Locus 5923

Sequence ID	3L_DroMel_CAF1
Location	15,908,613 – 15,908,886
Length	273
Max. P	0.924891

overview

Window 7

Location	15,908,613 – 15,908,726
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.46
Mean single sequence MFE	-23.20
Consensus MFE	-15.74
Energy contribution	-16.34
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.15
Structure conservation index	0.68
SVM decision value	1.16
SVM RNA-class probability	0.924891
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15908613 113 + 23771897
GCUAAAAGCACAAAAGACAGU-------CCCGAAAGGAAUCCCUGCCACACACGCCGUCAGACACUCGGCGAUUUCAAUUUGAUUUCAAUUCGAUUUCAAUUUGAUUUCAAUUGGCAAAC
((.....))............-------.((....))......(((((.....((((.........))))((..((((.((((..((.....))..)))).))))..))...)))))... ( -29.70)
>DroSec_CAF1 8089 113 + 1
GCUAAAAGCACAAAAGACAGC-------CCCGAAAGGAAUUCCUGCCACACACGCCGUCUGACACUCGACGAUUUCAAUUUGAUUUCAAUACGAAUUCAAUUUGAUUUCAAUUGGCAAAC
((.....))............-------.((....))......(((((........(((........)))((..((((.((((.(((.....))).)))).))))..))...)))))... ( -26.20)
>DroSim_CAF1 10594 113 + 1
GCUAAAAGCUCAAAAGACAGC-------CCCGAAAGGAAUUCCUGCCACACACGCCGUCUGACACUCGGCGAUUUCAAUUCGAUUUCAAUUCGAUUUCAAUUUGAUUUCAAUUGGCAAAC
.......(((........)))-------.((....))......(((((.....((((.........))))((..((((...((..((.....))..))...))))..))...)))))... ( -25.70)
>DroEre_CAF1 8170 90 + 1
UCUAAAAGCACAAAA-ACAGC-------CCCAAAAGGAACCACUGCCACACACGCCGUCUGACACUCGGCGAUUUCAAUUCGA----------------------UUUCAAUUGGCAAAA
...............-.....-------.((....))......(((((.....((((.........))))((..((.....))----------------------..))...)))))... ( -15.80)
>DroYak_CAF1 8150 98 + 1
GCUAAAAGCACAAAAGACAGCCAAAAUACCCAAAAGGAACGCCUGCCACACACGCCGUCUGACACUCGGCGAUUUCAAUUCGA----------------------UUUCAAUUGGCAAAC
((.....))..........(((((..........(((....)))........(((((.........)))))............----------------------......))))).... ( -18.60)
>consensus
GCUAAAAGCACAAAAGACAGC_______CCCGAAAGGAAUCCCUGCCACACACGCCGUCUGACACUCGGCGAUUUCAAUUCGAUUUCAAU_CGA_UUCAAUUUGAUUUCAAUUGGCAAAC
.............................((....))......(((((....(((((.........)))))..........((..((((............))))..))...)))))... (-15.74 = -16.34 +   0.60)

alignment

secondary structure

dotplot

Window 8

Location	15,908,646 – 15,908,766
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.51
Mean single sequence MFE	-27.22
Consensus MFE	-19.20
Energy contribution	-19.56
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-1.80
Structure conservation index	0.71
SVM decision value	0.39
SVM RNA-class probability	0.718308
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15908646 120 + 23771897
CCCUGCCACACACGCCGUCAGACACUCGGCGAUUUCAAUUUGAUUUCAAUUCGAUUUCAAUUUGAUUUCAAUUGGCAAACGGCAUCGGACUCUUUUGUUUUGGCCAAUUUUAUGUCCCAU
...(((((.....((((.........))))((..((((.((((..((.....))..)))).))))..))...)))))...(((...((((......))))..)))............... ( -31.60)
>DroSec_CAF1 8122 120 + 1
UCCUGCCACACACGCCGUCUGACACUCGACGAUUUCAAUUUGAUUUCAAUACGAAUUCAAUUUGAUUUCAAUUGGCAAACGGCAUCGGACUCUUGUGUUUUGCCCAAUUUUAUGUCCCAU
...(((((........(((........)))((..((((.((((.(((.....))).)))).))))..))...)))))...((((..(.((....)).)..))))................ ( -27.90)
>DroSim_CAF1 10627 120 + 1
UCCUGCCACACACGCCGUCUGACACUCGGCGAUUUCAAUUCGAUUUCAAUUCGAUUUCAAUUUGAUUUCAAUUGGCAAACGGCAUCGGACUCUUGUGUUUUGGCCAAUUUUAUGUCCCAU
...(((((.....((((.........))))((..((((...((..((.....))..))...))))..))...)))))...(((...((((......))))..)))............... ( -27.80)
>DroEre_CAF1 8202 98 + 1
CACUGCCACACACGCCGUCUGACACUCGGCGAUUUCAAUUCGA----------------------UUUCAAUUGGCAAAAGGCAACGGGCUCUUGUCUCUUGGCCAACUUUAUGUCCCAA
...(((((.....((((.........))))((..((.....))----------------------..))...)))))...(((...((((....))))....)))............... ( -24.00)
>DroYak_CAF1 8190 98 + 1
GCCUGCCACACACGCCGUCUGACACUCGGCGAUUUCAAUUCGA----------------------UUUCAAUUGGCAAACGGCAACGGGCUCUUGUGUUUUGGCCAGUUUUAUGUCCCAU
((((((((.....((((.........))))((..((.....))----------------------..))...)))))..((....)))))..........(((.((......))..))). ( -24.80)
>consensus
CCCUGCCACACACGCCGUCUGACACUCGGCGAUUUCAAUUCGAUUUCAAU_CGA_UUCAAUUUGAUUUCAAUUGGCAAACGGCAUCGGACUCUUGUGUUUUGGCCAAUUUUAUGUCCCAU
...((((.....(((((.........)))))...((((((.((..((((............))))..)))))))).....))))..((((.......................))))... (-19.20 = -19.56 +   0.36)

alignment

secondary structure

dotplot

Window 9

Location	15,908,766 – 15,908,886
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.58
Mean single sequence MFE	-30.06
Consensus MFE	-24.12
Energy contribution	-25.00
Covariance contribution	0.88
Combinations/Pair	1.08
Mean z-score	-1.44
Structure conservation index	0.80
SVM decision value	0.12
SVM RNA-class probability	0.591263
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15908766 120 - 23771897
ACUUUUUAACGGAUCGUGAUGAGGUAUAUUUUUGAGCUGGCAAUCCUUUUAGUCUGCCCAUUGAUUGAUGGAUUUGGCAAAGAUAAAUAUUUACGCACGAUUCUGGGAAACACAAUUCAG
..........((((((((...((((((...(((..((..(..((((..((((((........)))))).)))))..))..)))...))))))...))))))))(((....).))...... ( -29.90)
>DroSec_CAF1 8242 120 - 1
AUUUUUCAAUGGAUCGUGCUAAGGUAUAUUUUUGAGCUAACAAUCCUUUUAGGCUGCCCAUUGAUUGAUGGAUUUGGCAAAGAUAAAUAUUUACGCACGAUUCUGGGAAACACAAUUCAG
.(((..((..(((((((((((((...((((((((((((.............))))..(((((....)))))......))))))))....)))).)))))))))))..))).......... ( -30.02)
>DroSim_CAF1 10747 120 - 1
ACUUUUCAAUAGAUCGUGCUGAGGUAUAUUUUUGAGCUAACAAUCCUUUUAGUCUGCCCAUUGAUUGAUGGAUUUGGCAAAGAUAAAUAUUUACGCACGAUUCUGGGAAACACAAUUCAG
..((..((...((((((((..((((((...(((..(((((..((((..((((((........)))))).)))))))))..)))...))))))..)))))))).))..))........... ( -30.30)
>DroEre_CAF1 8300 118 - 1
ACUUUUCAAUGGAUCGUGGCGCGGUA-AUUUUUGAACUGGCAAUCCUUUUAGUCUGCCCAUUGAUUGAUGGAU-UUGCAGAGAUAAAUAUUUACGCACGGUUCUGGGAAACACAAUUCAG
...((((...((((((((.((((((.-........))))(((((((..((((((........)))))).))).-))))...............))))))))))...)))).......... ( -28.40)
>DroYak_CAF1 8288 120 - 1
ACUUUUCAAUGGAUCGUGGUGCGGUAUAUUUUUGAGCUGGCAAUCCUUUUAGUCUGCCCAUUGAUUGAUGGAUUUUGCACAGAUAAAUAUUUACGCACGGUUCUGGGAAAUACAAUUCAG
...((((...(((((...(((((..((((((.....((((((((((..((((((........)))))).))))..))).)))..))))))...))))))))))...)))).......... ( -31.70)
>consensus
ACUUUUCAAUGGAUCGUGCUGAGGUAUAUUUUUGAGCUGGCAAUCCUUUUAGUCUGCCCAUUGAUUGAUGGAUUUGGCAAAGAUAAAUAUUUACGCACGAUUCUGGGAAACACAAUUCAG
..(((((...((((((((...(((((((((((((.......(((((..((((((........)))))).)))))...))))))))..)))))...))))))))..))))).......... (-24.12 = -25.00 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:10 2006