Locus 8951

Sequence ID 3R_DroMel_CAF1
Location 23,997,242 – 23,997,340
Length 98
Max. P 0.990646
window14346 window14347

overview

Window 6

Location 23,997,242 – 23,997,340
Length 98
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 72.21
Mean single sequence MFE -28.78
Consensus MFE -13.52
Energy contribution -13.55
Covariance contribution 0.03
Combinations/Pair 1.06
Mean z-score -2.29
Structure conservation index 0.47
SVM decision value 1.81
SVM RNA-class probability 0.978461
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23997242 98 + 27905053
AUGGGCAG-AGU-GG-UUUCUCUCCUCACUUAUUUGCACUUUAAGUGAAUUGUUUGCUUGCGUUUUAACGCAAAUGCAAUUAUGCUCUG-----------GCCGGAUUUGUC--------
.(((.(((-(((-..-.........(((((((.........))))))).....((((((((((....))))))..))))....))))))-----------.)))........-------- ( -29.60)
>DroVir_CAF1 219784 99 + 1
-UCAGCUG-ACU-GA-CUGCUUUAUGCACUUAUUUACACUUUAAGUGAAUUGUUUGCUUGCGUUUUAACGCAAAUGCAAUUAUGCACAGGCAAUA------UCGCA---UUC--------
-((((...-.))-))-.(((......((((((.........)))))).((((((((.((((((....)))))).((((....)))))))))))).------..)))---...-------- ( -24.60)
>DroPse_CAF1 214358 118 + 1
AGAAACAG-AGCUGC-UGGAUUUCCUCACUUAUUUGCACUUUAAGUGAAUUGUUUGCUUGCGUUUUAACGCAAAUGCAAUUAUGCGCUGCCAGCGUCUGGGCCGGGUCCGGCUCGGGACG
........-....((-(((......(((((((.........))))))).......((((((((....))))))..(((....)))))..)))))((((((((((....)))))).)))). ( -41.20)
>DroGri_CAF1 175027 96 + 1
-UCAA----ACU-GG-CAGCUUUCUGCACUUAUUUACACUUUAAGUGAAUUGUUUGCUUGCGUUUUAACACAAAUGCAAUUAUGCGCUGCCAACA------ACGCU---GUC--------
-....----..(-((-((((......((((((.........))))))....((.((.((((((((......)))))))).)).)))))))))...------.....---...-------- ( -25.80)
>DroWil_CAF1 248080 100 + 1
--UUGCAC-AGUUGGUUGCCUUUCCUCACUUAUUUGCAGUUUAAGUGAAUUGUUUGCUUGCGUUUUAACGCAAAUGCAAUUAUUCACUGCCAGC------GCCACA---AUC--------
--......-.(((((((((................))).....(((((((...((((((((((....))))))..))))..)))))))))))))------......---...-------- ( -25.69)
>DroAna_CAF1 210169 99 + 1
AUGGAAGGAAGC-GG-CUGCUUUCCUCACUUAUUUGCACUCUGAGUGAAUUGUUUGCUUGCGUUUUAACGCAAAUGCAAUUAUGCGCUG-----------CCCGGAUUUGCC--------
......((..((-((-(.((.....(((((((.........))))))).....((((((((((....))))))..))))....))))))-----------))).........-------- ( -25.80)
>consensus
_UCAACAG_AGU_GG_CUGCUUUCCUCACUUAUUUGCACUUUAAGUGAAUUGUUUGCUUGCGUUUUAACGCAAAUGCAAUUAUGCGCUGCCA_C______GCCGCA___GUC________
..........................((((((.........))))))((((((....((((((....))))))..))))))....................................... (-13.52 = -13.55 +   0.03)

alignment

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secondary structure

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dotplot

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Window 7

Location 23,997,242 – 23,997,340
Length 98
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 72.21
Mean single sequence MFE -27.71
Consensus MFE -13.78
Energy contribution -13.92
Covariance contribution 0.14
Combinations/Pair 1.11
Mean z-score -2.42
Structure conservation index 0.50
SVM decision value 2.22
SVM RNA-class probability 0.990646
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23997242 98 - 27905053
--------GACAAAUCCGGC-----------CAGAGCAUAAUUGCAUUUGCGUUAAAACGCAAGCAAACAAUUCACUUAAAGUGCAAAUAAGUGAGGAGAGAAA-CC-ACU-CUGCCCAU
--------.........((.-----------(((((.....((((..((((((....)))))))))).(..((((((((.........))))))))..).....-..-.))-))).)).. ( -25.60)
>DroVir_CAF1 219784 99 - 1
--------GAA---UGCGA------UAUUGCCUGUGCAUAAUUGCAUUUGCGUUAAAACGCAAGCAAACAAUUCACUUAAAGUGUAAAUAAGUGCAUAAAGCAG-UC-AGU-CAGCUGA-
--------...---.((((------((((((.(((((((..((((..((((((....))))))))))......(((.....))).......)))))))..))))-).-.))-).))...- ( -25.40)
>DroPse_CAF1 214358 118 - 1
CGUCCCGAGCCGGACCCGGCCCAGACGCUGGCAGCGCAUAAUUGCAUUUGCGUUAAAACGCAAGCAAACAAUUCACUUAAAGUGCAAAUAAGUGAGGAAAUCCA-GCAGCU-CUGUUUCU
.(((..(.((((....)))))..)))(((((..(((((....)))..((((((....))))))))......((((((((.........)))))))).....)))-))....-........ ( -37.80)
>DroGri_CAF1 175027 96 - 1
--------GAC---AGCGU------UGUUGGCAGCGCAUAAUUGCAUUUGUGUUAAAACGCAAGCAAACAAUUCACUUAAAGUGUAAAUAAGUGCAGAAAGCUG-CC-AGU----UUGA-
--------...---.....------..(((((((((((....)))..((((((....))))))(((.......(((.....)))........))).....))))-))-)).----....- ( -26.96)
>DroWil_CAF1 248080 100 - 1
--------GAU---UGUGGC------GCUGGCAGUGAAUAAUUGCAUUUGCGUUAAAACGCAAGCAAACAAUUCACUUAAACUGCAAAUAAGUGAGGAAAGGCAACCAACU-GUGCAA--
--------...---....((------((.((((((.....)))))..((((((....))))))((......((((((((.........)))))))).....))......).-))))..-- ( -25.80)
>DroAna_CAF1 210169 99 - 1
--------GGCAAAUCCGGG-----------CAGCGCAUAAUUGCAUUUGCGUUAAAACGCAAGCAAACAAUUCACUCAGAGUGCAAAUAAGUGAGGAAAGCAG-CC-GCUUCCUUCCAU
--------.((........)-----------).((((....((((..((((((....)))))))))).....((.....))))))......(..(((((.((..-..-)))))))..).. ( -24.70)
>consensus
________GAC___UCCGGC______G_UGGCAGCGCAUAAUUGCAUUUGCGUUAAAACGCAAGCAAACAAUUCACUUAAAGUGCAAAUAAGUGAGGAAAGCAA_CC_ACU_CUGCUCA_
.........................................((((..((((((....))))))))))....((((((((.........))))))))........................ (-13.78 = -13.92 +   0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:23:23 2006