Locus 3696

Sequence ID X_DroMel_CAF1
Location 9,857,726 – 9,857,846
Length 120
Max. P 0.819418
window6052 window6053

overview

Window 2

Location 9,857,726 – 9,857,846
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 72.72
Mean single sequence MFE -39.98
Consensus MFE -15.54
Energy contribution -15.40
Covariance contribution -0.14
Combinations/Pair 1.39
Mean z-score -1.85
Structure conservation index 0.39
SVM decision value -0.05
SVM RNA-class probability 0.506752
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9857726 120 + 22224390
GAGAUAUUAUUGUGGCCAAGAAGCCACCAGAGCAGCACAAAGUUCUGCCCAAGAUCAUCCUCACCAAGGGAGCACCCAUUCUGCUGAAUCUUAACAAAGUGCAACAAAAUGCUGCUUUGC
...........(((((......)))))((((((((((....(.(((.....))).).((((......))))((((..((((....)))).........)))).......)))))))))). ( -31.10)
>DroVir_CAF1 2971 120 + 1
GCUCCAUUGUGGUGGCCCAAACGCCGCCAAUGCAGCACAAGAUGCUGCCUCGCGUCAUCGGCAGCAAAGGUGGUCCCAUAUUGCGUCCAUUGAACAAGGUGCAGCAGAUGGCCGCCCUGC
(((.(((..(((((((......)))))))))).)))......(((((((..........)))))))..(((((..((((.((((...((((......))))..))))))))))))).... ( -45.90)
>DroGri_CAF1 8327 120 + 1
GUUCCAUCGUGGUGGCAAGGACACCGCCAAAGCAGCACAAAGUUGUGCCACGCAUUAUUGGAAGCAAGGGCGGACCCAUGCUGCGUCCGCUGAACAAGGUGCAACAGCUGGCCGCUUUGA
........((((((.......))))))((((((.((.((..((((..((........(((....))).(((((((.(.....).)))))))......))..))))...)))).)))))). ( -45.20)
>DroEre_CAF1 2498 120 + 1
GAGAUAUUAUUGUGGCCAAGAAGCCACCAGAGCAGCACAAAGUUCUGCCCAAGAUCAUUCUCACCAAAGGGGCACCCAUGCUGCUGCAACUAAACAAAGUACAACAAAAUGCUGCCUUGC
((((.......(((((......)))))((((((........))))))...........))))....((((((((....(((....)))(((......))).........)))).)))).. ( -28.20)
>DroYak_CAF1 1930 120 + 1
GAGAUAUUAUUGUCGCCAAGAAGCCACCAGAGCAGCACAAAGUGCUGCCCAAGAUCAUCCUCACCAAAGGAGCGCCCAUGCUGCUGAAACUUAACAAAGUACAACAGAAUGCUGCUUUGC
(((........((.((......)).))..(.(((((((...))))))).).........)))..(((((.((((......(((.((..((((....)))).)).)))..)))).))))). ( -27.90)
>DroMoj_CAF1 2857 120 + 1
GCUCCAUUGUGAUAGGCCGGACACGGCCAAAGCAGCAAAAGGUGCUGCCUCGCAUCAUUGGCAGCAAGGGCGGGCCCAUGCUGCGCGCCUUGAAUAAGGUGCAGCAGGUGGCUGCCUUGC
((((((.(((((..(((((....)))))...((((((.....)))))).)))))....))).))).(((((((.(((.((((((..(((((....))))))))))))).).))))))).. ( -61.60)
>consensus
GAGACAUUAUGGUGGCCAAGAAGCCACCAAAGCAGCACAAAGUGCUGCCCAACAUCAUCCGCACCAAAGGAGCACCCAUGCUGCGGCAACUGAACAAAGUGCAACAGAAGGCUGCCUUGC
...........(((((......)))))....((((((...............((....))........((.....)).))))))..........((((((((........).))))))). (-15.54 = -15.40 +  -0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 9,857,726 – 9,857,846
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 72.72
Mean single sequence MFE -44.37
Consensus MFE -21.50
Energy contribution -20.25
Covariance contribution -1.25
Combinations/Pair 1.50
Mean z-score -1.85
Structure conservation index 0.48
SVM decision value 0.68
SVM RNA-class probability 0.819418
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9857726 120 - 22224390
GCAAAGCAGCAUUUUGUUGCACUUUGUUAAGAUUCAGCAGAAUGGGUGCUCCCUUGGUGAGGAUGAUCUUGGGCAGAACUUUGUGCUGCUCUGGUGGCUUCUUGGCCACAAUAAUAUCUC
.((.((((((((....((((.((..(...(..((((.(((...(((....)))))).))))..)...)..))))))......)))))))).))((((((....))))))........... ( -39.20)
>DroVir_CAF1 2971 120 - 1
GCAGGGCGGCCAUCUGCUGCACCUUGUUCAAUGGACGCAAUAUGGGACCACCUUUGCUGCCGAUGACGCGAGGCAGCAUCUUGUGCUGCAUUGGCGGCGUUUGGGCCACCACAAUGGAGC
.((.((.((((...((((((..((((((((.(((..((((...((.....)).))))..))).))).)))))(((((((...)))))))....))))))....)))).))....)).... ( -49.20)
>DroGri_CAF1 8327 120 - 1
UCAAAGCGGCCAGCUGUUGCACCUUGUUCAGCGGACGCAGCAUGGGUCCGCCCUUGCUUCCAAUAAUGCGUGGCACAACUUUGUGCUGCUUUGGCGGUGUCCUUGCCACCACGAUGGAAC
.....(((.((.((((..((.....)).)))))).)))((((.(((....))).))))((((.......(..(((((....)))))..)..(((.(((......))).)))...)))).. ( -44.90)
>DroEre_CAF1 2498 120 - 1
GCAAGGCAGCAUUUUGUUGUACUUUGUUUAGUUGCAGCAGCAUGGGUGCCCCUUUGGUGAGAAUGAUCUUGGGCAGAACUUUGUGCUGCUCUGGUGGCUUCUUGGCCACAAUAAUAUCUC
.((..(((((....(((((((((......)).)))))))(((.((.(((((.......((((....)))))))))...)).))))))))..))((((((....))))))........... ( -40.41)
>DroYak_CAF1 1930 120 - 1
GCAAAGCAGCAUUCUGUUGUACUUUGUUAAGUUUCAGCAGCAUGGGCGCUCCUUUGGUGAGGAUGAUCUUGGGCAGCACUUUGUGCUGCUCUGGUGGCUUCUUGGCGACAAUAAUAUCUC
.(((((.(((.(((((((((((((....))))....)))))).))).))).)))))....(((((.....(((((((((...)))))))))..((.(((....))).)).....))))). ( -39.20)
>DroMoj_CAF1 2857 120 - 1
GCAAGGCAGCCACCUGCUGCACCUUAUUCAAGGCGCGCAGCAUGGGCCCGCCCUUGCUGCCAAUGAUGCGAGGCAGCACCUUUUGCUGCUUUGGCCGUGUCCGGCCUAUCACAAUGGAGC
(((((((.(((.(.((((((.((((....))))...)))))).))))..).))))))..(((.(((((.(((((((((.....)))))))))(((((....))))))))))...)))... ( -53.30)
>consensus
GCAAAGCAGCAAUCUGUUGCACCUUGUUCAGUGGCAGCAGCAUGGGUCCGCCCUUGCUGACAAUGAUCCGGGGCAGAACUUUGUGCUGCUCUGGCGGCGUCUUGGCCACAACAAUAGAUC
((((((((((.....)))))..))))).........((((((..((.....(((.((..........)).)))......))..))))))......(((......)))............. (-21.50 = -20.25 +  -1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:53 2006