Locus 7143

Sequence ID	3L_DroMel_CAF1
Location	19,188,337 – 19,188,457
Length	120
Max. P	0.601008

overview

Window 8

Location	19,188,337 – 19,188,457
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.35
Mean single sequence MFE	-29.71
Consensus MFE	-23.68
Energy contribution	-23.44
Covariance contribution	-0.24
Combinations/Pair	1.05
Mean z-score	-1.56
Structure conservation index	0.80
SVM decision value	0.14
SVM RNA-class probability	0.601008
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19188337 120 + 23771897
CACUUGCAACGUGCAACAAAAAUUGUCAGGCUUUUAAGCCCUGAACAAAGCCAUACGCCCCCGCAGCUCGAUUAAGGGCCUCUUAAUCAAACUAAUUUGGGCGGCUGCUGUCGCUUCUAU
.....((.(((.((........((((((((((....)).)))).))))((((....((((....((...(((((((.....)))))))...)).....))))))))))))).))...... ( -30.70)
>DroSec_CAF1 16875 108 + 1
CACUUGCAACUUGCAACAAAAAUUGUCAGGCUUUUAAGCCCUGAACAAAGCC------------AGCCCGAUUAAGGGCCUUUUAAUCAAACUAAUUUGGGCGGCUGCUGUCGCUUCUAU
...((((.....))))((((..((((((((((....)).)))).))))....------------.((((......))))................))))((((((....))))))..... ( -28.80)
>DroSim_CAF1 20336 108 + 1
CACUUGCAACUUGCAACAAAAAUUGUCAGGCUUUUAAGCCCUGAACAAAGCC------------AGCCCGAUUAAGGGCCUGUUAAUCAAACUAAUUUGGGCGGCUGCUGUCGCUUCUAU
...((((.....))))((((..((((((((((....)).)))).))))(((.------------.((((......))))..)))...........))))((((((....))))))..... ( -30.20)
>DroEre_CAF1 19698 113 + 1
CACUUU-------CAACAAAAAUUGUCAGGCUUUUGAGCCCUGAAUAAAGCCAUUCGCCCCCGAAGCCCGUUUAAGGGCCUGUUAAUCAAACUAAUUUGGGCGGCUGCUGUCGCUCCUAU
......-------........((((.(((((((((((((...((((......))))((.......))..))))))))))))).))))...........(((((((....))))))).... ( -29.90)
>DroYak_CAF1 44669 113 + 1
CACUUU-------CAACAAAAAUCGUCAGGCUUUUAAGCCCUGAAUAUAGCCAAACGGCCACGAAGCUCGUUUAAGGGCCUGUUAAUCAAACUAAUUUGGGCGGCUGCUGUCGCUUCUAU
......-------.............(((((((((((((..........(((....)))..........)))))))))))))................(((((((....))))))).... ( -28.95)
>consensus
CACUUGCAAC_UGCAACAAAAAUUGUCAGGCUUUUAAGCCCUGAACAAAGCCA__CG_CC_CG_AGCCCGAUUAAGGGCCUGUUAAUCAAACUAAUUUGGGCGGCUGCUGUCGCUUCUAU
................((((.....(((((((....)).))))).....................((((......))))................))))((((((....))))))..... (-23.68 = -23.44 +  -0.24)

alignment

secondary structure

dotplot

Window 9

Location	19,188,337 – 19,188,457
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.35
Mean single sequence MFE	-35.10
Consensus MFE	-23.52
Energy contribution	-24.32
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.78
Structure conservation index	0.67
SVM decision value	0.03
SVM RNA-class probability	0.550492
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19188337 120 - 23771897
AUAGAAGCGACAGCAGCCGCCCAAAUUAGUUUGAUUAAGAGGCCCUUAAUCGAGCUGCGGGGGCGUAUGGCUUUGUUCAGGGCUUAAAAGCCUGACAAUUUUUGUUGCACGUUGCAAGUG
......(((((.((((((((((....(((((((((((((.....)))))))))))))...))))).......(((((..(((((....)))))))))).....)))))..)))))..... ( -45.90)
>DroSec_CAF1 16875 108 - 1
AUAGAAGCGACAGCAGCCGCCCAAAUUAGUUUGAUUAAAAGGCCCUUAAUCGGGCU------------GGCUUUGUUCAGGGCUUAAAAGCCUGACAAUUUUUGUUGCAAGUUGCAAGUG
......(((((.(((((.(((((((....)))).......(((((......)))))------------))).(((((..(((((....)))))))))).....)))))..)))))..... ( -34.50)
>DroSim_CAF1 20336 108 - 1
AUAGAAGCGACAGCAGCCGCCCAAAUUAGUUUGAUUAACAGGCCCUUAAUCGGGCU------------GGCUUUGUUCAGGGCUUAAAAGCCUGACAAUUUUUGUUGCAAGUUGCAAGUG
......(((((.(((((.(((((((....)))).......(((((......)))))------------))).(((((..(((((....)))))))))).....)))))..)))))..... ( -34.50)
>DroEre_CAF1 19698 113 - 1
AUAGGAGCGACAGCAGCCGCCCAAAUUAGUUUGAUUAACAGGCCCUUAAACGGGCUUCGGGGGCGAAUGGCUUUAUUCAGGGCUCAAAAGCCUGACAAUUUUUGUUG-------AAAGUG
......((....)).(((.(((......(((.....)))((((((......)))))).)))))).....(((((..(((((.((....)))))))((((....))))-------))))). ( -33.40)
>DroYak_CAF1 44669 113 - 1
AUAGAAGCGACAGCAGCCGCCCAAAUUAGUUUGAUUAACAGGCCCUUAAACGAGCUUCGUGGCCGUUUGGCUAUAUUCAGGGCUUAAAAGCCUGACGAUUUUUGUUG-------AAAGUG
.......((((((.(((((..(......(((.....))).((((.....(((.....))))))))..)))))....(((((.((....)))))))......))))))-------...... ( -27.20)
>consensus
AUAGAAGCGACAGCAGCCGCCCAAAUUAGUUUGAUUAACAGGCCCUUAAUCGGGCU_CG_GG_CG__UGGCUUUGUUCAGGGCUUAAAAGCCUGACAAUUUUUGUUGCA_GUUGCAAGUG
......(((((((.((((...((((....)))).......(((((......)))))............))))....(((((.((....)))))))......)))))))............ (-23.52 = -24.32 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:39:09 2006