Locus 3350

Sequence ID 3L_DroMel_CAF1
Location 9,821,272 – 9,821,432
Length 160
Max. P 0.975900
window5224 window5225

overview

Window 4

Location 9,821,272 – 9,821,362
Length 90
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 76.72
Mean single sequence MFE -16.80
Consensus MFE -11.94
Energy contribution -11.31
Covariance contribution -0.63
Combinations/Pair 1.19
Mean z-score -2.09
Structure conservation index 0.71
SVM decision value 1.76
SVM RNA-class probability 0.975900
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9821272 90 + 23771897
----------AAAAAAAAAACAGUAAACUUCAUUCAUAAAAUAAUAGUGGUAGUAA--AUCUAUGGUAGAAAGA--GGAAGUUGAACG-GGGGAAACCCGGCCAG---------------
----------............((.((((((.(((......((...((((......--..))))..))....))--)))))))..)).-(((....)))......--------------- ( -16.60)
>DroSec_CAF1 115242 96 + 1
AGCAAAGCAAA-----AAAACAGUAAAUUUCAUUCAUAAAAUAAUAGUGGUAGUAA--AUCUAUGAUAGAAAGG-GGGAAGUCGAAUG-GGGGAAACCCGGCAAG---------------
......((...-----..............(((((...........((.((((...--..)))).)).....((-......)))))))-(((....))).))...--------------- ( -17.10)
>DroSim_CAF1 118561 102 + 1
AGCAAAGCAAAAAAAAAAAACAGUAAAUUUCAUUCAUAAAAUAAUAGUGGUAGUAA--AUCUAUGAUAGAAAGGGGGGAAGUCGAAUG-GGGGAAACCCGGCAAG---------------
......((......................(((((...........((.((((...--..)))).))..........(....))))))-(((....))).))...--------------- ( -17.00)
>DroYak_CAF1 128253 109 + 1
-G--------AAAAGCAAAACAGUAAAUUUCAUUCAUAAAAUAAUAGUGGUAGUAUAUAUCUGUGGUAGAAAGA--GGAAGUCAAACGCGGGGAAACCCGGCAAAAUACAAAACAAAAGA
-.--------....((......((..(((((.(((........((((..(((.....)))))))........))--))))))...)).((((....)))))).................. ( -16.49)
>consensus
_G________AAAAAAAAAACAGUAAAUUUCAUUCAUAAAAUAAUAGUGGUAGUAA__AUCUAUGAUAGAAAGA__GGAAGUCGAACG_GGGGAAACCCGGCAAG_______________
......................((..(((((..((........((((.............))))........))...))))).......(((....))).)).................. (-11.94 = -11.31 +  -0.63)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,821,338 – 9,821,432
Length 94
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.99
Mean single sequence MFE -24.50
Consensus MFE -15.86
Energy contribution -15.30
Covariance contribution -0.56
Combinations/Pair 1.14
Mean z-score -2.00
Structure conservation index 0.65
SVM decision value 0.68
SVM RNA-class probability 0.821995
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9821338 94 + 23771897
GUUGAACG-GGGGAAACCCGGCCAG---------------------AAA-AAAGUGUUGAAAUUUUUG-GUUUCUGUGACGUAUAUAAUUUAUUUAUGCGUGUUUU--UUUAUGGCUUUG
........-(((....)))(((((.---------------------(((-((((....(((((.....-)))))....(((((((.........))))))).))))--))).)))))... ( -25.60)
>DroSec_CAF1 115314 97 + 1
GUCGAAUG-GGGGAAACCCGGCAAG---------------------AAAAAAAGUGUUGAAAUAUUUGCGUUUCUGUGACGUUUAUAAUUUAUUUAUGCGUGUUUU-UUGUAUGGCUUUG
((((....-(((....))).(((((---------------------(((....((((((((.(((..(((((.....)))))..))).))))...))))...))))-)))).)))).... ( -25.10)
>DroSim_CAF1 118639 97 + 1
GUCGAAUG-GGGGAAACCCGGCAAG---------------------AAA-AAAGUGUUGAAAUAUUUGCGUUUCUGUGACGUUUAUAAUUUAUUUAUGCGUGUUUUUUUUUAUGGCUUUG
((((....-(((....)))...(((---------------------(((-((.((((((((.(((..(((((.....)))))..))).))))...))))...))))))))..)))).... ( -21.60)
>DroYak_CAF1 128322 115 + 1
GUCAAACGCGGGGAAACCCGGCAAAAUACAAAACAAAAGACAAAAAAAA-AAUGUGUUGAAAUUUUUGCGUUUCUGUGACGUUUAUAAUUUAUUUAUGUGUGUUU---UUUAUGACUU-U
((((...(((((....))).))............((((((((.......-.(((((...(((((...(((((.....)))))....)))))...))))).)))))---))).))))..-. ( -25.70)
>consensus
GUCGAACG_GGGGAAACCCGGCAAG_____________________AAA_AAAGUGUUGAAAUAUUUGCGUUUCUGUGACGUUUAUAAUUUAUUUAUGCGUGUUUU__UUUAUGGCUUUG
((((.....(((....))).......................................(((((......)))))...((((..(((((.....)))))..))))........)))).... (-15.86 = -15.30 +  -0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:46 2006