Locus 5903

Sequence ID	2L_DroMel_CAF1
Location	16,683,578 – 16,683,681
Length	103
Max. P	0.918768

overview

Window 5

Location	16,683,578 – 16,683,681
Length	103
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	81.52
Mean single sequence MFE	-27.42
Consensus MFE	-18.69
Energy contribution	-19.49
Covariance contribution	0.80
Combinations/Pair	1.16
Mean z-score	-1.55
Structure conservation index	0.68
SVM decision value	-0.04
SVM RNA-class probability	0.510787
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16683578 103 + 22407834
CUUGGAGUAGCCAUUAACCAACGUCAUUACAGGGUUUUCUGGCAUCAGCCAAUAAAGCUAAAGCCAGCUGGCUUGACCAUGGUCUGACUUACUCUUGUGCCCA
...((((((((((..((((...((....))..))))...)))).(((((((...((((((........)))))).....))).))))..))))))........ ( -28.00)
>DroSec_CAF1 138455 103 + 1
CUUGGAGUAGCCAUUAACCAACGUCAUUACAGGGUUUUCUGGCAUCAGCCAAUAAAGCUAAAGCCAGCUGGCUUGACCAUGGUCUGACUUACUCUUGUGCCCA
...((((((((((..((((...((....))..))))...)))).(((((((...((((((........)))))).....))).))))..))))))........ ( -28.00)
>DroEre_CAF1 138906 97 + 1
CUUGGAGUAGCCAUUAACCAACGUCAUUACAGGGUUUUCUGGCAUCAGCCAAUAA------AGCCAGCUGGCUUGACCAUGGUCUGACUUACUCUUGUGCUCA
...((((((((((..((((...((....))..))))...)))).(((((((...(------((((....))))).....))).))))..))))))........ ( -29.50)
>DroYak_CAF1 138219 97 + 1
CAUGGAGUAGCCAUUAACCAACGUCAUUACAGGGUUUUCUGGCAUCAGCCAAUAA------AGCCAGCUGGCUUGACCAUGGUCUGACUUACUCUUGUGCCCA
...((((((((((..((((...((....))..))))...)))).(((((((...(------((((....))))).....))).))))..))))))........ ( -29.50)
>DroAna_CAF1 78741 80 + 1
CUGGGGUGAACUUUUAACCAACAUCAUUACUGGCUUCUGGGGCAUUAGCCAUUAA------AGCCAACUGGCU-GGCCAUGGCCUGG----------------
(..((((.........)))...........((((((....(((....)))....)------))))).)..)..-(((....)))...---------------- ( -22.10)
>consensus
CUUGGAGUAGCCAUUAACCAACGUCAUUACAGGGUUUUCUGGCAUCAGCCAAUAA______AGCCAGCUGGCUUGACCAUGGUCUGACUUACUCUUGUGCCCA
...((((((((((..((((.............))))...)))).(((((((..........((((....))))......))).))))..))))))........ (-18.69 = -19.49 +   0.80)

alignment

secondary structure

dotplot

Window 6

Location	16,683,578 – 16,683,681
Length	103
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	81.52
Mean single sequence MFE	-31.30
Consensus MFE	-22.74
Energy contribution	-24.66
Covariance contribution	1.92
Combinations/Pair	1.11
Mean z-score	-2.11
Structure conservation index	0.73
SVM decision value	1.12
SVM RNA-class probability	0.918768
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16683578 103 - 22407834
UGGGCACAAGAGUAAGUCAGACCAUGGUCAAGCCAGCUGGCUUUAGCUUUAUUGGCUGAUGCCAGAAAACCCUGUAAUGACGUUGGUUAAUGGCUACUCCAAG
.........(((((.(((((((((..((((...((((((((.((((((.....)))))).)))))......)))...))))..)))))..))))))))).... ( -35.50)
>DroSec_CAF1 138455 103 - 1
UGGGCACAAGAGUAAGUCAGACCAUGGUCAAGCCAGCUGGCUUUAGCUUUAUUGGCUGAUGCCAGAAAACCCUGUAAUGACGUUGGUUAAUGGCUACUCCAAG
.........(((((.(((((((((..((((...((((((((.((((((.....)))))).)))))......)))...))))..)))))..))))))))).... ( -35.50)
>DroEre_CAF1 138906 97 - 1
UGAGCACAAGAGUAAGUCAGACCAUGGUCAAGCCAGCUGGCU------UUAUUGGCUGAUGCCAGAAAACCCUGUAAUGACGUUGGUUAAUGGCUACUCCAAG
.........(((((.(((((((((..((((((((....))))------...(((((....)))))............))))..)))))..))))))))).... ( -30.80)
>DroYak_CAF1 138219 97 - 1
UGGGCACAAGAGUAAGUCAGACCAUGGUCAAGCCAGCUGGCU------UUAUUGGCUGAUGCCAGAAAACCCUGUAAUGACGUUGGUUAAUGGCUACUCCAUG
.........(((((.(((((((((..((((((((....))))------...(((((....)))))............))))..)))))..))))))))).... ( -30.80)
>DroAna_CAF1 78741 80 - 1
----------------CCAGGCCAUGGCC-AGCCAGUUGGCU------UUAAUGGCUAAUGCCCCAGAAGCCAGUAAUGAUGUUGGUUAAAAGUUCACCCCAG
----------------...(((....)))-((((((((((((------((...(((....)))...))))))))........))))))............... ( -23.90)
>consensus
UGGGCACAAGAGUAAGUCAGACCAUGGUCAAGCCAGCUGGCU______UUAUUGGCUGAUGCCAGAAAACCCUGUAAUGACGUUGGUUAAUGGCUACUCCAAG
.........(((((.(((((((((..((((((((....)))).........(((((....)))))............))))..)))))..))))))))).... (-22.74 = -24.66 +   1.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:53 2006