Locus 3911

Sequence ID	X_DroMel_CAF1
Location	10,464,252 – 10,464,361
Length	109
Max. P	0.669212

overview

Window 6

Location	10,464,252 – 10,464,361
Length	109
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	83.26
Mean single sequence MFE	-38.67
Consensus MFE	-26.26
Energy contribution	-28.14
Covariance contribution	1.88
Combinations/Pair	1.07
Mean z-score	-1.74
Structure conservation index	0.68
SVM decision value	0.29
SVM RNA-class probability	0.669212
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10464252 109 + 22224390
CGUGUGAAGCAAAAAGGAAAAACUGAAAA----CUGACAGAGCUGUCACUGCCAACGUCGA------CGCAGACGCCGACUGCGACUGCGACAGCGACAGCGAUGGAGGCGCU-ACGCGA
(((((..(((...................----.(((((....)))))..(((..((((..------(((((.(((.....))).)))))...((....))))))..))))))-))))). ( -38.20)
>DroSec_CAF1 8558 109 + 1
CGUGUGAAGCAAAAAGGAAAAACUGAAAA----CUGGCGGAGCUGUCACUGUCCACGUCGA------CGCAGACGCCGACUGCGACUGCGACAGCGACAGCGAUGGAGGAGCA-ACGCGA
(((((...((....((......)).....----((..((..((((((.(((((...(....------)((((.(((.....))).))))))))).))))))..))..)).)).-))))). ( -38.20)
>DroSim_CAF1 8529 103 + 1
CGUGUGAAGCAAAAAGGAAAAACUGAAAA----CUGGCGGAGCUGUCACUGUCCACCUCGA------CGCCGACGCCGACU------GCGACAGCGACAGCGAUGGAGGAGCA-ACGCGA
(((((...((....((......)).....----((..((..((((((.(((((((..(((.------((....)).))).)------).))))).))))))..))..)).)).-))))). ( -33.50)
>DroYak_CAF1 8768 120 + 1
CGUUUGGGCCAAAAAGGAAAAACUGAAUAUCUGCUGACGGAGCUGUCGCUGUACACGUCGACGUAGACGCAGACGCCGACGCCGACGCCGACUGCGACAGCGACGGAGGGGCAAACGCGA
(((.(..(((....((......)).........((..((..((((((((.((...(((((.(((....((....))..))).)))))...)).))))))))..))..)))))..).))). ( -44.80)
>consensus
CGUGUGAAGCAAAAAGGAAAAACUGAAAA____CUGACGGAGCUGUCACUGUCCACGUCGA______CGCAGACGCCGACUGCGACUGCGACAGCGACAGCGAUGGAGGAGCA_ACGCGA
(((((...((....((......)).........((..((..((((((.(((((...((((........((....))......))))...))))).))))))..))..)).))..))))). (-26.26 = -28.14 +   1.88)

alignment

secondary structure

dotplot

Window 7

Location	10,464,252 – 10,464,361
Length	109
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	83.26
Mean single sequence MFE	-40.48
Consensus MFE	-23.92
Energy contribution	-25.04
Covariance contribution	1.12
Combinations/Pair	1.10
Mean z-score	-1.96
Structure conservation index	0.59
SVM decision value	0.05
SVM RNA-class probability	0.559318
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10464252 109 - 22224390
UCGCGU-AGCGCCUCCAUCGCUGUCGCUGUCGCAGUCGCAGUCGGCGUCUGCG------UCGACGUUGGCAGUGACAGCUCUGUCAG----UUUUCAGUUUUUCCUUUUUGCUUCACACG
..(.(.-(((.........((((((((((((((....)).(((((((....))------)))))...)))))))))))).(((....----....)))............))).).)... ( -40.80)
>DroSec_CAF1 8558 109 - 1
UCGCGU-UGCUCCUCCAUCGCUGUCGCUGUCGCAGUCGCAGUCGGCGUCUGCG------UCGACGUGGACAGUGACAGCUCCGCCAG----UUUUCAGUUUUUCCUUUUUGCUUCACACG
..(((.-((......))..((((((((((((((....)).(((((((....))------)))))...))))))))))))..)))...----............................. ( -37.60)
>DroSim_CAF1 8529 103 - 1
UCGCGU-UGCUCCUCCAUCGCUGUCGCUGUCGC------AGUCGGCGUCGGCG------UCGAGGUGGACAGUGACAGCUCCGCCAG----UUUUCAGUUUUUCCUUUUUGCUUCACACG
..(((.-((......))..((((((((((((((------..((((((....))------)))).)).))))))))))))..)))...----............................. ( -33.60)
>DroYak_CAF1 8768 120 - 1
UCGCGUUUGCCCCUCCGUCGCUGUCGCAGUCGGCGUCGGCGUCGGCGUCUGCGUCUACGUCGACGUGUACAGCGACAGCUCCGUCAGCAGAUAUUCAGUUUUUCCUUUUUGGCCCAAACG
....((((((.....((..((((((((.((..((((((((((.((((....)))).))))))))))..)).))))))))..))...)))))).....((((..((.....))...)))). ( -49.90)
>consensus
UCGCGU_UGCUCCUCCAUCGCUGUCGCUGUCGCAGUCGCAGUCGGCGUCUGCG______UCGACGUGGACAGUGACAGCUCCGCCAG____UUUUCAGUUUUUCCUUUUUGCUUCACACG
..((....)).........((((((((((((...((((.......((....)).......))))...))))))))))))......................................... (-23.92 = -25.04 +   1.12)

alignment

secondary structure

dotplot

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