Locus 1277

Sequence ID 3L_DroMel_CAF1
Location 3,689,165 – 3,689,300
Length 135
Max. P 0.921849
window1994 window1995

overview

Window 4

Location 3,689,165 – 3,689,265
Length 100
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 82.39
Mean single sequence MFE -27.57
Consensus MFE -15.59
Energy contribution -17.60
Covariance contribution 2.00
Combinations/Pair 1.12
Mean z-score -2.26
Structure conservation index 0.57
SVM decision value 0.01
SVM RNA-class probability 0.537673
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3689165 100 + 23771897
---------GGUGGAAAAAUGCAACGAGAAUUAUAAAAAGUGAUAUUAUAAAAGCAUUGACAGUCGCC-UAAUGGCCGUUUGUUGGCGCU--UUGGUGUCAACA-UGGCCUGG
---------(((((...(((((....((.(((((.....))))).))......))))).....)))))-....(((((..(((((((((.--...)))))))))-)))))... ( -30.60)
>DroGri_CAF1 65784 96 + 1
---------UCUAGGAAAAUGCAACAAGAAUUAUAAAAAGUUAUA--AUAAAAGCAUUGACAGUCGCU-UAAUGGCCAACUAUUGUCGCUGGCAGGCGUUUC---UA--AUAA
---------..((((((..(((.......(((((((....)))))--)).....((.(((((((.(((-....))).....))))))).)))))....))))---))--.... ( -17.70)
>DroSec_CAF1 84543 100 + 1
---------GGUGGAAAAAUGCAACGAGAAUUAUAAAAAGUUAUAUUAUAAAAGCAUUGACAGUCGCC-UAAUGGCCGUUUGUUGGCGCU--UUGGUGUCAACA-UGGCCUAG
---------(((((...(((((.........(((((....)))))........))))).....)))))-....(((((..(((((((((.--...)))))))))-)))))... ( -30.83)
>DroWil_CAF1 111277 111 + 1
AGCCGAGAAGCGGGAAAAAUGCAACAAGAAUUAUAAAAACUUAUA--AUAAAAGCAUUGACAGUCGCCUUAAUGGCCGUCUGUUGGCGCUGCUUGGUGUCAACACUGGCAUAA
.((((((.((((.....(((((.......(((((((....)))))--))....)))))(((((.((((.....)).)).)))))..)))).))))))((((....)))).... ( -32.70)
>DroYak_CAF1 66625 100 + 1
---------GCUGGAAAAAUGCAACGAGAAUUAUAAAAAGUGAUAUUAUAAAAGCAUUGACAGUCGCC-UAAUGGCCGUUUGUUGGCGCU--UUGGUGUCAACA-UGGCCUGG
---------((((....(((((....((.(((((.....))))).))......)))))..))))..((-....(((((..(((((((((.--...)))))))))-))))).)) ( -28.40)
>DroAna_CAF1 83058 98 + 1
---------GGUGGCAAAAUGCAAUGAGAAUUAUAAAAAGUUAUA--AUAAAAGCAUUGACAGUCGCC-UAAUGGCCGUUUGUUCGCUCU--UUGGUGUCAACA-UGGUCUGG
---------((((((....(((((((...(((((((....)))))--)).....))))).))))))))-....(((((((((..((((..--..)))).))).)-)))))... ( -25.20)
>consensus
_________GCUGGAAAAAUGCAACGAGAAUUAUAAAAAGUUAUA__AUAAAAGCAUUGACAGUCGCC_UAAUGGCCGUUUGUUGGCGCU__UUGGUGUCAACA_UGGCCUAG
.................(((((.........(((((....)))))........)))))...............((((...((((((((((....))))))))))..))))... (-15.59 = -17.60 +   2.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,689,196 – 3,689,300
Length 104
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 90.15
Mean single sequence MFE -31.83
Consensus MFE -26.59
Energy contribution -27.28
Covariance contribution 0.70
Combinations/Pair 1.04
Mean z-score -2.54
Structure conservation index 0.84
SVM decision value 1.14
SVM RNA-class probability 0.921849
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3689196 104 + 23771897
UGAUAUUAUAAAAGCAUUGACAGUCGCC-UAAUGGCCGUUUGUUGGCGCU--UUGGUGUCAACA-UGGCCUGGGC-AAAGUUAAUGGAUUGGCUAAUUAGGUAUGGUAA
...((((((.....(((((((..(.(((-((..(((((..(((((((((.--...)))))))))-))))))))))-)..))))))).....(((.....))))))))). ( -34.90)
>DroSec_CAF1 84574 104 + 1
UUAUAUUAUAAAAGCAUUGACAGUCGCC-UAAUGGCCGUUUGUUGGCGCU--UUGGUGUCAACA-UGGCCUAGGC-AAAGUUAAUGGAUUGGCUAAUUAGGUAUGGUAA
...((((((.....(((((((..(.(((-((..(((((..(((((((((.--...)))))))))-))))))))))-)..))))))).....(((.....))))))))). ( -35.20)
>DroEre_CAF1 79138 104 + 1
UGAUAUUAUAAAAGCAUUGACAGUCGCC-UAAUGGCCGUUUGUUGGCGCU--UUGGUGUCAACA-UGGCCUGGGC-AAAGUUAAUGGAUUGGCUAAUUAGGUAUGGAAA
..............(((((((..(.(((-((..(((((..(((((((((.--...)))))))))-))))))))))-)..))))))).....(((.....)))....... ( -33.20)
>DroWil_CAF1 111317 105 + 1
UUAUA--AUAAAAGCAUUGACAGUCGCCUUAAUGGCCGUCUGUUGGCGCUGCUUGGUGUCAACACUGGCAUAAGCCAACGUUAAUGGAUUGGCUAAUUAGA--UGGAAA
.....--.......(((((((((.((((.....)).)).))((((((..((((.((((....))))))))...)))))))))))))...............--...... ( -30.40)
>DroYak_CAF1 66656 104 + 1
UGAUAUUAUAAAAGCAUUGACAGUCGCC-UAAUGGCCGUUUGUUGGCGCU--UUGGUGUCAACA-UGGCCUGGGC-CAAGUUAAUGGAUUGGCUAAUUAGGUAUGGUAA
....................((...(((-(((((((((..(((((((((.--...)))))))))-)))))..(((-(((.........)))))).))))))).)).... ( -35.30)
>DroAna_CAF1 83089 102 + 1
UUAUA--AUAAAAGCAUUGACAGUCGCC-UAAUGGCCGUUUGUUCGCUCU--UUGGUGUCAACA-UGGUCUGGGC-CACAUUAAUGGAUCGACUAAUUAGAUAUGAAUA
.....--.......((((((..((.(((-((..(((((((((..((((..--..)))).))).)-))))))))))-.)).))))))....................... ( -22.00)
>consensus
UGAUAUUAUAAAAGCAUUGACAGUCGCC_UAAUGGCCGUUUGUUGGCGCU__UUGGUGUCAACA_UGGCCUGGGC_AAAGUUAAUGGAUUGGCUAAUUAGGUAUGGAAA
..............(((((((....(((.....((((...((((((((((....))))))))))..))))..)))....)))))))....................... (-26.59 = -27.28 +   0.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:38 2006