Locus 4568

Sequence ID	3R_DroMel_CAF1
Location	12,070,353 – 12,070,497
Length	144
Max. P	0.994492

overview

Window 8

Location	12,070,353 – 12,070,457
Length	104
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.10
Mean single sequence MFE	-36.92
Consensus MFE	-27.66
Energy contribution	-27.90
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.72
Structure conservation index	0.75
SVM decision value	0.27
SVM RNA-class probability	0.662881
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12070353 104 + 27905053
UCGCACAAUAUGCUAAAUAGCCGCUGCUUGCGUCAACGUCUCCGUUGGCG------UCGCUGUCGCCGGCUUAGCCGCUGCGCUUGUCUAAUGCAACGCAAC--------AGCAACA--A
..((.......((((...((((((.((..(((((((((....))))))))------)....)).).))))))))).(.((((.((((.....)))))))).)--------.))....--. ( -34.30)
>DroSec_CAF1 6893 104 + 1
UCGCACAAUAUGCUAAAUAGCCGCUGCUUGCGUCAACGUCUACGUUGGCG------UCGCUGUCGCCGGCUUAGCCGCUGCGCUUGUCUAAUGCAACGCAAC--------AGCAACA--A
..((.......((((...((((((.((..(((((((((....))))))))------)....)).).))))))))).(.((((.((((.....)))))))).)--------.))....--. ( -35.20)
>DroSim_CAF1 7329 104 + 1
UCGCACAAUAUGCUAAAUAGCCGCUGCUUGCGUCAAUGUCUACGUUGGCG------UCGCUGUCGCCGGCUUAGCCGCUGCGCUUGUCUAAUGCAACGCAAC--------AGCAACA--A
..((.......((((...((((((.((..(((((((((....))))))))------)....)).).))))))))).(.((((.((((.....)))))))).)--------.))....--. ( -33.40)
>DroEre_CAF1 8903 120 + 1
UCGCACAAUAUGCUAAAUAGCCGCUGCUUGCGUCAACGUCUCAGUCGGCGUCGUCGUCGCUGUUGCCGGCUUAGCCGCUGCGUUUGUCUAAUGCAACGCAACAAUUGGACAGCAGCAGCA
..((.......((((...((((((.....))......((..(((.(((((....))))))))..)).)))))))).(((((...((((((((...........))))))))))))).)). ( -41.30)
>DroYak_CAF1 9007 111 + 1
UCGCACAAUAUGCUAAAUAGCCGCUGCUUGCGUCAACAGCUCCGUCGGCG------UCGCUGUCGCCGGCUUAGCCGCUGCGCUUGUCUAAUGCAACGCAACAAUUGGACAGCA---GCA
..(((.....))).........(((((..(((.((.(.(((..(((((((------.......)))))))..))).).))))).((((((((...........)))))))))))---)). ( -40.40)
>consensus
UCGCACAAUAUGCUAAAUAGCCGCUGCUUGCGUCAACGUCUCCGUUGGCG______UCGCUGUCGCCGGCUUAGCCGCUGCGCUUGUCUAAUGCAACGCAAC________AGCAACA__A
..........((((....(((.((((....(((((((......)))))))........((((....)))).)))).)))(((.((((.....)))))))...........))))...... (-27.66 = -27.90 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	12,070,353 – 12,070,457
Length	104
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.10
Mean single sequence MFE	-43.16
Consensus MFE	-34.20
Energy contribution	-34.48
Covariance contribution	0.28
Combinations/Pair	1.12
Mean z-score	-2.42
Structure conservation index	0.79
SVM decision value	1.80
SVM RNA-class probability	0.977770
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12070353 104 - 27905053
U--UGUUGCU--------GUUGCGUUGCAUUAGACAAGCGCAGCGGCUAAGCCGGCGACAGCGA------CGCCAACGGAGACGUUGACGCAAGCAGCGGCUAUUUAGCAUAUUGUGCGA
.--.((((((--------((((((((((...........)))))(((...))).))))))))))------)..(((((....))))).((((.......(((....)))......)))). ( -45.02)
>DroSec_CAF1 6893 104 - 1
U--UGUUGCU--------GUUGCGUUGCAUUAGACAAGCGCAGCGGCUAAGCCGGCGACAGCGA------CGCCAACGUAGACGUUGACGCAAGCAGCGGCUAUUUAGCAUAUUGUGCGA
.--.((((((--------((((((((((...........)))))(((...))).))))))))))------)(((((..(...(((((.(....))))))(((....))))..))).)).. ( -42.50)
>DroSim_CAF1 7329 104 - 1
U--UGUUGCU--------GUUGCGUUGCAUUAGACAAGCGCAGCGGCUAAGCCGGCGACAGCGA------CGCCAACGUAGACAUUGACGCAAGCAGCGGCUAUUUAGCAUAUUGUGCGA
.--.((((((--------((((((((((...........)))))(((...))).))))))))))------)(((((..(.........(((.....)))(((....))))..))).)).. ( -37.40)
>DroEre_CAF1 8903 120 - 1
UGCUGCUGCUGUCCAAUUGUUGCGUUGCAUUAGACAAACGCAGCGGCUAAGCCGGCAACAGCGACGACGACGCCGACUGAGACGUUGACGCAAGCAGCGGCUAUUUAGCAUAUUGUGCGA
.(((((((((.......(((((((((((...........)))))(((...))).))))))(((.(((((.(.........).))))).))).)))))))))......((((...)))).. ( -45.70)
>DroYak_CAF1 9007 111 - 1
UGC---UGCUGUCCAAUUGUUGCGUUGCAUUAGACAAGCGCAGCGGCUAAGCCGGCGACAGCGA------CGCCGACGGAGCUGUUGACGCAAGCAGCGGCUAUUUAGCAUAUUGUGCGA
.((---((((((....(((((...........)))))(((((((((((..(.(((((.......------))))).)..)))))))).)))..))))))))......((((...)))).. ( -45.20)
>consensus
U__UGUUGCU________GUUGCGUUGCAUUAGACAAGCGCAGCGGCUAAGCCGGCGACAGCGA______CGCCAACGGAGACGUUGACGCAAGCAGCGGCUAUUUAGCAUAUUGUGCGA
...(((((((........((((((((..........))))))))(((...))))))))))..........((((((......(((((.(....))))))(((....)))...))).))). (-34.20 = -34.48 +   0.28)

alignment

secondary structure

dotplot

Window 0

Location	12,070,393 – 12,070,497
Length	104
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	92.97
Mean single sequence MFE	-43.20
Consensus MFE	-38.20
Energy contribution	-38.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.02
Structure conservation index	0.88
SVM decision value	1.18
SVM RNA-class probability	0.926429
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12070393 104 + 27905053
UCCGUUGGCGUCGCUGUCGCCGGCUUAGCCGCUGCGCUUGUCUAAUGCAACGCAAC--------AGCAACA--AGCGUCGGCAGCAGCAAAGCAGCAGACAGCUGACUUUUGGG
.(((.....(((((((((((..((((.((.(((((((((((....(((........--------.))))))--)))....))))).)).)))).)).)))))).)))...))). ( -41.00)
>DroSec_CAF1 6933 104 + 1
UACGUUGGCGUCGCUGUCGCCGGCUUAGCCGCUGCGCUUGUCUAAUGCAACGCAAC--------AGCAACA--AGCGUCGGCAGCAGCAAAGCAGCAGACAGCUGACUUUUGGG
...((..((((((((((.((..(((..((((..((((((((....(((........--------.))))))--)))))))))))).))...))))).))).))..))....... ( -40.50)
>DroSim_CAF1 7369 104 + 1
UACGUUGGCGUCGCUGUCGCCGGCUUAGCCGCUGCGCUUGUCUAAUGCAACGCAAC--------AGCAACA--AGCGUCGGCAGCAGCAAAGCAGCAGACAGCUGACUUUUGGG
...((..((((((((((.((..(((..((((..((((((((....(((........--------.))))))--)))))))))))).))...))))).))).))..))....... ( -40.50)
>DroYak_CAF1 9047 111 + 1
UCCGUCGGCGUCGCUGUCGCCGGCUUAGCCGCUGCGCUUGUCUAAUGCAACGCAACAAUUGGACAGCA---GCAGCGUCGGCAGCAGCAAAGCAGCAGACAGCUGACUUUUGGG
...((((((((((((((((.((((...)))((((((((.(((((((...........)))))))))).---)))))).))))))).((......)).))).))))))....... ( -50.80)
>consensus
UACGUUGGCGUCGCUGUCGCCGGCUUAGCCGCUGCGCUUGUCUAAUGCAACGCAAC________AGCAACA__AGCGUCGGCAGCAGCAAAGCAGCAGACAGCUGACUUUUGGG
.........(((((((((((..((((.((.(((((((((((.....)))).))............((.......))....))))).)).)))).)).)))))).)))....... (-38.20 = -38.20 +  -0.00)

alignment

secondary structure

dotplot

Window 1

Location	12,070,393 – 12,070,497
Length	104
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	92.97
Mean single sequence MFE	-47.60
Consensus MFE	-43.40
Energy contribution	-43.40
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-3.17
Structure conservation index	0.91
SVM decision value	2.48
SVM RNA-class probability	0.994492
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12070393 104 - 27905053
CCCAAAAGUCAGCUGUCUGCUGCUUUGCUGCUGCCGACGCU--UGUUGCU--------GUUGCGUUGCAUUAGACAAGCGCAGCGGCUAAGCCGGCGACAGCGACGCCAACGGA
((.....(((.((((((.(((((((.((((((((....(((--((((..(--------((......)))...))))))))))))))).))).)))))))))))))......)). ( -48.50)
>DroSec_CAF1 6933 104 - 1
CCCAAAAGUCAGCUGUCUGCUGCUUUGCUGCUGCCGACGCU--UGUUGCU--------GUUGCGUUGCAUUAGACAAGCGCAGCGGCUAAGCCGGCGACAGCGACGCCAACGUA
.......(((.((((((.(((((((.((((((((....(((--((((..(--------((......)))...))))))))))))))).))).)))))))))))))......... ( -48.00)
>DroSim_CAF1 7369 104 - 1
CCCAAAAGUCAGCUGUCUGCUGCUUUGCUGCUGCCGACGCU--UGUUGCU--------GUUGCGUUGCAUUAGACAAGCGCAGCGGCUAAGCCGGCGACAGCGACGCCAACGUA
.......(((.((((((.(((((((.((((((((....(((--((((..(--------((......)))...))))))))))))))).))).)))))))))))))......... ( -48.00)
>DroYak_CAF1 9047 111 - 1
CCCAAAAGUCAGCUGUCUGCUGCUUUGCUGCUGCCGACGCUGC---UGCUGUCCAAUUGUUGCGUUGCAUUAGACAAGCGCAGCGGCUAAGCCGGCGACAGCGACGCCGACGGA
((.....(((.((((((.(((((((.((((((((.(((((.((---............)).)))))((.........)))))))))).))).)))))))))))))......)). ( -45.90)
>consensus
CCCAAAAGUCAGCUGUCUGCUGCUUUGCUGCUGCCGACGCU__UGUUGCU________GUUGCGUUGCAUUAGACAAGCGCAGCGGCUAAGCCGGCGACAGCGACGCCAACGGA
.......(((.((((((.(((((((.((((((((.(((((.....................)))))((.........)))))))))).))).)))))))))))))......... (-43.40 = -43.40 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:55 2006