Locus 1895

Sequence ID 2R_DroMel_CAF1
Location 7,140,087 – 7,140,211
Length 124
Max. P 0.988764
window3141 window3142 window3143

overview

Window 1

Location 7,140,087 – 7,140,189
Length 102
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 77.38
Mean single sequence MFE -41.09
Consensus MFE -26.25
Energy contribution -26.42
Covariance contribution 0.17
Combinations/Pair 1.09
Mean z-score -1.87
Structure conservation index 0.64
SVM decision value 1.10
SVM RNA-class probability 0.915715
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7140087 102 + 20766785
UAUCACAGAUGUGCUCCUCAGCCUC---CGAUGGCAUCUCGCCCUUGGCCAGACCCAUCUUCCUGAGGAACUGAUCACAGUGCGGCCCGUGUUUGGGCCGCGA------------UG
((((...(((..(.(((((((....---.(((((..(((.(((...))).))).)))))...))))))).)..))).....((((((((....))))))))))------------)) ( -43.30)
>DroVir_CAF1 4803 106 + 1
UAUCACAGAAAUGCUCCUCAGCGUC---GGCAG---ACUCGCCCUUGGCGAGGCCCAUCUUUCUGAGGAACUGAUCACAGUGUGGCCCGUGUUUGGGCCGCGUGGUGCAGCU-----
((((((........(((((((.((.---(((..---.((((((...))))))))).))....)))))))((((....))))((((((((....)))))))))))))).....----- ( -45.90)
>DroPse_CAF1 3344 114 + 1
UAUCACAGAUGUGCUCCUCAGAUUC---GGCUGUGGCCUCGCCCUUGGCCAGACCCAUCUUCCUGAGGAACUGAUCACAGUGUGGCCCGUGCUUGGGCCUGGUGGUGGUUGUGGUGG
((((((........(((((((....---((.(.(((((........))))).).))......)))))))...((((((.....((((((....)))))).....)))))))))))). ( -46.40)
>DroGri_CAF1 4827 106 + 1
UAUCACAGAAAUGCUCCUCAGCGUC---GGCAG---ACUCGCCCUUGGCAAGCCCCAUCUUCCUGAGGAACUGAUCACAGUGUGGCCCAUGUUUGGGCCGUGUGUUGCAACU-----
...........((((((((((.(((---....)---))..(((...))).............)))))))......((((...(((((((....)))))))))))..)))...----- ( -34.50)
>DroWil_CAF1 3909 99 + 1
UAUCACAGAAAUGUUCCUCAUUGUCAUUGGCUGAAUCUUGGCUCUUGGCCAAACCCAUUUUUCUGAGGAACUGAUCACAGUGUGGCCCAUGUUUGGGCC------------------
...(((.((...((((((((.......(((.......(((((.....)))))..)))......))))))))...))...))).((((((....))))))------------------ ( -30.72)
>DroPer_CAF1 3341 114 + 1
UAUCACAGAUGUGCUCCUCAGAUUC---GGCUGUGGCCUCGCCCUUGGCCAGACCCAUCUUCCUGAGGAACUGAUCACAGUGCGGCCCGUGCUUGGGCCUGGUGGUGGUUGUGGUGG
((((((........(((((((....---((.(.(((((........))))).).))......)))))))...((((((.....((((((....)))))).....)))))))))))). ( -45.70)
>consensus
UAUCACAGAAAUGCUCCUCAGCGUC___GGCUG___CCUCGCCCUUGGCCAGACCCAUCUUCCUGAGGAACUGAUCACAGUGUGGCCCGUGUUUGGGCCGCGUGGUG____U_____
..............(((((((.......(((.........)))..(((......))).....)))))))((((....))))..((((((....)))))).................. (-26.25 = -26.42 +   0.17)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,140,087 – 7,140,189
Length 102
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 77.38
Mean single sequence MFE -45.46
Consensus MFE -32.06
Energy contribution -32.22
Covariance contribution 0.17
Combinations/Pair 1.12
Mean z-score -3.61
Structure conservation index 0.71
SVM decision value 2.13
SVM RNA-class probability 0.988764
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7140087 102 - 20766785
CA------------UCGCGGCCCAAACACGGGCCGCACUGUGAUCAGUUCCUCAGGAAGAUGGGUCUGGCCAAGGGCGAGAUGCCAUCG---GAGGCUGAGGAGCACAUCUGUGAUA
.(------------(((((((((......)))))))((...(((..(((((((((...(((((((((.(((...))).)))).))))).---....)))))))))..))).))))). ( -50.40)
>DroVir_CAF1 4803 106 - 1
-----AGCUGCACCACGCGGCCCAAACACGGGCCACACUGUGAUCAGUUCCUCAGAAAGAUGGGCCUCGCCAAGGGCGAGU---CUGCC---GACGCUGAGGAGCAUUUCUGUGAUA
-----.((........))(((((......))))).(((...((...(((((((((...(.(.(((((((((...)))))).---..)))---.)).)))))))))...)).)))... ( -45.30)
>DroPse_CAF1 3344 114 - 1
CCACCACAACCACCACCAGGCCCAAGCACGGGCCACACUGUGAUCAGUUCCUCAGGAAGAUGGGUCUGGCCAAGGGCGAGGCCACAGCC---GAAUCUGAGGAGCACAUCUGUGAUA
....((((..(((.....(((((......))))).....)))....((((((((((..(.(((((((.(((...))).))))).))..)---...)))))))))).....))))... ( -46.80)
>DroGri_CAF1 4827 106 - 1
-----AGUUGCAACACACGGCCCAAACAUGGGCCACACUGUGAUCAGUUCCUCAGGAAGAUGGGGCUUGCCAAGGGCGAGU---CUGCC---GACGCUGAGGAGCAUUUCUGUGAUA
-----.((..((.((((.((((((....))))))....))))....(((((((((...(.(((((((((((...)))))))---)..))---).).))))))))).....))..)). ( -46.20)
>DroWil_CAF1 3909 99 - 1
------------------GGCCCAAACAUGGGCCACACUGUGAUCAGUUCCUCAGAAAAAUGGGUUUGGCCAAGAGCCAAGAUUCAGCCAAUGACAAUGAGGAACAUUUCUGUGAUA
------------------((((((....)))))).(((...((...((((((((........((((((((.....)))))......)))........))))))))...)).)))... ( -36.19)
>DroPer_CAF1 3341 114 - 1
CCACCACAACCACCACCAGGCCCAAGCACGGGCCGCACUGUGAUCAGUUCCUCAGGAAGAUGGGUCUGGCCAAGGGCGAGGCCACAGCC---GAAUCUGAGGAGCACAUCUGUGAUA
....((((..(((.....(((((......))))).....)))....((((((((((..(.(((((((.(((...))).))))).))..)---...)))))))))).....))))... ( -47.90)
>consensus
_____A____CACCACCCGGCCCAAACACGGGCCACACUGUGAUCAGUUCCUCAGGAAGAUGGGUCUGGCCAAGGGCGAGG___CAGCC___GACGCUGAGGAGCACAUCUGUGAUA
..................(((((......))))).(((...((...(((((((((.......(((((.((.....)).))......))).......)))))))))...)).)))... (-32.06 = -32.22 +   0.17)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,140,121 – 7,140,211
Length 90
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 76.71
Mean single sequence MFE -37.68
Consensus MFE -24.04
Energy contribution -25.27
Covariance contribution 1.22
Combinations/Pair 1.13
Mean z-score -1.91
Structure conservation index 0.64
SVM decision value 1.28
SVM RNA-class probability 0.939545
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7140121 90 - 20766785
---AGCAGCGGAGCAAGCAGCUCCGCA------------UCGCGGCCCAAACACGGGCCGCACUGUGAUCAGUUCCUCAGGAAGAUGGGUCUGGCCAAGGGCGAG
---.((.(((((((.....))))))).------------..(((((((......))))))).((.((..(((..((((.....)).))..)))..)).))))... ( -44.50)
>DroVir_CAF1 4834 96 - 1
UGCGGAAACGG---AACCAGCUCC------AGCUGCACCACGCGGCCCAAACACGGGCCACACUGUGAUCAGUUCCUCAGAAAGAUGGGCCUCGCCAAGGGCGAG
.(((....)((---...((((...------.))))..))..))(((((...(((((......)))))(((..(((....))).))))))))(((((...))))). ( -35.90)
>DroPse_CAF1 3378 102 - 1
---AGCAGCGGAGCAAGUAGUUCUGCCACCACAACCACCACCAGGCCCAAGCACGGGCCACACUGUGAUCAGUUCCUCAGGAAGAUGGGUCUGGCCAAGGGCGAG
---.((.(((((((.....)))))))........((....(((((((((..(((((......))))).....((((...))))..)))))))))....))))... ( -38.20)
>DroMoj_CAF1 4340 96 - 1
ACUAGUUCAGG---UUCCAGCUCC------AGUUGCACCACACGGCCCAAACACGGGCCACACUGUGAUCAGUUCCUCAGAAAGAUGGGCCUCGCCAAGGGCGAC
.........((---(..((((...------.)))).)))....(((((...(((((......)))))(((..(((....))).))))))))(((((...))))). ( -30.60)
>DroAna_CAF1 3220 90 - 1
---AGCAACGGAGCCACUGGCUCCGCA------------UCGAGGCCCAAACACGGGCCGCAUUGUGAUCAGUUCCUCAGGAAGAUGGGUCUGGCCAAGGGCGAG
---.....(((((((...)))))))..------------((..(((((......)))))((....((..(((..((((.....)).))..)))..))...)))). ( -36.30)
>DroPer_CAF1 3375 102 - 1
---AGCAGCGGAGCAAGCAGCUCUGCCACCACAACCACCACCAGGCCCAAGCACGGGCCGCACUGUGAUCAGUUCCUCAGGAAGAUGGGUCUGGCCAAGGGCGAG
---.((.(((((((.....)))))))........((....(((((((((..(((((......))))).....((((...))))..)))))))))....))))... ( -40.60)
>consensus
___AGCAGCGGAGCAACCAGCUCCGC____A____CACCACGAGGCCCAAACACGGGCCACACUGUGAUCAGUUCCUCAGGAAGAUGGGUCUGGCCAAGGGCGAG
........((((((.....))))))...................((((...(((((......))))).((((..((((.....)).))..))))....))))... (-24.04 = -25.27 +   1.22)

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 10:15:50 2006