Locus 4198

Sequence ID	3R_DroMel_CAF1
Location	11,349,254 – 11,349,494
Length	240
Max. P	0.999624

overview

Window 4

Location	11,349,254 – 11,349,374
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.63
Mean single sequence MFE	-39.44
Consensus MFE	-35.12
Energy contribution	-36.12
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.54
Structure conservation index	0.89
SVM decision value	3.67
SVM RNA-class probability	0.999509
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11349254 120 + 27905053
UCCUGCGAAGGACAUGCAGGCCAUUCAGGACAGUUGGCAGCGGGAAAUGCGAAUGCAUUUAUUUAUUUUAAUUCCGCCACAACACUUCCGCUGUGCAAUCAAUGCACGCGCAGGCACAAU
..(((((.......)))))(((.....(((..((((...(((((((((((....)))))............))))))..))))...)))((((((((.....)))))).)).)))..... ( -37.20)
>DroSec_CAF1 88124 120 + 1
UCCUGCGGAGGACAUGCCGGCCAUUCAGGACAGUUGGCAGCGGGAAAUGCGAAUGCAUUUAUUUAUUUUAAUUCCGCCACAACACUUCCGCUGUGCAAUCAAUGCACGCGCAGGCACAAU
.((((((((((...(((((((...........)))))))(((((((((((....)))))............)))))).......)))))((.(((((.....))))))))))))...... ( -42.70)
>DroSim_CAF1 86708 120 + 1
UCCUGCGGAGGACAUGCCGGCCAUUCAGGACAGUUGGCAGCGGGAAAUGCGAAUGCAUUUAUUUAUUUUAAUUCCGCCACAACACUUCCGCUGUGCAAUCAAUGCACGCGCAGGCACAAU
.((((((((((...(((((((...........)))))))(((((((((((....)))))............)))))).......)))))((.(((((.....))))))))))))...... ( -42.70)
>DroEre_CAF1 84373 111 + 1
UCCUGCGGAGGACA---------UCCAGGACAGUUGGCAGCGGGAAAUGCGAAUGCAUUUAUUUAUUUUAAUUCCGCCACAACACUUCCGCUGUGCAAUCAAUGCACGCGCAGGCACAAU
.((((((((.....---------))).(((..((((...(((((((((((....)))))............))))))..))))...)))((.(((((.....))))))))))))...... ( -37.50)
>DroYak_CAF1 86671 111 + 1
UCCUGCGGAGGACA---------UUCAGGACAGUUGGCAGCGGGAAAUGCGAAUGCAUUUAUUUAUUUUAAUUCCGCCACAACACUUCCGCUGUGCAAUCAAUGCACGCGCAGGCACAAU
.((((((((((.(.---------....)....((((...(((((((((((....)))))............))))))..)))).)))))((.(((((.....))))))))))))...... ( -37.10)
>consensus
UCCUGCGGAGGACAUGC_GGCCAUUCAGGACAGUUGGCAGCGGGAAAUGCGAAUGCAUUUAUUUAUUUUAAUUCCGCCACAACACUUCCGCUGUGCAAUCAAUGCACGCGCAGGCACAAU
.((((((((((.........((.....))...((((...(((((((((((....)))))............))))))..)))).)))))((.(((((.....))))))))))))...... (-35.12 = -36.12 +   1.00)

alignment

secondary structure

dotplot

Window 5

Location	11,349,254 – 11,349,374
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.63
Mean single sequence MFE	-40.70
Consensus MFE	-38.30
Energy contribution	-38.30
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.20
Structure conservation index	0.94
SVM decision value	3.80
SVM RNA-class probability	0.999624
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11349254 120 - 27905053
AUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUUGUGGCGGAAUUAAAAUAAAUAAAUGCAUUCGCAUUUCCCGCUGCCAACUGUCCUGAAUGGCCUGCAUGUCCUUCGCAGGA
......((((((((((((.....))))).))(((...((((..((((.(((......)))((((((....)))))).))))..).)))..))).(((.(((......))).)))))))). ( -41.20)
>DroSec_CAF1 88124 120 - 1
AUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUUGUGGCGGAAUUAAAAUAAAUAAAUGCAUUCGCAUUUCCCGCUGCCAACUGUCCUGAAUGGCCGGCAUGUCCUCCGCAGGA
......((((((((((((.....))))).))(((.((((((.(((((.(((......)))((((((....)))))).)))))((((...........)))))))))).)))...))))). ( -42.00)
>DroSim_CAF1 86708 120 - 1
AUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUUGUGGCGGAAUUAAAAUAAAUAAAUGCAUUCGCAUUUCCCGCUGCCAACUGUCCUGAAUGGCCGGCAUGUCCUCCGCAGGA
......((((((((((((.....))))).))(((.((((((.(((((.(((......)))((((((....)))))).)))))((((...........)))))))))).)))...))))). ( -42.00)
>DroEre_CAF1 84373 111 - 1
AUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUUGUGGCGGAAUUAAAAUAAAUAAAUGCAUUCGCAUUUCCCGCUGCCAACUGUCCUGGA---------UGUCCUCCGCAGGA
......((((((((((((.....))))).))(((...((((..((((.(((......)))((((((....)))))).))))..).)))..))).(((---------.....)))))))). ( -40.00)
>DroYak_CAF1 86671 111 - 1
AUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUUGUGGCGGAAUUAAAAUAAAUAAAUGCAUUCGCAUUUCCCGCUGCCAACUGUCCUGAA---------UGUCCUCCGCAGGA
......((((((((((((.....))))).))(((...((((..((((.(((......)))((((((....)))))).))))..).)))..)))....---------........))))). ( -38.30)
>consensus
AUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUUGUGGCGGAAUUAAAAUAAAUAAAUGCAUUCGCAUUUCCCGCUGCCAACUGUCCUGAAUGGCC_GCAUGUCCUCCGCAGGA
......((((((((((((.....))))).))(((...((((..((((.(((......)))((((((....)))))).))))..).)))..))).....................))))). (-38.30 = -38.30 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	11,349,294 – 11,349,414
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.65
Mean single sequence MFE	-31.76
Consensus MFE	-31.28
Energy contribution	-31.12
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.33
Structure conservation index	0.98
SVM decision value	0.67
SVM RNA-class probability	0.817602
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11349294 120 - 27905053
UGGAUAUGUAUUUACAUGUAUGCAUAUGGUUAUAUGUCUCAUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUUGUGGCGGAAUUAAAAUAAAUAAAUGCAUUCGCAUUUCCCG
.(((((((((....(((((....)))))..))))))))).(((.((((.((..(((((.....))))).((....))))...)))).)))..........((((((....)))))).... ( -31.90)
>DroSec_CAF1 88164 118 - 1
--GAUAUGUAUUUACAUGUAUGCAUAUGGUUAUAUGUCUCAUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUUGUGGCGGAAUUAAAAUAAAUAAAUGCAUUCGCAUUUCCCG
--((((((((....(((((....)))))..))))))))..(((.((((.((..(((((.....))))).((....))))...)))).)))..........((((((....)))))).... ( -31.20)
>DroSim_CAF1 86748 118 - 1
--GAUAUGUAUUUACAUGUAUGCAUAUGGUUAUAUGUCUCAUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUUGUGGCGGAAUUAAAAUAAAUAAAUGCAUUCGCAUUUCCCG
--((((((((....(((((....)))))..))))))))..(((.((((.((..(((((.....))))).((....))))...)))).)))..........((((((....)))))).... ( -31.20)
>DroEre_CAF1 84404 118 - 1
--GAUAUGUAUUUACAUGUAUGCAUAUGGCUAUAUGUCUCAUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUUGUGGCGGAAUUAAAAUAAAUAAAUGCAUUCGCAUUUCCCG
--.((((((((........))))))))(((.(((........)))))).((..(((((.....))))).))((((((((....(((..(((......)))...)))....)))))))).. ( -31.60)
>DroYak_CAF1 86702 118 - 1
--GAUAUGUAUUCACAUGUAUGCAUAUGGUUAUAUGUCUCAUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUUGUGGCGGAAUUAAAAUAAAUAAAUGCAUUCGCAUUUCCCG
--((((((((..((.(((....))).))..))))))))..(((.((((.((..(((((.....))))).((....))))...)))).)))..........((((((....)))))).... ( -32.90)
>consensus
__GAUAUGUAUUUACAUGUAUGCAUAUGGUUAUAUGUCUCAUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUUGUGGCGGAAUUAAAAUAAAUAAAUGCAUUCGCAUUUCCCG
..((((((((.(((.(((....))).))).))))))))..(((.((((.((..(((((.....))))).((....))))...)))).)))..........((((((....)))))).... (-31.28 = -31.12 +  -0.16)

alignment

secondary structure

dotplot

Window 7

Location	11,349,334 – 11,349,454
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.25
Mean single sequence MFE	-22.36
Consensus MFE	-20.10
Energy contribution	-20.10
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.55
Structure conservation index	0.90
SVM decision value	1.37
SVM RNA-class probability	0.947433
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11349334 120 + 27905053
AACACUUCCGCUGUGCAAUCAAUGCACGCGCAGGCACAAUGAGACAUAUAACCAUAUGCAUACAUGUAAAUACAUAUCCAUCCAUUUAUGGAGGCAGCUCUUCAUACAUAUAUGUACUAU
....(((.(((.(((((.....)))))))).))).......(((((((((...(((((....)))))...................((((((((....))))))))..))))))).)).. ( -25.10)
>DroSec_CAF1 88204 105 + 1
AACACUUCCGCUGUGCAAUCAAUGCACGCGCAGGCACAAUGAGACAUAUAACCAUAUGCAUACAUGUAAAUACAUAUC----CAUUUAUGGAGGCAGCUCUUCAUACA-----------U
....(((.(((.(((((.....)))))))).)))...((((.(((((((....))))).....((((....)))).))----))))((((((((....))))))))..-----------. ( -20.70)
>DroSim_CAF1 86788 105 + 1
AACACUUCCGCUGUGCAAUCAAUGCACGCGCAGGCACAAUGAGACAUAUAACCAUAUGCAUACAUGUAAAUACAUAUC----CAUUUAUGGAGGCAGCUCUUCAUACA-----------U
....(((.(((.(((((.....)))))))).)))...((((.(((((((....))))).....((((....)))).))----))))((((((((....))))))))..-----------. ( -20.70)
>DroEre_CAF1 84444 105 + 1
AACACUUCCGCUGUGCAAUCAAUGCACGCGCAGGCACAAUGAGACAUAUAGCCAUAUGCAUACAUGUAAAUACAUAUC----CAUUUAUGGAGGCAGCUCUUCAUACG-----------C
....(((.(((.(((((.....)))))))).)))....(((((.......((((((((....))))).........((----((....))))))).....)))))...-----------. ( -22.40)
>DroYak_CAF1 86742 102 + 1
AACACUUCCGCUGUGCAAUCAAUGCACGCGCAGGCACAAUGAGACAUAUAACCAUAUGCAUACAUGUGAAUACAUAUC----CAUUUAUGGAGGCAGCUCUUCAUA--------------
....(((.(((.(((((.....)))))))).)))...((((.((.((.((..((((((....))))))..)).)).))----))))((((((((....))))))))-------------- ( -22.90)
>consensus
AACACUUCCGCUGUGCAAUCAAUGCACGCGCAGGCACAAUGAGACAUAUAACCAUAUGCAUACAUGUAAAUACAUAUC____CAUUUAUGGAGGCAGCUCUUCAUACA___________U
....(((.(((.(((((.....)))))))).)))...((((.(.(((((....))))))....((((....)))).......))))((((((((....)))))))).............. (-20.10 = -20.10 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	11,349,334 – 11,349,454
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.25
Mean single sequence MFE	-30.38
Consensus MFE	-25.92
Energy contribution	-26.12
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.65
Structure conservation index	0.85
SVM decision value	1.18
SVM RNA-class probability	0.926696
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11349334 120 - 27905053
AUAGUACAUAUAUGUAUGAAGAGCUGCCUCCAUAAAUGGAUGGAUAUGUAUUUACAUGUAUGCAUAUGGUUAUAUGUCUCAUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUU
...(((((((((((((..........((((((....)))).)).........)))))))))((((((....))))))......))))((((..(((((.....))))).))))....... ( -32.81)
>DroSec_CAF1 88204 105 - 1
A-----------UGUAUGAAGAGCUGCCUCCAUAAAUG----GAUAUGUAUUUACAUGUAUGCAUAUGGUUAUAUGUCUCAUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUU
.-----------.(((..(.((((.(((((((....))----))(((((((........))))))).))).....).))).)..)))((((..(((((.....))))).))))....... ( -29.30)
>DroSim_CAF1 86788 105 - 1
A-----------UGUAUGAAGAGCUGCCUCCAUAAAUG----GAUAUGUAUUUACAUGUAUGCAUAUGGUUAUAUGUCUCAUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUU
.-----------.(((..(.((((.(((((((....))----))(((((((........))))))).))).....).))).)..)))((((..(((((.....))))).))))....... ( -29.30)
>DroEre_CAF1 84444 105 - 1
G-----------CGUAUGAAGAGCUGCCUCCAUAAAUG----GAUAUGUAUUUACAUGUAUGCAUAUGGCUAUAUGUCUCAUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUU
.-----------.(((..(.((((.(((((((....))----))(((((((........))))))).))).....).))).)..)))((((..(((((.....))))).))))....... ( -31.20)
>DroYak_CAF1 86742 102 - 1
--------------UAUGAAGAGCUGCCUCCAUAAAUG----GAUAUGUAUUCACAUGUAUGCAUAUGGUUAUAUGUCUCAUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUU
--------------........((.((...(((((..(----((((((((..((.(((....))).))..)))))))))..)))))...))))(((((.....))))).((....))... ( -29.30)
>consensus
A___________UGUAUGAAGAGCUGCCUCCAUAAAUG____GAUAUGUAUUUACAUGUAUGCAUAUGGUUAUAUGUCUCAUUGUGCCUGCGCGUGCAUUGAUUGCACAGCGGAAGUGUU
.............(((..(.((((.....(((((..((.....((((((....))))))...)))))))......).))).)..)))((((..(((((.....))))).))))....... (-25.92 = -26.12 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	11,349,374 – 11,349,494
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.78
Mean single sequence MFE	-27.77
Consensus MFE	-19.08
Energy contribution	-20.70
Covariance contribution	1.62
Combinations/Pair	1.08
Mean z-score	-2.06
Structure conservation index	0.69
SVM decision value	0.93
SVM RNA-class probability	0.884585
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11349374 120 + 27905053
GAGACAUAUAACCAUAUGCAUACAUGUAAAUACAUAUCCAUCCAUUUAUGGAGGCAGCUCUUCAUACAUAUAUGUACUAUGUGCGCUUGUGUGUGUACUUAUGCAUGUCCAGUGUCCUGU
..(((((......(((((((((...(((.((((((((((((......)))))(((.((.(....((((....))))....).)))))))))))).))).)))))))))...))))).... ( -31.00)
>DroSec_CAF1 88244 105 + 1
GAGACAUAUAACCAUAUGCAUACAUGUAAAUACAUAUC----CAUUUAUGGAGGCAGCUCUUCAUACA-----------UGUGCGCUUGUGUGUGUACUUAUGCAUGUCCUGUGUCCCCU
..((((((.....(((((((((...(((.(((((((.(----(((.((((((((....)))))))).)-----------)).)....))))))).))).)))))))))..)))))).... ( -29.90)
>DroSim_CAF1 86828 100 + 1
GAGACAUAUAACCAUAUGCAUACAUGUAAAUACAUAUC----CAUUUAUGGAGGCAGCUCUUCAUACA-----------UGUGCGCUUGUGUGUGAACUUAUGCAUGUCCUGUGU-----
...(((((.....(((((((((...((..(((((((.(----(((.((((((((....)))))))).)-----------)).)....)))))))..)).)))))))))..)))))----- ( -25.10)
>DroEre_CAF1 84484 97 + 1
GAGACAUAUAGCCAUAUGCAUACAUGUAAAUACAUAUC----CAUUUAUGGAGGCAGCUCUUCAUACG-----------CG--------UAUAUGUAGGUGUGCAUGUCCUGCGUCCUGC
..........((...(((((.(((((((..(((((((.----(...((((((((....))))))))..-----------.)--------.)))))))....)))))))..)))))...)) ( -25.10)
>consensus
GAGACAUAUAACCAUAUGCAUACAUGUAAAUACAUAUC____CAUUUAUGGAGGCAGCUCUUCAUACA___________UGUGCGCUUGUGUGUGUACUUAUGCAUGUCCUGUGUCCUGU
..((((((.....(((((((((...(((.(((((((..........((((((((....))))))))((((.......))))......))))))).))).)))))))))..)))))).... (-19.08 = -20.70 +   1.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:23 2006