Locus 6858

Sequence ID 2L_DroMel_CAF1
Location 19,186,654 – 19,186,747
Length 93
Max. P 0.827653
window10932 window10933

overview

Window 2

Location 19,186,654 – 19,186,747
Length 93
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 79.47
Mean single sequence MFE -23.13
Consensus MFE -15.48
Energy contribution -15.65
Covariance contribution 0.17
Combinations/Pair 1.32
Mean z-score -1.40
Structure conservation index 0.67
SVM decision value 0.27
SVM RNA-class probability 0.661344
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19186654 93 + 22407834
AAGAUGGCCC---------CCAACUUGCUAACAAUCGGAUUACUUUUGACCCUGAUCGCCAGCGGUCAGGCCCAUCUCAAUAUUUUCCUCAACUUGCACGAG
.((((((...---------...............(((((.....))))).((((((((....)))))))).))))))......................... ( -21.10)
>DroGri_CAF1 20627 102 + 1
AUAAUGGAGAAUAACUUUAAAGGCAUCUUCACAAUCGGAUUAUGUUUGGCGCUGCUCAGCAGCGGACAAACCCAUUUGAAUAUAUUUCUCAAUUUGCACGAG
......(((((....((((((((.((((........))))...(((((.((((((...))))))..))))))).)))))).....)))))............ ( -22.40)
>DroSim_CAF1 7920 93 + 1
AAGAUGGCCC---------CCAACUUGCUCACAAUCGGAUUACUUUUGACCCUGAUCGCCAGCGGUCAGGCCCAUCUCAAUAUUUUCCUCAACUUGCACGAG
.((((((...---------...............(((((.....))))).((((((((....)))))))).))))))......................... ( -21.10)
>DroEre_CAF1 6872 93 + 1
AAGAUGGCCC---------GCAACUUCCUCACAAUCGGAUUACUUUUGACCCUGAUCGCCAGCGGUCAGGCUCAUCUAAAUAUUUUCCUCAACUUGCAUGAG
.((((((((.---------......(((........))).......((((((((.....))).)))))))).)))))..........((((.......)))) ( -24.00)
>DroYak_CAF1 7836 93 + 1
AAGAUGGCCC---------GCAACUUCCUCUCAAUCGGAUUACUUUUGACCCUGAUCGCCAGCGGUCAGGCUCAUCUAAACAUUUUCCUCAACUUGCACGAG
.((((((((.---------......(((........))).......((((((((.....))).)))))))).)))))......................... ( -22.70)
>DroAna_CAF1 56954 102 + 1
AAGAUGGCCAACAGCCGGAGCAAUUUGCUGACAAUCGGAUUAAUUCUGACCCUGGUAGCCAGUGGUCAGGCCCACCUCAACAUCUUCCUCAACUUGCACGAG
((((((((.....)))((.((((((..(((.....)))...))))((((((((((...)))).))))))))))........)))))................ ( -27.50)
>consensus
AAGAUGGCCC_________GCAACUUCCUCACAAUCGGAUUACUUUUGACCCUGAUCGCCAGCGGUCAGGCCCAUCUCAAUAUUUUCCUCAACUUGCACGAG
.((((((...........................(((((.....))))).((((((((....)))))))).))))))......................... (-15.48 = -15.65 +   0.17)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,186,654 – 19,186,747
Length 93
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 79.47
Mean single sequence MFE -30.45
Consensus MFE -18.93
Energy contribution -19.05
Covariance contribution 0.12
Combinations/Pair 1.27
Mean z-score -1.93
Structure conservation index 0.62
SVM decision value 0.70
SVM RNA-class probability 0.827653
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19186654 93 - 22407834
CUCGUGCAAGUUGAGGAAAAUAUUGAGAUGGGCCUGACCGCUGGCGAUCAGGGUCAAAAGUAAUCCGAUUGUUAGCAAGUUGG---------GGGCCAUCUU
((((.......)))).........(((((((.((..((.((((((((((.((((........))))))))))))))..))..)---------.).))))))) ( -34.50)
>DroGri_CAF1 20627 102 - 1
CUCGUGCAAAUUGAGAAAUAUAUUCAAAUGGGUUUGUCCGCUGCUGAGCAGCGCCAAACAUAAUCCGAUUGUGAAGAUGCCUUUAAAGUUAUUCUCCAUUAU
((((.......))))...........((((((((((..((((((...)))))).))))).......((((.(((((....))))).)))).....))))).. ( -23.80)
>DroSim_CAF1 7920 93 - 1
CUCGUGCAAGUUGAGGAAAAUAUUGAGAUGGGCCUGACCGCUGGCGAUCAGGGUCAAAAGUAAUCCGAUUGUGAGCAAGUUGG---------GGGCCAUCUU
((((.......)))).........(((((((.((..((.(((.((((((.((((........)))))))))).)))..))..)---------.).))))))) ( -33.40)
>DroEre_CAF1 6872 93 - 1
CUCAUGCAAGUUGAGGAAAAUAUUUAGAUGAGCCUGACCGCUGGCGAUCAGGGUCAAAAGUAAUCCGAUUGUGAGGAAGUUGC---------GGGCCAUCUU
((((.......))))..........(((((.((((((((.(((.....)))))))....(((((((........)))..))))---------))))))))). ( -28.50)
>DroYak_CAF1 7836 93 - 1
CUCGUGCAAGUUGAGGAAAAUGUUUAGAUGAGCCUGACCGCUGGCGAUCAGGGUCAAAAGUAAUCCGAUUGAGAGGAAGUUGC---------GGGCCAUCUU
((((.......))))..........(((((.((((((((.(((.....)))))))....(((((((........)))..))))---------))))))))). ( -27.80)
>DroAna_CAF1 56954 102 - 1
CUCGUGCAAGUUGAGGAAGAUGUUGAGGUGGGCCUGACCACUGGCUACCAGGGUCAGAAUUAAUCCGAUUGUCAGCAAAUUGCUCCGGCUGUUGGCCAUCUU
((((.......)))).........(((((((..((((((.((((...)))))))))).......(((((.((((((.....)))..))).)))))))))))) ( -34.70)
>consensus
CUCGUGCAAGUUGAGGAAAAUAUUGAGAUGGGCCUGACCGCUGGCGAUCAGGGUCAAAAGUAAUCCGAUUGUGAGCAAGUUGC_________GGGCCAUCUU
((((.......))))..........(((((.((((((((.((((...))))))))).........(((((.......)))))...........)))))))). (-18.93 = -19.05 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:21:26 2006