Locus 4972

Sequence ID 2R_DroMel_CAF1
Location 16,215,477 – 16,215,608
Length 131
Max. P 0.993981
window7958 window7959

overview

Window 8

Location 16,215,477 – 16,215,581
Length 104
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 72.28
Mean single sequence MFE -24.09
Consensus MFE -6.21
Energy contribution -7.33
Covariance contribution 1.12
Combinations/Pair 1.24
Mean z-score -2.47
Structure conservation index 0.26
SVM decision value 2.44
SVM RNA-class probability 0.993981
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16215477 104 - 20766785
GGAAAAUUGUAUAAAAAUGCAAUUUACUG---------UUUUCAGAGAUGACAAACGACGAGCUGAAAACGGAAAGUAG---AAAAUUGCUAGCCGCUGAAAGCUAAAAAGUGCAA
((.(((((((((....))))))))).))(---------(((((((.(.((.....)).)...))))))))((..(((((---....)))))..)).......((........)).. ( -21.80)
>DroPse_CAF1 8218 111 - 1
GGAAAAUUAUGUGAAAAUUCAUGUUGAUGGCUUGUUUCUUCUCUGCCUGGACAAACAAA-AGC-AAAGAGGGAGAGAAGGGAAAACAUUCUGU---UUGUAAGCUGAAUAUGGCAA
..................(((((((..((((((((..(((((((.(((...........-...-....))).)))))))..)((((.....))---)).))))))))))))))... ( -25.97)
>DroEre_CAF1 1338 101 - 1
GGAAAAUUGUAUAAAAAUGCAAUUUACUG---------UUUUCAGAGAUGACAAACGGCGAGCUGAAAACGGAAACUAG---AAAAUUGCUAG---CUGAAAGCUAAAAAGUGCAA
......((((((......(((((((.(((---------(((((((.(.((.....)).)...))))))))(....).))---.)))))))(((---(.....))))....)))))) ( -24.00)
>DroYak_CAF1 7708 101 - 1
GGAAAAUUGUAUAAAAAUGCAAUUUGCUG---------UUUUCAGUGAUGACAAACGGCGGGCUGAAAACGGAAAGUAG---AAAAUUGCUAG---CUGAAAGCUAAAAAGUGCAA
......((((((......(((((((.(((---------((((((((..((........)).))))))))))).......---.)))))))(((---(.....))))....)))))) ( -25.80)
>DroPer_CAF1 8115 111 - 1
GGAAAAUUAUUUGAAAAUUCAUGUUGAUGACUUGUUUCUUCUCUGCCUGGACAAACAAA-AGC-AAAGAGGGAGAGAAGGGAAAACAUUCUGU---UUGUAAGCUGAAUAUGGCAA
..................(((((((.(.(.(((((..(((((((.(((...........-...-....))).)))))))..)((((.....))---)).)))))).)))))))... ( -22.87)
>consensus
GGAAAAUUGUAUAAAAAUGCAAUUUGCUG_________UUUUCAGAGAUGACAAACGACGAGCUGAAAACGGAAAGUAG___AAAAUUGCUAG___CUGAAAGCUAAAAAGUGCAA
..................(((((((.............((((((((...............))))))))..............)))))))............((........)).. ( -6.21 =  -7.33 +   1.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,215,511 – 16,215,608
Length 97
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 72.21
Mean single sequence MFE -22.90
Consensus MFE -4.26
Energy contribution -5.46
Covariance contribution 1.20
Combinations/Pair 1.14
Mean z-score -1.88
Structure conservation index 0.19
SVM decision value 0.89
SVM RNA-class probability 0.874454
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16215511 97 - 20766785
------AGAC--GAACAACUGCCAAGUCAAAUGAUGGAAAAUUGUAUAAAAAUGCAAUUUACUG---------UUUUCAGAGAUGACAAACGACGAGCUGAAAACGGAAAGUAG-
------....--......((((...(((....)))...(((((((((....))))))))).(((---------(((((((.(.((.....)).)...))))))))))...))))- ( -20.40)
>DroPse_CAF1 8251 113 - 1
GACGACGGACGAGAACAAUUUCCAUGGAAAAUUAUGGAAAAUUAUGUGAAAAUUCAUGUUGAUGGCUUGUUUCUUCUCUGCCUGGACAAACAAA-AGC-AAAGAGGGAGAGAAGG
......(((((((.....(((((((((....)))))))))(((((((((....))))).))))..)))))))(((((((.(((...........-...-....))).))))))). ( -27.57)
>DroEre_CAF1 1369 97 - 1
------AGAC--GAACAACUGCCAAGUCAAAUGAUGGAAAAUUGUAUAAAAAUGCAAUUUACUG---------UUUUCAGAGAUGACAAACGGCGAGCUGAAAACGGAAACUAG-
------.(((--.............)))......(((.(((((((((....))))))))).(((---------(((((((.(.((.....)).)...))))))))))...))).- ( -20.42)
>DroYak_CAF1 7739 97 - 1
------AGAC--GAACAACUGCCAAGUCAAAUGAUGGAAAAUUGUAUAAAAAUGCAAUUUGCUG---------UUUUCAGUGAUGACAAACGGCGGGCUGAAAACGGAAAGUAG-
------...(--(.......(((..(((....)))...(((((((((....)))))))))((((---------((((((....))).))))))).)))......))........- ( -22.62)
>DroPer_CAF1 8148 113 - 1
GACGACGGACGAGAACAAUUGCCAUGGAAAAUUAUGGAAAAUUAUUUGAAAAUUCAUGUUGAUGACUUGUUUCUUCUCUGCCUGGACAAACAAA-AGC-AAAGAGGGAGAGAAGG
......(((((((........((((((....))))))................((((....)))))))))))(((((((.(((...........-...-....))).))))))). ( -23.47)
>consensus
______AGAC__GAACAACUGCCAAGUCAAAUGAUGGAAAAUUGUAUAAAAAUGCAAUUUGCUG_________UUUUCAGAGAUGACAAACGACGAGCUGAAAACGGAAAGUAG_
.....................((...............(((((((((....)))))))))................(((....)))...................))........ ( -4.26 =  -5.46 +   1.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:27 2006