Locus 6466

Sequence ID	X_DroMel_CAF1
Location	16,222,076 – 16,222,178
Length	102
Max. P	0.949957

overview

Window 7

Location	16,222,076 – 16,222,178
Length	102
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	76.96
Mean single sequence MFE	-35.52
Consensus MFE	-23.37
Energy contribution	-23.99
Covariance contribution	0.62
Combinations/Pair	1.28
Mean z-score	-1.96
Structure conservation index	0.66
SVM decision value	1.40
SVM RNA-class probability	0.949957
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16222076 102 + 22224390
AGGCGUGAACAUUUUUGCUCUCGAGGAUCAGCGCACUUGGUUGGGUGUGCCAGCA---GCUGUUCCUCGACUCCGACUCCUUCACGCCGAGUGUAAGCCCUCGAA
.((((((((.....(((...(((((((.((((.......(((((.....))))).---)))).)))))))...)))....))))))))(((.(....).)))... ( -39.70)
>DroSec_CAF1 1164 101 + 1
AGGCGUGAACAUUUUUGCUCUCGAGGAUCAG--CACUUGGUUGGGUGUGCCAGCAGCAGCUGUA-CUCGACU-CGACUCCUUCACGACGAGUGUAAGCCAUCGAA
.((((....)....((((...((((...(((--(.....(((((.....)))))....))))..-))))(((-((.(........).))))))))))))...... ( -29.60)
>DroSim_CAF1 1161 103 + 1
AGGCGUGAACAUUUUUGCUCUCGAGGAUCAG--CACUUGGUUGGGUGUGCCAGCAGCAGCUGUUCCUCGACUCCGACUCCUUCACGCCGAGUGUAAGCCCUCGAA
.((((((((.....(((...(((((((.(((--(.....(((((.....)))))....)))).)))))))...)))....))))))))(((.(....).)))... ( -41.00)
>DroEre_CAF1 1157 92 + 1
AGGCGUGAAAGU--UUGCUCUUGAGGAUCAG--CACUUGGUUGGGUGUGCCA------GCUGUUCCUCGACUCCGAC---UUCACGCCGAGUAUAAGCCCUCGAA
.((((((((.((--(.(...(((((((.(((--(...((((.......))))------)))).)))))))..).)))---))))))))(((........)))... ( -36.80)
>DroYak_CAF1 1146 92 + 1
AGGCGUGAAAGU--UUGCUCUUGAGGAUCAG--CACUUGGUUGGGUGUGCCA------GCUGUUCCUCGACUCCGAU---UUCACGCCGAGUGUAAGCCCUCGAA
.(((((((((..--(((...(((((((.(((--(...((((.......))))------)))).)))))))...))))---))))))))(((.(....).)))... ( -36.90)
>DroAna_CAF1 1104 86 + 1
GAGCGUGCACAUC---AUUCUUGAGGACUAG--CA----GUGGGGUGUGUCU------GCUAGUCAUUGAUUUUGAU---UUCGCACG-GGACCAUGGCCCCUAU
....((((..(((---(...(..(.((((((--((----(..........))------))))))).)..)...))))---...))))(-((.(....).)))... ( -29.10)
>consensus
AGGCGUGAACAUU_UUGCUCUCGAGGAUCAG__CACUUGGUUGGGUGUGCCA______GCUGUUCCUCGACUCCGAC___UUCACGCCGAGUGUAAGCCCUCGAA
.((((((((.....(((...(((((((.(((......((((.......)))).......))).)))))))...)))....))))))))(((.(....).)))... (-23.37 = -23.99 +   0.62)

alignment

secondary structure

dotplot

Window 8

Location	16,222,076 – 16,222,178
Length	102
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	76.96
Mean single sequence MFE	-33.90
Consensus MFE	-16.44
Energy contribution	-17.91
Covariance contribution	1.47
Combinations/Pair	1.14
Mean z-score	-2.22
Structure conservation index	0.48
SVM decision value	0.85
SVM RNA-class probability	0.866840
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16222076 102 - 22224390
UUCGAGGGCUUACACUCGGCGUGAAGGAGUCGGAGUCGAGGAACAGC---UGCUGGCACACCCAACCAAGUGCGCUGAUCCUCGAGAGCAAAAAUGUUCACGCCU
...(((........)))((((((((.(..(..(..(((((((.((((---((((((.........)).)))).)))).)))))))...)..)..).)))))))). ( -38.30)
>DroSec_CAF1 1164 101 - 1
UUCGAUGGCUUACACUCGUCGUGAAGGAGUCG-AGUCGAG-UACAGCUGCUGCUGGCACACCCAACCAAGUG--CUGAUCCUCGAGAGCAAAAAUGUUCACGCCU
((((((..(((.(((.....))))))..))))-))(((((-..((((....))))((((..........)))--).....)))))(((((....)))))...... ( -30.30)
>DroSim_CAF1 1161 103 - 1
UUCGAGGGCUUACACUCGGCGUGAAGGAGUCGGAGUCGAGGAACAGCUGCUGCUGGCACACCCAACCAAGUG--CUGAUCCUCGAGAGCAAAAAUGUUCACGCCU
...(((........)))((((((((.(..(..(..(((((((.((((.(((..(((.....)))....))))--))).)))))))...)..)..).)))))))). ( -38.80)
>DroEre_CAF1 1157 92 - 1
UUCGAGGGCUUAUACUCGGCGUGAA---GUCGGAGUCGAGGAACAGC------UGGCACACCCAACCAAGUG--CUGAUCCUCAAGAGCAA--ACUUUCACGCCU
...(((........)))((((((((---((..(....(((((.((((------(((.........)))...)--))).))))).....)..--)).)))))))). ( -32.70)
>DroYak_CAF1 1146 92 - 1
UUCGAGGGCUUACACUCGGCGUGAA---AUCGGAGUCGAGGAACAGC------UGGCACACCCAACCAAGUG--CUGAUCCUCAAGAGCAA--ACUUUCACGCCU
...(((........)))((((((((---(...(....(((((.((((------(((.........)))...)--))).))))).....)..--..))))))))). ( -31.40)
>DroAna_CAF1 1104 86 - 1
AUAGGGGCCAUGGUCC-CGUGCGAA---AUCAAAAUCAAUGACUAGC------AGACACACCCCAC----UG--CUAGUCCUCAAGAAU---GAUGUGCACGCUC
...(((((....))))-)(((((..---((((........(((((((------((..........)----))--))))))........)---))).))))).... ( -31.89)
>consensus
UUCGAGGGCUUACACUCGGCGUGAA___GUCGGAGUCGAGGAACAGC______UGGCACACCCAACCAAGUG__CUGAUCCUCAAGAGCAA_AAUGUUCACGCCU
...(((........)))((((((((............(((((.(((.......(((.........)))......))).))))).............)))))))). (-16.44 = -17.91 +   1.47)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:28 2006