Locus 2038

Sequence ID 3L_DroMel_CAF1
Location 5,612,920 – 5,613,075
Length 155
Max. P 0.969913
window3183 window3184

overview

Window 3

Location 5,612,920 – 5,613,035
Length 115
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 88.32
Mean single sequence MFE -18.95
Consensus MFE -14.38
Energy contribution -14.58
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.71
Structure conservation index 0.76
SVM decision value 0.32
SVM RNA-class probability 0.687006
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5612920 115 + 23771897
AUAAAAAAAUCCUAUUGAUUUAUUGCCAUUAAAAGCAACAGCUGCUAAAGUUGGAAAAACAAUUAGUCAAACGCCAAAAGAUAAUUCAGCAGAGCAGCAACUGACCAAGUUAUAC
......(((((.....))))).((((........))))..((((((...((((((..........((.....))..........))))))..))))))((((.....)))).... ( -18.75)
>DroSec_CAF1 31991 115 + 1
AUAAAAAAAUCCUAUUGAUUUAUUGCCAUUAAAAGCAACAGCUGCUAGAGUUGGAAAAACAAUUAGUCAAACGCCAAAAGAUAAUUCAGUAGAGCAGCAACAAACCANNNNNNNN
......(((((.....))))).((((........))))..((((((..(((((......)))))...............((....)).....))))))................. ( -16.50)
>DroSim_CAF1 31372 114 + 1
AUCAA-AAAUCCUAUUGAUUUAUUGCCAUUAAAAGCAACAGCUGCUAGAGUUGGAAAAACAAUUAGUCAAACGCCAAAAGAUAAUUCAGUAGAGCAGCAACAAACCAAGUUAUAC
.....-.........((((((.((((........))))..((((((..(((((......)))))...............((....)).....))))))........))))))... ( -16.90)
>DroEre_CAF1 33446 114 + 1
AUAAA-AAAUCCUAUUGAUUUAUUGCCGCUAACAGCAAAAGCUGCUAGAGUUGCAAAAACAAUUAGUUAAGCGCCAAGCGACAAUUCAGUAGAGCAGCAACAGGCCAAGUUAUAU
.....-.........((((((...(((((.....))....((((((.(((((((...(((.....)))..((.....))).)))))).....))))))....))).))))))... ( -24.80)
>DroYak_CAF1 31905 113 + 1
AUAAA-AAAUCCUAUUGAUUUAUUGCCAUUAACAGCAACAGCUGCUAGAGUUGCAA-AACAAUUAGUAAAACACCUAAAGAUAAUUCAGUAGAGCAACAACAAACCCAGUUAUAC
.....-.....(((((((.(((((((.(((..((((....))))....))).))..-.....((((........)))).))))).)))))))....................... ( -17.80)
>consensus
AUAAA_AAAUCCUAUUGAUUUAUUGCCAUUAAAAGCAACAGCUGCUAGAGUUGGAAAAACAAUUAGUCAAACGCCAAAAGAUAAUUCAGUAGAGCAGCAACAAACCAAGUUAUAC
......(((((.....))))).((((........))))..((((((..(((((......)))))...............((....)).....))))))................. (-14.38 = -14.58 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,612,955 – 5,613,075
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 70.55
Mean single sequence MFE -16.38
Consensus MFE -11.40
Energy contribution -11.60
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.65
Structure conservation index 0.70
SVM decision value 1.65
SVM RNA-class probability 0.969913
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5612955 120 + 23771897
CAACAGCUGCUAAAGUUGGAAAAACAAUUAGUCAAACGCCAAAAGAUAAUUCAGCAGAGCAGCAACUGACCAAGUUAUACAACAACAAUUCCCAUUCGCUUUUUAUUGUUCUUAACAAAA
.....((((((...((((((..........((.....))..........))))))..))))))..........((((...(((((.((..............)).)))))..)))).... ( -16.99)
>DroSec_CAF1 32026 103 + 1
CAACAGCUGCUAGAGUUGGAAAAACAAUUAGUCAAACGCCAAAAGAUAAUUCAGUAGAGCAGCAACAAACCANNNNNNNNNNNNNNNNNNNNNNNNNNN-----------------NNNN
.....((((((..(((((......)))))...............((....)).....))))))....................................-----------------.... ( -13.40)
>DroSim_CAF1 31406 103 + 1
CAACAGCUGCUAGAGUUGGAAAAACAAUUAGUCAAACGCCAAAAGAUAAUUCAGUAGAGCAGCAACAAACCAAGUUAUACAACAACAAUUCCCAUUUGC-----------------AAAA
.....((((((..(((((......)))))...............((....)).....))))))....................................-----------------.... ( -13.40)
>DroEre_CAF1 33480 118 + 1
CAAAAGCUGCUAGAGUUGCAAAAACAAUUAGUUAAGCGCCAAGCGACAAUUCAGUAGAGCAGCAACAGGCCAAGUUAUAUAACAA-AUUUCCUAUUUG-UAUAUAUUGUUCUAAACAAAA
.....((((((.(((((((...(((.....)))..((.....))).)))))).....))))))...((..(((..((((((.(((-((.....)))))-)))))))))..))........ ( -25.20)
>DroYak_CAF1 31939 113 + 1
CAACAGCUGCUAGAGUUGCAA-AACAAUUAGUAAAACACCUAAAGAUAAUUCAGUAGAGCAACAACAAACCCAGUUAUACAACCA-AAUCACUAUUAG-UUAUUAUUCUUCUU----AAA
....(((((.(((.(((((..-.((.....)).......(((..((....))..))).)))))(((.......))).........-.....))).)))-))............----... ( -12.90)
>consensus
CAACAGCUGCUAGAGUUGGAAAAACAAUUAGUCAAACGCCAAAAGAUAAUUCAGUAGAGCAGCAACAAACCAAGUUAUACAACAA_AAUUCCCAUUUG_U___UAUU_UUCU____AAAA
.....((((((..(((((......)))))...............((....)).....))))))......................................................... (-11.40 = -11.60 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:00 2006