Locus 5878

Sequence ID	X_DroMel_CAF1
Location	15,145,586 – 15,145,729
Length	143
Max. P	0.995350

overview

Window 4

Location	15,145,586 – 15,145,689
Length	103
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	73.84
Mean single sequence MFE	-36.65
Consensus MFE	-22.42
Energy contribution	-23.43
Covariance contribution	1.00
Combinations/Pair	1.17
Mean z-score	-2.37
Structure conservation index	0.61
SVM decision value	2.57
SVM RNA-class probability	0.995350
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15145586 103 - 22224390
AAAAAUA--------UAUUAGCAGCGCCCACGGCCGCC-UAAUCAAAUGGUUUUCGGUGGUU-UGGGGUGCUUAGUUGGU------GGCACAAGUGAAGCAAGUGCCGCA-AGUGCCACA
.......--------...(((((((((((..(((((((-.((((....))))...)))))))-..)))))))..))))((------(((((..(((..((....))))).-.))))))). ( -42.50)
>DroSim_CAF1 48037 98 - 1
AAAAAUA--------UAUUAGCAGCGCCCACGGCCUCC-UAAUCAAGUGGUUUUCGGUGGUU-UGGGGUGCUUAGUUGGU------GCCACAAGUGAAGCAAGUGCCGCA-AGUG-----
.......--------((((((((((((((..((((.((-.((((....))))...)).))))-..)))))))..))))))------).(((..(((..((....))))).-.)))----- ( -29.20)
>DroEre_CAF1 63298 86 - 1
AAAAAUA--------UAUUUGAAGCGCCCACGGCCGCCUUAAUCAAGUGAUUUUCGGUGGUG-UGGGGUGCUCAGUUG------------------------GUGCCACAA-GUGCCGCA
.......--------...((((.((((((...((((((..((((....))))...)))))).-..))))))))))..(------------------------(..(.....-)..))... ( -32.60)
>DroYak_CAF1 64277 118 - 1
AAAAAUACAUAUAUGUAUUAGCAGCGCCCACGGCCUCC-CAGUCAAGUGGUUUUCGGUGGUUUUGUGGUGCUUUGUUGUUGGUGGUGCGACAAGAGCCGCAAGUGCCACA-AGUGCCGCA
...((((((....)))))).((.(((((((((((....-..)))..))))......(((((((((((((..((((((((.......)))))))).)))))))).))))).-.)))).)). ( -42.30)
>consensus
AAAAAUA________UAUUAGCAGCGCCCACGGCCGCC_UAAUCAAGUGGUUUUCGGUGGUU_UGGGGUGCUUAGUUGGU______GCCACAAGUGAAGCAAGUGCCACA_AGUGCCGCA
......................(((((((..(((((((..((((....))))...)))))))...)))))))..............................(((.(((...))).))). (-22.42 = -23.43 +   1.00)

alignment

secondary structure

dotplot

Window 5

Location	15,145,619 – 15,145,729
Length	110
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.94
Mean single sequence MFE	-36.00
Consensus MFE	-28.92
Energy contribution	-29.79
Covariance contribution	0.87
Combinations/Pair	1.10
Mean z-score	-2.63
Structure conservation index	0.80
SVM decision value	1.88
SVM RNA-class probability	0.981310
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15145619 110 - 22224390
GUCGUCUCGUUGACGAAAAUAAAUCAAACGAAAUGUUGAUAAAAAUA--------UAUUAGCAGCGCCCACGGCCGCC-UAAUCAAAUGGUUUUCGGUGGUU-UGGGGUGCUUAGUUGGU
.(((((.....)))))......(((((......((((((((......--------))))))))((((((..(((((((-.((((....))))...)))))))-..))))))....))))) ( -37.40)
>DroSim_CAF1 48065 110 - 1
GUCGUCUCGUUGACGAAAAUAAACCAAACGAAAUGUUGAUAAAAAUA--------UAUUAGCAGCGCCCACGGCCUCC-UAAUCAAGUGGUUUUCGGUGGUU-UGGGGUGCUUAGUUGGU
.(((((.....)))))......(((((......((((((((......--------))))))))((((((..((((.((-.((((....))))...)).))))-..))))))....))))) ( -36.40)
>DroEre_CAF1 63315 109 - 1
GUCGUCUCGGUGACGAAAAUAAAUCAAGCAAAAUGCUGAUAAAAAUA--------UAUUUGAAGCGCCCACGGCCGCCUUAAUCAAGUGAUUUUCGGUGGUG-UGGGGUGCUCAGUUG--
.(((((.....)))))......((((.((.....)))))).......--------...((((.((((((...((((((..((((....))))...)))))).-..))))))))))...-- ( -37.60)
>DroYak_CAF1 64316 119 - 1
GUCGUCUCGGUGACGAAAAUAAAUCAUGAAAAAUGCUGAUAAAAAUACAUAUAUGUAUUAGCAGCGCCCACGGCCUCC-CAGUCAAGUGGUUUUCGGUGGUUUUGUGGUGCUUUGUUGUU
.(((((.....))))).((((((..........((((((((...(((....))).))))))))(((((((..(((.((-.(..(....)..)...)).)))..)).)))))))))))... ( -32.60)
>consensus
GUCGUCUCGGUGACGAAAAUAAAUCAAACAAAAUGCUGAUAAAAAUA________UAUUAGCAGCGCCCACGGCCGCC_UAAUCAAGUGGUUUUCGGUGGUU_UGGGGUGCUUAGUUGGU
.(((((.....))))).................((((((((..............))))))))((((((..(((((((..((((....))))...)))))))...))))))......... (-28.92 = -29.79 +   0.87)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:40 2006