Locus 3070

Sequence ID 2L_DroMel_CAF1
Location 8,761,407 – 8,761,546
Length 139
Max. P 0.861339
window4882 window4883 window4884

overview

Window 2

Location 8,761,407 – 8,761,510
Length 103
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.90
Mean single sequence MFE -31.27
Consensus MFE -17.19
Energy contribution -16.28
Covariance contribution -0.91
Combinations/Pair 1.27
Mean z-score -2.65
Structure conservation index 0.55
SVM decision value 0.07
SVM RNA-class probability 0.569292
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8761407 103 - 22407834
--------UUGCUCCUUUUUGUU-UUAGCC--GAGGGUUAACCCUUUUAACCCCUGGCAAGCAACUA-CUCUUUGGUUAACCACGGACAGCGCUGG-AUGACAUUUUUUCC----AGGAC
--------..(((.....(((((-(..(((--(.(((((((.....))))))).))))))))))...-.(((.(((....))).))).))).((((-(..........)))----))... ( -30.50)
>DroPse_CAF1 86224 110 - 1
--------UUUUUGCGUUUUGUU-UUAGCUUUUGGGGUUAACCCUUUUAACCCUUGGCAACUGACUGCCUCUCCGGUUAACCACGGACAGCGUUAGCCUGACAUUU-UUCCAGGCAGGAC
--------.......((((((..-...(((...((((((((.....)))))))).)))..(((((.((...((((........))))..)))))))((((......-...)))))))))) ( -30.70)
>DroSim_CAF1 68284 102 - 1
--------UUGCUCCUUUUUGUU-UUAGCC--GAGGGUUAACCCUUUUAACCCUUGGCAAGCAACUA-CUCUUUGGUUAACCACGGACAGCGCUGG-AUGACAUUU-UUCC----AGGAC
--------..(((.....(((((-(..(((--(((((((((.....))))))))))))))))))...-.(((.(((....))).))).))).((((-(........-.)))----))... ( -35.10)
>DroEre_CAF1 69522 110 - 1
CGCAGCGCUCGCUCCUUUUUGUU-UCAGCC--AAGGGUUAACCCUUUUAACCCUGGGCCAGCAACUC-CUCUUUGGUUAACCACGGACAGCGCUGG-AUGACAUUU-UUCC----AGGAC
..(((((((.(.(((...(((((-...(((--.((((((((.....)))))))).))).)))))...-.....(((....))).))))))))))).-.........-....----..... ( -35.30)
>DroYak_CAF1 68553 102 - 1
--------UCGCUGCUUUUUGUU-UCAGUC--GUGGGUUAACCCUUUUAACCCUUGGCAAGCAACUC-CUCUUCGGUUAACCACGGACAGCGCUGG-AUGACAUUU-UUCC----AGCAC
--------..((((((..(((((-(..(((--(.(((((((.....))))))).))))))))))...-......((....))..)).))))(((((-(........-.)))----))).. ( -32.90)
>DroAna_CAF1 67287 100 - 1
--------U--AUCCUUUCUGUUUUUAGCA--AGGGGUUAACUCUUUUAACCCUUGGCAAGCAACUA-CUCUUCGGUUAACCACGGACAACGUUAG-AUGACAUU--UUCC----AGGAC
--------.--.((((...(((((...((.--(((((((((.....))))))))).)))))))....-......((....))..(((.((.(((..-..))).))--.)))----)))). ( -23.10)
>consensus
________UUGCUCCUUUUUGUU_UUAGCC__GAGGGUUAACCCUUUUAACCCUUGGCAAGCAACUA_CUCUUCGGUUAACCACGGACAGCGCUGG_AUGACAUUU_UUCC____AGGAC
............((((...((((.(((((.....(((((((.....)))))))...............((.((((........)))).)).)))))...))))............)))). (-17.19 = -16.28 +  -0.91)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,761,442 – 8,761,546
Length 104
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 82.77
Mean single sequence MFE -27.02
Consensus MFE -16.35
Energy contribution -17.68
Covariance contribution 1.33
Combinations/Pair 1.05
Mean z-score -2.32
Structure conservation index 0.61
SVM decision value 0.15
SVM RNA-class probability 0.608672
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8761442 104 + 22407834
UUAACCAAAGAG-UAGUUGCUUGCCAGGGGUUAAAAGGGUUAACCCUC--GGCUAAAACAAAAAGGAGCAA-----------UGGAAGAAAAAACCAA-CGAAAAUGGUAGCUGGCAGG
....(((.....-..((((((((((..(((((((.....)))))))..--))).....(.....)))))))-----------)..........((((.-......))))...))).... ( -25.60)
>DroPse_CAF1 86263 104 + 1
UUAACCGGAGAGGCAGUCAGUUGCCAAGGGUUAAAAGGGUUAACCCCAAAAGCUAAAACAAAACGCAAAAA-----------GG---CGA-AAACCUCUAAAAAAUGUGAGUUGGCAGG
....((.....(((((....)))))..(((((((.....))))))).....(((((.......(((.....-----------.)---)).-....(((..........)))))))).)) ( -23.90)
>DroSec_CAF1 65683 103 + 1
UUAACCAAAGAG-UAGUUGCUUGCCAAGGGUUAAAAGGGUUAACCCUC--GGCUAAAACAAAAAGGAGCAA-----------UGGAAGGA-AAACCAA-CGAAAAUGGUAGCUGGCAGG
....((......-..((((((((((.((((((((.....)))))))).--))).....(.....)))))))-----------).(..((.-..((((.-......))))..))..).)) ( -26.20)
>DroSim_CAF1 68318 103 + 1
UUAACCAAAGAG-UAGUUGCUUGCCAAGGGUUAAAAGGGUUAACCCUC--GGCUAAAACAAAAAGGAGCAA-----------UGGAAGGA-AAACCAA-CGAAAAUGGUAGCUGGCAGG
....((......-..((((((((((.((((((((.....)))))))).--))).....(.....)))))))-----------).(..((.-..((((.-......))))..))..).)) ( -26.20)
>DroEre_CAF1 69556 114 + 1
UUAACCAAAGAG-GAGUUGCUGGCCCAGGGUUAAAAGGGUUAACCCUU--GGCUGAAACAAAAAGGAGCGAGCGCUGCGAUGUGGAAGGA-AACCCAA-CGAAAAUGGUUGUUGGCAGG
....(((....(-.(((.(((.((((.(((((((.....)))))))((--(.......)))...)).)).)))))).)....)))..(..-..)((((-(((......))))))).... ( -34.90)
>DroYak_CAF1 68587 103 + 1
UUAACCGAAGAG-GAGUUGCUUGCCAAGGGUUAAAAGGGUUAACCCAC--GACUGAAACAAAAAGCAGCGA-----------UGGAAGGA-AAACCAA-CGAAAAUGGUAGUUGGCAGG
....((.....)-).....(((((((((((((((.....))))))).(--(.(((..........))))).-----------........-..((((.-......))))..)))))))) ( -25.30)
>consensus
UUAACCAAAGAG_UAGUUGCUUGCCAAGGGUUAAAAGGGUUAACCCUC__GGCUAAAACAAAAAGGAGCAA___________UGGAAGGA_AAACCAA_CGAAAAUGGUAGCUGGCAGG
...................(((((((((((((((.....)))))))...............................................((((........))))..)))))))) (-16.35 = -17.68 +   1.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,761,442 – 8,761,546
Length 104
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 82.77
Mean single sequence MFE -26.00
Consensus MFE -16.89
Energy contribution -17.25
Covariance contribution 0.36
Combinations/Pair 1.22
Mean z-score -3.12
Structure conservation index 0.65
SVM decision value 0.83
SVM RNA-class probability 0.861339
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8761442 104 - 22407834
CCUGCCAGCUACCAUUUUCG-UUGGUUUUUUCUUCCA-----------UUGCUCCUUUUUGUUUUAGCC--GAGGGUUAACCCUUUUAACCCCUGGCAAGCAACUA-CUCUUUGGUUAA
...((((((..........)-)))))........(((-----------..(.......((((((..(((--(.(((((((.....))))))).))))))))))...-..)..))).... ( -24.50)
>DroPse_CAF1 86263 104 - 1
CCUGCCAACUCACAUUUUUUAGAGGUUU-UCG---CC-----------UUUUUGCGUUUUGUUUUAGCUUUUGGGGUUAACCCUUUUAACCCUUGGCAACUGACUGCCUCUCCGGUUAA
..((((((...........((((((((.-.((---(.-----------.....))).........))))))))(((((((.....)))))))))))))..((((((......)))))). ( -24.60)
>DroSec_CAF1 65683 103 - 1
CCUGCCAGCUACCAUUUUCG-UUGGUUU-UCCUUCCA-----------UUGCUCCUUUUUGUUUUAGCC--GAGGGUUAACCCUUUUAACCCUUGGCAAGCAACUA-CUCUUUGGUUAA
...((((((..........)-)))))..-.....(((-----------..(.......((((((..(((--(((((((((.....))))))))))))))))))...-..)..))).... ( -29.00)
>DroSim_CAF1 68318 103 - 1
CCUGCCAGCUACCAUUUUCG-UUGGUUU-UCCUUCCA-----------UUGCUCCUUUUUGUUUUAGCC--GAGGGUUAACCCUUUUAACCCUUGGCAAGCAACUA-CUCUUUGGUUAA
...((((((..........)-)))))..-.....(((-----------..(.......((((((..(((--(((((((((.....))))))))))))))))))...-..)..))).... ( -29.00)
>DroEre_CAF1 69556 114 - 1
CCUGCCAACAACCAUUUUCG-UUGGGUU-UCCUUCCACAUCGCAGCGCUCGCUCCUUUUUGUUUCAGCC--AAGGGUUAACCCUUUUAACCCUGGGCCAGCAACUC-CUCUUUGGUUAA
.........(((((.....(-(.(((..-....)))))...(((((....))).............(((--.((((((((.....)))))))).)))..)).....-.....))))).. ( -27.40)
>DroYak_CAF1 68587 103 - 1
CCUGCCAACUACCAUUUUCG-UUGGUUU-UCCUUCCA-----------UCGCUGCUUUUUGUUUCAGUC--GUGGGUUAACCCUUUUAACCCUUGGCAAGCAACUC-CUCUUCGGUUAA
...((((((..........)-)))))..-.......(-----------(((..(....((((((..(((--(.(((((((.....))))))).))))))))))...-..)..))))... ( -21.50)
>consensus
CCUGCCAACUACCAUUUUCG_UUGGUUU_UCCUUCCA___________UUGCUCCUUUUUGUUUUAGCC__GAGGGUUAACCCUUUUAACCCUUGGCAAGCAACUA_CUCUUUGGUUAA
...(((.....(((........))).................................((((((..(((...((((((((.....)))))))).)))))))))..........)))... (-16.89 = -17.25 +   0.36)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:35 2006