Locus 5748

Sequence ID	3L_DroMel_CAF1
Location	15,621,551 – 15,621,737
Length	186
Max. P	0.804904

overview

Window 4

Location	15,621,551 – 15,621,666
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.94
Mean single sequence MFE	-24.27
Consensus MFE	-20.50
Energy contribution	-20.34
Covariance contribution	-0.16
Combinations/Pair	1.11
Mean z-score	-1.50
Structure conservation index	0.84
SVM decision value	0.63
SVM RNA-class probability	0.804904
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15621551 115 + 23771897
UUUAUGGCAUCAAGAAAAUCAAAAACAUUUCGUUUGAAAAAUUAUGUUUUGGA-----GUAAGAAGGAGUGGAGUGAGAAGUUUUGAGGAACUGCCAGACGAGAUGACGAGGAUGCAUCA
......(((((..(.....).....(((((((((((........(.((((...-----...)))).)............(((((....)))))..))))))))))).....))))).... ( -22.50)
>DroSec_CAF1 44350 115 + 1
UUUAUGGCAUCAAGAAAAUCAAAAACAUUUCGUUUGAAAAAUUAUGCUUUGGA-----AAAAGAUGGAGGGGAGUGAGGAGUUUUGAAGAACUGCCAGACGAGAUGACGAGGAUGCAUCA
......(((((..(.....).....(((((((((((.....((((.((((...-----.))))))))..........(.(((((....))))).)))))))))))).....))))).... ( -27.20)
>DroSim_CAF1 44921 115 + 1
UUUAUGGCAUCAAGAAAAUCAAAAACAUUUCGUUUGAAAAAUUAUGCUUUGGA-----AAAAGAUGGAGGGGAGUGAGAAGUUUUGAAGAACUGCCAGACGAGAUGACGAGGAUGCAUCA
......(((((..(.....).....(((((((((((.....((((.((((...-----.))))))))............(((((....)))))..))))))))))).....))))).... ( -25.70)
>DroEre_CAF1 45007 115 + 1
UUUAUGGCAUCAAGAAAAUCAAAAACAUUUCGUUUGAAAAAUUAUGUUUCGGG-----AUGAAAAGGAGGGCAGGGAGAGGUUUUGAAGAACUGCCAGACGAUAUGACGAGGAUGCAUCA
......(((((..(.....).....(((.((((((((((.......))))...-----...........(((((.................))))))))))).))).....))))).... ( -22.53)
>DroYak_CAF1 47558 119 + 1
UUUAUGGCAUCAAGAAAAUCAAAAACAUUUCGU-UGAAAAAUUAUGUUUUGGAAAGCGAAGGAGAGGAGGGGAGGGAGGAGUUUUGAAGAACUGCCAGACGAGAUGACGAGGAUGCAUCA
......(((((..(.....).....((((((((-(.........(.(((((.....))))).)..............(((((((....))))).)).))))))))).....))))).... ( -23.40)
>consensus
UUUAUGGCAUCAAGAAAAUCAAAAACAUUUCGUUUGAAAAAUUAUGUUUUGGA_____AAAAGAAGGAGGGGAGUGAGAAGUUUUGAAGAACUGCCAGACGAGAUGACGAGGAUGCAUCA
......(((((..(.....).....(((((((((((..........((((...............))))........(.(((((....))))).)))))))))))).....))))).... (-20.50 = -20.34 +  -0.16)

alignment

secondary structure

dotplot

Window 5

Location	15,621,626 – 15,621,737
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.24
Mean single sequence MFE	-31.96
Consensus MFE	-30.68
Energy contribution	-30.72
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.16
Structure conservation index	0.96
SVM decision value	0.54
SVM RNA-class probability	0.776234
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15621626 111 - 23771897
GUCCAGACCAGCAUCGCGAUGAGUUGAGCCAGGCACGCACA---------UCGUGCACAUCGUCAUGCUUGUCUUACACUUGAUGCAUCCUCGUCAUCUCGUCUGGCAGUUCCUCAAAAC
(.((((((.(((((.((((((.(.....)...(((((....---------.))))).)))))).)))))...........(((((......)))))....)))))))............. ( -31.30)
>DroSec_CAF1 44425 111 - 1
GUCCAGACCAGCAUCGCGAUGAGUUGAGCCAGGCACGCACA---------UCGUGCACAUCGUCAUGCUUGUCUUACACUUGAUGCAUCCUCGUCAUCUCGUCUGGCAGUUCUUCAAAAC
(.((((((.(((((.((((((.(.....)...(((((....---------.))))).)))))).)))))...........(((((......)))))....)))))))............. ( -31.30)
>DroSim_CAF1 44996 111 - 1
GUCCAGACCAGCAUCGCGAUGAGUUGAGCCAGGCACGCACA---------UCGUGCACAUCGUCAUGCUUGUCUUGCACUUGAUGCAUCCUCGUCAUCUCGUCUGGCAGUUCUUCAAAAC
(.((((((.(((((.((((((.(.....)...(((((....---------.))))).)))))).)))))...........(((((......)))))....)))))))............. ( -31.30)
>DroEre_CAF1 45082 120 - 1
CUCCAGACCAGCAUCGCGAUGAGUUGAGCCAGGCACGCACAUCGUCCACAUCGUGCACAUCGUCAUGCUUGUCUUACACUUGAUGCAUCCUCGUCAUAUCGUCUGGCAGUUCUUCAAAAC
((((((((.(((((.((((((.(((......)))..((((............)))).)))))).)))))...........(((((......)))))....)))))).))........... ( -31.80)
>DroYak_CAF1 47637 111 - 1
GUCCAGACCAGCAUCGCGAUGAGCUGAGCCCGGCACGCACA---------UCGGGCACAUCGUCAUGCUUGUCUUGCACUUGAUGCAUCCUCGUCAUCUCGUCUGGCAGUUCUUCAAAAC
(.((((((..((...))((((((.((.((((((........---------)))))).(((((...(((.......)))..)))))))..)))))).....)))))))............. ( -34.10)
>consensus
GUCCAGACCAGCAUCGCGAUGAGUUGAGCCAGGCACGCACA_________UCGUGCACAUCGUCAUGCUUGUCUUACACUUGAUGCAUCCUCGUCAUCUCGUCUGGCAGUUCUUCAAAAC
..((((((.(((((.((((((.(((......)))..((((............)))).)))))).)))))...........(((((......)))))....)))))).............. (-30.68 = -30.72 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:39 2006