Locus 8828

Sequence ID 3R_DroMel_CAF1
Location 23,626,707 – 23,626,800
Length 93
Max. P 0.651610
window14174 window14175

overview

Window 4

Location 23,626,707 – 23,626,800
Length 93
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 80.84
Mean single sequence MFE -23.03
Consensus MFE -16.92
Energy contribution -17.75
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -1.36
Structure conservation index 0.73
SVM decision value 0.25
SVM RNA-class probability 0.651610
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23626707 93 + 27905053
AGAGCA-----------GGGGAAACAACGGAC--CAAAGGCCGACCAACGGACAUGUUGUUUGUCUGAGCGCAAUUUAUUGCAUGUCGGAAAGGCCAAUAUUAUAA
......-----------..(....)...((.(--(.....(((((...((((((.......))))))...((((....))))..)))))...)))).......... ( -24.10)
>DroVir_CAF1 122804 101 + 1
CGAGCAAAACAUAGUUAG-AGAAAGAGAGAAAGAGAGAUG----CCAACCGACAUGUUGUUUGCCAGAGCGCAAUUUAUUGCAUGUCGGAAAGGCCAAUAUUAUAA
..................-....................(----((..(((((((((...((((......))))......)))))))))...)))........... ( -21.30)
>DroPse_CAF1 89274 83 + 1
---------------------CCACAACGGAC--CAAAGGCCGACCAACGGACAUGUUGUUUGUCUGAGCGCAAUUUAUUGCAUGUCGGAAAGGCCAAUAUUAUAA
---------------------.......((.(--(.....(((((...((((((.......))))))...((((....))))..)))))...)))).......... ( -22.60)
>DroEre_CAF1 88934 92 + 1
AAAGCA-----------G-GGACUGAACGGAC--CAAAGGCCGACCAACGGACAUGUUGUUUGUCUGAGCGCAAUUUAUUGCAUGUCGGAAAGGCCAAUAUUAUAA
......-----------(-(..(.....)..)--)...((((..((..((((((.......))))))...((((....)))).....))...)))).......... ( -25.10)
>DroAna_CAF1 88243 89 + 1
---ACA-----------C-GGACGAGGAGGAC--CAAAGGCCGACCAACGGACAUGUUGUUUGUCUGAGCGCAAUUUAUUGCAUGUCGGAAAGGCCAAUAUUAUAA
---...-----------.-.........((.(--(.....(((((...((((((.......))))))...((((....))))..)))))...)))).......... ( -22.50)
>DroPer_CAF1 87640 83 + 1
---------------------CCACAACGGAC--CAAAGGCCGACCAACGGACAUGUUGUUUGUCUGAGCGCAAUUUAUUGCAUGUCGGAAAGGCCAAUAUUAUAA
---------------------.......((.(--(.....(((((...((((((.......))))))...((((....))))..)))))...)))).......... ( -22.60)
>consensus
___GCA___________G_GGACACAACGGAC__CAAAGGCCGACCAACGGACAUGUUGUUUGUCUGAGCGCAAUUUAUUGCAUGUCGGAAAGGCCAAUAUUAUAA
......................................((((..((..((((((.......))))))...((((....)))).....))...)))).......... (-16.92 = -17.75 +   0.83)

alignment

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secondary structure

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dotplot

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Window 5

Location 23,626,707 – 23,626,800
Length 93
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 80.84
Mean single sequence MFE -21.13
Consensus MFE -17.49
Energy contribution -17.85
Covariance contribution 0.36
Combinations/Pair 1.06
Mean z-score -1.17
Structure conservation index 0.83
SVM decision value 0.07
SVM RNA-class probability 0.571093
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23626707 93 - 27905053
UUAUAAUAUUGGCCUUUCCGACAUGCAAUAAAUUGCGCUCAGACAAACAACAUGUCCGUUGGUCGGCCUUUG--GUCCGUUGUUUCCCC-----------UGCUCU
......((..((((...(((((..((((....)))).....((((.......)))).)))))..))))..))--...............-----------...... ( -20.40)
>DroVir_CAF1 122804 101 - 1
UUAUAAUAUUGGCCUUUCCGACAUGCAAUAAAUUGCGCUCUGGCAAACAACAUGUCGGUUGG----CAUCUCUCUUUCUCUCUUUCU-CUAACUAUGUUUUGCUCG
...........(((...(((((((((((....))))((....)).......)))))))..))----)....................-.................. ( -21.30)
>DroPse_CAF1 89274 83 - 1
UUAUAAUAUUGGCCUUUCCGACAUGCAAUAAAUUGCGCUCAGACAAACAACAUGUCCGUUGGUCGGCCUUUG--GUCCGUUGUGG---------------------
.((((((...((((...(((((..((((....))))...........((((......))))))))).....)--))).)))))).--------------------- ( -20.80)
>DroEre_CAF1 88934 92 - 1
UUAUAAUAUUGGCCUUUCCGACAUGCAAUAAAUUGCGCUCAGACAAACAACAUGUCCGUUGGUCGGCCUUUG--GUCCGUUCAGUCC-C-----------UGCUUU
..........((((...(((((..((((....)))).....((((.......)))).)))))..))))...(--(..(.....)..)-)-----------...... ( -22.20)
>DroAna_CAF1 88243 89 - 1
UUAUAAUAUUGGCCUUUCCGACAUGCAAUAAAUUGCGCUCAGACAAACAACAUGUCCGUUGGUCGGCCUUUG--GUCCUCCUCGUCC-G-----------UGU---
..........((((...(((((..((((....)))).....((((.......)))).)))))..))))...(--(.(......).))-.-----------...--- ( -21.30)
>DroPer_CAF1 87640 83 - 1
UUAUAAUAUUGGCCUUUCCGACAUGCAAUAAAUUGCGCUCAGACAAACAACAUGUCCGUUGGUCGGCCUUUG--GUCCGUUGUGG---------------------
.((((((...((((...(((((..((((....))))...........((((......))))))))).....)--))).)))))).--------------------- ( -20.80)
>consensus
UUAUAAUAUUGGCCUUUCCGACAUGCAAUAAAUUGCGCUCAGACAAACAACAUGUCCGUUGGUCGGCCUUUG__GUCCGUUGUGUCC_C___________UGC___
..........((((...(((((..((((....)))).....((((.......)))).)))))..))))...................................... (-17.49 = -17.85 +   0.36)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:20:41 2006