Locus 2679

Sequence ID 2R_DroMel_CAF1
Location 9,456,673 – 9,456,849
Length 176
Max. P 0.998805
window4405 window4406 window4407 window4408 window4409

overview

Window 5

Location 9,456,673 – 9,456,788
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 87.36
Mean single sequence MFE -34.75
Consensus MFE -24.81
Energy contribution -26.78
Covariance contribution 1.97
Combinations/Pair 1.06
Mean z-score -3.85
Structure conservation index 0.71
SVM decision value 0.71
SVM RNA-class probability 0.829938
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9456673 115 - 20766785
UAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUGUCAGAGCAAGAGUCAUGUGUGAG--CCGCAACCCGCUCCCUC---UGACGCAGGUGCGUUUAUCUACAGUCGUACCUGCCUAUCCC
((((((((((....)))))))))).........(((((((...((((....((((..--.))))....)))).)))---))))(((((((((............)))))))))....... ( -38.10)
>DroSec_CAF1 43535 115 - 1
UAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUGUCAGAGCAAGAGUCAUGUGUGAG--UCGCAAUCCGCUCCCUC---UGACGCAGGUGCGUUUAUCUACAGUCGUACCUGCCUAACCC
((((((((((....)))))))))).........(((((((...((((....((((..--.))))....)))).)))---))))(((((((((............)))))))))....... ( -38.10)
>DroSim_CAF1 52065 115 - 1
UAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUGUCAGAGCAAGAGUCAUGUGUGAG--CCGCAACCCGCUCCCUC---UGACGCAGGUGCGUUUAUCUACAGUCGUACCUGCCUAACCC
((((((((((....)))))))))).........(((((((...((((....((((..--.))))....)))).)))---))))(((((((((............)))))))))....... ( -38.10)
>DroEre_CAF1 43684 114 - 1
UAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUGUCAGAUCAAGAGUCAUGUGUGAG---CGCAACCCGCUCCCUC---UGACGCAGGUGCGUUGAUCUACAGUCGUGCCUGCCUAACCC
((((((((((....)))))))))).........((((((....((((..((((....---))))....))))..))---))))(((((..(((((.....))).))..)))))....... ( -36.80)
>DroYak_CAF1 43870 117 - 1
UAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUGUCAGAGCAAGAGUCAUGUGUGUGAUCCACAACCCGCUCCCUC---UGACGCAGGUGCGUUUAUCUACAGUCGUGCCUGCCUAACCC
((((((((((....)))))))))).........(((((((...((((....((((.....))))....)))).)))---))))(((((..((............))..)))))....... ( -38.80)
>DroAna_CAF1 45011 94 - 1
UAAACAAAUUAAAUAAUUUGUUUAUAA-ACUGUGUCAGAGC---------------------CAACCCGCUCCCUCCUAUGACGUAGCGGC----AUCGACAGUCGAACAUCCCUAACCC
((((((((((....))))))))))...-.((((((((((((---------------------......)))).......))))))))((((----.......)))).............. ( -18.61)
>consensus
UAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUGUCAGAGCAAGAGUCAUGUGUGAG__CCGCAACCCGCUCCCUC___UGACGCAGGUGCGUUUAUCUACAGUCGUACCUGCCUAACCC
((((((((((....)))))))))).........(((((((...((((....((((.....))))....)))).)))...))))(((((((((............)))))))))....... (-24.81 = -26.78 +   1.97)

alignment

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secondary structure

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Window 6

Location 9,456,713 – 9,456,815
Length 102
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 93.87
Mean single sequence MFE -27.30
Consensus MFE -23.30
Energy contribution -23.66
Covariance contribution 0.36
Combinations/Pair 1.11
Mean z-score -1.28
Structure conservation index 0.85
SVM decision value 0.14
SVM RNA-class probability 0.602299
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9456713 102 + 20766785
AGAGGGAGCGGGUUGCGG--CUCACACAUGACUCUUGCUCUGACACAGUUUUAUAAACAAAUUAUUUAAUUUGUUUACCCGCCCCCGUACAAUAAAGCAACGGC
...(((.(((((..((((--.(((....)))...))))...............((((((((((....))))))))))))))).))).................. ( -24.90)
>DroSec_CAF1 43575 102 + 1
AGAGGGAGCGGAUUGCGA--CUCACACAUGACUCUUGCUCUGACACAGUUUUAUAAACAAAUUAUUUAAUUUGUUUACCCGCCCCCGCACCAUAAGGCAACGGC
.(.(((.((((...((((--.(((....)))...))))...............((((((((((....)))))))))).)))).))).).......(....)... ( -24.00)
>DroSim_CAF1 52105 102 + 1
AGAGGGAGCGGGUUGCGG--CUCACACAUGACUCUUGCUCUGACACAGUUUUAUAAACAAAUUAUUUAAUUUGUUUACCCGCCCCCGCACCAUAAGGCAACGGC
....((.(((((..((((--.........((((..((......)).))))...((((((((((....)))))))))).)))).))))).))....(....)... ( -27.10)
>DroEre_CAF1 43724 101 + 1
AGAGGGAGCGGGUUGCG---CUCACACAUGACUCUUGAUCUGACACAGUUUUAUAAACAAAUUAUUUAAUUUGUUUACCCGCCCCCGCAGCAAAAGGCCGCGGC
...(((.((((((((.(---.(((..((.......))...)))).))).....((((((((((....))))))))))))))))))(((.((.....)).))).. ( -29.20)
>DroYak_CAF1 43910 104 + 1
AGAGGGAGCGGGUUGUGGAUCACACACAUGACUCUUGCUCUGACACAGUUUUAUAAACAAAUUAUUUAAUUUGUUUACCCGCCCCCGCAGCAUAAGGCAGCGGC
...(((.(((((.((((.....))))...........................((((((((((....))))))))))))))))))(((.((.....)).))).. ( -31.30)
>consensus
AGAGGGAGCGGGUUGCGG__CUCACACAUGACUCUUGCUCUGACACAGUUUUAUAAACAAAUUAUUUAAUUUGUUUACCCGCCCCCGCACCAUAAGGCAACGGC
...(((.(((((..((((...(((....)))...))))...............((((((((((....))))))))))))))).)))((........))...... (-23.30 = -23.66 +   0.36)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,456,713 – 9,456,815
Length 102
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 93.87
Mean single sequence MFE -35.72
Consensus MFE -30.06
Energy contribution -29.94
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -2.89
Structure conservation index 0.84
SVM decision value 3.23
SVM RNA-class probability 0.998805
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9456713 102 - 20766785
GCCGUUGCUUUAUUGUACGGGGGCGGGUAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUGUCAGAGCAAGAGUCAUGUGUGAG--CCGCAACCCGCUCCCUCU
...((.((......))))(((((((((((((((((((....))))))))).......(((((((..(((.......))).))).--.))))))))))))))... ( -32.20)
>DroSec_CAF1 43575 102 - 1
GCCGUUGCCUUAUGGUGCGGGGGCGGGUAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUGUCAGAGCAAGAGUCAUGUGUGAG--UCGCAAUCCGCUCCCUCU
(((((......)))))..(((((((((((((((((((....)))))))))))..............((..((.(((....))).--))))...))))))))... ( -34.70)
>DroSim_CAF1 52105 102 - 1
GCCGUUGCCUUAUGGUGCGGGGGCGGGUAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUGUCAGAGCAAGAGUCAUGUGUGAG--CCGCAACCCGCUCCCUCU
(((((......)))))..(((((((((((((((((((....))))))))).......(((((((..(((.......))).))).--.))))))))))))))... ( -35.90)
>DroEre_CAF1 43724 101 - 1
GCCGCGGCCUUUUGCUGCGGGGGCGGGUAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUGUCAGAUCAAGAGUCAUGUGUGAG---CGCAACCCGCUCCCUCU
...(((((.....)))))(((((((((((((((((((....))))))))).......(((((((.((..........)).))).---))))))))))))))... ( -39.50)
>DroYak_CAF1 43910 104 - 1
GCCGCUGCCUUAUGCUGCGGGGGCGGGUAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUGUCAGAGCAAGAGUCAUGUGUGUGAUCCACAACCCGCUCCCUCU
((.((........)).))(((((((((((((((((((....))))))))).......(((((((..(((.......)))...)))..))))))))))))))... ( -36.30)
>consensus
GCCGUUGCCUUAUGGUGCGGGGGCGGGUAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUGUCAGAGCAAGAGUCAUGUGUGAG__CCGCAACCCGCUCCCUCU
...((.(((....)))))(((((((((((((((((((....))))))))).....(((.((......))..)))....((((.....))))))))))))))... (-30.06 = -29.94 +  -0.12)

alignment

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secondary structure

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Window 8

Location 9,456,748 – 9,456,849
Length 101
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.86
Mean single sequence MFE -19.62
Consensus MFE -11.27
Energy contribution -11.72
Covariance contribution 0.45
Combinations/Pair 1.05
Mean z-score -1.88
Structure conservation index 0.57
SVM decision value 0.96
SVM RNA-class probability 0.890637
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9456748 101 + 20766785
CUCUGACACAGUUUUAUAAACAAAUUAUUUAAUUUGUUUACCCGCCCCCGU-------------ACAAUAAAGCAACGGCUGUCGGUUUAAAAAUUCCACUCACACA--A---UA-GCCG
..........((((((((((((((((....)))))))))...((....)).-------------...)))))))..(((((((.(....................).--)---))-)))) ( -16.85)
>DroPse_CAF1 42403 95 + 1
------CACAGUUUUAUAAACAAAUUAUUUAAUUUGUUUACCCGCCCUCGACUCA---------AACAGAAGGCAGCGGCUGUUCCACACAAAAUUUCACUCGCAGA--A---UG-----
------.((((((...((((((((((....))))))))))...(((.((......---------....)).)))...))))))........................--.---..----- ( -16.70)
>DroEre_CAF1 43758 106 + 1
AUCUGACACAGUUUUAUAAACAAAUUAUUUAAUUUGUUUACCCGCCCCCGC-------------AGCAAAAGGCCGCGGCUGUCGGUUUAAAAAUUCCACUCACACACAGUCGCC-GCCG
..(((.....((....((((((((((....))))))))))...)).....)-------------)).....(((.((((((((.(....................))))))))).-))). ( -25.65)
>DroYak_CAF1 43947 101 + 1
CUCUGACACAGUUUUAUAAACAAAUUAUUUAAUUUGUUUACCCGCCCCCGC-------------AGCAUAAGGCAGCGGCUGUCGGUUUAAAAAUUCCACUCACACA--A---UC-GUCG
....(((.........((((((((((....)))))))))).((((..((((-------------.((.....)).))))..).))).....................--.---..-))). ( -22.30)
>DroAna_CAF1 45066 110 + 1
CUCUGACACAGU-UUAUAAACAAAUUAUUUAAUUUGUUUACCCGCCCCCGCCUCCACACUUCACAACAUAAGGCCACGGCUG----UUUAAAAAUUCCACUCACACA--C---UUGGCAG
..(((.((.(((-...((((((((((....))))))))))...(((...((((.................))))...)))..----....................)--)---))).))) ( -17.23)
>DroPer_CAF1 43224 95 + 1
------CACAGUUUUAUAAACAAAUUAUUUAAUUUGUUUACCCGCCCUCGCCUCC---------AACAGAAGGCAGCGGCUGUUCCACACAAAAUUUCACUCGCAGA--A---UG-----
------.((((.....((((((((((....)))))))))).((((....((((.(---------....).)))).))))))))........................--.---..----- ( -19.00)
>consensus
CUCUGACACAGUUUUAUAAACAAAUUAUUUAAUUUGUUUACCCGCCCCCGC_____________AACAUAAGGCAGCGGCUGUCGGUUUAAAAAUUCCACUCACACA__A___UC_GCCG
.......((((.....((((((((((....)))))))))).((((..((......................))..))))))))..................................... (-11.27 = -11.72 +   0.45)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,456,748 – 9,456,849
Length 101
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.86
Mean single sequence MFE -28.32
Consensus MFE -17.22
Energy contribution -16.80
Covariance contribution -0.42
Combinations/Pair 1.13
Mean z-score -1.75
Structure conservation index 0.61
SVM decision value 0.94
SVM RNA-class probability 0.886095
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9456748 101 - 20766785
CGGC-UA---U--UGUGUGAGUGGAAUUUUUAAACCGACAGCCGUUGCUUUAUUGU-------------ACGGGGGCGGGUAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUGUCAGAG
((((-(.---(--((.((...((((...)))).))))).)))))........(((.-------------(((.((....(((((((((((....)))))))))))....)).)))))).. ( -23.90)
>DroPse_CAF1 42403 95 - 1
-----CA---U--UCUGCGAGUGAAAUUUUGUGUGGAACAGCCGCUGCCUUCUGUU---------UGAGUCGAGGGCGGGUAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUG------
-----..---(--((((((((......)))))).)))((((...((((((((....---------......))))))))(((((((((((....)))))))))))....)))).------ ( -25.90)
>DroEre_CAF1 43758 106 - 1
CGGC-GGCGACUGUGUGUGAGUGGAAUUUUUAAACCGACAGCCGCGGCCUUUUGCU-------------GCGGGGGCGGGUAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUGUCAGAU
.(((-.(((.((((((.((((.......)))).))..)))).))).))).....((-------------(((.((....(((((((((((....)))))))))))....)).)).))).. ( -32.40)
>DroYak_CAF1 43947 101 - 1
CGAC-GA---U--UGUGUGAGUGGAAUUUUUAAACCGACAGCCGCUGCCUUAUGCU-------------GCGGGGGCGGGUAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUGUCAGAG
.(((-(.---.--.((..................(((.(..((((.((.....)).-------------))))..))))(((((((((((....)))))))))))...))..)))).... ( -27.40)
>DroAna_CAF1 45066 110 - 1
CUGCCAA---G--UGUGUGAGUGGAAUUUUUAAA----CAGCCGUGGCCUUAUGUUGUGAAGUGUGGAGGCGGGGGCGGGUAAACAAAUUAAAUAAUUUGUUUAUAA-ACUGUGUCAGAG
(((((..---.--(((.((((.......)))).)----))(((.(.((((((..((....))..).))))).).)))))(((((((((((....)))))))))))..-.......))).. ( -29.10)
>DroPer_CAF1 43224 95 - 1
-----CA---U--UCUGCGAGUGAAAUUUUGUGUGGAACAGCCGCUGCCUUCUGUU---------GGAGGCGAGGGCGGGUAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUG------
-----..---(--((((((((......)))))).)))(((((((((((((((....---------))))))...)))))(((((((((((....)))))))))))....)))).------ ( -31.20)
>consensus
CGGC_CA___U__UGUGUGAGUGGAAUUUUUAAACCGACAGCCGCUGCCUUAUGUU_____________GCGGGGGCGGGUAAACAAAUUAAAUAAUUUGUUUAUAAAACUGUGUCAGAG
.....................................((((((((..((((....................))))))))(((((((((((....)))))))))))....))))....... (-17.22 = -16.80 +  -0.42)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:09 2006