Locus 1860

Sequence ID 3R_DroMel_CAF1
Location 5,337,776 – 5,337,883
Length 107
Max. P 0.779311
window3060 window3061

overview

Window 0

Location 5,337,776 – 5,337,883
Length 107
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 78.01
Mean single sequence MFE -23.48
Consensus MFE -11.12
Energy contribution -12.52
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.47
SVM decision value 0.26
SVM RNA-class probability 0.658108
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5337776 107 + 27905053
--UAAACGGGAAACCAAACCAGCGAAAGGGUGCAGAAAUCUCUAGAGUAUUUGGACCUGUGCAGCCCUAGCUUUGCCAGAUCUAAGUACAUAUAACUCACCGAUAACCA
--.....((....)).......(....)((((.((...((....))(((((((((.(((.(((((....))..)))))).)))))))))......))))))........ ( -29.70)
>DroSec_CAF1 590 107 + 1
--UAAACGGGAAACCAAACCAGCGAAAGGGUGCAGAAAUCUCUAGAGGCUUUGGACCUCUGCACCCCUUUUUAUGCCAGAUCUAACUACAUAUAACUCACCGAUAACCA
--.....((....))......(((((((((((((((..(((..((...))..)))..)))))).)))))))...))................................. ( -25.00)
>DroSim_CAF1 593 100 + 1
--UAAACGGGAAACCAAACCAGCGAAAGGGUGCAGAAAUCUCUAGAGGAU-------CCUGCACCCCUUUUUAUGCCAGAUCUUACUACAUAUUACUCACCGAUAACCA
--.....((....))......((((((((((((((..((((.....))))-------.))))).)))))))...))................................. ( -22.80)
>DroEre_CAF1 589 104 + 1
UCAAGA-GGUACCCCAAAACAGCAAAAGAAAGCAGAAAUCUCUAGAGGCUUAAGACCUCUGCACCCUUUGCAAUACCAGAUUUUAGU----AUAACUCACCGAUAACCA
....((-(((((.........((........)).(((((((..((((((....).)))))(((.....)))......))))))).))----))..)))........... ( -17.90)
>DroYak_CAF1 569 96 + 1
UUUAUAUGGGAAACCAGAGCAGCGAAAGGGCGCAGAAAUCUCUAGAGACU---------UGCACCCUUUGAAAUACCAGAUUUUAGU----AUAACUCACCGAUAACCA
......(((....)))(((.....((((((.((((...((....))...)---------))).))))))...((((.........))----))..)))........... ( -22.00)
>consensus
__UAAACGGGAAACCAAACCAGCGAAAGGGUGCAGAAAUCUCUAGAGGCUU__GACCUCUGCACCCCUUGCUAUGCCAGAUCUUAGUACAUAUAACUCACCGAUAACCA
.......((....))............((((((((.......................))))))))........................................... (-11.12 = -12.52 +   1.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 5,337,776 – 5,337,883
Length 107
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 78.01
Mean single sequence MFE -30.52
Consensus MFE -17.82
Energy contribution -19.42
Covariance contribution 1.60
Combinations/Pair 1.27
Mean z-score -1.90
Structure conservation index 0.58
SVM decision value 0.55
SVM RNA-class probability 0.779311
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5337776 107 - 27905053
UGGUUAUCGGUGAGUUAUAUGUACUUAGAUCUGGCAAAGCUAGGGCUGCACAGGUCCAAAUACUCUAGAGAUUUCUGCACCCUUUCGCUGGUUUGGUUUCCCGUUUA--
.......((((((((.......)))))((((..((..(((.((((.((((.((((((..........).))))).))))))))...))).))..))))..)))....-- ( -23.80)
>DroSec_CAF1 590 107 - 1
UGGUUAUCGGUGAGUUAUAUGUAGUUAGAUCUGGCAUAAAAAGGGGUGCAGAGGUCCAAAGCCUCUAGAGAUUUCUGCACCCUUUCGCUGGUUUGGUUUCCCGUUUA--
.....((((((((....(((((((......)).)))))...((((((((((((((((..........).)))))))))))))))))))))))..((....)).....-- ( -34.70)
>DroSim_CAF1 593 100 - 1
UGGUUAUCGGUGAGUAAUAUGUAGUAAGAUCUGGCAUAAAAAGGGGUGCAGG-------AUCCUCUAGAGAUUUCUGCACCCUUUCGCUGGUUUGGUUUCCCGUUUA--
.....((((((((....(((((((......)).)))))...(((((((((((-------(..((....))..))))))))))))))))))))..((....)).....-- ( -32.70)
>DroEre_CAF1 589 104 - 1
UGGUUAUCGGUGAGUUAU----ACUAAAAUCUGGUAUUGCAAAGGGUGCAGAGGUCUUAAGCCUCUAGAGAUUUCUGCUUUCUUUUGCUGUUUUGGGGUACC-UCUUGA
......((((.(((.((.----.(((((((........((((((((.(((((((((((.((...)).)))))))))))..)))))))).)))))))..)).)-)))))) ( -31.90)
>DroYak_CAF1 569 96 - 1
UGGUUAUCGGUGAGUUAU----ACUAAAAUCUGGUAUUUCAAAGGGUGCA---------AGUCUCUAGAGAUUUCUGCGCCCUUUCGCUGCUCUGGUUUCCCAUAUAAA
.((..(((((.((((.((----((((.....))))))...((((((((((---------(((((....)))))..)))))))))).))).).)))))..))........ ( -29.50)
>consensus
UGGUUAUCGGUGAGUUAUAUGUACUAAGAUCUGGCAUAACAAGGGGUGCAGAGGUC__AAGCCUCUAGAGAUUUCUGCACCCUUUCGCUGGUUUGGUUUCCCGUUUA__
.....((((((((..............(......)......(((((((((((((((.............)))))))))))))))))))))))..((....))....... (-17.82 = -19.42 +   1.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:20 2006