Locus 8068

Sequence ID	3R_DroMel_CAF1
Location	21,654,959 – 21,655,067
Length	108
Max. P	0.915928

overview

Window 8

Location	21,654,959 – 21,655,067
Length	108
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	82.60
Mean single sequence MFE	-21.11
Consensus MFE	-11.50
Energy contribution	-12.70
Covariance contribution	1.20
Combinations/Pair	1.08
Mean z-score	-2.53
Structure conservation index	0.54
SVM decision value	0.75
SVM RNA-class probability	0.841886
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21654959 108 + 27905053
AAG-AAAGAGAAAUAAAAUAUAAACUUUCUACACCUAACUGGCAAA--ACAUGA---AG--CCAUAGCAAUCUAGUUUGUAAUGUAAAGCUGCUUACUAACUACGUUUAUAUUUUA
...-.........((((((((((((.........(((..((((...--......---.)--)))))).....(((((.((((.(((....))))))).))))).)))))))))))) ( -20.20)
>DroSec_CAF1 144233 109 + 1
AAUAAAAGAGAAAUAAAAUAUAAACUUUCUACACCUAACUGGCAAA--ACAUGU---AG--GUAUAGCAAUCUAGUUUGUAAUGUAAAGCUGCUUACUAACUACGUUUAUAUUUCA
...............((((((((((...(((.(((((..((.....--.))..)---))--)).))).....(((((.((((.(((....))))))).))))).)))))))))).. ( -22.00)
>DroSim_CAF1 142360 109 + 1
AAUAAAAGAGAAAUAAAAUAUAAACUUUCUACACCUAACUGGCAAA--ACAUGU---AG--GUAUAGCAAUCUAGUUUGUAAUGUAAAGCUGCUUACUAACUACGUUUAUAUUUCA
...............((((((((((...(((.(((((..((.....--.))..)---))--)).))).....(((((.((((.(((....))))))).))))).)))))))))).. ( -22.00)
>DroEre_CAF1 141333 112 + 1
AAA-U-UUGAAAAUAAAAUAUAAACUUUCCAUACCAAACUGGAAAA--ACAUCUACUAUGGGUAUAGCAAUCUAGUUUGUAAUGGAUAGCUGCAUACUAACUACGUUUAUAUUUUG
...-.-.......((((((((((((..(((((..(((((((((...--..((((.....)))).......)))))))))..)))))(((.......))).....)))))))))))) ( -24.60)
>DroYak_CAF1 142554 109 + 1
AAA-GGAUGAAAAUAAAAUAUAAACAUUCUAAACCAAACUGGAAAAAAACAUCA---AGGUAUAUGGCAAUCUAGUUCGUAAUGAAAAGUU---UGCUAACUACGCUUAUAUUUUG
..(-(((((...............))))))...((.....))..........((---(((((((.(((....(((((.((((........)---))).))))).)))))))))))) ( -16.76)
>consensus
AAA_AAAGAGAAAUAAAAUAUAAACUUUCUACACCUAACUGGCAAA__ACAUGU___AG__GUAUAGCAAUCUAGUUUGUAAUGUAAAGCUGCUUACUAACUACGUUUAUAUUUUA
.............((((((((((((........((.....))..............................(((((.((((.(((....))))))).))))).)))))))))))) (-11.50 = -12.70 +   1.20)

alignment

secondary structure

dotplot

Window 9

Location	21,654,959 – 21,655,067
Length	108
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	82.60
Mean single sequence MFE	-24.60
Consensus MFE	-13.67
Energy contribution	-13.47
Covariance contribution	-0.20
Combinations/Pair	1.25
Mean z-score	-2.72
Structure conservation index	0.56
SVM decision value	1.10
SVM RNA-class probability	0.915928
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21654959 108 - 27905053
UAAAAUAUAAACGUAGUUAGUAAGCAGCUUUACAUUACAAACUAGAUUGCUAUGG--CU---UCAUGU--UUUGCCAGUUAGGUGUAGAAAGUUUAUAUUUUAUUUCUCUUU-CUU
(((((((((((((((((..(((((....))))))))))...(((.(((....(((--(.---......--...))))....))).)))...)))))))))))).........-... ( -24.10)
>DroSec_CAF1 144233 109 - 1
UGAAAUAUAAACGUAGUUAGUAAGCAGCUUUACAUUACAAACUAGAUUGCUAUAC--CU---ACAUGU--UUUGCCAGUUAGGUGUAGAAAGUUUAUAUUUUAUUUCUCUUUUAUU
((((((((((((.(((((.((((...........)))).))))).....((((((--((---(..((.--.....))..)))))))))...))))))))))))............. ( -26.60)
>DroSim_CAF1 142360 109 - 1
UGAAAUAUAAACGUAGUUAGUAAGCAGCUUUACAUUACAAACUAGAUUGCUAUAC--CU---ACAUGU--UUUGCCAGUUAGGUGUAGAAAGUUUAUAUUUUAUUUCUCUUUUAUU
((((((((((((.(((((.((((...........)))).))))).....((((((--((---(..((.--.....))..)))))))))...))))))))))))............. ( -26.60)
>DroEre_CAF1 141333 112 - 1
CAAAAUAUAAACGUAGUUAGUAUGCAGCUAUCCAUUACAAACUAGAUUGCUAUACCCAUAGUAGAUGU--UUUUCCAGUUUGGUAUGGAAAGUUUAUAUUUUAUUUUCAA-A-UUU
.(((((((((((.(((((.(....))))))(((((..((((((.((..((..(((.....)))...))--...)).))))))..)))))..)))))))))))........-.-... ( -26.80)
>DroYak_CAF1 142554 109 - 1
CAAAAUAUAAGCGUAGUUAGCA---AACUUUUCAUUACGAACUAGAUUGCCAUAUACCU---UGAUGUUUUUUUCCAGUUUGGUUUAGAAUGUUUAUAUUUUAUUUUCAUCC-UUU
.(((((((((((((((((....---)))).........(((((((((((......((..---....)).......)))))))))))...)))))))))))))..........-... ( -18.92)
>consensus
UAAAAUAUAAACGUAGUUAGUAAGCAGCUUUACAUUACAAACUAGAUUGCUAUAC__CU___ACAUGU__UUUGCCAGUUAGGUGUAGAAAGUUUAUAUUUUAUUUCUCUUU_AUU
.(((((((((((.(((((.((((...........)))).))))).....((((((........((.......))........))))))...))))))))))).............. (-13.67 = -13.47 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:01:49 2006