MFE -11.81
Energy contribution -12.04
Covariance contribution 0.23
Combinations/Pair 1.10
Mean z-score -2.44
Structure conservation index 0.73
SVM decision value 1.80
SVM RNA-class probability 0.977786
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7772058 111 - 22224390
CCUU-UUUGUUUCUAUAUUUAUUCACACCUCA---CUACUAAUAUUAGUAGAACAUUUGUGUUCUCUUU-CGCUUAUUUAAGCAUUCGCAAUUUUUUGUUUGCGAUA----UUGACAACU
....-.(((((..((........((((.....---((((((....))))))......))))........-.((((....))))..((((((........))))))))----..))))).. ( -19.10)
>DroSec_CAF1 6174 104 - 1
CCUU-UUUGUUUCUAUAUUUAUUCACACCUCA---CUACUAAUAUUAGUAGAACAUUUAUGUUCUCUUUCCGCUUA--------UUCGCAAUUUUUUGUUUGCGAUA----UUGACACCC
....-..((((..((.................---.(((((....)))))(((((....)))))............--------.((((((........))))))))----..))))... ( -13.60)
>DroYak_CAF1 6374 118 - 1
CCUUUUUUGUUUCUAUAUUUCUCAACACCCCCAGCUUACUACUAUUAUUAGUACUUUUGUGUUCUCUUU-UGCUUAUUUAAGCAUUCGCAGUU-UGUGUUUGCGAUACAAUUUGACAUCU
.....................((((..............(((((....)))))...(((((........-(((((....))))).((((((..-.....))))))))))).))))..... ( -16.00)
>consensus
CCUU_UUUGUUUCUAUAUUUAUUCACACCUCA___CUACUAAUAUUAGUAGAACAUUUGUGUUCUCUUU_CGCUUAUUUAAGCAUUCGCAAUUUUUUGUUUGCGAUA____UUGACAACU
.......((((.............((((.......((((((....)))))).......)))).......................((((((........))))))........))))... (-11.81 = -12.04 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:46:17 2006