Locus 3017

Sequence ID	3R_DroMel_CAF1
Location	8,066,725 – 8,066,848
Length	123
Max. P	0.848589

overview

Window 3

Location	8,066,725 – 8,066,825
Length	100
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	88.21
Mean single sequence MFE	-35.42
Consensus MFE	-25.70
Energy contribution	-25.90
Covariance contribution	0.20
Combinations/Pair	1.08
Mean z-score	-1.64
Structure conservation index	0.73
SVM decision value	0.02
SVM RNA-class probability	0.545986
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8066725 100 + 27905053
GACAUCCGUAUGUGGCCAGUGGCUGGCCAAAAUAACGCCGCUUCUCCAUUGGCGCAUCUC----CACUGGUGCAGUGGCUACUGCACAGCUGCAACUGCAACUG-------
.......(((..(((((((...))))))).......((((((.(.(((.(((.......)----)).))).).))))))...))).(((.(((....))).)))------- ( -34.60)
>DroSec_CAF1 12801 100 + 1
GACAUCCGUAUGUGGCCAGUGGCUGGCCAAAAUAAUGCCCCUUCUCCAUUGGCGCAUAUC----UACUGGCACAGUGGCUACUGCCCAGCUGCAACUGCAACUG-------
.......(((.(((((((.((....((((.....((((.((.........)).))))...----...)))).)).)))))))))).(((.(((....))).)))------- ( -32.80)
>DroSim_CAF1 12811 100 + 1
GACAUCCGUAUGUGGCCAGUGGCUGGCCAAAAUAAUGCCCCUUCUCCAUUGGCGCAUAUC----CACUGGCGCAGUGGCUACUGCACAGCUGCAACUGCAACUG-------
.......(((.((.((((((((.(((((((..................))))).))...)----)))))))(((((.((....))...))))).))))).....------- ( -33.87)
>DroEre_CAF1 11345 106 + 1
GACAUCCGUAUGUGGCCAGUGGCUGGCCAAAAUAAAGCCGCUUCUCCACUGGCGCAUCUC----C-UUGGAGCACUGGCUACUGCACAGCUGCAACUGCAACUGCAAGUGC
.((....(((.((((((((((((.(((.........)))))..(((((..((.......)----)-.)))))))))))))))))).(((.(((....))).)))...)).. ( -37.70)
>DroYak_CAF1 11607 103 + 1
GACAUCCGUAUGUGGCCGGUGGCUUGCCAAAAUAAUGCCGCUUCUCCACUGGCGCAUCUGUGUGC-AUGUGGCAGUGGCUACUGCACAGCUGCAACUGCAACUG-------
.......(((.((((((((((((.............)))))).((((((..(((((....)))))-..)))).)).))))))))).(((.(((....))).)))------- ( -38.12)
>consensus
GACAUCCGUAUGUGGCCAGUGGCUGGCCAAAAUAAUGCCGCUUCUCCAUUGGCGCAUCUC____CACUGGCGCAGUGGCUACUGCACAGCUGCAACUGCAACUG_______
.........(((((.(((((((..(((.........)))......))))))))))))..............(((((....))))).(((.(((....))).)))....... (-25.70 = -25.90 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	8,066,758 – 8,066,848
Length	90
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	83.69
Mean single sequence MFE	-31.36
Consensus MFE	-18.98
Energy contribution	-19.78
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.86
Structure conservation index	0.61
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8066758 90 + 27905053
AACGCCGCUUCUCCAUUGGCGCAUCUC----CACUGGUGCAGUGGCUACUGCACAGCUGCAACUGCAACUG------------CAGCCCCAAGAUCGAGAUG--GAGA
.........((((((((..((.((((.----.....(((((((....))))))).((((((........))------------))))....)))))).))))--)))) ( -34.50)
>DroSec_CAF1 12834 92 + 1
AAUGCCCCUUCUCCAUUGGCGCAUAUC----UACUGGCACAGUGGCUACUGCCCAGCUGCAACUGCAACUG------------CAGCCCCAAGAUCGAGAUGAAGAGA
.......(((((((..(((.(((((.(----(((((...)))))).)).))))))((((((........))------------)))).........).)).))))... ( -25.60)
>DroSim_CAF1 12844 92 + 1
AAUGCCCCUUCUCCAUUGGCGCAUAUC----CACUGGCGCAGUGGCUACUGCACAGCUGCAACUGCAACUG------------CAGCCCCAAGAUCGAGAUGAAGAGA
.........((((..((((.(((((.(----(((((...)))))).)).)))...((((((........))------------)))).))))....))))........ ( -27.10)
>DroEre_CAF1 11378 99 + 1
AAAGCCGCUUCUCCACUGGCGCAUCUC----C-UUGGAGCACUGGCUACUGCACAGCUGCAACUGCAACUGCAAGUGCAAGUGCAGCCCCA--AUCGAGAUG--GAGA
...((((.........)))).((((((----.-((((.((((((((....)).))).)))..(((((..(((....)))..)))))..)))--)..))))))--.... ( -36.00)
>DroYak_CAF1 11640 91 + 1
AAUGCCGCUUCUCCACUGGCGCAUCUGUGUGC-AUGUGGCAGUGGCUACUGCACAGCUGCAACUGCAACUG------------CAGCCCCA--AUCGAGAUG--GAGA
.........((((((((.(........(((((-(.(((((....)))))))))))((((((........))------------))))....--..).)).))--)))) ( -33.60)
>consensus
AAUGCCGCUUCUCCAUUGGCGCAUCUC____CACUGGCGCAGUGGCUACUGCACAGCUGCAACUGCAACUG____________CAGCCCCAAGAUCGAGAUG__GAGA
.........((((..((((.((................(((((....))))).(((.(((....))).)))..............)).))))....))))........ (-18.98 = -19.78 +   0.80)

alignment

secondary structure

dotplot

Window 5

Location	8,066,758 – 8,066,848
Length	90
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	83.69
Mean single sequence MFE	-36.42
Consensus MFE	-27.66
Energy contribution	-27.46
Covariance contribution	-0.20
Combinations/Pair	1.09
Mean z-score	-1.96
Structure conservation index	0.76
SVM decision value	0.78
SVM RNA-class probability	0.848589
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8066758 90 - 27905053
UCUC--CAUCUCGAUCUUGGGGCUG------------CAGUUGCAGUUGCAGCUGUGCAGUAGCCACUGCACCAGUG----GAGAUGCGCCAAUGGAGAAGCGGCGUU
((((--(((...........(((((------------(((......))))))))(((((((....)))))))..)))----)))).(((((...........))))). ( -36.40)
>DroSec_CAF1 12834 92 - 1
UCUCUUCAUCUCGAUCUUGGGGCUG------------CAGUUGCAGUUGCAGCUGGGCAGUAGCCACUGUGCCAGUA----GAUAUGCGCCAAUGGAGAAGGGGCAUU
(((((((.(((.....(((((((((------------(....))))))(((((((((((((....))))).))))).----....))).)))).)))))))))).... ( -32.00)
>DroSim_CAF1 12844 92 - 1
UCUCUUCAUCUCGAUCUUGGGGCUG------------CAGUUGCAGUUGCAGCUGUGCAGUAGCCACUGCGCCAGUG----GAUAUGCGCCAAUGGAGAAGGGGCAUU
(((((((.......(((...(((.(------------(((((((....))))))))(((....((((((...)))))----)...))))))...)))))))))).... ( -36.61)
>DroEre_CAF1 11378 99 - 1
UCUC--CAUCUCGAU--UGGGGCUGCACUUGCACUUGCAGUUGCAGUUGCAGCUGUGCAGUAGCCAGUGCUCCAA-G----GAGAUGCGCCAGUGGAGAAGCGGCUUU
....--..((((.((--(((.((.(((((.((((((((((((((....))))))))).))).)).)))))((...-.----))...)).))))).))))......... ( -42.30)
>DroYak_CAF1 11640 91 - 1
UCUC--CAUCUCGAU--UGGGGCUG------------CAGUUGCAGUUGCAGCUGUGCAGUAGCCACUGCCACAU-GCACACAGAUGCGCCAGUGGAGAAGCGGCAUU
....--..((((.((--(((.((.(------------(((((((....))))))))(((((....))))).....-..........)).))))).))))......... ( -34.80)
>consensus
UCUC__CAUCUCGAUCUUGGGGCUG____________CAGUUGCAGUUGCAGCUGUGCAGUAGCCACUGCGCCAGUG____GAGAUGCGCCAAUGGAGAAGCGGCAUU
........((((.((..(((.((..............(((((((....))))))).(((((....)))))................)).))))).))))......... (-27.66 = -27.46 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:16 2006