Locus 4468

Sequence ID	2L_DroMel_CAF1
Location	12,808,934 – 12,809,053
Length	119
Max. P	0.922117

overview

Window 8

Location	12,808,934 – 12,809,053
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.30
Mean single sequence MFE	-31.16
Consensus MFE	-21.88
Energy contribution	-21.84
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.84
Structure conservation index	0.70
SVM decision value	-0.00
SVM RNA-class probability	0.531413
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12808934 119 + 22407834
AGUUUGUCAAGGUUCGGGAGAUGGCAUGACAAGAUAUAAAGUCCAUAUCAUGGACAUGCAAUCCCACGGGAAAAGAGUUACGGAAGCGGAAAGAGGCCGCAAAAUGGUUCGGAGUCAAA-
..........(..((((((....(((((.((.(((((.......))))).))..)))))..)))).........(((..(.....((((.......))))....)..))).))..)...- ( -29.00)
>DroSec_CAF1 74677 112 + 1
AGUUUGUCAAGGUUCGGGAGAUGGCAUGACAAGAUAUAAAGUCCAUAUCAUGGACAUGCAAUCCCACGGGAAAAGAGUUACGGAAGCGGAAAGAGGCCGC-------UUCGGAAGGAAA-
............(((((((....(((((.((.(((((.......))))).))..)))))..))))...............(.(((((((.......))))-------))).)...))).- ( -32.30)
>DroSim_CAF1 77925 113 + 1
AGUUUGUCAAGGUUCGGGAGAUGGCAUGACAAGAUAUAAAGUCCAUAUCAUGGACAUGCAAUCCCACGGGAAAAGAGUUACGGAAGCGGAAAGAGGCCGC-------UUCGGAAGGAAAA
............(((((((....(((((.((.(((((.......))))).))..)))))..))))...............(.(((((((.......))))-------))).)...))).. ( -32.30)
>DroEre_CAF1 78051 118 + 1
AGUUUGUCAGGGCUCG-AAGAUGGCAUGACUAGAUAUAAAGUCCAUAUCAUGGACAUGCAAUCCCACGGGAAAAGAGUUACGGAAGCGGAAAGAGGGCGCAAAAUGGCUGGGUAAUGAA-
.....((((.(((((.-......(((((.((((((((.......))))).))).)))))..(((....)))...)))))......(((.........)))....))))...........- ( -26.30)
>DroYak_CAF1 78247 119 + 1
AGUUUGUCAGGGCUCGGGAGAUGGCAUGACAAGAUAUAAAGUCCAUAUCAUGGACAUGCAAUCCCACGGGAAAAGAGUUACGGAAGCGGAAAGCGGCAGCAAAAUGCUUUGGUAAUGAA-
......((....((((((.(((.(((((.((.(((((.......))))).))..))))).))))).))))....))(((((.((((((....((....))....)))))).)))))...- ( -35.90)
>consensus
AGUUUGUCAAGGUUCGGGAGAUGGCAUGACAAGAUAUAAAGUCCAUAUCAUGGACAUGCAAUCCCACGGGAAAAGAGUUACGGAAGCGGAAAGAGGCCGCAAAAUG_UUCGGAAAGAAA_
..(((((((.(.(((....)).).).))))))).......((((((...))))))..((..(((....))).........((....))..........)).................... (-21.88 = -21.84 +  -0.04)

alignment

secondary structure

dotplot

Window 9

Location	12,808,934 – 12,809,053
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.30
Mean single sequence MFE	-25.33
Consensus MFE	-20.84
Energy contribution	-21.08
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.85
Structure conservation index	0.82
SVM decision value	1.15
SVM RNA-class probability	0.922117
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12808934 119 - 22407834
-UUUGACUCCGAACCAUUUUGCGGCCUCUUUCCGCUUCCGUAACUCUUUUCCCGUGGGAUUGCAUGUCCAUGAUAUGGACUUUAUAUCUUGUCAUGCCAUCUCCCGAACCUUGACAAACU
-((((...............((((.......)))).................((.(((((.(((((..((.((((((.....)))))).)).))))).))))).))........)))).. ( -24.40)
>DroSec_CAF1 74677 112 - 1
-UUUCCUUCCGAA-------GCGGCCUCUUUCCGCUUCCGUAACUCUUUUCCCGUGGGAUUGCAUGUCCAUGAUAUGGACUUUAUAUCUUGUCAUGCCAUCUCCCGAACCUUGACAAACU
-.........(((-------((((.......)))))))..............((.(((((.(((((..((.((((((.....)))))).)).))))).))))).)).............. ( -28.80)
>DroSim_CAF1 77925 113 - 1
UUUUCCUUCCGAA-------GCGGCCUCUUUCCGCUUCCGUAACUCUUUUCCCGUGGGAUUGCAUGUCCAUGAUAUGGACUUUAUAUCUUGUCAUGCCAUCUCCCGAACCUUGACAAACU
..........(((-------((((.......)))))))..............((.(((((.(((((..((.((((((.....)))))).)).))))).))))).)).............. ( -28.80)
>DroEre_CAF1 78051 118 - 1
-UUCAUUACCCAGCCAUUUUGCGCCCUCUUUCCGCUUCCGUAACUCUUUUCCCGUGGGAUUGCAUGUCCAUGAUAUGGACUUUAUAUCUAGUCAUGCCAUCUU-CGAGCCCUGACAAACU
-................((((((..(((...((((..................))))(((.(((((.(...((((((.....))))))..).))))).)))..-.)))...)).)))).. ( -19.07)
>DroYak_CAF1 78247 119 - 1
-UUCAUUACCAAAGCAUUUUGCUGCCGCUUUCCGCUUCCGUAACUCUUUUCCCGUGGGAUUGCAUGUCCAUGAUAUGGACUUUAUAUCUUGUCAUGCCAUCUCCCGAGCCCUGACAAACU
-.(((((((..((((.....((....)).....))))..)))).........((.(((((.(((((..((.((((((.....)))))).)).))))).))))).)).....)))...... ( -25.60)
>consensus
_UUUACUUCCGAA_CAUUUUGCGGCCUCUUUCCGCUUCCGUAACUCUUUUCCCGUGGGAUUGCAUGUCCAUGAUAUGGACUUUAUAUCUUGUCAUGCCAUCUCCCGAACCUUGACAAACU
....................((((.......)))).................((.(((((.(((((.(...((((((.....))))))..).))))).))))).)).............. (-20.84 = -21.08 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:31 2006