Locus 81

Sequence ID	3L_DroMel_CAF1
Location	299,106 – 299,296
Length	190
Max. P	0.858785

overview

Window 5

Location	299,106 – 299,220
Length	114
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	86.11
Mean single sequence MFE	-30.05
Consensus MFE	-20.94
Energy contribution	-21.00
Covariance contribution	0.06
Combinations/Pair	1.28
Mean z-score	-1.44
Structure conservation index	0.70
SVM decision value	-0.03
SVM RNA-class probability	0.519711
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 299106 114 + 23771897
AUCAACUCCAUAAUAAACCUUUUGUUGCUGCACCUGCAGUGAAAUCGCGAAUCUUUCAAGUAGUUGUUCGCCUAGUCGCAUUCUCAGCAUUUUUCUGCCAGCGGGCAGUUAGCA
......................(((((((((.((.((.((((....((((((((.......))..))))))....)))).......(((......)))..)))))))).))))) ( -26.20)
>DroSec_CAF1 9024 114 + 1
AUUAACUGCAUAAUAAACCUUUUGUUGCUGCACCUGCAGUUAAGUCGCGAAUCUUUCAAGUGGUUGUUCGCUUAGUCGCAUUCUCAGCAUAUUUCUGCUGACAGGCAGGCUGCA
......((((((((((.....)))))).))))...((((((..(((((((.......((((((....))))))..))))....((((((......))))))..))).)))))). ( -31.60)
>DroSim_CAF1 11355 114 + 1
AUUAACUGCAUAAUAAACCUUUUGUUGCUGCACCUGCAGUUAAGUCGCGAAUCUUUCAAGUGGUUGUUCGCUUAGUCGCAUUCUCAGCAUAUUUCUGCUGACAGGCAGGCUGCA
......((((((((((.....)))))).))))...((((((..(((((((.......((((((....))))))..))))....((((((......))))))..))).)))))). ( -31.60)
>DroYak_CAF1 9950 106 + 1
AUUAACUGCAUAGUAAACCUUUUGUGGCUGCACCUGCAGUCAACUCGCGAAUCUUUCAGGUGGUUG--------UUCGCAUUCUCAGCAUAUUUCUGCUUGGAGGCGGACUGUA
...(((..(..((...........(((((((....)))))))..........)).....)..)))(--------(((((.((((.((((......)))).)))))))))).... ( -30.80)
>consensus
AUUAACUGCAUAAUAAACCUUUUGUUGCUGCACCUGCAGUUAAGUCGCGAAUCUUUCAAGUGGUUGUUCGCUUAGUCGCAUUCUCAGCAUAUUUCUGCUGACAGGCAGGCUGCA
..(((((((...............(((((((....)))))))......((.....))..)))))))....................(((....((((((....)))))).))). (-20.94 = -21.00 +   0.06)

alignment

secondary structure

dotplot

Window 6

Location	299,140 – 299,260
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	76.39
Mean single sequence MFE	-35.00
Consensus MFE	-18.27
Energy contribution	-20.34
Covariance contribution	2.06
Combinations/Pair	1.24
Mean z-score	-2.28
Structure conservation index	0.52
SVM decision value	0.82
SVM RNA-class probability	0.858785
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 299140 120 + 23771897
UGCAGUGAAAUCGCGAAUCUUUCAAGUAGUUGUUCGCCUAGUCGCAUUCUCAGCAUUUUUCUGCCAGCGGGCAGUUAGCAUCGUCAGUUUUUGCGUAUUCGUAAAAAUUGAACAGUGCAC
....((((....((((((((.......))..))))))....))))...............(((((....)))))...((((..((((((((((((....))))))))))))...)))).. ( -36.00)
>DroSec_CAF1 9058 120 + 1
UGCAGUUAAGUCGCGAAUCUUUCAAGUGGUUGUUCGCUUAGUCGCAUUCUCAGCAUAUUUCUGCUGACAGGCAGGCUGCAUCAUCAAUUGUUGCGUAUUCGUAAAAAUUGAACAGUGCAC
(((((((..(((((((.......((((((....))))))..))))....((((((......))))))..))).)))))))...((((((.(((((....))))).))))))......... ( -35.90)
>DroSim_CAF1 11389 120 + 1
UGCAGUUAAGUCGCGAAUCUUUCAAGUGGUUGUUCGCUUAGUCGCAUUCUCAGCAUAUUUCUGCUGACAGGCAGGCUGCAUUGUCAAUUGUUGCGUAUUCGUAAAAAUUGAACAGUGCAC
........((((((((((...((....))..))))))......((....((((((......))))))...)).))))((((((((((((.(((((....))))).))))).))))))).. ( -38.80)
>DroYak_CAF1 9984 90 + 1
UGCAGUCAACUCGCGAAUCUUUCAGGUGGUUG--------UUCGCAUUCUCAGCAUAUUUCUGCUUGGAGGCGGACUGUAUCGCCAAUUGUUGCGUUC----------------------
.((((.(((.....((.....)).((((((.(--------(((((.((((.((((......)))).))))))))))...))))))..)))))))....---------------------- ( -29.30)
>consensus
UGCAGUUAAGUCGCGAAUCUUUCAAGUGGUUGUUCGCUUAGUCGCAUUCUCAGCAUAUUUCUGCUGACAGGCAGGCUGCAUCGUCAAUUGUUGCGUAUUCGUAAAAAUUGAACAGUGCAC
((((((......((((......(((....))).........))))...............(((((....)))))))))))...((((((.(((((....))))).))))))......... (-18.27 = -20.34 +   2.06)

alignment

secondary structure

dotplot

Window 7

Location	299,180 – 299,296
Length	116
Sequences	3
Columns	116
Reading direction	forward
Mean pairwise identity	90.80
Mean single sequence MFE	-32.03
Consensus MFE	-23.34
Energy contribution	-23.23
Covariance contribution	-0.11
Combinations/Pair	1.07
Mean z-score	-2.56
Structure conservation index	0.73
SVM decision value	0.13
SVM RNA-class probability	0.598650
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 299180 116 + 23771897
GUCGCAUUCUCAGCAUUUUUCUGCCAGCGGGCAGUUAGCAUCGUCAGUUUUUGCGUAUUCGUAAAAAUUGAACAGUGCACCACGUCGAUUCUUAACAUGAAGUUUCUGUUUAACUU
(((((...............(((((....)))))...((((..((((((((((((....))))))))))))...)))).....).))))..........(((((.......))))) ( -29.20)
>DroSec_CAF1 9098 116 + 1
GUCGCAUUCUCAGCAUAUUUCUGCUGACAGGCAGGCUGCAUCAUCAAUUGUUGCGUAUUCGUAAAAAUUGAACAGUGCACCACAUCGAUUCUUAACAUGCAGUUUCUGUUUAACUU
.........((((((......)))))).(((((((((((((..((((((.(((((....))))).))))))...(((...))).............)))))))..))))))..... ( -30.20)
>DroSim_CAF1 11429 116 + 1
GUCGCAUUCUCAGCAUAUUUCUGCUGACAGGCAGGCUGCAUUGUCAAUUGUUGCGUAUUCGUAAAAAUUGAACAGUGCACCACAUCGAUUCUUAUCAUGCAGUUUCUGUGUAACUU
((..(((..((((((......))))))...(((((.(((((((((((((.(((((....))))).))))).)))))))))).....(((....))).))).......)))..)).. ( -36.70)
>consensus
GUCGCAUUCUCAGCAUAUUUCUGCUGACAGGCAGGCUGCAUCGUCAAUUGUUGCGUAUUCGUAAAAAUUGAACAGUGCACCACAUCGAUUCUUAACAUGCAGUUUCUGUUUAACUU
...(((....(.((((....(((((....)))))...((((..((((((.(((((....))))).))))))...))))..................)))).)....)))....... (-23.34 = -23.23 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:52 2006