Locus 4784

Sequence ID 3R_DroMel_CAF1
Location 12,514,419 – 12,514,594
Length 175
Max. P 0.875599
window7849 window7850

overview

Window 9

Location 12,514,419 – 12,514,534
Length 115
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 93.74
Mean single sequence MFE -23.10
Consensus MFE -20.36
Energy contribution -20.76
Covariance contribution 0.40
Combinations/Pair 1.06
Mean z-score -1.21
Structure conservation index 0.88
SVM decision value 0.15
SVM RNA-class probability 0.609436
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12514419 115 + 27905053
AGCCAACAUUUACUGACUCGUGAUUUAAUGUUGCGCUACCGAAAAGUUUUCUUUGUUUAUGGUGAAACUUAAAUUGGCUAAGUGCCAGAAAUAUCUUUAAAUUAUUCACCUACUU
(((((((((((((......))))....)))))).))).....((((....))))......((((((........((((.....))))((....)).........))))))..... ( -22.10)
>DroSec_CAF1 3494 115 + 1
AGCCAACAUUUACUGACUUGUGAUUUAAUGUUGCGCUACCGAAAAGUUUUGUUGGUUUAUGGCGAAACUUAAAUUGGCUAAGUGCCACAAAUAUCUUUAAAUAUUUUACCUACUU
(((((((((((((......))))....)))))).)))......(((((((((((.....)))))))))))....((((.....))))............................ ( -23.70)
>DroSim_CAF1 3573 115 + 1
AGCCAACAUUUACUGACUCGUGAUUUAAUGUUGCGCUACCGAAAAGUUUUCUUGGUUUAUGGCGAAACUUAAAUUGGCUAAGUGCCACAAAUAUCUUUAAAUAUUUUACCUACUU
((((((...((((......))))(((((.(((.(((((((((.........)))))....)))).))))))))))))))(((((....((((((......))))))....))))) ( -21.10)
>DroEre_CAF1 931 115 + 1
AGCCAACAUUUACUGAGUCGUGAUUUAAUGUUGCGCUACAGAAAAGUUUUCUUUGUUUAUGGCGAAACUUAAAUUGGCUAAGUGCCACAAAUAUCUGUAAAUUAUUCACCUACUU
.((((((((((((......))))....)))))).))((((((.(((((((((........)).)))))))....((((.....))))......))))))................ ( -24.30)
>DroYak_CAF1 357 114 + 1
AGCCAACAUUUACUAAGUCGUGAUUUAAUGUUGCGCUACCGAAAAGUUUUGUUUGUUUAUGGCGAAACUUAAAUUGGCUAAGUGCCACAAAUAUCUUUAAAUUAUUCACCCAUU-
(((((((((((((......))))....)))))).)))...(((((((((((((.......))))))))))....((((.....)))).................))).......- ( -24.30)
>consensus
AGCCAACAUUUACUGACUCGUGAUUUAAUGUUGCGCUACCGAAAAGUUUUCUUUGUUUAUGGCGAAACUUAAAUUGGCUAAGUGCCACAAAUAUCUUUAAAUUAUUCACCUACUU
(((((((((((((......))))....)))))).)))...(((.(((((....(((((.((((...(((((.......))))))))).))))).....))))).)))........ (-20.36 = -20.76 +   0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,514,494 – 12,514,594
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 74.46
Mean single sequence MFE -21.28
Consensus MFE -13.84
Energy contribution -14.52
Covariance contribution 0.68
Combinations/Pair 1.19
Mean z-score -1.70
Structure conservation index 0.65
SVM decision value 0.89
SVM RNA-class probability 0.875599
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12514494 100 + 27905053
GGCUAAGUGCCAGAAAUAUCUUUAAAUUAUUCACCUACUUACAUAUUUACGGAAAUGUUC-CUUGGUGUAUUUAAAGACAUUUUAUAGAUCUU--------UGU--------UUGUU---
(((.....))).(((((.(((((((((....((((.....((((.((....)).))))..-...)))).))))))))).))))).........--------...--------.....--- ( -21.50)
>DroSec_CAF1 3569 95 + 1
GGCUAAGUGCCACAAAUAUCUUUAAAUAUUUUACCUACUUACAUAUUUACAGAAAUGUUC-CUUGGUGUAUUUGAAGACGUUUUAUAGAUAUU--------UGA----------------
(((.....))).(((((((((..(((..((((.......(((((....(((....)))..-....)))))....))))..)))...)))))))--------)).---------------- ( -22.50)
>DroSim_CAF1 3648 95 + 1
GGCUAAGUGCCACAAAUAUCUUUAAAUAUUUUACCUACUUACAUAUUUACGGAAAUGUUC-CUUGGUGUAUUUGAAGACAUUUUAUAGAUAUU--------UGA----------------
(((.....))).(((((((((..((((.((((.......(((((......(((.....))-)...)))))....)))).))))...)))))))--------)).---------------- ( -20.20)
>DroEre_CAF1 1006 120 + 1
GGCUAAGUGCCACAAAUAUCUGUAAAUUAUUCACCUACUUGCAUAUUUACGGCGAUGUUGCAUUGGUGUAUUUGAAAACAUUUUGUAGAUCUUAUUAGACUUGAGAUUUUUUUUGUCUCA
(((.....)))(((((......(((((....((((....((((((((......)))).))))..)))).))))).......)))))...............((((((.......)))))) ( -23.42)
>DroYak_CAF1 432 107 + 1
GGCUAAGUGCCACAAAUAUCUUUAAAUUAUUCACCCAUU-----CUUCACGGAAAUGUUGCAUUGGUGUAUUUAAAAGCAUUUCAUAGAUCCUAAAAGAUUUAAGAUGGUUU--------
(((.....))).......................(((((-----.......((((((((...((((.....)))).)))))))).((((((......)))))).)))))...-------- ( -18.80)
>consensus
GGCUAAGUGCCACAAAUAUCUUUAAAUUAUUCACCUACUUACAUAUUUACGGAAAUGUUC_CUUGGUGUAUUUGAAGACAUUUUAUAGAUCUU________UGA________________
(((.....)))..((((.(((((((((....((((.....((((.((....)).))))......)))).))))))))).))))..................................... (-13.84 = -14.52 +   0.68)

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 11:38:51 2006