Locus 3509

Sequence ID	X_DroMel_CAF1
Location	9,420,749 – 9,420,869
Length	120
Max. P	0.953068

overview

Window 3

Location	9,420,749 – 9,420,869
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.08
Mean single sequence MFE	-41.64
Consensus MFE	-39.18
Energy contribution	-39.18
Covariance contribution	-0.00
Combinations/Pair	1.06
Mean z-score	-1.43
Structure conservation index	0.94
SVM decision value	1.43
SVM RNA-class probability	0.953068
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9420749 120 + 22224390
GAUUGGCCACAUCGGCGAAUGCCUGCGAGUCCAGUUGCUCCCUGAUGCUCUCGAUGUCCCGCAGCACAUACUUGCAGUAGGCACUCAUAAAAAUGGCCGAUGCGCCGCCGAUCCCGGCUA
....(((..(((((((...(((((((((((.(((.......)))..))))..........((((.......)))).)))))))..(((....)))))))))).)))((((....)))).. ( -43.20)
>DroSec_CAF1 2501 120 + 1
GAUUGGCCACAUCGGCAAAUGCCUGCGAGUCCAGUUGCUCCCUGAUGCUUUCGAUGUCCCGCAGCACAUACUUGCAGUAGGCACUCAUAAAGAUGGCCGAUGCGCCGCCGAUCCCGGCUA
....(((..(((((((...(((((((((((......)))).....(((.....((((........))))....))))))))))..(((....)))))))))).)))((((....)))).. ( -43.00)
>DroSim_CAF1 2486 120 + 1
GAUUGGCCACAUCGGCAAACGCCUGCGAGUCCAGUUGCUCCCUGAUGCUUUCGAUGUCCCGCAGCACAUACUUGCAGUAGGCACUCAUAAAGAUGGCCGAUGCGCCGCCGAUCCCGGCUA
....(((..(((((((....((((((((((......)))).....(((.....((((........))))....)))))))))...(((....)))))))))).)))((((....)))).. ( -42.60)
>DroEre_CAF1 2550 120 + 1
GAUUGGCCACGUCGGCGAACGCCUGCGAGUCCAACUGCUCCCUGAUGCUAUCGAUGUCCCGCAGCACAUACUUGCAAUAGGCACUCAUGAAGAUGGCCGAUGCGCCGCCAAUCCCAGCCA
((((((((.(((((((....((((((((((....((((.....(((.........)))..)))).....))))))...))))...(((....)))))))))).)..)))))))....... ( -38.60)
>DroYak_CAF1 2530 120 + 1
GAUUGGCCACAUCGGCGAAUGCCUGCGAGUCCAGUUGCUCCCUGAUGCCAUCGAUGUCCCGCAGCACAUACUUGCAGUAGGCACUCAUAAAGAUAGCCGAUGCGCCGCCAAUCCCCGCCA
((((((((.(((((((((.(((((((((((......)))).....(((.....((((........))))....)))))))))).))((....)).))))))).)..)))))))....... ( -40.80)
>consensus
GAUUGGCCACAUCGGCGAAUGCCUGCGAGUCCAGUUGCUCCCUGAUGCUAUCGAUGUCCCGCAGCACAUACUUGCAGUAGGCACUCAUAAAGAUGGCCGAUGCGCCGCCGAUCCCGGCUA
((((((((.(((((((....((((((((((......)))).....(((.....((((........))))....)))))))))...(((....)))))))))).)..)))))))....... (-39.18 = -39.18 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	9,420,749 – 9,420,869
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.08
Mean single sequence MFE	-46.96
Consensus MFE	-42.34
Energy contribution	-41.74
Covariance contribution	-0.60
Combinations/Pair	1.14
Mean z-score	-1.12
Structure conservation index	0.90
SVM decision value	0.00
SVM RNA-class probability	0.534495
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9420749 120 - 22224390
UAGCCGGGAUCGGCGGCGCAUCGGCCAUUUUUAUGAGUGCCUACUGCAAGUAUGUGCUGCGGGACAUCGAGAGCAUCAGGGAGCAACUGGACUCGCAGGCAUUCGCCGAUGUGGCCAAUC
..((((....))))(((((((((((.........((((((((.(((((.((....)))))))......(.(((..((((.......)))).))).))))))))))))))))).))).... ( -48.90)
>DroSec_CAF1 2501 120 - 1
UAGCCGGGAUCGGCGGCGCAUCGGCCAUCUUUAUGAGUGCCUACUGCAAGUAUGUGCUGCGGGACAUCGAAAGCAUCAGGGAGCAACUGGACUCGCAGGCAUUUGCCGAUGUGGCCAAUC
..((((....))))(((((((((((.........((((((((...(((......))).(((((....(....)..((((.......)))).))))))))))))))))))))).))).... ( -47.50)
>DroSim_CAF1 2486 120 - 1
UAGCCGGGAUCGGCGGCGCAUCGGCCAUCUUUAUGAGUGCCUACUGCAAGUAUGUGCUGCGGGACAUCGAAAGCAUCAGGGAGCAACUGGACUCGCAGGCGUUUGCCGAUGUGGCCAAUC
..((((....))))(((((((((((......((((..(((.....)))..))))..(((((((....(....)..((((.......)))).)))))))......)))))))).))).... ( -45.10)
>DroEre_CAF1 2550 120 - 1
UGGCUGGGAUUGGCGGCGCAUCGGCCAUCUUCAUGAGUGCCUAUUGCAAGUAUGUGCUGCGGGACAUCGAUAGCAUCAGGGAGCAGUUGGACUCGCAGGCGUUCGCCGACGUGGCCAAUC
((((((.(.((((((((((............((((..(((.....)))..))))..(((((((...(((((.((........)).))))).)))))))))).)))))))).))))))... ( -46.00)
>DroYak_CAF1 2530 120 - 1
UGGCGGGGAUUGGCGGCGCAUCGGCUAUCUUUAUGAGUGCCUACUGCAAGUAUGUGCUGCGGGACAUCGAUGGCAUCAGGGAGCAACUGGACUCGCAGGCAUUCGCCGAUGUGGCCAAUC
.......(((((((..(((((((((((....)).((((((((...((.(((..(((((((((....))).))))))(((.......))).))).)))))))))))))))))))))))))) ( -47.30)
>consensus
UAGCCGGGAUCGGCGGCGCAUCGGCCAUCUUUAUGAGUGCCUACUGCAAGUAUGUGCUGCGGGACAUCGAAAGCAUCAGGGAGCAACUGGACUCGCAGGCAUUCGCCGAUGUGGCCAAUC
..((((....))))(((((((((((.........((((((((...(((......))).(((((....(....)..((((.......)))).))))))))))))))))))))).))).... (-42.34 = -41.74 +  -0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:09 2006