Locus 2472

Sequence ID	3R_DroMel_CAF1
Location	6,804,908 – 6,805,056
Length	148
Max. P	0.988465

overview

Window 0

Location	6,804,908 – 6,805,027
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	89.05
Mean single sequence MFE	-35.18
Consensus MFE	-29.33
Energy contribution	-29.83
Covariance contribution	0.51
Combinations/Pair	1.23
Mean z-score	-2.20
Structure conservation index	0.83
SVM decision value	0.68
SVM RNA-class probability	0.820722
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6804908 119 + 27905053
AGGCCCUUACUGGGCUUGCAAAACUUUUGCGACGCGUAUGAAAAUGAUGCCAGCACACGCAUGAAUGUCUGUGGGCAAGCACAUCAUUUUUGCCUUUGCUGUCGUCUUUUGAUAUUAUU-
((((((.....))))))((((.....)))).....((((.((((.((((.(((((...(((.(((((..((((......)))).))))).)))...))))).)))))))).))))....- ( -38.10)
>DroSec_CAF1 63202 119 + 1
AGGUCCUUACUGGGCUUGCAAAACUUGUGCGACGCGUAUGAAAAUGAUGCCAGCACACGCAUAAAUGUCUGUGGGCAAGCACAUCAUUUUUGCCUUUGCUGUCGUCUUUUGAUAUUAUU-
((((((.....))))))(((.......))).....((((.((((.((((.(((((...(((.(((((..((((......)))).))))).)))...))))).)))))))).))))....- ( -34.00)
>DroSim_CAF1 68745 119 + 1
AGGCCCUUACUGGGCUUGCAAAACUUUUGCGUCGCGUAUGAAAAUGAUGCCAGCACACGCAUGAAUGUCUGUGGGCAAGCACAUCAUUUUUGCCUUUGCUGUCGUCUUUUGAUAUUAUU-
((((((.....))))))((((.....)))).....((((.((((.((((.(((((...(((.(((((..((((......)))).))))).)))...))))).)))))))).))))....- ( -38.10)
>DroEre_CAF1 48924 119 + 1
AGGCCUUUGCCGGGCUUGCAAAACUUUUGCGACGCAUAUGAAAAUGAUGCCAGCACACGCAUGAAUGUCUGUGGACAAGCACAUCAUUUUUGCCUUUGCUGUCGUCUUUUGAUAUUAUU-
.(((....)))..((((((((.....)))))).))((((.((((.((((.(((((...(((.(((((..((((......)))).))))).)))...))))).)))))))).))))....- ( -36.70)
>DroYak_CAF1 61755 119 + 1
AGGCCUUUGCCGGGCUUGCAAAACUUUUGCGACGCAUAUGAAAAUGAUGCCAGCACACGCAUGAAUGUCUGUGGACAAGCACAUCAUUUUUGCCAUUCCUGCCGUCUUUUGAUAUUAUU-
.(((....)))..((((((((.....)))))).))((((.((((.((((.(((.....(((.(((((..((((......)))).))))).))).....))).)))))))).))))....- ( -31.40)
>DroAna_CAF1 20996 111 + 1
AGGCC-UGGCUUGGCUUGCAAAACUUUUGCGACGCAUAUGAAAACGAUGCCCCUGCACGCAUGUGUGUGU-------AGCACAUCAUU-UUGCCUUUGCCUCUGUUUUUUGAUAUUAUUU
((((.-.(((...((((((((.....)))))).)).....((((.((((...((((((((....))))))-------))..)))).))-)))))...))))................... ( -32.80)
>consensus
AGGCCCUUACUGGGCUUGCAAAACUUUUGCGACGCAUAUGAAAAUGAUGCCAGCACACGCAUGAAUGUCUGUGGGCAAGCACAUCAUUUUUGCCUUUGCUGUCGUCUUUUGAUAUUAUU_
((((((.....))))))((((.....)))).....((((.((((.((((.(((((...(((.(((((..((((......)))).))))).)))...))))).)))))))).))))..... (-29.33 = -29.83 +   0.51)

alignment

secondary structure

dotplot

Window 1

Location	6,804,948 – 6,805,056
Length	108
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	94.90
Mean single sequence MFE	-22.73
Consensus MFE	-21.42
Energy contribution	-21.46
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.63
Structure conservation index	0.94
SVM decision value	2.12
SVM RNA-class probability	0.988465
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6804948 108 + 27905053
AAAAUGAUGCCAGCACACGCAUGAAUGUCUGUGGGCAAGCACAUCAUUUUUGCCUUUGCUGUCGUCUUUUGAUAUUAUUCAUACCCUAAAAGAAAGUAUUUUCAUAUU
.....((((.(((((...(((.(((((..((((......)))).))))).)))...))))).))))....((((((.(((...........)))))))))........ ( -22.90)
>DroSec_CAF1 63242 107 + 1
AAAAUGAUGCCAGCACACGCAUAAAUGUCUGUGGGCAAGCACAUCAUUUUUGCCUUUGCUGUCGUCUUUUGAUAUUAUUCAUACCCUAAAA-AAAGUAUUUUCAUAUU
.....((((.(((((...(((.(((((..((((......)))).))))).)))...))))).))))...(((......)))..........-................ ( -22.40)
>DroSim_CAF1 68785 107 + 1
AAAAUGAUGCCAGCACACGCAUGAAUGUCUGUGGGCAAGCACAUCAUUUUUGCCUUUGCUGUCGUCUUUUGAUAUUAUUCAUACACUAAAA-AAAGUAUUUUCAUAUU
.....((((.(((((...(((.(((((..((((......)))).))))).)))...))))).))))...(((......)))..........-................ ( -22.60)
>DroEre_CAF1 48964 108 + 1
AAAAUGAUGCCAGCACACGCAUGAAUGUCUGUGGACAAGCACAUCAUUUUUGCCUUUGCUGUCGUCUUUUGAUAUUAUUCAUACCCUAAAAAGAGGGAUUUUCAUAUU
.....((((.(((((...(((.(((((..((((......)))).))))).)))...))))).))))...(((......)))..((((......))))........... ( -28.10)
>DroYak_CAF1 61795 107 + 1
AAAAUGAUGCCAGCACACGCAUGAAUGUCUGUGGACAAGCACAUCAUUUUUGCCAUUCCUGCCGUCUUUUGAUAUUAUUCAUACCCUAA-AAGAAGAAUUUUCAUAUU
.....((((.(((.....(((.(((((..((((......)))).))))).))).....))).))))...(((....((((.........-.....))))..))).... ( -17.64)
>consensus
AAAAUGAUGCCAGCACACGCAUGAAUGUCUGUGGGCAAGCACAUCAUUUUUGCCUUUGCUGUCGUCUUUUGAUAUUAUUCAUACCCUAAAA_AAAGUAUUUUCAUAUU
.....((((.(((((...(((.(((((..((((......)))).))))).)))...))))).))))...(((......)))........................... (-21.42 = -21.46 +   0.04)

alignment

secondary structure

dotplot

Window 2

Location	6,804,948 – 6,805,056
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	94.90
Mean single sequence MFE	-23.60
Consensus MFE	-19.70
Energy contribution	-20.30
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.32
Structure conservation index	0.83
SVM decision value	-0.02
SVM RNA-class probability	0.522858
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6804948 108 - 27905053
AAUAUGAAAAUACUUUCUUUUAGGGUAUGAAUAAUAUCAAAAGACGACAGCAAAGGCAAAAAUGAUGUGCUUGCCCACAGACAUUCAUGCGUGUGCUGGCAUCAUUUU
...((((........(((((...(((((.....))))).)))))...(((((.(.(((..((((.((((......))))..))))..))).).)))))...))))... ( -24.70)
>DroSec_CAF1 63242 107 - 1
AAUAUGAAAAUACUUU-UUUUAGGGUAUGAAUAAUAUCAAAAGACGACAGCAAAGGCAAAAAUGAUGUGCUUGCCCACAGACAUUUAUGCGUGUGCUGGCAUCAUUUU
.((((....(((((((-....))))))).....)))).....((.(.(((((.(.(((.(((((.((((......))))..))))).))).).))))).).))..... ( -24.80)
>DroSim_CAF1 68785 107 - 1
AAUAUGAAAAUACUUU-UUUUAGUGUAUGAAUAAUAUCAAAAGACGACAGCAAAGGCAAAAAUGAUGUGCUUGCCCACAGACAUUCAUGCGUGUGCUGGCAUCAUUUU
...((((..(((((..-....))))).....................(((((.(.(((..((((.((((......))))..))))..))).).)))))...))))... ( -22.00)
>DroEre_CAF1 48964 108 - 1
AAUAUGAAAAUCCCUCUUUUUAGGGUAUGAAUAAUAUCAAAAGACGACAGCAAAGGCAAAAAUGAUGUGCUUGUCCACAGACAUUCAUGCGUGUGCUGGCAUCAUUUU
...((((.....(.((((((...(((((.....))))))))))).).(((((.(.(((..((((.((((......))))..))))..))).).)))))...))))... ( -24.30)
>DroYak_CAF1 61795 107 - 1
AAUAUGAAAAUUCUUCUU-UUAGGGUAUGAAUAAUAUCAAAAGACGGCAGGAAUGGCAAAAAUGAUGUGCUUGUCCACAGACAUUCAUGCGUGUGCUGGCAUCAUUUU
...((((.......((((-(...(((((.....))))).)))))(((((.(....(((..((((.((((......))))..))))..))).).)))))...))))... ( -22.20)
>consensus
AAUAUGAAAAUACUUU_UUUUAGGGUAUGAAUAAUAUCAAAAGACGACAGCAAAGGCAAAAAUGAUGUGCUUGCCCACAGACAUUCAUGCGUGUGCUGGCAUCAUUUU
...((((................(((((.....))))).......(.(((((.(.(((..((((.((((......))))..))))..))).).))))).).))))... (-19.70 = -20.30 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:15 2006