Locus 6005

Sequence ID	3R_DroMel_CAF1
Location	15,800,016 – 15,800,176
Length	160
Max. P	0.895293

overview

Window 1

Location	15,800,016 – 15,800,136
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	89.03
Mean single sequence MFE	-39.47
Consensus MFE	-30.66
Energy contribution	-32.72
Covariance contribution	2.06
Combinations/Pair	1.11
Mean z-score	-2.20
Structure conservation index	0.78
SVM decision value	0.99
SVM RNA-class probability	0.895293
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15800016 120 - 27905053
AUUUCCUUCGGAAUUUUUCCCUGCAAGGGGCAAAAGGGCUCCUUGGUGAAAAACUGAAGACCCAUAUCGGAGCGGACACCAAUAUCUUCUUUGGAAUGGAUAGCUCCAUGGCUGAGGGAC
...((((((((..((((((((...(((((((......))))))))).))))))........((((...(((((...((((((........))))..))....))))))))))))))))). ( -40.70)
>DroSec_CAF1 21220 120 - 1
AUUUCCUUCGGAAUUUGUCUUUGCAAGGGGCAAAAGCGCUCCUUGGUGAAACACUGAAGACACAUUUCGGAGCGGACACCAAUAUCUUCUUUGGAAUGGAUAGGUCCAUGGCUGAGGCAC
..((((((((((((.(((((((.((((((((......))))))))(((...))).))))))).))))))))).)))............(((..(.(((((....)))))..)..)))... ( -41.90)
>DroSim_CAF1 25741 120 - 1
AUUUCCUUCGGAAUUUGUCUUUGCAAGGGGCAAAAGCGCUCCUUGGUGAAAAACUGAAGACACAUUUCGGAGCGGACACCAAUAUCUUCUUUGGAAUGGAUAGGUCCAUGGCUGAGGCAC
..((((((((((((.(((((((.((((((((......))))))))((.....)).))))))).))))))))).)))............(((..(.(((((....)))))..)..)))... ( -41.30)
>DroYak_CAF1 48977 120 - 1
AUUUCCAUUGGAUGAUUUCUUUGAAAGGGGAAGAAGCGGCCCUUGGUGGAAAACUGAAGAUACAUAUCGGUGUGGACACCAAUAUCUUUUUUGGCAUGGAUAGUUCCAUGGCUGAGGCAC
.(((((((..(.((.(((((((....)))))))...))....)..))))))).(..((((...((((.((((....)))).))))..))))..)((((((....))))))((....)).. ( -34.00)
>consensus
AUUUCCUUCGGAAUUUGUCUUUGCAAGGGGCAAAAGCGCUCCUUGGUGAAAAACUGAAGACACAUAUCGGAGCGGACACCAAUAUCUUCUUUGGAAUGGAUAGGUCCAUGGCUGAGGCAC
..((((((((((((.(((((((.((((((((......))))))))((.....)).))))))).))))))))).)))............(((..(.(((((....)))))..)..)))... (-30.66 = -32.72 +   2.06)

alignment

secondary structure

dotplot

Window 2

Location	15,800,056 – 15,800,176
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	83.19
Mean single sequence MFE	-39.50
Consensus MFE	-28.39
Energy contribution	-30.45
Covariance contribution	2.06
Combinations/Pair	1.11
Mean z-score	-1.97
Structure conservation index	0.72
SVM decision value	0.79
SVM RNA-class probability	0.850585
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15800056 120 - 27905053
GGUAGAUAAUCGGUUGUCUCGUUGGAUGGGCUGCGGGUAAAUUUCCUUCGGAAUUUUUCCCUGCAAGGGGCAAAAGGGCUCCUUGGUGAAAAACUGAAGACCCAUAUCGGAGCGGACACC
...........(((.(((.((((..(((((((.((((.(((.((((...)))).))).)))..((((((((......))))))))..........).)).))))).....)))))))))) ( -38.60)
>DroSec_CAF1 21260 120 - 1
GGUAGAUAAACGGUUGUCCUGUUGGAUUCGUUCCGGGUAAAUUUCCUUCGGAAUUUGUCUUUGCAAGGGGCAAAAGCGCUCCUUGGUGAAACACUGAAGACACAUUUCGGAGCGGACACC
...........(((.((((..(((((.....))))).........(((((((((.(((((((.((((((((......))))))))(((...))).))))))).))))))))).))))))) ( -43.20)
>DroSim_CAF1 25781 120 - 1
GGUAGAUAAACGGUUGUCCAGUUGGAUUCGUUCCGGGUAAAUUUCCUUCGGAAUUUGUCUUUGCAAGGGGCAAAAGCGCUCCUUGGUGAAAAACUGAAGACACAUUUCGGAGCGGACACC
...........(((.(((((.(((((.....))))).).......(((((((((.(((((((.((((((((......))))))))((.....)).))))))).))))))))).))))))) ( -43.50)
>DroYak_CAF1 49017 120 - 1
GAUUAGUAAACGGUUGUCCCAAUGGAGAAGUUAUGGGUGAAUUUCCAUUGGAUGAUUUCUUUGAAAGGGGAAGAAGCGGCCCUUGGUGGAAAACUGAAGAUACAUAUCGGUGUGGACACC
(((..(((...((((((.((((((((((..(((....))).))))))))))....(((((((....)))))))..)))))).(..((.....))..)...)))..)))((((....)))) ( -32.70)
>consensus
GGUAGAUAAACGGUUGUCCCGUUGGAUUCGUUCCGGGUAAAUUUCCUUCGGAAUUUGUCUUUGCAAGGGGCAAAAGCGCUCCUUGGUGAAAAACUGAAGACACAUAUCGGAGCGGACACC
...........(((.((((...............(((......)))((((((((.(((((((.((((((((......))))))))((.....)).))))))).))))))))..))))))) (-28.39 = -30.45 +   2.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:17 2006