Locus 1930

Sequence ID	2R_DroMel_CAF1
Location	7,278,678 – 7,278,777
Length	99
Max. P	0.950653

overview

Window 9

Location	7,278,678 – 7,278,777
Length	99
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	88.57
Mean single sequence MFE	-35.02
Consensus MFE	-23.39
Energy contribution	-24.31
Covariance contribution	0.92
Combinations/Pair	1.07
Mean z-score	-2.15
Structure conservation index	0.67
SVM decision value	0.02
SVM RNA-class probability	0.545588
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7278678 99 + 20766785
UGCCAGCCAUCGGGCGACUCUCUUCGGAUCUUUGGCUAUAUGUGUAGC--------UAUAUAGCCAUAUAGCUGGCCAACAACUCAAUUAGAUGGCAGUCUGGGGUU
.((((((.....(((.....((....))....(((((((....)))))--------))....))).....))))))....(((((...(((((....)))))))))) ( -30.90)
>DroSec_CAF1 74601 107 + 1
UGCCAGCCAUCGGGCGACUCUCUUCGGAUCUUCGGCCAUAUGUGUAACUAUAUAGCUAUAUAGCCAUAUAGCUGGCAAACAACUCAAUUAGAUGGCAGUCUGGGGUU
(((((((....((.(((...((....))...))).)).((((((...((((((....)))))).)))))))))))))...(((((...(((((....)))))))))) ( -35.00)
>DroSim_CAF1 78061 107 + 1
UGCCAGCCAUCGGGCGACUCUCUUCGGAUCUUCGGCCAUAUGUGUAGCUAUAUAGCUAUAUAGCCAUAUAGCUGGCCAACAACUCAAUUAGAUGGCAGUCUGGGGUU
..(((((((((((.(((...((....))...))).))...((..(((((((((.(((....))).)))))))))..))............))))))....))).... ( -37.40)
>DroEre_CAF1 74710 105 + 1
UGCCAGCCAUCGGGCGACUCUCUUUGGAUCCUC-GCUAUAUGUGCAGCUAUACAGCGAGAUGGCCAUAUAGCUGGCCAACAACUCAAUUAGAUGGCAGCCCGGG-UU
....((((..(((((..((.(((((((...(((-(((.((((......)))).)))))).((((((......)))))).....))))..))).))..)))))))-)) ( -37.70)
>DroYak_CAF1 76540 100 + 1
UGCCAGCCAUCGGGCGACUCUCUUCGGAUCUUCGGCUAUAUGUG------UAUGGCGAUAUAGCCAUAUAGCUGGCCAACAACUCAAUUAGAUGGCAGUCUGGG-GU
.((((((....((.(((...((....))...))).)).....((------((((((......)))))))))))))).....((((...(((((....)))))))-)) ( -34.10)
>consensus
UGCCAGCCAUCGGGCGACUCUCUUCGGAUCUUCGGCUAUAUGUGUAGCUAUAUAGCUAUAUAGCCAUAUAGCUGGCCAACAACUCAAUUAGAUGGCAGUCUGGGGUU
..(((((((((.(((((..(.....)..))..((((((((((.((.................))))))))))))))).............))))))....))).... (-23.39 = -24.31 +   0.92)

alignment

secondary structure

dotplot

Window 0

Location	7,278,678 – 7,278,777
Length	99
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	88.57
Mean single sequence MFE	-34.52
Consensus MFE	-26.63
Energy contribution	-26.75
Covariance contribution	0.12
Combinations/Pair	1.11
Mean z-score	-2.32
Structure conservation index	0.77
SVM decision value	1.40
SVM RNA-class probability	0.950653
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7278678 99 - 20766785
AACCCCAGACUGCCAUCUAAUUGAGUUGUUGGCCAGCUAUAUGGCUAUAUA--------GCUACACAUAUAGCCAAAGAUCCGAAGAGAGUCGCCCGAUGGCUGGCA
.......(((.((((......)).)).))).(((((((((.(((((((((.--------.......)))))))))..((..(.....)..)).....))))))))). ( -31.40)
>DroSec_CAF1 74601 107 - 1
AACCCCAGACUGCCAUCUAAUUGAGUUGUUUGCCAGCUAUAUGGCUAUAUAGCUAUAUAGUUACACAUAUGGCCGAAGAUCCGAAGAGAGUCGCCCGAUGGCUGGCA
......((((.((((......)).)).))))(((((((((((((((....)))))))))......(((.(((.(((...((....))...))).)))))))))))). ( -32.80)
>DroSim_CAF1 78061 107 - 1
AACCCCAGACUGCCAUCUAAUUGAGUUGUUGGCCAGCUAUAUGGCUAUAUAGCUAUAUAGCUACACAUAUGGCCGAAGAUCCGAAGAGAGUCGCCCGAUGGCUGGCA
...........(((((((..(((..((.((((((((((((((((((....)))))))))))........))))))).))..)))..)))...(((....))))))). ( -39.20)
>DroEre_CAF1 74710 105 - 1
AA-CCCGGGCUGCCAUCUAAUUGAGUUGUUGGCCAGCUAUAUGGCCAUCUCGCUGUAUAGCUGCACAUAUAGC-GAGGAUCCAAAGAGAGUCGCCCGAUGGCUGGCA
..-..(((((.((..(((..(((..((..((((((......)))))).((((((((((........)))))))-)))))..))))))..)).))))).......... ( -39.60)
>DroYak_CAF1 76540 100 - 1
AC-CCCAGACUGCCAUCUAAUUGAGUUGUUGGCCAGCUAUAUGGCUAUAUCGCCAUA------CACAUAUAGCCGAAGAUCCGAAGAGAGUCGCCCGAUGGCUGGCA
..-....(((.((((......)).)).))).(((((((((.(((((((((.......------...)))))))))..((..(.....)..)).....))))))))). ( -29.60)
>consensus
AACCCCAGACUGCCAUCUAAUUGAGUUGUUGGCCAGCUAUAUGGCUAUAUAGCUAUAUAGCUACACAUAUAGCCGAAGAUCCGAAGAGAGUCGCCCGAUGGCUGGCA
.......(((.((((......)).)).))).(((((((((.(((((((((................)))))))))..((..(.....)..)).....))))))))). (-26.63 = -26.75 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:36 2006