Locus 6477

Sequence ID	2R_DroMel_CAF1
Location	20,230,173 – 20,230,289
Length	116
Max. P	0.966394

overview

Window 6

Location	20,230,173 – 20,230,289
Length	116
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	96.72
Mean single sequence MFE	-35.98
Consensus MFE	-31.88
Energy contribution	-32.32
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.78
Structure conservation index	0.89
SVM decision value	1.59
SVM RNA-class probability	0.966394
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20230173 116 + 20766785
GCAGGAUGGCAAACUGCAAUGGGAAAUUACCACAAUUGAUGCAUAUAGACAUCUGGGCAUUGAGCUGGCGAUAUUCCGCAGAACUGGCAUCGUUUGCCUGCAGGCGGAAAAUUUAU
....((((.((..((((...((((.((..(((...(..((((...(((....))).))))..)..)))..)).))))))))...)).)))).((((((....))))))........ ( -36.50)
>DroSec_CAF1 23054 116 + 1
GCAGGAUGGCAAACUGCAAUGGGAAAUUACCACAAUUGAUGCAUAUAGACAUCUGGGCAUGGAGCUGGCGAUAUUCCGCAGAACUGGCAUCGUUUGCCUGCAGGCGGAAAAUUUAU
....((((.((..((((...((((.((..(((...((.((((...(((....))).)))).))..)))..)).))))))))...)).)))).((((((....))))))........ ( -35.30)
>DroSim_CAF1 21884 116 + 1
GCAGGAUGGCAAACUGCAAUGGGAAAUUACCACAAUUGAUGCAUAUAGACAUCUGGGCAUGGAGCUGGCGAUAUUCCGCAGAACUGGCAUCGUUUGCCUGCAGGCGGAAAAUUUAU
....((((.((..((((...((((.((..(((...((.((((...(((....))).)))).))..)))..)).))))))))...)).)))).((((((....))))))........ ( -35.30)
>DroEre_CAF1 24085 116 + 1
GCAGGCUGGCAAACAGCAAUGGGAAAUUACCACAAUUGAUGCAUAUAGACAUCUGGGCAUUGAGCUGGCGAUACUCCGCAGAACUGGCAUCGUUUGCCUGCUGGCGGAAAAUUUAU
((.(((.((((((((((..(((.......)))...(..((((...(((....))).))))..)))).(((......)))............))))))).))).))........... ( -36.90)
>DroYak_CAF1 22747 116 + 1
GCAGGAUGGCAAACAGCAAUGGGAAAUUACCACAAUUGAUGCAUAUAGACAUCUGGGCAUUGAGCUGGCGAUGUUCCACAGAACUGGCAUCGUUUGCCUGCUGGCGAAAAAUUUAU
.(((.(.(((((.((((..(((.......)))...(..((((...(((....))).))))..)))))((((((..(((......))))))))))))))).)))............. ( -35.90)
>consensus
GCAGGAUGGCAAACUGCAAUGGGAAAUUACCACAAUUGAUGCAUAUAGACAUCUGGGCAUUGAGCUGGCGAUAUUCCGCAGAACUGGCAUCGUUUGCCUGCAGGCGGAAAAUUUAU
((.....((((((((((..(((((.((..(((...(..((((...(((....))).))))..)..)))..)).)))))((....)))))..))))))).....))........... (-31.88 = -32.32 +   0.44)

alignment

secondary structure

dotplot

Window 7

Location	20,230,173 – 20,230,289
Length	116
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	96.72
Mean single sequence MFE	-30.04
Consensus MFE	-27.76
Energy contribution	-27.12
Covariance contribution	-0.64
Combinations/Pair	1.07
Mean z-score	-1.23
Structure conservation index	0.92
SVM decision value	0.34
SVM RNA-class probability	0.696396
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20230173 116 - 20766785
AUAAAUUUUCCGCCUGCAGGCAAACGAUGCCAGUUCUGCGGAAUAUCGCCAGCUCAAUGCCCAGAUGUCUAUAUGCAUCAAUUGUGGUAAUUUCCCAUUGCAGUUUGCCAUCCUGC
.......((((((..((.((((.....)))).))...))))))....((.(((((((((....(((((......)))))......((......))))))).)))).))........ ( -29.60)
>DroSec_CAF1 23054 116 - 1
AUAAAUUUUCCGCCUGCAGGCAAACGAUGCCAGUUCUGCGGAAUAUCGCCAGCUCCAUGCCCAGAUGUCUAUAUGCAUCAAUUGUGGUAAUUUCCCAUUGCAGUUUGCCAUCCUGC
...........(((....)))....((((.(((..((((((((.((..(((((.....))...(((((......))))).....)))..))))))....)))).))).)))).... ( -28.80)
>DroSim_CAF1 21884 116 - 1
AUAAAUUUUCCGCCUGCAGGCAAACGAUGCCAGUUCUGCGGAAUAUCGCCAGCUCCAUGCCCAGAUGUCUAUAUGCAUCAAUUGUGGUAAUUUCCCAUUGCAGUUUGCCAUCCUGC
...........(((....)))....((((.(((..((((((((.((..(((((.....))...(((((......))))).....)))..))))))....)))).))).)))).... ( -28.80)
>DroEre_CAF1 24085 116 - 1
AUAAAUUUUCCGCCAGCAGGCAAACGAUGCCAGUUCUGCGGAGUAUCGCCAGCUCAAUGCCCAGAUGUCUAUAUGCAUCAAUUGUGGUAAUUUCCCAUUGCUGUUUGCCAGCCUGC
...............((((((...(((...((((..((.((((.((..(((((.....))...(((((......))))).....)))..))))))))..)))).)))...)))))) ( -32.30)
>DroYak_CAF1 22747 116 - 1
AUAAAUUUUUCGCCAGCAGGCAAACGAUGCCAGUUCUGUGGAACAUCGCCAGCUCAAUGCCCAGAUGUCUAUAUGCAUCAAUUGUGGUAAUUUCCCAUUGCUGUUUGCCAUCCUGC
.............(((..((((((((((((......((((((.((((....((.....))...)))))))))).)))))......((((((.....)))))))))))))...))). ( -30.70)
>consensus
AUAAAUUUUCCGCCUGCAGGCAAACGAUGCCAGUUCUGCGGAAUAUCGCCAGCUCAAUGCCCAGAUGUCUAUAUGCAUCAAUUGUGGUAAUUUCCCAUUGCAGUUUGCCAUCCUGC
...........(((((((((((.....)))).....((.((((.((..(((((.....))...(((((......))))).....)))..)))))))).)))))...))........ (-27.76 = -27.12 +  -0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:55 2006