Locus 8742

Sequence ID	3L_DroMel_CAF1
Location	22,836,857 – 22,837,097
Length	240
Max. P	0.834841

overview

Window 4

Location	22,836,857 – 22,836,977
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.69
Mean single sequence MFE	-39.40
Consensus MFE	-31.33
Energy contribution	-32.70
Covariance contribution	1.37
Combinations/Pair	1.14
Mean z-score	-1.87
Structure conservation index	0.80
SVM decision value	0.73
SVM RNA-class probability	0.834841
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22836857 120 - 23771897
AAAAUAACACCGUUGCUUCUUGCCUGCCAGCUAUGGACCUGCUGCCUAACCUCCAGGUCUGCAGUCUGGUAGUAAGGUAGGCAACUGUAGUGUUGAACUUCCAAAGCUGCCACGAGGCAU
....((((((.((((((((((..(((((((((..(((((((..(......)..)))))))..)).)))))))..))).)))))))....))))))............((((....)))). ( -45.10)
>DroSec_CAF1 25436 120 - 1
AGAAUAACACCGUUGCUUCUUGCCCGCCAGCUAUGCACCUGCCGUCUAACCUCCAGGUCCGAAGUCUGGUAGUAGGGCAGGCAGCUGUAGUUUCGAUCUUCCAAAGCUGCCACAAGGCAC
.............(((((..((((((((((((.((.(((((..(......)..))))).)).)).)))))....)))))(((((((..((.......)).....)))))))...))))). ( -39.30)
>DroSim_CAF1 24903 120 - 1
AGAAUAACACCGUUGCUUCUUGCCCGCCAGCUAUGCACCUGCCGCCUAACCUCCAGGUCCGAAGUCUGGUAGUAGGGCAGGCAGCUGUAGUUUCGAUCUUCCAAAGCUGCCACAAGGCAC
.............(((((..((((((((((((.((.(((((..(......)..))))).)).)).)))))....)))))(((((((..((.......)).....)))))))...))))). ( -39.00)
>DroEre_CAF1 31453 120 - 1
AGUAUGACACCAUGACUUCGUGCCUGCCAGCUAUGGACCUGCUUCAAAACCCCCAAGUCCGCAGUCUGGUAGUAAGGCAGACAUCGGUAGUUCCUAUCUUCCAGAGCUGCCACAAGACAC
.((((((..........))))))(((((((((.(((((.((............)).))))).)).)))))))...(((((...((((.((.......)).)).)).)))))......... ( -34.20)
>consensus
AGAAUAACACCGUUGCUUCUUGCCCGCCAGCUAUGCACCUGCCGCCUAACCUCCAGGUCCGAAGUCUGGUAGUAAGGCAGGCAGCUGUAGUUUCGAUCUUCCAAAGCUGCCACAAGGCAC
.........((((((((...((((((((((((.((((((((............)))))))).)).)))))....))))))))))).(((((((.(......).))))))).....))... (-31.33 = -32.70 +   1.37)

alignment

secondary structure

dotplot

Window 5

Location	22,836,977 – 22,837,097
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.75
Mean single sequence MFE	-37.65
Consensus MFE	-34.60
Energy contribution	-35.10
Covariance contribution	0.50
Combinations/Pair	1.10
Mean z-score	-1.58
Structure conservation index	0.92
SVM decision value	0.49
SVM RNA-class probability	0.757093
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22836977 120 - 23771897
AGAUUGUCGGAUAUUUUGAGGUGCCUUAACUUAAACUUGCUCCACGAGUGACUCAUACUGUGAUGAAUUAUGGUGUGCGCAUCUCGAAUGUCCAGCUCCGGACAAUUGUCUGUGCACAGC
...((((.((((((((.(((((((..........(((((.....)))))....((((((((((....)))))))))).))))))))))))))).((..(((((....))))).)))))). ( -39.20)
>DroSec_CAF1 25556 120 - 1
AGAUUGUCGGAUAUUUUGAGGUGCCUUAACUUAAAAUUCCUCCACGAGCGACUCAUACUGUGAUGAAUUAUGGUGUGCGCAUCUCGAAUGUCCAGCUCCGGGCAAUUGUCUGUGCACAGC
...((((.((((((((.(((((((.............(((((...))).))..((((((((((....)))))))))).))))))))))))))).((..(((((....))))).)))))). ( -36.50)
>DroSim_CAF1 25023 120 - 1
AGAUUGUCGGAUAUUUUGAGGUGCCUUAACUUAAAAUUCCUCCACGAGCGACUCAUACUGUGAUGAAUUAUGGUGUGCGCAUCUCGAAUGUCCAGCUCCGGGCAAUUGUCUGUGCACAGC
...((((.((((((((.(((((((.............(((((...))).))..((((((((((....)))))))))).))))))))))))))).((..(((((....))))).)))))). ( -36.50)
>DroEre_CAF1 31573 120 - 1
AGAUUGUUGGAUAUUUUGAGGUGUCUUAAUUUAAACGUGCUCCACGACUGACUCAUACUGUGAUGGAUUAGGGUGUGCGCAUCUCGGAUGUCCAGCUCCGGGCAGUUGUCCGUGCACAGC
.....(((((((((((.(((((((...........((((...)))).......((((((.(((....))).)))))).))))))))))))))))))..(((((....)))))........ ( -38.40)
>consensus
AGAUUGUCGGAUAUUUUGAGGUGCCUUAACUUAAAAUUCCUCCACGAGCGACUCAUACUGUGAUGAAUUAUGGUGUGCGCAUCUCGAAUGUCCAGCUCCGGGCAAUUGUCUGUGCACAGC
...((((.((((((((.(((((((............((((((...))))))..((((((((((....)))))))))).))))))))))))))).((..(((((....))))).)))))). (-34.60 = -35.10 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:23:32 2006