Locus 535

Sequence ID	X_DroMel_CAF1
Location	1,529,364 – 1,529,466
Length	102
Max. P	0.921543

overview

Window 3

Location	1,529,364 – 1,529,466
Length	102
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	89.76
Mean single sequence MFE	-31.02
Consensus MFE	-25.72
Energy contribution	-26.24
Covariance contribution	0.52
Combinations/Pair	1.08
Mean z-score	-1.56
Structure conservation index	0.83
SVM decision value	0.57
SVM RNA-class probability	0.783971
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1529364 102 + 22224390
UGAGCUCUGCAUCUCCCUUCUCCCAGUGGGGCGAGGGUUUU-----GGUUUGGUUUUAGAUCGCCAUUAGAUCGUUAUUAGAUCGUGAUCGUGAUCGCGAUGCUAAA
..(((..(((.....(((((.(((....))).)))))....-----............((((((.((((((((.......)))).)))).)))))))))..)))... ( -33.50)
>DroSec_CAF1 2351 96 + 1
UGAGCUCUGCAUCUCCCUUCUCCCAGUGGGGCGAGGGUUUU-----GGUUUGGUUUUAGAUCGCCAUUAGAUCGUUAUUAGAUCGU------GAUCGCGAUGCUAAA
.(((((..((....(((((.((((...)))).)))))....-----.))..)))))((((((((.((((((((.......)))).)------))).))))).))).. ( -31.40)
>DroSim_CAF1 1806 102 + 1
UGAGCUCUGCAUCUCCCUUCUCCCAGUGGGGCGAGGGUUUU-----GGUUUGGUUUUAGAUCGCCAUUAGAUCGUUAUUAGAUCGUGAUCGUGAUCGCGAUGCUAAA
..(((..(((.....(((((.(((....))).)))))....-----............((((((.((((((((.......)))).)))).)))))))))..)))... ( -33.50)
>DroEre_CAF1 2433 101 + 1
UGAUUUCUGCACCUCCCUUCUCCCAGUGGGGCGAGGGUUUUGGUUUGGUUUGGUUUUAAAUCGUCAUUAGAUCGAUACUAGAUCGU------GUUCGCGAUGCCAAA
......(((.(((.(((((.((((...)))).)))))....))).)))((((((.....(((((.....((((.......))))..------....))))))))))) ( -27.40)
>DroYak_CAF1 2319 97 + 1
UGAGCUCUGCACCUCCCUUCUCCCAGUGGGGCGAGGGUUUU----CGGUUUGGUUUUAGAUCGUCAUUAGAUCGAUAUUAGAUCGU------GAUCGCGAUUCUAAA
.(((((..((....(((((.((((...)))).)))))....----..))..)))))((((((((.((((((((.......)))).)------))).)))).)))).. ( -29.30)
>consensus
UGAGCUCUGCAUCUCCCUUCUCCCAGUGGGGCGAGGGUUUU_____GGUUUGGUUUUAGAUCGCCAUUAGAUCGUUAUUAGAUCGU______GAUCGCGAUGCUAAA
..(((..(((.....(((((.(((....))).))))).........((((((((....((((.......))))...))))))))............)))..)))... (-25.72 = -26.24 +   0.52)

alignment

secondary structure

dotplot

Window 4

Location	1,529,364 – 1,529,466
Length	102
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	89.76
Mean single sequence MFE	-24.50
Consensus MFE	-21.74
Energy contribution	-21.74
Covariance contribution	0.00
Combinations/Pair	1.10
Mean z-score	-1.61
Structure conservation index	0.89
SVM decision value	1.14
SVM RNA-class probability	0.921543
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1529364 102 - 22224390
UUUAGCAUCGCGAUCACGAUCACGAUCUAAUAACGAUCUAAUGGCGAUCUAAAACCAAACC-----AAAACCCUCGCCCCACUGGGAGAAGGGAGAUGCAGAGCUCA
....(((((..((((.(.((...((((.......))))..)).).))))............-----....(((((.(((....))).).)))).)))))........ ( -27.30)
>DroSec_CAF1 2351 96 - 1
UUUAGCAUCGCGAUC------ACGAUCUAAUAACGAUCUAAUGGCGAUCUAAAACCAAACC-----AAAACCCUCGCCCCACUGGGAGAAGGGAGAUGCAGAGCUCA
(((((.(((((.((.------..((((.......))))..)).))))))))))........-----....(((((.(((....))).).)))).((.((...)))). ( -25.00)
>DroSim_CAF1 1806 102 - 1
UUUAGCAUCGCGAUCACGAUCACGAUCUAAUAACGAUCUAAUGGCGAUCUAAAACCAAACC-----AAAACCCUCGCCCCACUGGGAGAAGGGAGAUGCAGAGCUCA
....(((((..((((.(.((...((((.......))))..)).).))))............-----....(((((.(((....))).).)))).)))))........ ( -27.30)
>DroEre_CAF1 2433 101 - 1
UUUGGCAUCGCGAAC------ACGAUCUAGUAUCGAUCUAAUGACGAUUUAAAACCAAACCAAACCAAAACCCUCGCCCCACUGGGAGAAGGGAGGUGCAGAAAUCA
....(((((......------..((((.......))))................................(((((.(((....))).).)))).)))))........ ( -21.10)
>DroYak_CAF1 2319 97 - 1
UUUAGAAUCGCGAUC------ACGAUCUAAUAUCGAUCUAAUGACGAUCUAAAACCAAACCG----AAAACCCUCGCCCCACUGGGAGAAGGGAGGUGCAGAGCUCA
....((.((((((((------.((((.....)))).((....)).)))).........(((.----....(((((.(((....))).).)))).))))).))..)). ( -21.80)
>consensus
UUUAGCAUCGCGAUC______ACGAUCUAAUAACGAUCUAAUGGCGAUCUAAAACCAAACC_____AAAACCCUCGCCCCACUGGGAGAAGGGAGAUGCAGAGCUCA
....(((((..((((........((((.......)))).......)))).....................(((((.(((....))).).)))).)))))........ (-21.74 = -21.74 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:10 2006