Locus 3476

Sequence ID 3L_DroMel_CAF1
Location 10,221,761 – 10,221,865
Length 104
Max. P 0.564073
window5428 window5429

overview

Window 8

Location 10,221,761 – 10,221,865
Length 104
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 80.40
Mean single sequence MFE -24.65
Consensus MFE -15.23
Energy contribution -16.28
Covariance contribution 1.06
Combinations/Pair 1.10
Mean z-score -1.57
Structure conservation index 0.62
SVM decision value 0.06
SVM RNA-class probability 0.564073
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10221761 104 + 23771897
UUAUAAAAUCAUAGAAAUCAUAUGAC-AAACA-UUUUUUCAAGUGCAACUGCAGUCGAAGUUGAA-UUCAAAGCUG--UAUCUGGAGAUGGAUGUGGGAUAUGCACCUG
........(((((.......))))).-...((-(..(..((.((.((.((.(((....((((...-.....)))).--...))).)).)).)).))..).)))...... ( -18.20)
>DroSec_CAF1 97903 103 + 1
UUUAAAAAUCAUGGACA-CAUAUGAC-AUACA-UUUUCCCAAGUGCAACUGCAGAUGAAGUUGAA-UUCAAAGCUG--UAUCUGGAGAUGGAUGUGGGAUAUGCACCUG
........(((((....-..))))).-...((-(..(((((.((.((.((.((((((.((((...-.....)))).--)))))).)).)).)).))))).)))...... ( -27.70)
>DroSim_CAF1 103252 103 + 1
UUAUAAAAUCAUAGAAA-CAUAUGAC-AAACA-UUUUUCCAAGUGCAACUGCAGAUGAAGUUGAA-UUCAAAGCUG--UAUCUGGAGAUGGAUGUGGGAUAUGCACCUG
........(((((....-..))))).-...((-(..(((((.((.((.((.((((((.((((...-.....)))).--)))))).)).)).)).))))).)))...... ( -25.30)
>DroEre_CAF1 103580 103 + 1
AUGUAAAAUUAUAAAAG-CAUAUGAC-AAACA-UUUUUCCAAGUGCAGCUGCAGAUGAAGUUAAA-UUCAAAGCUG--UAUCUGGAGAUGGAUGUGGGAUAUGCACCUG
................(-(((((..(-(....-..((((((..(((((((.....((((......-)))).)))))--))..))))))......))..))))))..... ( -30.70)
>DroYak_CAF1 103269 94 + 1
---------AAAAGAAA-CAGAUGGC-AAACA-UUUUUCCAAGUGCAACUGCAGAUGAAGUUGAA-UUCAAAGCUG--UAUCUGGAGAUGGAUGUGGGAUAUGCACCUG
---------........-(((...((-(....-...(((((.((.((.((.((((((.((((...-.....)))).--)))))).)).)).)).)))))..)))..))) ( -24.40)
>DroAna_CAF1 99427 96 + 1
------------GCUAA-CUUAAGCCCAAUUAUUUUUUCCAAGUGCAUCUGCCGAUGAAGUCAGCCUGUGGAGCUGGGAACCUAGAGAUGGAUGCGGGAUAUGCACCUG
------------(((..-....)))..............((.((((((.(.(((......((((((....).)))))...((.......))...))).).)))))).)) ( -21.60)
>consensus
UU_UAAAAUCAUAGAAA_CAUAUGAC_AAACA_UUUUUCCAAGUGCAACUGCAGAUGAAGUUGAA_UUCAAAGCUG__UAUCUGGAGAUGGAUGUGGGAUAUGCACCUG
....................................(((((.((.((.((.((((((.((((.........))))...)))))).)).)).)).))))).......... (-15.23 = -16.28 +   1.06)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,221,761 – 10,221,865
Length 104
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 80.40
Mean single sequence MFE -19.90
Consensus MFE -13.22
Energy contribution -13.47
Covariance contribution 0.25
Combinations/Pair 1.12
Mean z-score -1.28
Structure conservation index 0.66
SVM decision value -0.03
SVM RNA-class probability 0.518482
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10221761 104 - 23771897
CAGGUGCAUAUCCCACAUCCAUCUCCAGAUA--CAGCUUUGAA-UUCAACUUCGACUGCAGUUGCACUUGAAAAAA-UGUUU-GUCAUAUGAUUUCUAUGAUUUUAUAA
((((((((............(((....))).--..((.(((((-......)))))..))...))))))))......-(((..-((((((.(....)))))))...))). ( -19.40)
>DroSec_CAF1 97903 103 - 1
CAGGUGCAUAUCCCACAUCCAUCUCCAGAUA--CAGCUUUGAA-UUCAACUUCAUCUGCAGUUGCACUUGGGAAAA-UGUAU-GUCAUAUG-UGUCCAUGAUUUUUAAA
((((((((............(((....))).--..((..((((-......))))...))...))))))))(((..(-(((..-...)))).-..)))............ ( -19.80)
>DroSim_CAF1 103252 103 - 1
CAGGUGCAUAUCCCACAUCCAUCUCCAGAUA--CAGCUUUGAA-UUCAACUUCAUCUGCAGUUGCACUUGGAAAAA-UGUUU-GUCAUAUG-UUUCUAUGAUUUUAUAA
((((((((............(((....))).--..((..((((-......))))...))...))))))))......-(((..-((((((..-....))))))...))). ( -19.60)
>DroEre_CAF1 103580 103 - 1
CAGGUGCAUAUCCCACAUCCAUCUCCAGAUA--CAGCUUUGAA-UUUAACUUCAUCUGCAGCUGCACUUGGAAAAA-UGUUU-GUCAUAUG-CUUUUAUAAUUUUACAU
.....((((((...(((..(((.(((((...--(((((.((((-......)))).....)))))...)))))...)-))..)-)).)))))-)................ ( -20.70)
>DroYak_CAF1 103269 94 - 1
CAGGUGCAUAUCCCACAUCCAUCUCCAGAUA--CAGCUUUGAA-UUCAACUUCAUCUGCAGUUGCACUUGGAAAAA-UGUUU-GCCAUCUG-UUUCUUUU---------
((((((((............(((....))).--..((..((((-......))))...))...))))))))((((.(-((...-..)))...-))))....--------- ( -16.70)
>DroAna_CAF1 99427 96 - 1
CAGGUGCAUAUCCCGCAUCCAUCUCUAGGUUCCCAGCUCCACAGGCUGACUUCAUCGGCAGAUGCACUUGGAAAAAAUAAUUGGGCUUAAG-UUAGC------------
(((((((((...(((...((.......))....(((((.....))))).......)))...)))))))))..............(((....-..)))------------ ( -23.20)
>consensus
CAGGUGCAUAUCCCACAUCCAUCUCCAGAUA__CAGCUUUGAA_UUCAACUUCAUCUGCAGUUGCACUUGGAAAAA_UGUUU_GUCAUAUG_UUUCUAUGAUUUUA_AA
((((((((............(((....))).....((..((((.......))))...))...))))))))....................................... (-13.22 = -13.47 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:04 2006