Locus 3040

Sequence ID 2R_DroMel_CAF1
Location 10,483,647 – 10,483,766
Length 119
Max. P 0.844043
window5006 window5007

overview

Window 6

Location 10,483,647 – 10,483,747
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.48
Mean single sequence MFE -28.60
Consensus MFE -17.26
Energy contribution -16.90
Covariance contribution -0.36
Combinations/Pair 1.18
Mean z-score -1.66
Structure conservation index 0.60
SVM decision value 0.07
SVM RNA-class probability 0.566795
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10483647 100 - 20766785
UUUGUCGCUGUCGAGAGCCGUUAAAGUUUACUGGCAUGAGUAAUCAGCCAAAUGGAGCGCAAUAAAAUGGCAA-----A------CGGUAACACG----GC--CAAUCUAUCACCAG---
......(((((.(...((((((...((((..((((.(((....)))))))....))))((.........)).)-----)------))))..))))----))--..............--- ( -24.70)
>DroVir_CAF1 114394 99 - 1
AUCGUCGCUGU---GCGCCGUUAAAGUUUACUGGCAUGAGUAAUCAGCCAAAUGGAGCGCAAUAAAAUGGCAACGGCAA------CGGCAACACG----GC--CAAUCUAUCAG------
...((.(((((---..((((((...((((..((((.(((....)))))))....)))).......)))))).))))).)------)(((......----))--)..........------ ( -31.50)
>DroPse_CAF1 81400 98 - 1
AUUGUAUCGG--GAGAACCGUUAAAGUUUACUGGCAUGAGUAAUCGGCCAAAUGGAGCGCAAUAAAAUGGCAA-----A------CGGUAACACG----GC--CAAUAUAUCACAAG---
(((((..(((--.....))).....((((..((((.(((....)))))))....)))))))))....((((..-----.------((......))----))--))............--- ( -22.40)
>DroGri_CAF1 102754 107 - 1
GUUGUC----------GCCGUUAAAGUUUACUGGCAUGAGUAAUCAGCCAAAUGGAGCGCAAUAAAAUGGCAACGGCAACGGCAACAGCAACACAGGCGGCAACAAUCUAUCAGCAG---
((((((----------(((......((((..((((.(((....)))))))....))))((........(....)(....)(....).))......))))))))).............--- ( -34.80)
>DroMoj_CAF1 136744 104 - 1
GUUGUCGCGGU---GAGCCGUUAAAGUUUACUGGCAUGAGUAAUCAGCCAAAUGGAGCGCAAUAAAAUGGCAACGGCAACGG-AACGGCAACACG----GC--CAAUCUAUCAG------
((((((((.((---..((((((...((((..((((.(((....)))))))....))))((.........)))))))).)).)-..)))))))...----..--...........------ ( -32.40)
>DroAna_CAF1 90850 103 - 1
UCUGUCGCUGUCGAGGGCCGUUAAAGUUUACUGGCAUGAGUAAUCAGCCAAAUGGAGCGCAAUAAAAUGGCAA-----A------CGGUAACACG----GC--CAAUCUAUCACACAAGU
......(((((.(...((((((...((((..((((.(((....)))))))....))))((.........)).)-----)------))))..))))----))--................. ( -25.80)
>consensus
AUUGUCGCUGU___GAGCCGUUAAAGUUUACUGGCAUGAGUAAUCAGCCAAAUGGAGCGCAAUAAAAUGGCAA_____A______CGGCAACACG____GC__CAAUCUAUCAC_AG___
................((((.....((((..((((.(((....)))))))....))))((.........))..............))))............................... (-17.26 = -16.90 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,483,673 – 10,483,766
Length 93
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 74.29
Mean single sequence MFE -24.98
Consensus MFE -15.56
Energy contribution -15.67
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -1.52
Structure conservation index 0.62
SVM decision value 0.76
SVM RNA-class probability 0.844043
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10483673 93 - 20766785
----UCUUUUCUUU-CAUAG---------------CGUUUUUGUCGCUGUCGAGAGCCGUUAAAGUUUACUGGCAUGAGUAAUCAGCCAAAUGGAGCGCAAUAAAAUGGCAA-----A-
----.......(((-(((((---------------((.......)))))).))))((((((...((((..((((.(((....)))))))....)))).......))))))..-----.- ( -26.80)
>DroPse_CAF1 81426 92 - 1
----UCCCCCCCUUUUUUCC---------------CACUAUUGUAUCGG--GAGAACCGUUAAAGUUUACUGGCAUGAGUAAUCGGCCAAAUGGAGCGCAAUAAAAUGGCAA-----A-
----...............(---------------((.((((((..(((--.....))).....((((..((((.(((....)))))))....))))))))))...)))...-----.- ( -19.90)
>DroGri_CAF1 102791 92 - 1
GUUAAAUUGUCAAU-CA-AU---------------UGCUGUUGUC----------GCCGUUAAAGUUUACUGGCAUGAGUAAUCAGCCAAAUGGAGCGCAAUAAAAUGGCAACGGCAAC
..............-..-.(---------------((((((((((----------(...(((..((((..((((.(((....)))))))....))))....)))..)))))))))))). ( -27.50)
>DroYak_CAF1 88407 93 - 1
----UUUUCUCUUU-CAUAG---------------CGUUUUUGUCGCUGUCGAGAGCCGUUAAAGUUUACUGGCAUGAGUAAUCAGCCAAAUGGAGCGCAAUAAAAUGGCAA-----A-
----...((((...-.((((---------------((.......)))))).))))((((((...((((..((((.(((....)))))))....)))).......))))))..-----.- ( -27.20)
>DroAna_CAF1 90879 107 - 1
----UCUUCGG-UU-UAUAGUUUCUGACUCUCUUUAGUCUCUGUCGCUGUCGAGGGCCGUUAAAGUUUACUGGCAUGAGUAAUCAGCCAAAUGGAGCGCAAUAAAAUGGCAA-----A-
----.(((((.-..-.(((((..(.((((......))))...)..))))))))))((((((...((((..((((.(((....)))))))....)))).......))))))..-----.- ( -28.40)
>DroPer_CAF1 87947 92 - 1
----UCCCCCCCUU-UUUCC---------------CACUAUUGUAUCGG-GGAGAACCGUUAAAGUUUACUGGCAUGAGUAAUCGGCCAAAUGGAGCGCAAUAAAAUGGCAA-----A-
----..........-....(---------------((.((((((..(((-......))).....((((..((((.(((....)))))))....))))))))))...)))...-----.- ( -20.10)
>consensus
____UCUUCUCCUU_CAUAG_______________CGCUUUUGUCGCUG_CGAGAGCCGUUAAAGUUUACUGGCAUGAGUAAUCAGCCAAAUGGAGCGCAAUAAAAUGGCAA_____A_
.......................................................((((((...((((..((((.(((....)))))))....)))).......))))))......... (-15.56 = -15.67 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:47 2006