Locus 9198

Sequence ID 3R_DroMel_CAF1
Location 24,528,968 – 24,529,098
Length 130
Max. P 0.976571
window14712 window14713

overview

Window 2

Location 24,528,968 – 24,529,058
Length 90
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 81.50
Mean single sequence MFE -25.26
Consensus MFE -19.62
Energy contribution -18.48
Covariance contribution -1.14
Combinations/Pair 1.29
Mean z-score -1.49
Structure conservation index 0.78
SVM decision value 0.33
SVM RNA-class probability 0.693519
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24528968 90 + 27905053
--------------UUUUC--UUGUGC---CGCCACUGCCACUUGGCCAAAGCAUCA--CACUGCAAGUUGGCAACAAAGUGGUUAAGACAAAUGGGUUACGUGAUAAAAU
--------------((((.--(..((.---.(((...(((((((.(((((.(((...--...)))...)))))....)))))))...........)))..))..).)))). ( -23.24)
>DroVir_CAF1 17628 93 + 1
--------------UUUAG--UUGCGCGAAUGCUGCUGCCACUUGGCCAAAGCAUCA--CACUGCAAGUUGGCAACAAAGUGGUUAAGACAAAUGGGUUACGUGAUAAAAU
--------------....(--(.((.((..((((...(((((((.(((((.(((...--...)))...)))))....)))))))..)).))..)).)).)).......... ( -26.20)
>DroGri_CAF1 31415 85 + 1
------------------------CCCAUCUGCUGCUACUGCUUAGCCAAAGCAUCA--CACUGCAACUUGGCAACAAAGUGGUUAAGACAAAUGGGUUACGUGAUAAAAU
------------------------(((((.((((((((((.....(((((.(((...--...)))...))))).....))))))..)).)).))))).............. ( -23.20)
>DroWil_CAF1 31403 94 + 1
--------------CUUUCGCUGGCAC---UGCCACUGCCACUUGGCCGAAGCAUCACACACUGCAAGUUGGCAACAAAGUGGUUAAGACAAAUGGGUUACGUGAUAAAAU
--------------...((((((((..---.))))(((((((((.(((((.(((........)))...)))))....)))))))..)).............))))...... ( -25.20)
>DroMoj_CAF1 36229 107 + 1
CCCCGCAUGCUUCUUUUGG--AUGCGCGAAUGCUGCUGCCACUUGGCCAAAGCAUCA--CACUGCAAGUUGGCAACAAAGUGGUUAAGACAAAUGGGUUACGUGAUAAAAU
.(((((((.(.......).--)))).....((((...(((((((.(((((.(((...--...)))...)))))....)))))))..)).))...))).............. ( -31.90)
>DroAna_CAF1 27905 90 + 1
--------------UUUUC--UUCUGC---CGGCACUGCCACUUGGCCGAAGCAUCA--CACUGCAAGUUGGCAACAAAGUGGUUAAGACAAAUGGGUUACGUGAUAAAAU
--------------....(--(((.((---((((...)))....))).)))).((((--(((..(...(((....))).)..))...(((......)))..)))))..... ( -21.80)
>consensus
______________UUUUC__UUGCGC___UGCCACUGCCACUUGGCCAAAGCAUCA__CACUGCAAGUUGGCAACAAAGUGGUUAAGACAAAUGGGUUACGUGAUAAAAU
.................................(((.(((((((.(((((.(((........)))...)))))....)))))))...(((......)))..)))....... (-19.62 = -18.48 +  -1.14)

alignment

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secondary structure

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dotplot

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Window 3

Location 24,528,980 – 24,529,098
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 95.17
Mean single sequence MFE -32.00
Consensus MFE -30.41
Energy contribution -29.50
Covariance contribution -0.91
Combinations/Pair 1.18
Mean z-score -1.40
Structure conservation index 0.95
SVM decision value 1.77
SVM RNA-class probability 0.976571
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24528980 118 + 27905053
GCCACUGCCACUUGGCCAAAGCAUCA--CACUGCAAGUUGGCAACAAAGUGGUUAAGACAAAUGGGUUACGUGAUAAAAUGCGGUUACUCAAAUUGCAUGUAUGCAAGCUUACAUGUUGU
....(((((((((.(((((.(((...--...)))...)))))....)))))))..))(((..(((((..(((........)))...)))))....(((((((.(....).)))))))))) ( -33.20)
>DroPse_CAF1 34143 118 + 1
GCCGCUGCCACUUGGCCAGAGCAUCA--CACUGCAAGUUGGCAACAAAGUGGUUAAGACAAAUGGGUUACGUGAUAAAAUGCGGUUACUCAAAUUGCAUGUAUGCAAGCUUACAUGUUGU
..(...(((((((.(((((.(((...--...)))...)))))....)))))))...)(((..(((((..(((........)))...)))))....(((((((.(....).)))))))))) ( -33.50)
>DroGri_CAF1 31422 117 + 1
GCUGCUACUGCUUAGCCAAAGCAUCA--CACUGCAACUUGGCAACAAAGUGGUUAAGACAAAUGGGUUACGUGAUAAAAUGCGGUUACUCAAAUUGCAUGUAUGCAAGUUUACAUCUU-U
..((((((((((((((((..(((...--...)))...(((....)))..)))))))......(((((..(((........)))...)))))....))).))).)))............-. ( -27.40)
>DroWil_CAF1 31417 120 + 1
GCCACUGCCACUUGGCCGAAGCAUCACACACUGCAAGUUGGCAACAAAGUGGUUAAGACAAAUGGGUUACGUGAUAAAAUGCGGUUACUCAAAUUGCAUGUAUGCAAGCUUACAUGUUGU
....(((((((((.(((((.(((........)))...)))))....)))))))..))(((..(((((..(((........)))...)))))....(((((((.(....).)))))))))) ( -32.70)
>DroMoj_CAF1 36258 118 + 1
GCUGCUGCCACUUGGCCAAAGCAUCA--CACUGCAAGUUGGCAACAAAGUGGUUAAGACAAAUGGGUUACGUGAUAAAAUGCGGUUACUCAAAUUGCAUGUAUGCAAGCUUACAUCUUCU
.((...(((((((.(((((.(((...--...)))...)))))....)))))))..)).....(((((..(((........)))...)))))..(((((....)))))............. ( -31.70)
>DroPer_CAF1 13651 118 + 1
GCCGCUGCCACUUGGCCAGAGCAUCA--CACUGCAAGUUGGCAACAAAGUGGUUAAGACAAAUGGGUUACGUGAUAAAAUGCGGUUACUCAAAUUGCAUGUAUGCAAGCUUACAUGUUGU
..(...(((((((.(((((.(((...--...)))...)))))....)))))))...)(((..(((((..(((........)))...)))))....(((((((.(....).)))))))))) ( -33.50)
>consensus
GCCGCUGCCACUUGGCCAAAGCAUCA__CACUGCAAGUUGGCAACAAAGUGGUUAAGACAAAUGGGUUACGUGAUAAAAUGCGGUUACUCAAAUUGCAUGUAUGCAAGCUUACAUGUUGU
......(((((((.(((((.(((........)))...)))))....)))))))((((.(...(((((..(((........)))...)))))..(((((....))))))))))........ (-30.41 = -29.50 +  -0.91)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:28:45 2006