Locus 135

Sequence ID sp_pn.0
Location 1,242,028 – 1,242,146
Length 118
Max. P 0.999256
window840 window841

overview

Window 0

Location 1,242,028 – 1,242,146
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 74.02
Mean single sequence MFE -24.95
Consensus MFE -20.13
Energy contribution -21.47
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -1.79
Structure conservation index 0.81
SVM decision value 2.62
SVM RNA-class probability 0.995816
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 1242028 118 + 2038615/0-120
CAAAAGACAAGCUCAUAUCACGAAGGGCGAA-AAACCGCGGUACCACCUUCAUUCAAUGAACUUGUCAUUCUCUUGUUCUUAUGCAAUUGUAUGAUUGAGUAGCAUGACUUCCUAGCU-U
.....((((((.((((.....((((((((..-....)))(....).))))).....)))).))))))....((.((((((((..((......))..)))).)))).))..........-. ( -26.80)
>sp_ag.0 1351795 116 - 2160267/0-120
CAAAAGACAAGUCCAU--UACGAAGGGCGAA-AA-CCGCGGUACCACCUUCAUUCAAUGAACUUGUCAUUCUCAUUUAUUUUUAGUUUUACCCCAUUGAGUAGCAUCUUUUUCUGAUUAU
.....(((((((.(((--(..((((((((..-..-.)))(....).)))))....)))).)))))))...((((......................)))).................... ( -22.75)
>sp_mu.0 1422527 119 - 2030921/0-120
CAAAAAACAAGUUCACUGUAAGAAGGGCGAAGAAACCGCGGUACCACCUUCAUUCAAUGAACUUGUCAUUCUUAUUAUGUUAUUCUGUUUAUCAAUCAAGCAGCCAAAUUUUUCUAUU-U
......(((((((((.((...((((((((.......)))(....).)))))...)).)))))))))..................((((((.......))))))...............-. ( -25.30)
>consensus
CAAAAGACAAGUUCAU__UACGAAGGGCGAA_AAACCGCGGUACCACCUUCAUUCAAUGAACUUGUCAUUCUCAUUUUCUUAUACUAUUAAACAAUUGAGUAGCAUAAUUUUCUAAUU_U
.....(((((((((((.....((((((((.......)))(....).))))).....)))))))))))..................................................... (-20.13 = -21.47 +   1.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 1,242,028 – 1,242,146
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 74.02
Mean single sequence MFE -30.08
Consensus MFE -26.75
Energy contribution -26.20
Covariance contribution -0.55
Combinations/Pair 1.15
Mean z-score -1.86
Structure conservation index 0.89
SVM decision value 3.46
SVM RNA-class probability 0.999256
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 1242028 118 + 2038615/0-120
A-AGCUAGGAAGUCAUGCUACUCAAUCAUACAAUUGCAUAAGAACAAGAGAAUGACAAGUUCAUUGAAUGAAGGUGGUACCGCGGUUU-UUCGCCCUUCGUGAUAUGAGCUUGUCUUUUG
.-............((((.................)))).........((((.(((((((((((...(((((((.(....)((((...-.)))))))))))...))))))))))))))). ( -31.23)
>sp_ag.0 1351795 116 - 2160267/0-120
AUAAUCAGAAAAAGAUGCUACUCAAUGGGGUAAAACUAAAAAUAAAUGAGAAUGACAAGUUCAUUGAAUGAAGGUGGUACCGCGG-UU-UUCGCCCUUCGUA--AUGGACUUGUCUUUUG
.....(((((........(((((....))))).....................((((((((((((..((((((((((.((....)-).-.))).))))))))--)))))))))))))))) ( -30.20)
>sp_mu.0 1422527 119 - 2030921/0-120
A-AAUAGAAAAAUUUGGCUGCUUGAUUGAUAAACAGAAUAACAUAAUAAGAAUGACAAGUUCAUUGAAUGAAGGUGGUACCGCGGUUUCUUCGCCCUUCUUACAGUGAACUUGUUUUUUG
.-..........((((..(((......).))..))))............(((.(((((((((((((...(((((.(....)((((.....)))))))))...))))))))))))).))). ( -28.80)
>consensus
A_AAUAAGAAAAUCAUGCUACUCAAUCGAAAAAAAGAAUAAAAAAAUGAGAAUGACAAGUUCAUUGAAUGAAGGUGGUACCGCGGUUU_UUCGCCCUUCGUA__AUGAACUUGUCUUUUG
.................................................(((.(((((((((((...(((((((.(....)((((.....)))))))))))...))))))))))).))). (-26.75 = -26.20 +  -0.55) 
# Strand winner: reverse (1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 19:02:17 2006