Locus 6007

Sequence ID	3R_DroMel_CAF1
Location	15,806,892 – 15,807,030
Length	138
Max. P	0.871526

overview

Window 4

Location	15,806,892 – 15,806,999
Length	107
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	91.81
Mean single sequence MFE	-29.23
Consensus MFE	-28.41
Energy contribution	-27.85
Covariance contribution	-0.56
Combinations/Pair	1.10
Mean z-score	-1.21
Structure conservation index	0.97
SVM decision value	-0.02
SVM RNA-class probability	0.524981
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15806892 107 + 27905053
UGGCUGCACUUUGCAUAACUUUGUUGCAUACUUUUGAGCGUGUUUCGGCCCCGGAUCGUGUUUCACAGCUCCCGUUGGAGCUGUUUCCCCAACCAGGUCUGUUC---CAU
.((((((.....))........(..(((..((....))..)))..))))).((((((.((....((((((((....)))))))).....))....))))))...---... ( -29.50)
>DroSec_CAF1 28069 110 + 1
UGGCUGCACUUUGCAUAACUUUGUUGCAUACUUUUGAGCGUGUUUCGUCCCCGGAUCGCGUUUCACAGCUCCCGUUGGAGCUGUAUCCCCAACCUGGCCUCUCCCACCAU
.((((((.....))........((((.........(((((((.((((....)))).))))))).((((((((....)))))))).....))))..))))........... ( -32.60)
>DroSim_CAF1 32675 110 + 1
UGGCUGCACUUUGCAUAACUUUGUUGCAUACUUUUGAGCGUGUUUCGUCACCGGAUCGUGUUUCACAGCUCCCGUUGGAGCUGUAUCCCCAACCUGGCCUGUCCCACCAU
.((((((.....))........((((.........(((((((.((((....)))).))))))).((((((((....)))))))).....))))..))))........... ( -27.80)
>DroEre_CAF1 31987 106 + 1
CGGCUGCACUUUGCAUAACUUUGUUGCAUACUUUUGAGCGUGUUUCGUCCCCGGAUCGUGUUUCACAGCUCCCAUUGGAGCUGU-UCCCCGACCUCGCCUGUCCCA---U
.((((((.....))).......(..(((..((....))..)))..)......((.(((.(....((((((((....))))))))-...))))))..))).......---. ( -27.00)
>consensus
UGGCUGCACUUUGCAUAACUUUGUUGCAUACUUUUGAGCGUGUUUCGUCCCCGGAUCGUGUUUCACAGCUCCCGUUGGAGCUGUAUCCCCAACCUGGCCUGUCCCA_CAU
.((((((.....))).......((((.........(((((((.((((....)))).))))))).((((((((....)))))))).....))))...)))........... (-28.41 = -27.85 +  -0.56)

alignment

secondary structure

dotplot

Window 5

Location	15,806,892 – 15,806,999
Length	107
Sequences	4
Columns	110
Reading direction	reverse
Mean pairwise identity	91.81
Mean single sequence MFE	-33.33
Consensus MFE	-29.11
Energy contribution	-29.18
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-1.83
Structure conservation index	0.87
SVM decision value	0.87
SVM RNA-class probability	0.871526
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15806892 107 - 27905053
AUG---GAACAGACCUGGUUGGGGAAACAGCUCCAACGGGAGCUGUGAAACACGAUCCGGGGCCGAAACACGCUCAAAAGUAUGCAACAAAGUUAUGCAAAGUGCAGCCA
.((---(......(((((((((....((((((((....))))))))....).))).))))).)))......(((((...((((((......).)))))....)).))).. ( -31.50)
>DroSec_CAF1 28069 110 - 1
AUGGUGGGAGAGGCCAGGUUGGGGAUACAGCUCCAACGGGAGCUGUGAAACGCGAUCCGGGGACGAAACACGCUCAAAAGUAUGCAACAAAGUUAUGCAAAGUGCAGCCA
.((((..(((.(....(((((.(..(((((((((....)))))))))...).)))))((....)).....).)))....(((((((.........))))...))).)))) ( -34.20)
>DroSim_CAF1 32675 110 - 1
AUGGUGGGACAGGCCAGGUUGGGGAUACAGCUCCAACGGGAGCUGUGAAACACGAUCCGGUGACGAAACACGCUCAAAAGUAUGCAACAAAGUUAUGCAAAGUGCAGCCA
.((((.(.((.(((..((((((...(((((((((....)))))))))...).)))))((....))......))).....((((((......).)))))...)).).)))) ( -33.80)
>DroEre_CAF1 31987 106 - 1
A---UGGGACAGGCGAGGUCGGGGA-ACAGCUCCAAUGGGAGCUGUGAAACACGAUCCGGGGACGAAACACGCUCAAAAGUAUGCAACAAAGUUAUGCAAAGUGCAGCCG
.---.......(((..((((((...-((((((((....))))))))....).)))))((....))...((((((....))).((((.........))))..)))..))). ( -33.80)
>consensus
AUG_UGGGACAGGCCAGGUUGGGGAUACAGCUCCAACGGGAGCUGUGAAACACGAUCCGGGGACGAAACACGCUCAAAAGUAUGCAACAAAGUUAUGCAAAGUGCAGCCA
...........(((..(((((.(...((((((((....))))))))....).)))))((....))...((((((....))).((((.........))))..)))..))). (-29.11 = -29.18 +   0.06)

alignment

secondary structure

dotplot

Window 6

Location	15,806,925 – 15,807,030
Length	105
Sequences	4
Columns	108
Reading direction	reverse
Mean pairwise identity	84.23
Mean single sequence MFE	-33.96
Consensus MFE	-27.01
Energy contribution	-26.57
Covariance contribution	-0.44
Combinations/Pair	1.09
Mean z-score	-1.68
Structure conservation index	0.80
SVM decision value	0.41
SVM RNA-class probability	0.725610
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15806925 105 - 27905053
AUAAUGUGGCAGCGGUACAGCACAGAGCAGCAUG---GAACAGACCUGGUUGGGGAAACAGCUCCAACGGGAGCUGUGAAACACGAUCCGGGGCCGAAACACGCUCAA
.....(((....((((.((((........)).))---.......(((((((((....((((((((....))))))))....).))).)))))))))...)))...... ( -36.30)
>DroSec_CAF1 28102 108 - 1
AUAAUGUGGCAGUGGUACAGCACAGAGUAGCAUGGUGGGAGAGGCCAGGUUGGGGAUACAGCUCCAACGGGAGCUGUGAAACGCGAUCCGGGGACGAAACACGCUCAA
....((.(((.(((.(((........))).))).(((((.....)).(((((.(..(((((((((....)))))))))...).)))))((....))...)))))))). ( -35.60)
>DroSim_CAF1 32708 108 - 1
AUAAUGUGGCAGUGGUACAGCACAGAGUAGCAUGGUGGGACAGGCCAGGUUGGGGAUACAGCUCCAACGGGAGCUGUGAAACACGAUCCGGUGACGAAACACGCUCAA
....((.(((.(((.(((........))).))).(((......(((.((((((...(((((((((....)))))))))...).))))).))).......)))))))). ( -34.12)
>DroEre_CAF1 32020 92 - 1
ACAAUGUGGUAGCGGUAGA------------A---UGGGACAGGCGAGGUCGGGGA-ACAGCUCCAAUGGGAGCUGUGAAACACGAUCCGGGGACGAAACACGCUCAA
........(.((((((...------------.---............((((((...-((((((((....))))))))....).)))))((....))..)).))))).. ( -29.80)
>consensus
AUAAUGUGGCAGCGGUACAGCACAGAGUAGCAUG_UGGGACAGGCCAGGUUGGGGAUACAGCUCCAACGGGAGCUGUGAAACACGAUCCGGGGACGAAACACGCUCAA
........(.((((((...............................(((((.(...((((((((....))))))))....).)))))((....))..)).))))).. (-27.01 = -26.57 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:20 2006