Locus 3619

Sequence ID	2R_DroMel_CAF1
Location	12,004,934 – 12,005,083
Length	149
Max. P	0.986941

overview

Window 1

Location	12,004,934 – 12,005,043
Length	109
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	84.97
Mean single sequence MFE	-43.64
Consensus MFE	-27.28
Energy contribution	-28.25
Covariance contribution	0.97
Combinations/Pair	1.11
Mean z-score	-3.94
Structure conservation index	0.63
SVM decision value	2.06
SVM RNA-class probability	0.986941
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12004934 109 - 20766785
CAUUGCCAUGGUU--AUGUGUGCGACUGUAUGUAGCCA------UGGCGGUGAAUCUGGUUCCGGAUUGUGGAUGUGGCCAAAGGGUAUGGGCAUGGGCGUGUUGGCGACAUUACGC
(((((((((((((--(((((........))))))))))------))))))))((((((....))))))((((((((.(((((.(.((..........)).).))))).))))).))) ( -45.20)
>DroSec_CAF1 6249 103 - 1
CAUUGCCAUGGUU--AUAUGUUCGACUGUAUGUAGCCA------UGGCGGUGAAUCUGGAUCCGGAUUGUGGAUGUGGCCAAAGGGUAUG------GGCGUGUUGGCGACAUUACGC
(((((((((((((--(((((........))))))))))------))))))))((((((....))))))((((((((.(((((.(.((...------.)).).))))).))))).))) ( -47.10)
>DroSim_CAF1 6024 103 - 1
CAUUGCCAUGGUU--AUAUGUUCGACUGUAUGUAGCCA------UGGCGGUGAAUCUGGAUCCGGAUUGUGGAUGUGGCCAAAGGGUAUG------GGCGUGUUGGCGACAUUACGC
(((((((((((((--(((((........))))))))))------))))))))((((((....))))))((((((((.(((((.(.((...------.)).).))))).))))).))) ( -47.10)
>DroEre_CAF1 3986 110 - 1
CAUGGUUAUACGUACAUAUGUGCGACUUUAUGUAGCCAUGGCCAUGGCGGUGAAUCUGGAUACGGAUUGUGGAUGUGGCCAA-GGGUAUG------GGCGUGUUGGCGACAUUACGC
(((((((((((((((....)))))......))))))))))((....))....((((((....))))))((((((((.(((((-.(((...------.)).).))))).))))).))) ( -39.00)
>DroYak_CAF1 6076 98 - 1
CAUGGUACUACUCGUAUACGAG------UAUGUAGCCA------UGGCGGUGAAUCUGGAUCCGGAUUGUGGAUGUGGCCAA-GGGUAUG------GGCGUGUUGGCGACAUUACGC
((((((((((((((....))))------)).)).))))------))(((...((((((....))))))...(((((.(((((-.(((...------.)).).))))).))))).))) ( -39.80)
>consensus
CAUUGCCAUGGUU__AUAUGUGCGACUGUAUGUAGCCA______UGGCGGUGAAUCUGGAUCCGGAUUGUGGAUGUGGCCAAAGGGUAUG______GGCGUGUUGGCGACAUUACGC
((((((((........(((((((....)))))))..........))))))))((((((....))))))((((((((.(((((.(.((..........)).).))))).))))).))) (-27.28 = -28.25 +   0.97)

alignment

secondary structure

dotplot

Window 2

Location	12,004,973 – 12,005,083
Length	110
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	77.66
Mean single sequence MFE	-21.92
Consensus MFE	-7.13
Energy contribution	-8.47
Covariance contribution	1.33
Combinations/Pair	1.00
Mean z-score	-2.65
Structure conservation index	0.33
SVM decision value	0.25
SVM RNA-class probability	0.651272
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12004973 110 + 20766785
CCACAUCCACAAUCCGGAACCAGAUUCACCGCCA------UGGCUACAUACAGUCGCACACAU--AACCAUGGCAAU-GGCAAUGGCCAUGUCCCACCUCGCCAUCCUCAACAUCCUUC
...............(((............((((------(((....................--..)))))))..(-((..(((((...(.....)...)))))..)))...)))... ( -20.65)
>DroSec_CAF1 6282 107 + 1
CCACAUCCACAAUCCGGAUCCAGAUUCACCGCCA------UGGCUACAUACAGUCGAACAUAU--AACCAUGGCAAU-GGCAAUGGCCAUGUCC---CUCGCCAUCCUCAACAUCCUUC
...............((((...((......((((------(((....................--..))))))).((-(((....)))))....---.))...))))............ ( -21.95)
>DroSim_CAF1 6057 107 + 1
CCACAUCCACAAUCCGGAUCCAGAUUCACCGCCA------UGGCUACAUACAGUCGAACAUAU--AACCAUGGCAAU-GGCAAUGGCCAUGUCC---CUCGCCAUCCUCAACAUCCUUC
...............((((...((......((((------(((....................--..))))))).((-(((....)))))....---.))...))))............ ( -21.95)
>DroEre_CAF1 4018 111 + 1
CCACAUCCACAAUCCGUAUCCAGAUUCACCGCCAUGGCCAUGGCUACAUAAAGUCGCACAUAUGUACGUAUAACCAU-GGCAAUGGCCACGUCC---CUCGC----CUCAACAUCCUUC
..............................(((((.((((((((((((((..........)))))).).....))))-))).))))).......---.....----............. ( -21.30)
>DroYak_CAF1 6108 99 + 1
CCACAUCCACAAUCCGGAUCCAGAUUCACCGCCA------UGGCUACAUA------CUCGUAUACGAGUAGUACCAU-GGCAAUGGCCAUGUCC---CUUGC----CUCAACAUCCUUC
...............((((...((......((((------(((.(((.((------((((....)))))))))))))-)))...(((.......---...))----)))...))))... ( -30.00)
>DroAna_CAF1 2404 97 + 1
CCACAUCCUCAUU-CACAUCCACUUGCACAACCA------------UAUCCUGAUUCACAUAU--AACCAUGGCAGCGGGCAAUGGCCAUGUCC---AUGCC----CUCAGCAUCCUUC
.............-..........(((.......------------....(((.....(((..--....))).))).(((((.(((......))---)))))----)...)))...... ( -15.70)
>consensus
CCACAUCCACAAUCCGGAUCCAGAUUCACCGCCA______UGGCUACAUACAGUCGCACAUAU__AACCAUGGCAAU_GGCAAUGGCCAUGUCC___CUCGC____CUCAACAUCCUUC
...............((((...........((((......))))..................................(((....)))........................))))... ( -7.13 =  -8.47 +   1.33)

alignment

secondary structure

dotplot

Window 3

Location	12,004,973 – 12,005,083
Length	110
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	77.66
Mean single sequence MFE	-36.73
Consensus MFE	-11.79
Energy contribution	-11.68
Covariance contribution	-0.11
Combinations/Pair	1.37
Mean z-score	-2.65
Structure conservation index	0.32
SVM decision value	0.20
SVM RNA-class probability	0.631124
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12004973 110 - 20766785
GAAGGAUGUUGAGGAUGGCGAGGUGGGACAUGGCCAUUGCC-AUUGCCAUGGUU--AUGUGUGCGACUGUAUGUAGCCA------UGGCGGUGAAUCUGGUUCCGGAUUGUGGAUGUGG
.....(((((.(.(((((((((((.(....).))).)))))-)))(((((((((--(((((........))))))))))------))))....((((((....)))))).).))))).. ( -40.10)
>DroSec_CAF1 6282 107 - 1
GAAGGAUGUUGAGGAUGGCGAG---GGACAUGGCCAUUGCC-AUUGCCAUGGUU--AUAUGUUCGACUGUAUGUAGCCA------UGGCGGUGAAUCUGGAUCCGGAUUGUGGAUGUGG
...((((.(.((.((((((.(.---.....).))))))..(-((((((((((((--(((((........))))))))))------))))))))..)).).))))............... ( -40.70)
>DroSim_CAF1 6057 107 - 1
GAAGGAUGUUGAGGAUGGCGAG---GGACAUGGCCAUUGCC-AUUGCCAUGGUU--AUAUGUUCGACUGUAUGUAGCCA------UGGCGGUGAAUCUGGAUCCGGAUUGUGGAUGUGG
...((((.(.((.((((((.(.---.....).))))))..(-((((((((((((--(((((........))))))))))------))))))))..)).).))))............... ( -40.70)
>DroEre_CAF1 4018 111 - 1
GAAGGAUGUUGAG----GCGAG---GGACGUGGCCAUUGCC-AUGGUUAUACGUACAUAUGUGCGACUUUAUGUAGCCAUGGCCAUGGCGGUGAAUCUGGAUACGGAUUGUGGAUGUGG
.....(((((.(.----.....---...(((.(((((.(((-((((((((((((((....)))))......)))))))))))).))))).)))((((((....)))))).).))))).. ( -39.00)
>DroYak_CAF1 6108 99 - 1
GAAGGAUGUUGAG----GCAAG---GGACAUGGCCAUUGCC-AUGGUACUACUCGUAUACGAG------UAUGUAGCCA------UGGCGGUGAAUCUGGAUCCGGAUUGUGGAUGUGG
......(((....----)))..---..((((...(((((((-(((((((((((((....))))------)).)).))))------))))))))((((((....))))))....)))).. ( -37.00)
>DroAna_CAF1 2404 97 - 1
GAAGGAUGCUGAG----GGCAU---GGACAUGGCCAUUGCCCGCUGCCAUGGUU--AUAUGUGAAUCAGGAUA------------UGGUUGUGCAAGUGGAUGUG-AAUGAGGAUGUGG
...(.((.((.((----(((((---((......))).)))))(((..(((..((--((((.(......).)))------------)))..)))..))).......-..).)).)).).. ( -22.90)
>consensus
GAAGGAUGUUGAG____GCGAG___GGACAUGGCCAUUGCC_AUUGCCAUGGUU__AUAUGUGCGACUGUAUGUAGCCA______UGGCGGUGAAUCUGGAUCCGGAUUGUGGAUGUGG
............................(((.((((..((.....))((((......))))........................)))).)))((((((....)))))).......... (-11.79 = -11.68 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:03 2006