Locus 4682

Sequence ID	3L_DroMel_CAF1
Location	13,223,198 – 13,223,306
Length	108
Max. P	0.919642

overview

Window 6

Location	13,223,198 – 13,223,306
Length	108
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	89.73
Mean single sequence MFE	-29.70
Consensus MFE	-24.45
Energy contribution	-24.70
Covariance contribution	0.25
Combinations/Pair	1.12
Mean z-score	-2.12
Structure conservation index	0.82
SVM decision value	1.13
SVM RNA-class probability	0.919642
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13223198 108 + 23771897
CAGAAAAAAA-------AGAGAGAACGCGCUCUGGUAUGCUCCAUAAAGUGGGGCACCAUGGCGAUUACUAUGCUGCAA-ACGCAUUAAAAUCAAUUGAUUGCGGUGGAAAAUGUA
..........-------........((((((.((((..(((((((...))))))))))).)))((((...((((.....-..))))...))))........)))............ ( -28.20)
>DroSec_CAF1 16594 108 + 1
CAGAAAAAAA-------AGAGAGAACGCGCUCUGGUAUGCGCCAUAAAGUGGGGCAGCACGGAGAUUACUAUGCUGCGA-ACGCAUUAAAAUCAAUUGAUUGCGGUGGAAAAUGUA
..........-------........((((.(((((((((((((((...)))).((((((..(......)..))))))..-.)))))....))))...)).))))............ ( -25.20)
>DroEre_CAF1 6419 108 + 1
CAGAAAAAA--------AGAGAGAAUGCGCUCUGGUAUGCCCCAUAAAGUGGGGCAGCACGGCGAUUACUAUGCUGCAAAACGCACUAAAGUCAAUUGAUUGCGGUGGAAAAUGCA
.........--------..((((......)))).(((((((((((...)))))))..(((.(((((((((.((.(((.....))).)).))).....)))))).)))....)))). ( -31.60)
>DroYak_CAF1 16517 115 + 1
CAGCAAAAAAAAAAAAUAAAGAGAACGCGCUCUGGUAUGCCCCAUAAAGUGGGGCAGCGCGGCGAUUACUAUGCUGCAA-ACGCAUUAAAAUCAAUUGAUUGCGGUGGAGAAUGCA
..((...............((((......))))....((((((((...))))))))))((((((.......))))))..-..(((((....((.((((....)))).)).))))). ( -33.80)
>consensus
CAGAAAAAAA_______AGAGAGAACGCGCUCUGGUAUGCCCCAUAAAGUGGGGCAGCACGGCGAUUACUAUGCUGCAA_ACGCAUUAAAAUCAAUUGAUUGCGGUGGAAAAUGCA
...................((((......))))....((((((((...)))))))).(((.(((((((..((((........))))..........))))))).)))......... (-24.45 = -24.70 +   0.25)

alignment

secondary structure

dotplot

Window 7

Location	13,223,198 – 13,223,306
Length	108
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	89.73
Mean single sequence MFE	-26.98
Consensus MFE	-18.64
Energy contribution	-19.32
Covariance contribution	0.69
Combinations/Pair	1.14
Mean z-score	-2.07
Structure conservation index	0.69
SVM decision value	0.20
SVM RNA-class probability	0.629562
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13223198 108 - 23771897
UACAUUUUCCACCGCAAUCAAUUGAUUUUAAUGCGU-UUGCAGCAUAGUAAUCGCCAUGGUGCCCCACUUUAUGGAGCAUACCAGAGCGCGUUCUCUCU-------UUUUUUUCUG
............(((........((((...((((..-.....))))...))))((..((((((.(((.....))).))..))))..)))))........-------.......... ( -22.40)
>DroSec_CAF1 16594 108 - 1
UACAUUUUCCACCGCAAUCAAUUGAUUUUAAUGCGU-UCGCAGCAUAGUAAUCUCCGUGCUGCCCCACUUUAUGGCGCAUACCAGAGCGCGUUCUCUCU-------UUUUUUUCUG
...............((((....))))..(((((((-((((((((..(......)..)))))).........(((......))))))))))))......-------.......... ( -25.10)
>DroEre_CAF1 6419 108 - 1
UGCAUUUUCCACCGCAAUCAAUUGACUUUAGUGCGUUUUGCAGCAUAGUAAUCGCCGUGCUGCCCCACUUUAUGGGGCAUACCAGAGCGCAUUCUCUCU--------UUUUUUCUG
(((..........))).............(((((((((((.((((..((....))..))))((((((.....))))))....)))))))))))......--------......... ( -31.10)
>DroYak_CAF1 16517 115 - 1
UGCAUUCUCCACCGCAAUCAAUUGAUUUUAAUGCGU-UUGCAGCAUAGUAAUCGCCGCGCUGCCCCACUUUAUGGGGCAUACCAGAGCGCGUUCUCUUUAUUUUUUUUUUUUGCUG
.............((((......((((...((((..-.....))))...))))..((((((((((((.....)))))).......))))))...................)))).. ( -29.31)
>consensus
UACAUUUUCCACCGCAAUCAAUUGAUUUUAAUGCGU_UUGCAGCAUAGUAAUCGCCGUGCUGCCCCACUUUAUGGGGCAUACCAGAGCGCGUUCUCUCU_______UUUUUUUCUG
.............................(((((((.(((.(((((.(......).)))))((((((.....))))))....))).)))))))....................... (-18.64 = -19.32 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:39 2006