Locus 2326

Sequence ID	3L_DroMel_CAF1
Location	6,528,489 – 6,528,636
Length	147
Max. P	0.999626

overview

Window 0

Location	6,528,489 – 6,528,581
Length	92
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	96.41
Mean single sequence MFE	-23.88
Consensus MFE	-22.08
Energy contribution	-22.32
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-2.47
Structure conservation index	0.92
SVM decision value	3.80
SVM RNA-class probability	0.999626
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6528489 92 + 23771897
CAAACAAAAACAAGGCGGUACUUAUGCAAAUGGAAUUCAUCAUAUCCAAAGCAAACCUCCGCUGGUUGCACAUAAUGCAGCCAGAGGUCAGC
.............((.(((.....(((...((((..........))))..))).))).)).(((((((((.....)))))))))........ ( -23.40)
>DroSec_CAF1 19755 92 + 1
CAAACAAAAACAAGGCGGUACUUAUGCAAAUGGAAUUCAUCAUAUCCAAAGCAAACCUCCGCUGGUUGCACAUAAUGCAGCCAGAGGUCAGC
.............((.(((.....(((...((((..........))))..))).))).)).(((((((((.....)))))))))........ ( -23.40)
>DroSim_CAF1 19971 92 + 1
CAAACAAAAACAAGGCGGUACUUAUGCAAAUGGAAUUCAUCAUAUCCAAAGCAAACCUCCGCUGGUUGCACAUAAUGCAGCCAGAGGUCAGG
...........(((......))).(((...((((..........))))..)))..(((((.(((((((((.....))))))))).))..))) ( -23.90)
>DroEre_CAF1 19904 92 + 1
CAAACAAAAACAAGGCGGUACUUAUGCAAAUGGAAUUCAUCAUAUCCAAAGCAAACCUGCGCUGGCUGCACUUAAUGCAGCCAGAGGUCAGC
.............((((((.....(((...((((..........))))..))).)))..(.(((((((((.....))))))))).))))... ( -25.40)
>DroYak_CAF1 20223 92 + 1
CAAACAAAAACAGCGCGGUACUUAUGCAAAUGGAAUUCAUCAUAUCCAAAGCAAACCUGCGCUGGUUGCCCGUAAUGCAGCCAGAGGUCAGC
...........(((((((......(((...((((..........))))..)))...)))))))((((((.......)))))).......... ( -23.30)
>consensus
CAAACAAAAACAAGGCGGUACUUAUGCAAAUGGAAUUCAUCAUAUCCAAAGCAAACCUCCGCUGGUUGCACAUAAUGCAGCCAGAGGUCAGC
.............((((((.....(((...((((..........))))..))).)))..(.(((((((((.....))))))))).))))... (-22.08 = -22.32 +   0.24)

alignment

secondary structure

dotplot

Window 1

Location	6,528,511 – 6,528,616
Length	105
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	92.29
Mean single sequence MFE	-32.70
Consensus MFE	-25.84
Energy contribution	-27.12
Covariance contribution	1.28
Combinations/Pair	1.07
Mean z-score	-1.79
Structure conservation index	0.79
SVM decision value	0.69
SVM RNA-class probability	0.824384
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6528511 105 + 23771897
UAUGCAAAUGGAAUUCAUCAUAUCCAAAGCAAACCUCCGCUGGUUGCACAUAAUGCAGCCAGAGGUCAGCAGCUUAAAGCCAGGUCUUAUGGUCGU--CGUUUUGGG---
...((...((((..........))))..((..(((((...((((((((.....)))))))))))))..)).))(((((((..(..(....)..)..--.))))))).--- ( -30.80)
>DroSec_CAF1 19777 105 + 1
UAUGCAAAUGGAAUUCAUCAUAUCCAAAGCAAACCUCCGCUGGUUGCACAUAAUGCAGCCAGAGGUCAGCAGCUUAAAGCCAGGGCUUAUAGUCGU--CGUUUUGGG---
.......................(((((((......((.(((((((((.....))))))))).))...((.(((..((((....))))..))).))--.))))))).--- ( -32.60)
>DroSim_CAF1 19993 105 + 1
UAUGCAAAUGGAAUUCAUCAUAUCCAAAGCAAACCUCCGCUGGUUGCACAUAAUGCAGCCAGAGGUCAGGAGCUUAAAGCCAGGGCUUAUAGUCGU--CGUUUUGGG---
.......................(((((((...(((((.(((((((((.....))))))))).))..))).(((..((((....))))..)))...--.))))))).--- ( -34.20)
>DroEre_CAF1 19926 107 + 1
UAUGCAAAUGGAAUUCAUCAUAUCCAAAGCAAACCUGCGCUGGCUGCACUUAAUGCAGCCAGAGGUCAGCAGCUUAAAGCCAGGGCUUAUAGACGUGUGGUGUUUGU---
...(((((.......((((((((.....((..((((...(((((((((.....)))))))))))))..)).(((..((((....))))..)).))))))))))))))--- ( -34.31)
>DroYak_CAF1 20245 110 + 1
UAUGCAAAUGGAAUUCAUCAUAUCCAAAGCAAACCUGCGCUGGUUGCCCGUAAUGCAGCCAGAGGUCAGCAGCUUAAAGCCAGGGCUUAUAGUCGUGUGGUGUUUGGUUC
......(((.(((..((((((((.....((..((((...((((((((.......))))))))))))..)).(((..((((....))))..))).))))))))))).))). ( -31.60)
>consensus
UAUGCAAAUGGAAUUCAUCAUAUCCAAAGCAAACCUCCGCUGGUUGCACAUAAUGCAGCCAGAGGUCAGCAGCUUAAAGCCAGGGCUUAUAGUCGU__CGUUUUGGG___
.......................(((((((..((((...(((((((((.....)))))))))))))..((.(((..((((....))))..))).))...))))))).... (-25.84 = -27.12 +   1.28)

alignment

secondary structure

dotplot

Window 2

Location	6,528,541 – 6,528,636
Length	95
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	86.99
Mean single sequence MFE	-31.28
Consensus MFE	-21.26
Energy contribution	-22.14
Covariance contribution	0.88
Combinations/Pair	1.09
Mean z-score	-1.93
Structure conservation index	0.68
SVM decision value	0.12
SVM RNA-class probability	0.594110
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6528541 95 + 23771897
AAACCUCCGCUGGUUGCACAUAAUGCAGCCAGAGGUCAGCAGCUUAAAGCCAGGUCUUAUGGUCGU--CGUUUUGGG--------UAUAUGGUGACUU--UUACGAA
.......(((((((((((.....)))))))))((((((.(((((((((((..(..(....)..)..--.))))))))--------)...)).))))))--...)).. ( -32.70)
>DroSec_CAF1 19807 95 + 1
AAACCUCCGCUGGUUGCACAUAAUGCAGCCAGAGGUCAGCAGCUUAAAGCCAGGGCUUAUAGUCGU--CGUUUUGGG--------UAUAUGGUGACUU--UUACGAA
.......(((((((((((.....)))))))))((((((.(((((((((((.(.(((.....))).)--.))))))))--------)...)).))))))--...)).. ( -33.40)
>DroSim_CAF1 20023 95 + 1
AAACCUCCGCUGGUUGCACAUAAUGCAGCCAGAGGUCAGGAGCUUAAAGCCAGGGCUUAUAGUCGU--CGUUUUGGG--------UAUAUGGUGACUU--UUACGAA
...(((((.(((((((((.....))))))))).))..))).(((((((((.(.(((.....))).)--.))))))))--------)....(....)..--....... ( -32.30)
>DroEre_CAF1 19956 98 + 1
AAACCUGCGCUGGCUGCACUUAAUGCAGCCAGAGGUCAGCAGCUUAAAGCCAGGGCUUAUAGACGUGUGGUGUUUGU--------UAUAUGGUAACUU-UUUACGAA
....((((.(((((((((.....)))))))))......))))....((((....)))).....(((((((......)--------))))))((((...-.))))... ( -29.30)
>DroYak_CAF1 20275 107 + 1
AAACCUGCGCUGGUUGCCCGUAAUGCAGCCAGAGGUCAGCAGCUUAAAGCCAGGGCUUAUAGUCGUGUGGUGUUUGGUUCAUACAUAUAUGGUACAUUUUUAACGAA
....((((.((((((((.......))))))))......))))......((((.(((.....)))((((((........)))))).....)))).............. ( -28.70)
>consensus
AAACCUCCGCUGGUUGCACAUAAUGCAGCCAGAGGUCAGCAGCUUAAAGCCAGGGCUUAUAGUCGU__CGUUUUGGG________UAUAUGGUGACUU__UUACGAA
..(((.((.(((((((((.....))))))))).))...((.(((..((((....))))..))).))........................))).............. (-21.26 = -22.14 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:37 2006