Locus 8832

Sequence ID 3R_DroMel_CAF1
Location 23,644,794 – 23,644,899
Length 105
Max. P 0.910456
window14179 window14180

overview

Window 9

Location 23,644,794 – 23,644,899
Length 105
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 77.05
Mean single sequence MFE -25.95
Consensus MFE -16.43
Energy contribution -16.43
Covariance contribution 0.00
Combinations/Pair 1.22
Mean z-score -1.83
Structure conservation index 0.63
SVM decision value 1.07
SVM RNA-class probability 0.910456
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23644794 105 + 27905053
AGCCCC--------ACGCUGUCAACUUGUUCAUAAGCGUCACUUUUAUGCAUACUUCACUGUGUAAACAGCGUGA-AAUUUUGUAGCGAACGUUUUGCAAAAUUUAUAAGGAAA
...(((--------(((((((..............((((.......))))((((......))))..))))))))(-((((((((((........)))))))))))....))... ( -25.20)
>DroVir_CAF1 146721 98 + 1
GGCGGC--------AGGCUGUCAACUUGUGCAUAAGCGUCAAUUUUAUGCACACUUCGCUGUGUAAAUGGCGUAAAAAUGUUGUUGCAAA-GCGUUGCAAAAAAUAG-------
(((((.--------...)))))....((((((((((.......))))))))))...((((.((((.(..((((....))))..))))).)-))).............------- ( -28.60)
>DroPse_CAF1 109431 112 + 1
AGGCCCUCUGCCAGGCGCUGUCAACUUGUUCAUAAGCGUCACUUUCAUGCACACUUCACUGUGUAAACAGCGUAA-AAUUUUGUUGCGAGCGCUUUGCAAAAUGUAUAAAAAA-
.(((.....)))..(((((((..............((((.......))))((((......))))..)))))))..-.(((((((.((....))...)))))))..........- ( -27.00)
>DroGri_CAF1 139161 94 + 1
AAAUG----------CGCUGUCAACUUGUGCAUAAGCGUCAAUUUUAUGCACACUUCGGUGUUUAAAUAGCGUAA-AAUGUUGUUGCA-A-GCAUUGCAAAAAAAAA-------
...((----------((((((.(((..(((((((((.......)))))))))((....)))))...)))))))).-((((((......-)-)))))...........------- ( -25.30)
>DroAna_CAF1 107756 99 + 1
--------------GCGCUGUCAACUUGUUCAUAAGCGUCACUUUUAUGCAUACUUCACUGUGUAAACAGCGUAA-AAUUUUGUUGCGAGCGCUCUGCAAAAUUUAUAAAAAGA
--------------(((((((..............((((.......))))((((......))))..))))))).(-((((((((.((....))...)))))))))......... ( -22.60)
>DroPer_CAF1 107736 112 + 1
AGGCCCUCUGCCAGGCGCUGUCAACUUGUUCAUAAGCGUCACUUUCAUGCACACUUCACUGUGUAAACAGCGUAA-AAUUUUGUUGCGAGCGCUUUGCAAAAUGUAUAAAAAA-
.(((.....)))..(((((((..............((((.......))))((((......))))..)))))))..-.(((((((.((....))...)))))))..........- ( -27.00)
>consensus
AGCCCC________GCGCUGUCAACUUGUUCAUAAGCGUCACUUUUAUGCACACUUCACUGUGUAAACAGCGUAA_AAUUUUGUUGCGAACGCUUUGCAAAAUAUAUAAAAAA_
..............(((((((..............((((.......))))((((......))))..))))))).....((((((.((....))...))))))............ (-16.43 = -16.43 +   0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 23,644,794 – 23,644,899
Length 105
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 77.05
Mean single sequence MFE -25.59
Consensus MFE -15.68
Energy contribution -17.27
Covariance contribution 1.59
Combinations/Pair 1.17
Mean z-score -1.60
Structure conservation index 0.61
SVM decision value 0.52
SVM RNA-class probability 0.766753
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23644794 105 - 27905053
UUUCCUUAUAAAUUUUGCAAAACGUUCGCUACAAAAUU-UCACGCUGUUUACACAGUGAAGUAUGCAUAAAAGUGACGCUUAUGAACAAGUUGACAGCGU--------GGGGCU
..(((....((((((((..............)))))))-)(((((((((.((...((.((((...(((....)))..))))....))..)).))))))))--------)))).. ( -22.44)
>DroVir_CAF1 146721 98 - 1
-------CUAUUUUUUGCAACGC-UUUGCAACAACAUUUUUACGCCAUUUACACAGCGAAGUGUGCAUAAAAUUGACGCUUAUGCACAAGUUGACAGCCU--------GCCGCC
-------.........(((..((-(...((((..........(((..........)))...(((((((((.........))))))))).))))..))).)--------)).... ( -21.10)
>DroPse_CAF1 109431 112 - 1
-UUUUUUAUACAUUUUGCAAAGCGCUCGCAACAAAAUU-UUACGCUGUUUACACAGUGAAGUGUGCAUGAAAGUGACGCUUAUGAACAAGUUGACAGCGCCUGGCAGAGGGCCU
-...........((((((...(((((..((((......-...((((((....))))))((((((.(((....)))))))))........))))..)))))...))))))..... ( -35.20)
>DroGri_CAF1 139161 94 - 1
-------UUUUUUUUUGCAAUGC-U-UGCAACAACAUU-UUACGCUAUUUAAACACCGAAGUGUGCAUAAAAUUGACGCUUAUGCACAAGUUGACAGCG----------CAUUU
-------...........(((((-(-((((((......-...((............))...(((((((((.........))))))))).)))).))).)----------)))). ( -18.30)
>DroAna_CAF1 107756 99 - 1
UCUUUUUAUAAAUUUUGCAGAGCGCUCGCAACAAAAUU-UUACGCUGUUUACACAGUGAAGUAUGCAUAAAAGUGACGCUUAUGAACAAGUUGACAGCGC--------------
.....................(((((..((((......-...((((((....))))))((((...(((....)))..))))........))))..)))))-------------- ( -21.30)
>DroPer_CAF1 107736 112 - 1
-UUUUUUAUACAUUUUGCAAAGCGCUCGCAACAAAAUU-UUACGCUGUUUACACAGUGAAGUGUGCAUGAAAGUGACGCUUAUGAACAAGUUGACAGCGCCUGGCAGAGGGCCU
-...........((((((...(((((..((((......-...((((((....))))))((((((.(((....)))))))))........))))..)))))...))))))..... ( -35.20)
>consensus
_UUUUUUAUAAAUUUUGCAAAGCGCUCGCAACAAAAUU_UUACGCUGUUUACACAGUGAAGUGUGCAUAAAAGUGACGCUUAUGAACAAGUUGACAGCGC________GGGCCU
.....................(((((..((((..........((((((....))))))((((((.(((....)))))))))........))))..))))).............. (-15.68 = -17.27 +   1.59)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:20:47 2006