Locus 422

Sequence ID 2R_DroMel_CAF1
Location 2,460,908 – 2,461,049
Length 141
Max. P 0.990189
window821 window822 window823

overview

Window 1

Location 2,460,908 – 2,461,020
Length 112
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 82.73
Mean single sequence MFE -33.00
Consensus MFE -31.50
Energy contribution -31.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.25
Structure conservation index 0.95
SVM decision value 2.20
SVM RNA-class probability 0.990189
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2460908 112 + 20766785
--ACUAUUAAAAUUUGAAUAUUUACUACA-AAAUAUUGG---UCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAG
--............(.(((((((......-))))))).)---..((((..((((((.......))))))....((((((.....)))))).((((........)))).....)))).. ( -33.50)
>DroPse_CAF1 32327 110 + 1
--CCUAUUGCUUC---AAAAGAUAGACCAAAAAUAAAUG---UCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAU
--.(((((.....---....)))))..............---..((((..((((((.......))))))....((((((.....)))))).((((........)))).....)))).. ( -33.10)
>DroAna_CAF1 19152 115 + 1
GAAUGACAAAAAAAAGAAACGC--GACCA-AAAUAAUGAAAUGCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAU
....................((--(..((-......))...)))((((..((((((.......))))))....((((((.....)))))).((((........)))).....)))).. ( -32.30)
>DroPer_CAF1 23364 110 + 1
--CCUAUUGCUUC---AAAAGAUAGACCAAAAAUAAAUG---UCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAU
--.(((((.....---....)))))..............---..((((..((((((.......))))))....((((((.....)))))).((((........)))).....)))).. ( -33.10)
>consensus
__ACUAUUAAAAC___AAAAGAUAGACCA_AAAUAAAGG___UCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAU
............................................((((..((((((.......))))))....((((((.....)))))).((((........)))).....)))).. (-31.50 = -31.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,460,908 – 2,461,020
Length 112
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 82.73
Mean single sequence MFE -34.15
Consensus MFE -32.88
Energy contribution -32.88
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -0.93
Structure conservation index 0.96
SVM decision value -0.00
SVM RNA-class probability 0.532086
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2460908 112 - 20766785
CUGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGA---CCAAUAUUU-UGUAGUAAAUAUUCAAAUUUUAAUAGU--
.((((((((..((((........))))....((((((.......))))))(((((.......))))))))))))).---..(((((((-......)))))))..............-- ( -34.30)
>DroPse_CAF1 32327 110 - 1
AUGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGA---CAUUUAUUUUUGGUCUAUCUUUU---GAAGCAAUAGG--
..(((((((..((((........))))....((((((.......))))))(((((.......))))))))))))((---(...........)))........---...........-- ( -33.60)
>DroAna_CAF1 19152 115 - 1
AUGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGCAUUUCAUUAUUU-UGGUC--GCGUUUCUUUUUUUUGUCAUUC
..(((((((..((((........))))....((((((.......))))))(((((.......))))))))))))((...(((......-)))..--)).................... ( -35.10)
>DroPer_CAF1 23364 110 - 1
AUGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGA---CAUUUAUUUUUGGUCUAUCUUUU---GAAGCAAUAGG--
..(((((((..((((........))))....((((((.......))))))(((((.......))))))))))))((---(...........)))........---...........-- ( -33.60)
>consensus
AUGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGA___CAAUUAUUU_UGGUCUAUCUUUU___GAAGCAAUAGG__
.((((((((..((((........))))....((((((.......))))))(((((.......)))))))))))))........................................... (-32.88 = -32.88 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,460,944 – 2,461,049
Length 105
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 82.80
Mean single sequence MFE -37.78
Consensus MFE -31.50
Energy contribution -31.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.83
SVM decision value 0.28
SVM RNA-class probability 0.664855
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2460944 105 + 20766785
---UCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAGGUAAAU-----GAAUUUGCUGUCUGCCAAAAC-----UC
---..((((..((((((.......))))))....((((((.....)))))).((((........)))).....)))).((((.((-----.........)).)))).....-----.. ( -34.20)
>DroPse_CAF1 32361 115 + 1
---UCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAUGUGGGCCAAUCGAAUGCGAUCCGUAUCCGGCCAACACCU
---..((((..((((((.......))))))....((((((.....)))))).((((........)))).....)))).(((.((((....(.(((((...))))).))))).)))... ( -41.60)
>DroSim_CAF1 23173 105 + 1
---UCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAGGUAACC-----GAAUUUGGUGUCUGUGAAAAG-----UU
---..((((..((((((.......))))))....((((((.....)))))).((((........)))).....))))((..(.((-----(....))))..))........-----.. ( -34.10)
>DroYak_CAF1 21839 105 + 1
---UCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAGGUAAAC-----GAAUCCGCUGACUGUCAAAAC-----UC
---..((((..((((((.......))))))....((((((.....)))))).((((........)))).....)))).(((...(-----(....))...)))........-----.. ( -33.00)
>DroAna_CAF1 19188 106 + 1
AAUGCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAUGUGGGC-----GUAUCCGAUCGGUAUCAGAAC-------
.(((((((((.((((((.......)))))).(((((((((.....)))))).((((........)))).....)))....)))))-----))))((....)).........------- ( -42.20)
>DroPer_CAF1 23398 115 + 1
---UCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAUGUGGGCCAAUCGAAUGCGAUCCGUAUCCGGCCAACACCU
---..((((..((((((.......))))))....((((((.....)))))).((((........)))).....)))).(((.((((....(.(((((...))))).))))).)))... ( -41.60)
>consensus
___UCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAGGUAAGC_____GAAUCCGAUCCCUAUCAAAAC_____UU
.....((((..((((((.......))))))....((((((.....)))))).((((........)))).....))))......................................... (-31.50 = -31.50 +   0.00)

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 09:38:14 2006