Locus 1696

Sequence ID	2R_DroMel_CAF1
Location	6,419,113 – 6,419,393
Length	280
Max. P	0.999980

overview

Window 5

Location	6,419,113 – 6,419,233
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.97
Mean single sequence MFE	-45.28
Consensus MFE	-35.24
Energy contribution	-35.00
Covariance contribution	-0.24
Combinations/Pair	1.21
Mean z-score	-2.08
Structure conservation index	0.78
SVM decision value	1.10
SVM RNA-class probability	0.915637
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6419113 120 - 20766785
CUUUUGCGGUCCUGCAGGACAUAAAGUUCUCCAACUAACGGCGUAUUGGUCCUGCGGCGGUCGCAGGAUGAAGGUUUUCGCGGUUGGCUACGGUUAGCCCAAAUUACGGGCGACUUACUG
.(((((((..((((((((((....(((.(.((.......)).).))).))))))))).)..)))))))....(((..(((((((((((....)))))))(........)))))...))). ( -45.80)
>DroSec_CAF1 16670 120 - 1
CUUUUGCGGUCCUGCAGGACAUAAAGUUCACCAACUAACGGCGUAUUGGUCCUGCGGCGGUCGCAGGAUGAAGGUUUCCGCGGUUGGCUACGUUUAGCCCAAAUUACGGGGGACUUACUG
.(((((((..((((((((((....(((.(.((.......)).).))).))))))))).)..)))))))..(((.(..(((..((((((((....)))))..)))..)))..).))).... ( -47.80)
>DroSim_CAF1 17357 120 - 1
CUUUUGCGGUCCUGCAGGACAUAAAGUUCACCAACUAACGGCGUAUUGGUCCUGCGGCGGUCGCAGGAUGAAGGUUUCCGCGGUUGGCUACGGUUAGCCCAAAUUACAGGGGACUUACUG
.(((((((..((((((((((....(((.(.((.......)).).))).))))))))).)..)))))))...((((..((..(((((((....))))))).........))..)))).... ( -48.30)
>DroEre_CAF1 13847 117 - 1
CUUUUGCGGUCCUGCAGGACAUAAAGUCCUCUAACUAACGGCGGAUUGGUCCUGU---GGUCGCAGGAUGAAGAUUUCCGCGGUUGGCUACGGUUAGUCCAAAUUAUGGUGGAAUUACCA
....((((....))))((((.....)))).....(((((.(((((((.(((((((---....))))))).))....))))).)))))....(((...((((........))))...))). ( -42.60)
>DroYak_CAF1 14317 117 - 1
GUUUCGCGGUCCUGCAGGACAUAAAGUUCUCUAACUAACGGCGGAUUGGUCCUGU---GGUCGCAGGACGAAGGUUUCCGCGCUUGGCUACGGUUAGCCCAAAUUGUGGUGGAAUUACCA
(((..((((.((.(((((((....(((((.((.......)).))))).)))))))---))))))..)))...(((((((((((..(((((....)))))......)).))))))..))). ( -41.90)
>consensus
CUUUUGCGGUCCUGCAGGACAUAAAGUUCUCCAACUAACGGCGUAUUGGUCCUGCGGCGGUCGCAGGAUGAAGGUUUCCGCGGUUGGCUACGGUUAGCCCAAAUUACGGGGGACUUACUG
....((((..((((((((((....(((.(.((.......)).).))).))))))))).)..))))(((........)))(.(((((((....))))))))......(((........))) (-35.24 = -35.00 +  -0.24)

alignment

secondary structure

dotplot

Window 6

Location	6,419,153 – 6,419,273
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.49
Mean single sequence MFE	-38.11
Consensus MFE	-32.83
Energy contribution	-33.55
Covariance contribution	0.72
Combinations/Pair	1.06
Mean z-score	-1.55
Structure conservation index	0.86
SVM decision value	0.97
SVM RNA-class probability	0.891207
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6419153 120 - 20766785
CAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCCCUUUUGCGGUCCUGCAGGACAUAAAGUUCUCCAACUAACGGCGUAUUGGUCCUGCGGCGGUCGCAGGAUGAAGGUUUUCG
..(((((.................))))).......(((..(((((((..((((((((((....(((.(.((.......)).).))).))))))))).)..)))))))....)))..... ( -39.13)
>DroSec_CAF1 16710 120 - 1
CAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCCCUUUUGCGGUCCUGCAGGACAUAAAGUUCACCAACUAACGGCGUAUUGGUCCUGCGGCGGUCGCAGGAUGAAGGUUUCCG
..(((((.................))))).......(((..(((((((..((((((((((....(((.(.((.......)).).))).))))))))).)..)))))))....)))..... ( -39.53)
>DroSim_CAF1 17397 120 - 1
CAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCCCUUUUGCGGUCCUGCAGGACAUAAAGUUCACCAACUAACGGCGUAUUGGUCCUGCGGCGGUCGCAGGAUGAAGGUUUCCG
..(((((.................))))).......(((..(((((((..((((((((((....(((.(.((.......)).).))).))))))))).)..)))))))....)))..... ( -39.53)
>DroEre_CAF1 13887 117 - 1
CAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCCCUUUUGCGGUCCUGCAGGACAUAAAGUCCUCUAACUAACGGCGGAUUGGUCCUGU---GGUCGCAGGAUGAAGAUUUCCG
..(((((.................)))))...............(((((.((.(((((((....(((((.((.......)).))))).)))))))---)))))))(((........))). ( -35.93)
>DroYak_CAF1 14357 117 - 1
CAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCCGUUUCGCGGUCCUGCAGGACAUAAAGUUCUCUAACUAACGGCGGAUUGGUCCUGU---GGUCGCAGGACGAAGGUUUCCG
..(((((.................))))).......(((((((..((((.((.(((((((....(((((.((.......)).))))).)))))))---))))))..))))..)))..... ( -36.43)
>consensus
CAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCCCUUUUGCGGUCCUGCAGGACAUAAAGUUCUCCAACUAACGGCGUAUUGGUCCUGCGGCGGUCGCAGGAUGAAGGUUUCCG
..(((((.................))))).......(((..(((((((..((((((((((....(((.(.((.......)).).))).))))))))).)..)))))))....)))..... (-32.83 = -33.55 +   0.72)

alignment

secondary structure

dotplot

Window 7

Location	6,419,193 – 6,419,313
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.67
Mean single sequence MFE	-37.86
Consensus MFE	-37.78
Energy contribution	-37.62
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.15
Structure conservation index	1.00
SVM decision value	0.34
SVM RNA-class probability	0.694002
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6419193 120 + 20766785
CGUUAGUUGGAGAACUUUAUGUCCUGCAGGACCGCAAAAGGGGCAAUAAGUUGCGCUUAUUAUGAUAAUGGGUGCGCAUGUGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUGGC
.............(((....(((((((.((.((.(((((..(((........((((((((((...))))))))))((....)).))).)))))...)).))...)))))))...)))... ( -37.90)
>DroSec_CAF1 16750 120 + 1
CGUUAGUUGGUGAACUUUAUGUCCUGCAGGACCGCAAAAGGGGCAAUAAGUUGCGCUUAUUAUGAUAAUGGGUGCGCAUGUGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUGGC
.............(((....(((((((.((.((.(((((..(((........((((((((((...))))))))))((....)).))).)))))...)).))...)))))))...)))... ( -37.90)
>DroSim_CAF1 17437 120 + 1
CGUUAGUUGGUGAACUUUAUGUCCUGCAGGACCGCAAAAGGGGCAAUAAGUUGCGCUUAUUAUGAUAAUGGGUGCGCAUGUGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUGGC
.............(((....(((((((.((.((.(((((..(((........((((((((((...))))))))))((....)).))).)))))...)).))...)))))))...)))... ( -37.90)
>DroEre_CAF1 13924 120 + 1
CGUUAGUUAGAGGACUUUAUGUCCUGCAGGACCGCAAAAGGGGCAAUAAGUUGCGCUUAUUAUGAUAAUGGGUGCGCAUGUGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUAGC
.............(((....(((((((.((.((.(((((..(((........((((((((((...))))))))))((....)).))).)))))...)).))...)))))))...)))... ( -38.00)
>DroYak_CAF1 14394 120 + 1
CGUUAGUUAGAGAACUUUAUGUCCUGCAGGACCGCGAAACGGGCAAUAAGUUGCGCUUAUUAUGAUAAUGGGUGCGCAUGUGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUGGC
.............(((....(((((((....(((.....))).......((.((((((((((...))))))))))))...(((((((..........))))))))))))))...)))... ( -37.60)
>consensus
CGUUAGUUGGAGAACUUUAUGUCCUGCAGGACCGCAAAAGGGGCAAUAAGUUGCGCUUAUUAUGAUAAUGGGUGCGCAUGUGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUGGC
.............(((....(((((((.((.((.(((((..(((........((((((((((...))))))))))((....)).))).)))))...)).))...)))))))...)))... (-37.78 = -37.62 +  -0.16)

alignment

secondary structure

dotplot

Window 8

Location	6,419,193 – 6,419,313
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.67
Mean single sequence MFE	-28.47
Consensus MFE	-27.75
Energy contribution	-27.75
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.35
Structure conservation index	0.97
SVM decision value	3.83
SVM RNA-class probability	0.999645
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6419193 120 - 20766785
GCCACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCACAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCCCUUUUGCGGUCCUGCAGGACAUAAAGUUCUCCAACUAACG
..........((((((.((((((..........))))))...(((((.................))))).......(((.(....).)))...)))))).....((((....)))).... ( -28.03)
>DroSec_CAF1 16750 120 - 1
GCCACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCACAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCCCUUUUGCGGUCCUGCAGGACAUAAAGUUCACCAACUAACG
..........((((((.((((((..........))))))...(((((.................))))).......(((.(....).)))...)))))).....((((....)))).... ( -28.03)
>DroSim_CAF1 17437 120 - 1
GCCACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCACAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCCCUUUUGCGGUCCUGCAGGACAUAAAGUUCACCAACUAACG
..........((((((.((((((..........))))))...(((((.................))))).......(((.(....).)))...)))))).....((((....)))).... ( -28.03)
>DroEre_CAF1 13924 120 - 1
GCUACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCACAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCCCUUUUGCGGUCCUGCAGGACAUAAAGUCCUCUAACUAACG
((.((..(((....((.((((((..........))))))...(((((.................))))).......)).....)))..))...))(((((.....))))).......... ( -28.63)
>DroYak_CAF1 14394 120 - 1
GCCACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCACAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCCGUUUCGCGGUCCUGCAGGACAUAAAGUUCUCUAACUAACG
..........((((((.((((((..........))))))...(((((.................))))).........(((.....)))....)))))).....((((....)))).... ( -29.63)
>consensus
GCCACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCACAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCCCUUUUGCGGUCCUGCAGGACAUAAAGUUCUCCAACUAACG
..........((((((.((((((..........))))))...(((((.................)))))....(((((.......)))))...))))))..................... (-27.75 = -27.75 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	6,419,233 – 6,419,353
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.42
Mean single sequence MFE	-42.26
Consensus MFE	-39.66
Energy contribution	-40.50
Covariance contribution	0.84
Combinations/Pair	1.02
Mean z-score	-3.17
Structure conservation index	0.94
SVM decision value	4.45
SVM RNA-class probability	0.999900
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6419233 120 + 20766785
GGGCAAUAAGUUGCGCUUAUUAUGAUAAUGGGUGCGCAUGUGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUGGCACUGCUAAAUGCAGCGCCAGUUAUCAAACGUAAGUGAAUU
..((((....))))((((((..(((((((.(((((((((..((((((..........))))))(((((...(((....))))))))..)))).))))).)))))))...))))))..... ( -44.90)
>DroSec_CAF1 16790 120 + 1
GGGCAAUAAGUUGCGCUUAUUAUGAUAAUGGGUGCGCAUGUGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUGGCACUGCUAAAUGCAGAACCAGUUAUCAAGCGUAAGUGAAUU
........(.((((((((........(((((.((((....)))).))))).(((((((((..(.((......)).)..)).((((.....))))..)))))))..)))))))).)..... ( -41.10)
>DroSim_CAF1 17477 120 + 1
GGGCAAUAAGUUGCGCUUAUUAUGAUAAUGGGUGCGCAUGUGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUGGCACUGCUAAAUGCAGCGCCAGUUAUCAAGCGUAAGUGAAUU
........(.(((((((.....(((((((.(((((((((..((((((..........))))))(((((...(((....))))))))..)))).))))).)))))))))))))).)..... ( -45.00)
>DroEre_CAF1 13964 120 + 1
GGGCAAUAAGUUGCGCUUAUUAUGAUAAUGGGUGCGCAUGUGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUAGCAAUGCUAAAUGCAACGCCAGUUAUCAAGCGUAAGUGAAUU
........(.(((((((.....(((((((.((((.((((.(((((((..........)))))))..((.(((((....))))).))..))))..)))).)))))))))))))).)..... ( -39.90)
>DroYak_CAF1 14434 120 + 1
GGGCAAUAAGUUGCGCUUAUUAUGAUAAUGGGUGCGCAUGUGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUGGCAGUGCUAAAUGCAACGCCAGUUAUCAAACGUAAGUGAAUU
..((((....))))((((((..(((((((.((((.((((..(((((((((.(((((..((....))..))))).))))))..)))...))))..)))).)))))))...))))))..... ( -40.40)
>consensus
GGGCAAUAAGUUGCGCUUAUUAUGAUAAUGGGUGCGCAUGUGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUGGCACUGCUAAAUGCAGCGCCAGUUAUCAAGCGUAAGUGAAUU
..((((....))))((((((..(((((((.(((((((((..((((((..........))))))(((((...(((....))))))))..)))).))))).)))))))...))))))..... (-39.66 = -40.50 +   0.84)

alignment

secondary structure

dotplot

Window 0

Location	6,419,233 – 6,419,353
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.42
Mean single sequence MFE	-31.68
Consensus MFE	-31.99
Energy contribution	-32.03
Covariance contribution	0.04
Combinations/Pair	1.12
Mean z-score	-3.51
Structure conservation index	1.01
SVM decision value	5.23
SVM RNA-class probability	0.999980
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6419233 120 - 20766785
AAUUCACUUACGUUUGAUAACUGGCGCUGCAUUUAGCAGUGCCACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCACAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCC
...........((..(((...(((((((((.....))))))))).....)))..)).((((((..........))))))...(((((.................)))))........... ( -34.33)
>DroSec_CAF1 16790 120 - 1
AAUUCACUUACGCUUGAUAACUGGUUCUGCAUUUAGCAGUGCCACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCACAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCC
...........((..(((...((((.((((.....)))).)))).....)))..)).((((((..........))))))...(((((.................)))))........... ( -30.03)
>DroSim_CAF1 17477 120 - 1
AAUUCACUUACGCUUGAUAACUGGCGCUGCAUUUAGCAGUGCCACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCACAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCC
...........((..(((...(((((((((.....))))))))).....)))..)).((((((..........))))))...(((((.................)))))........... ( -35.93)
>DroEre_CAF1 13964 120 - 1
AAUUCACUUACGCUUGAUAACUGGCGUUGCAUUUAGCAUUGCUACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCACAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCC
...........(((((((((.(((.(((((((.(((.((((......)))).)))..((((((..........))))))..))))).))))))))))).....)))((((....)))).. ( -30.10)
>DroYak_CAF1 14434 120 - 1
AAUUCACUUACGUUUGAUAACUGGCGUUGCAUUUAGCACUGCCACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCACAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCC
...........((..(((...(((((.(((.....))).))))).....)))..)).((((((..........))))))...(((((.................)))))........... ( -28.03)
>consensus
AAUUCACUUACGCUUGAUAACUGGCGCUGCAUUUAGCAGUGCCACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCACAUGCGCACCCAUUAUCAUAAUAAGCGCAACUUAUUGCCC
...........((..(((...(((((((((.....))))))))).....)))..)).((((((..........))))))...(((((.................)))))........... (-31.99 = -32.03 +   0.04)

alignment

secondary structure

dotplot

Window 1

Location	6,419,273 – 6,419,393
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.58
Mean single sequence MFE	-43.84
Consensus MFE	-40.56
Energy contribution	-41.36
Covariance contribution	0.80
Combinations/Pair	1.06
Mean z-score	-3.23
Structure conservation index	0.93
SVM decision value	4.85
SVM RNA-class probability	0.999956
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6419273 120 + 20766785
UGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUGGCACUGCUAAAUGCAGCGCCAGUUAUCAAACGUAAGUGAAUUGAAUGUGCGCAGCUGCAUUGUCGGAAACCGGAAACGGAAA
.((((((..........))))))(((((...(((((((((.((((.....)))).))).((..((((((....))...))))....))...))))))))))).....(((....)))... ( -44.10)
>DroSec_CAF1 16830 120 + 1
UGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUGGCACUGCUAAAUGCAGAACCAGUUAUCAAGCGUAAGUGAAUUGAAUGUGCGCAGCUGCAUUGUCGGAAACCGGAAACGGAAA
((((((.....(((((((((..(.((......)).)..)).((((.....))))..)))))))....(((((.((.......)).))))).))))))..........(((....)))... ( -43.20)
>DroSim_CAF1 17517 120 + 1
UGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUGGCACUGCUAAAUGCAGCGCCAGUUAUCAAGCGUAAGUGAAUUGAAUGUGCGCAGCUGCAUUGUCGGAAACCGGAAACGGAAA
.((((((..........))))))(((((...(((((((((.((((.....)))).))).........(((((.((.......)).))))).))))))))))).....(((....)))... ( -47.80)
>DroEre_CAF1 14004 120 + 1
UGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUAGCAAUGCUAAAUGCAACGCCAGUUAUCAAGCGUAAGUGAAUUGAAUGUGCGCAGCUGCACUGUUGGCCACCGGAAACGGAAA
.((((((..........))))))(((..(((.((.(((((..(((.....))).(((((.(((....((....))....))).)).)))..))))))).))).))).(((....)))... ( -44.10)
>DroYak_CAF1 14474 120 + 1
UGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUGGCAGUGCUAAAUGCAACGCCAGUUAUCAAACGUAAGUGAAUUGAAUGUGCGCAGCUGCAUUGUUGAAAACCGGAAACGGAAA
.((((((..........))))))..(((.(.((((((.((..(((.....)))..((((.(((....((....))....))).)).)))).)))))).).)))....(((....)))... ( -40.00)
>consensus
UGCAGCCAUUUUGAUUGGGCUGCGGCAGGAUUGUAGUGGCACUGCUAAAUGCAGCGCCAGUUAUCAAGCGUAAGUGAAUUGAAUGUGCGCAGCUGCAUUGUCGGAAACCGGAAACGGAAA
.((((((..........))))))(((((...(((((((((.((((.....)))).))).........(((((.((.......)).))))).))))))))))).....(((....)))... (-40.56 = -41.36 +   0.80)

alignment

secondary structure

dotplot

Window 2

Location	6,419,273 – 6,419,393
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.58
Mean single sequence MFE	-31.08
Consensus MFE	-30.01
Energy contribution	-30.05
Covariance contribution	0.04
Combinations/Pair	1.12
Mean z-score	-1.80
Structure conservation index	0.97
SVM decision value	2.84
SVM RNA-class probability	0.997317
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6419273 120 - 20766785
UUUCCGUUUCCGGUUUCCGACAAUGCAGCUGCGCACAUUCAAUUCACUUACGUUUGAUAACUGGCGCUGCAUUUAGCAGUGCCACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCA
...(((....)))..........((((((((((((...((((...........))))....(((((((((.....))))))))).........)).))))))(((.......))).)))) ( -33.60)
>DroSec_CAF1 16830 120 - 1
UUUCCGUUUCCGGUUUCCGACAAUGCAGCUGCGCACAUUCAAUUCACUUACGCUUGAUAACUGGUUCUGCAUUUAGCAGUGCCACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCA
...(((....)))...........((((..(((.................)))........((((.((((.....)))).))))........)))).((((((..........)))))). ( -28.33)
>DroSim_CAF1 17517 120 - 1
UUUCCGUUUCCGGUUUCCGACAAUGCAGCUGCGCACAUUCAAUUCACUUACGCUUGAUAACUGGCGCUGCAUUUAGCAGUGCCACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCA
...(((....)))...........((((..(((.................)))........(((((((((.....)))))))))........)))).((((((..........)))))). ( -34.23)
>DroEre_CAF1 14004 120 - 1
UUUCCGUUUCCGGUGGCCAACAGUGCAGCUGCGCACAUUCAAUUCACUUACGCUUGAUAACUGGCGUUGCAUUUAGCAUUGCUACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCA
............(..((((...((((......)))).................(((((...(((.(((((...(((.((((......)))).)))..)))))))))))))..))))..). ( -31.60)
>DroYak_CAF1 14474 120 - 1
UUUCCGUUUCCGGUUUUCAACAAUGCAGCUGCGCACAUUCAAUUCACUUACGUUUGAUAACUGGCGUUGCAUUUAGCACUGCCACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCA
...........(((.......((((((((.((.((...((((...........))))....)))))))))))).......)))..............((((((..........)))))). ( -27.64)
>consensus
UUUCCGUUUCCGGUUUCCGACAAUGCAGCUGCGCACAUUCAAUUCACUUACGCUUGAUAACUGGCGCUGCAUUUAGCAGUGCCACUACAAUCCUGCCGCAGCCCAAUCAAAAUGGCUGCA
...(((....)))...........((((..(((.................)))........(((((((((.....)))))))))........)))).((((((..........)))))). (-30.01 = -30.05 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:59 2006