Locus 174

Sequence ID 2L_DroMel_CAF1
Location 540,875 – 540,985
Length 110
Max. P 0.992672
window263 window264

overview

Window 3

Location 540,875 – 540,985
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 73.77
Mean single sequence MFE -27.51
Consensus MFE -14.64
Energy contribution -15.36
Covariance contribution 0.72
Combinations/Pair 1.23
Mean z-score -2.38
Structure conservation index 0.53
SVM decision value 2.34
SVM RNA-class probability 0.992672
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 540875 110 + 22407834
GCUUCCCUGGUAAUUCAGUUCGAA--AU-------AUAUGAGCAUCCUCGGGAAAAAUAAUAAAUUCAGCUGUCAGUAUG-CCGGAUUCCCCAGACUGAAGUACCAGGCGAACACAAAUC
..((((((((((.((((((..(..--..-------....(((....)))((((..........((((.((.........)-).)))))))))..)))))).))))))).)))........ ( -30.40)
>DroSec_CAF1 86358 111 + 1
GCUCCCCUGGUAAUUCAGUUCAAAAAAU-------AUAAGAGCAUCCUCG-GAAAAAUAAUAAAUUUAGCUGUCAGUAUA-CCGGUUUCUACAAAUUGAAGUACCAGGCGAACAUAAAUC
(.((.(((((((.(((((((........-------....(((....))).-................(((((........-.)))))......))))))).))))))).)).)....... ( -21.20)
>DroSim_CAF1 88791 111 + 1
GCUCCCCUGGUAAUUCAGUUCGAAAAAU-------AUAAGAGCAUCCUCG-GAAAAAUAAUAAAUUUAGCUGUCAGUAUG-CCGGUUUCCACAAACUGAAGUACCAGGCGAACAUAAAUC
(.((.(((((((.(((((((.(......-------....(((....)))(-(((((((.....)))).((((.(.....)-.)))))))).).))))))).))))))).)).)....... ( -27.60)
>DroEre_CAF1 90082 103 + 1
GUUCCCCUGGUAUUUCAGAUCGAACAUUUUCAAU-UUAAG----CCCUCG-GA----------GCUAAACAGCU-GCUAGGCUGUAUUCCUCAAACUGAAGUACCAGGCGCACAGAAAUC
((.(.(((((((((((((...(((....)))...-.....----......-((----------(..(.((((((-....)))))).)..)))...))))))))))))).).))....... ( -33.60)
>DroYak_CAF1 89529 111 + 1
GCUCCCCUGGUAUAUCAAUUCGAAAAAUUCAAAUUUUAAG----UCCCCG-GAAA----AUAAGUUUAGCAGCUAGUUUGUCCGUUUUCGCCAAUCUGAAGUACCAGGCGAACAGAAAUC
(.((.((((((((.((((((((((((..............----....((-((((----((.(((......))).)))).))))))))))..))).))).)))))))).)).)....... ( -24.76)
>consensus
GCUCCCCUGGUAAUUCAGUUCGAAAAAU_______AUAAGAGCAUCCUCG_GAAAAAUAAUAAAUUUAGCUGUCAGUAUG_CCGGUUUCCACAAACUGAAGUACCAGGCGAACAGAAAUC
(.((.(((((((.(((((((...................(((....)))..............((......))....................))))))).))))))).)).)....... (-14.64 = -15.36 +   0.72)

alignment

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secondary structure

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dotplot

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Window 4

Location 540,875 – 540,985
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 73.77
Mean single sequence MFE -30.98
Consensus MFE -20.86
Energy contribution -24.42
Covariance contribution 3.56
Combinations/Pair 1.16
Mean z-score -1.96
Structure conservation index 0.67
SVM decision value 1.83
SVM RNA-class probability 0.979191
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 540875 110 - 22407834
GAUUUGUGUUCGCCUGGUACUUCAGUCUGGGGAAUCCGG-CAUACUGACAGCUGAAUUUAUUAUUUUUCCCGAGGAUGCUCAUAU-------AU--UUCGAACUGAAUUACCAGGGAAGC
........(((.(((((((.((((((.(((((((..(((-(.........))))(((.....))).)))))(((....)))....-------..--..)).)))))).)))))))))).. ( -32.30)
>DroSec_CAF1 86358 111 - 1
GAUUUAUGUUCGCCUGGUACUUCAAUUUGUAGAAACCGG-UAUACUGACAGCUAAAUUUAUUAUUUUUC-CGAGGAUGCUCUUAU-------AUUUUUUGAACUGAAUUACCAGGGGAGC
.......((((.(((((((.((((.....(((....(((-....)))....)))............(((-.(((((((......)-------)))))).))).)))).))))))).)))) ( -26.40)
>DroSim_CAF1 88791 111 - 1
GAUUUAUGUUCGCCUGGUACUUCAGUUUGUGGAAACCGG-CAUACUGACAGCUAAAUUUAUUAUUUUUC-CGAGGAUGCUCUUAU-------AUUUUUCGAACUGAAUUACCAGGGGAGC
.......((((.(((((((.(((((((((..(((...((-(((.((.......((((.....))))...-...))))))).....-------.)))..))))))))).))))))).)))) ( -34.52)
>DroEre_CAF1 90082 103 - 1
GAUUUCUGUGCGCCUGGUACUUCAGUUUGAGGAAUACAGCCUAGC-AGCUGUUUAGC----------UC-CGAGGG----CUUAA-AUUGAAAAUGUUCGAUCUGAAAUACCAGGGGAAC
..........(.(((((((.(((((.(((((.(..(((((.....-.)))))..(((----------(.-....))----))...-........).))))).))))).))))))).)... ( -32.90)
>DroYak_CAF1 89529 111 - 1
GAUUUCUGUUCGCCUGGUACUUCAGAUUGGCGAAAACGGACAAACUAGCUGCUAAACUUAU----UUUC-CGGGGA----CUUAAAAUUUGAAUUUUUCGAAUUGAUAUACCAGGGGAGC
.......((((.(((((((..((((.....((((((.(((.(((..((........))..)----))))-)(....----).............))))))..))))..))))))).)))) ( -28.80)
>consensus
GAUUUAUGUUCGCCUGGUACUUCAGUUUGGGGAAACCGG_CAUACUGACAGCUAAAUUUAUUAUUUUUC_CGAGGAUGCUCUUAU_______AUUUUUCGAACUGAAUUACCAGGGGAGC
.......((((.(((((((.((((((((((((((..(((.....)))........................(((....)))............)))))))))))))).))))))).)))) (-20.86 = -24.42 +   3.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:27:59 2006