Locus 4445

Sequence ID 3R_DroMel_CAF1
Location 11,752,049 – 11,752,149
Length 100
Max. P 0.925541
window7267 window7268

overview

Window 7

Location 11,752,049 – 11,752,149
Length 100
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 72.40
Mean single sequence MFE -26.25
Consensus MFE -15.72
Energy contribution -16.78
Covariance contribution 1.06
Combinations/Pair 1.24
Mean z-score -1.29
Structure conservation index 0.60
SVM decision value 0.14
SVM RNA-class probability 0.603698
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11752049 100 + 27905053
AUGGGAAAUAGUAACUGC--UUAAACU--CAUCGACUAUGUGAUUUUAGUCAAACGCAGAUGCCUUCAGCCACUGGAUGUGGGCAAAGGCAAGGCCUAUCUGCG
(((((....(((....))--)....))--))).(((((........)))))...((((((((((((...((((.....))))((....)))))))..))))))) ( -31.20)
>DroSec_CAF1 84803 95 + 1
-----AAGAAGUAACUUC--AUAAACU--CAUGGACUAUGUGAUUUUAGUCAAACGCAGAUGCCUCCAGCCACUGGAUGUGGGCAAAGGCAAGGCCUAUCUGCG
-----..((((...))))--.......--....(((((........)))))...((((((((((..((.((...)).))..)))..((((...))))))))))) ( -28.80)
>DroSim_CAF1 86501 95 + 1
-----AAAAAGUAACUUC--AUAAACU--CAUCGACUAUGUGAUUUUAGUCAAACGCAGAUGCCUCCAGCCACUGGAUGUGGGCAAAGGCAAGGCCUAUCUGCG
-----.............--.......--....(((((........)))))...((((((((((..((.((...)).))..)))..((((...))))))))))) ( -27.50)
>DroEre_CAF1 85162 83 + 1
----------------A---CCUAACU--AAUCGACCGUGCGAUUUUAGCCAAACGCAGAUGCCUUAGGCCCCUGCAUGUGGGCAAAGGUAAGGCCUAUAUGCG
----------------.---(((((..--.(((...(((((.......))...)))..)))...))))).....((((((((((.........)))))))))). ( -24.60)
>DroYak_CAF1 88869 99 + 1
UUGUGAAGAAGUAACUA---UUAAACU--CAUCUGCCAUGCGAUUUAAGUCAAACCCAGAUGCCUUAAGCCACUGGAUGUGGGCAAAGGUAAGGCGUAUCUGCG
..(((.((((((.....---....)))--..)))..)))(((((....)))........((((((((.(((((.....)).))).....))))))))....)). ( -19.00)
>DroPer_CAF1 91096 99 + 1
-----GGAGAGCAAACCCACAGAAACUUUUAAUAAAUAUUGGUUUUUAGUUAAGAAGAGAUGCCUGCUGCCGCUGGAACAGGGCAACGGCAAGGCCAUCCUCCG
-----((((...........(((((((..((.....))..)))))))...........(((((((((((((.(((...))))))...))).))).)))))))). ( -26.40)
>consensus
_____AAAAAGUAACUAC__AUAAACU__CAUCGACUAUGUGAUUUUAGUCAAACGCAGAUGCCUUCAGCCACUGGAUGUGGGCAAAGGCAAGGCCUAUCUGCG
.................................(((((........)))))...(((((((((((...(((..((........))..))).))))..))))))) (-15.72 = -16.78 +   1.06)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,752,049 – 11,752,149
Length 100
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 72.40
Mean single sequence MFE -26.35
Consensus MFE -18.14
Energy contribution -18.95
Covariance contribution 0.81
Combinations/Pair 1.33
Mean z-score -1.39
Structure conservation index 0.69
SVM decision value 1.17
SVM RNA-class probability 0.925541
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11752049 100 - 27905053
CGCAGAUAGGCCUUGCCUUUGCCCACAUCCAGUGGCUGAAGGCAUCUGCGUUUGACUAAAAUCACAUAGUCGAUG--AGUUUAA--GCAGUUACUAUUUCCCAU
.(.((((((....(((((((..((((.....))))..))))))).((((....((((...(((........))).--))))...--))))...)))))).)... ( -29.00)
>DroSec_CAF1 84803 95 - 1
CGCAGAUAGGCCUUGCCUUUGCCCACAUCCAGUGGCUGGAGGCAUCUGCGUUUGACUAAAAUCACAUAGUCCAUG--AGUUUAU--GAAGUUACUUCUU-----
((((((.......(((((((..((((.....))))..)))))))))))))...(((((........)))))....--.......--((((...))))..----- ( -26.71)
>DroSim_CAF1 86501 95 - 1
CGCAGAUAGGCCUUGCCUUUGCCCACAUCCAGUGGCUGGAGGCAUCUGCGUUUGACUAAAAUCACAUAGUCGAUG--AGUUUAU--GAAGUUACUUUUU-----
((((((.......(((((((..((((.....))))..))))))))))))).(((((((........)))))))..--.......--.............----- ( -28.01)
>DroEre_CAF1 85162 83 - 1
CGCAUAUAGGCCUUACCUUUGCCCACAUGCAGGGGCCUAAGGCAUCUGCGUUUGGCUAAAAUCGCACGGUCGAUU--AGUUAGG---U----------------
((((.....(((((((((((((......)))))))..))))))...))))((((((((..((((......)))))--)))))))---.---------------- ( -26.70)
>DroYak_CAF1 88869 99 - 1
CGCAGAUACGCCUUACCUUUGCCCACAUCCAGUGGCUUAAGGCAUCUGGGUUUGACUUAAAUCGCAUGGCAGAUG--AGUUUAA---UAGUUACUUCUUCACAA
..(((((..((((((.....(((.((.....))))).)))))))))))((..((((((((((..(((.....)))--.))))).---.)))))..))....... ( -20.50)
>DroPer_CAF1 91096 99 - 1
CGGAGGAUGGCCUUGCCGUUGCCCUGUUCCAGCGGCAGCAGGCAUCUCUUCUUAACUAAAAACCAAUAUUUAUUAAAAGUUUCUGUGGGUUUGCUCUCC-----
.((((((((.(((((((((((........))))))))..))))))).............(((((.(((...((.....))...))).)))))...))))----- ( -27.20)
>consensus
CGCAGAUAGGCCUUGCCUUUGCCCACAUCCAGUGGCUGAAGGCAUCUGCGUUUGACUAAAAUCACAUAGUCGAUG__AGUUUAU__GAAGUUACUUUUU_____
((((((...((((((((.(((........))).)))..))))).)))))).(((((((........)))))))............................... (-18.14 = -18.95 +   0.81)

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 11:29:28 2006