Locus 2278

Sequence ID	3L_DroMel_CAF1
Location	6,408,796 – 6,408,886
Length	90
Max. P	0.989393

overview

Window 1

Location	6,408,796 – 6,408,886
Length	90
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	77.95
Mean single sequence MFE	-28.50
Consensus MFE	-10.32
Energy contribution	-12.52
Covariance contribution	2.20
Combinations/Pair	1.00
Mean z-score	-2.12
Structure conservation index	0.36
SVM decision value	0.68
SVM RNA-class probability	0.821025
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6408796 90 + 23771897
CACAA---C---------UGCAC-A-UAUGUACAUAGAUGUAUAUAUUCGCCAAGAGCAAUUCAGCUGGCUGCAACUGAAGUG---------CAGCUCGGCGGAGCUUUCCUU
.....---.---------.((..-.-((((((((....))))))))((((((...(((......)))(((((((.(....)))---------))))).))))))))....... ( -29.00)
>DroSec_CAF1 146800 90 + 1
AUCAA---C---------UGCAC-A-UAUGUACAUAGAUGUAUAUAUUCGCCAAGAGCAAUUCAGCUGGCUGCAACUGAAGUG---------CAGCUCGGCGGAGCUUUCCUU
.....---.---------.((..-.-((((((((....))))))))((((((...(((......)))(((((((.(....)))---------))))).))))))))....... ( -29.00)
>DroSim_CAF1 153052 90 + 1
AUCAA---C---------UGCAC-A-UAUGUACAUAGAUGUAUAUAUUCGCCAAGAGCAAUUCAGCUGGCUGCAACUGAAGUG---------CAGCUCGGCGGAGCUUUCCUU
.....---.---------.((..-.-((((((((....))))))))((((((...(((......)))(((((((.(....)))---------))))).))))))))....... ( -29.00)
>DroEre_CAF1 151194 89 + 1
ACCAG---C---------UACACCA-GCUACACAUAGA--UACAUAUGCGCCAAGUGCAGUCGAGCUGCCUGCAUCUGAAGUG---------CAGCUCGGCAGAGCUUUCCUU
.....---.---------......(-(((.........--......(((((...)))))((((((((((((........)).)---------)))))))))..))))...... ( -29.00)
>DroYak_CAF1 159758 111 + 1
GCCAUACGCCAUACUCCGUACGCCAUACUACACAUGGA--UACAUAUUCGCCAAGAGCAGUCGAGCUGCCUGCAACUGAAGUGCAGCAAGUGCAGCGCGGCAGAGCUUUCCUU
((..((((........))))..((((.......)))).--.........))..(((((.((((.((((((((((.(....)))))).....))))).))))...))))).... ( -26.50)
>consensus
ACCAA___C_________UGCAC_A_UAUGUACAUAGAUGUAUAUAUUCGCCAAGAGCAAUUCAGCUGGCUGCAACUGAAGUG_________CAGCUCGGCGGAGCUUUCCUU
..............................................((((((..((((..(((((.((....)).))))).((((.....))))))))))))))......... (-10.32 = -12.52 +   2.20)

alignment

secondary structure

dotplot

Window 2

Location	6,408,796 – 6,408,886
Length	90
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	77.95
Mean single sequence MFE	-33.28
Consensus MFE	-16.32
Energy contribution	-16.00
Covariance contribution	-0.32
Combinations/Pair	1.21
Mean z-score	-2.65
Structure conservation index	0.49
SVM decision value	2.16
SVM RNA-class probability	0.989393
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6408796 90 - 23771897
AAGGAAAGCUCCGCCGAGCUG---------CACUUCAGUUGCAGCCAGCUGAAUUGCUCUUGGCGAAUAUAUACAUCUAUGUACAUA-U-GUGCA---------G---UUGUG
..(((....)))((((((..(---------((.((((((((....)))))))).))).)))))).......((((....(((((...-.-)))))---------.---.)))) ( -32.60)
>DroSec_CAF1 146800 90 - 1
AAGGAAAGCUCCGCCGAGCUG---------CACUUCAGUUGCAGCCAGCUGAAUUGCUCUUGGCGAAUAUAUACAUCUAUGUACAUA-U-GUGCA---------G---UUGAU
..(((....)))((((((..(---------((.((((((((....)))))))).))).))))))..........(((..(((((...-.-)))))---------.---..))) ( -32.20)
>DroSim_CAF1 153052 90 - 1
AAGGAAAGCUCCGCCGAGCUG---------CACUUCAGUUGCAGCCAGCUGAAUUGCUCUUGGCGAAUAUAUACAUCUAUGUACAUA-U-GUGCA---------G---UUGAU
..(((....)))((((((..(---------((.((((((((....)))))))).))).))))))..........(((..(((((...-.-)))))---------.---..))) ( -32.20)
>DroEre_CAF1 151194 89 - 1
AAGGAAAGCUCUGCCGAGCUG---------CACUUCAGAUGCAGGCAGCUCGACUGCACUUGGCGCAUAUGUA--UCUAUGUGUAGC-UGGUGUA---------G---CUGGU
......((((..(((.(((((---------(((...(((((((.((.((.(((......)))))))...))))--)))..)))))))-))))..)---------)---))... ( -35.80)
>DroYak_CAF1 159758 111 - 1
AAGGAAAGCUCUGCCGCGCUGCACUUGCUGCACUUCAGUUGCAGGCAGCUCGACUGCUCUUGGCGAAUAUGUA--UCCAUGUGUAGUAUGGCGUACGGAGUAUGGCGUAUGGC
.......(((..((((..((((((.((.((((......((((.(((((.....)))))....))))...))))--..)).))))))..))))(((((........)))))))) ( -33.60)
>consensus
AAGGAAAGCUCCGCCGAGCUG_________CACUUCAGUUGCAGCCAGCUGAAUUGCUCUUGGCGAAUAUAUACAUCUAUGUACAUA_U_GUGCA_________G___UUGAU
.......((..(((((((............((.((((((((....)))))))).))..))))))).(((((......)))))..........))................... (-16.32 = -16.00 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:31 2006