Locus 5268

Sequence ID	2R_DroMel_CAF1
Location	17,130,206 – 17,130,526
Length	320
Max. P	0.999853

overview

Window 8

Location	17,130,206 – 17,130,326
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.67
Mean single sequence MFE	-35.00
Consensus MFE	-31.28
Energy contribution	-31.68
Covariance contribution	0.40
Combinations/Pair	1.06
Mean z-score	-1.41
Structure conservation index	0.89
SVM decision value	0.79
SVM RNA-class probability	0.852199
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17130206 120 - 20766785
UGGUCCUAAGGAAUCGCCUUUCAAGCAGAAGUCAAUGGAUUUGCCGAUGCCGACACUCCAGGCAAAGACCACAGUGUCUACAUCAUCGAUGAAUCUCCUUCAGCGUCGGGGAUCCAAUCA
(((((((((((.....))))....((.((((.....((((((..(((((..((((((...((......))..)))))).....)))))..)))))).)))).))....)))).))).... ( -33.40)
>DroSec_CAF1 66097 120 - 1
UGGACCUAAGGAAUCGCCUUUCAAGCAGAAGUCAAUGGAUCUGCCGAUGCCGACACUCCAGGCAAAGAACACAGUGUCUACAUCAUCGAUGAAUCUCCUUCAGCGUCGGGGAUCCAACCA
.((....((((.....))))...............(((((((.(((((((.((((((...(........)..))))))..((((...))))...........)))))))))))))).)). ( -34.00)
>DroSim_CAF1 56942 120 - 1
UGGUCCUAAGGAAUCGCCUUUCAAGCAGAAGUCAAUGGAUCUGCCGAUGCCGACACUCCAGGCAAAGACCACAGUGUCUACAUCAUCGAUGAAUCUCCUUCAGCGUCGGGGAUCCAACCA
.(((...((((.....))))...............(((((((.(((((((.((((((...((......))..))))))..((((...))))...........))))))))))))))))). ( -36.70)
>DroEre_CAF1 71619 120 - 1
UGGUCCUAAGGAAUCGCCUUUCAAGCAGAAGUCAAUGGAUCUGCCGAUGCCGACACUGCAGGCAAAGACCACAGUGUCUACAUCAUCUAUGAAUCUCCUCCAACGUCGGGGAUCCAAUCA
..((...((((.....))))....)).........(((((((.((((((..(((((((..((......)).)))))))....(((....)))...........))))))))))))).... ( -33.00)
>DroYak_CAF1 73516 120 - 1
UGGUGCUAAGGAAUCGCCUUUCAAGCAGAAGUCUAUGGAUCUGCCGAUGCCGACACUCCAGGCAAAGACCACAGUGUCCACAUCAUCGAUGAAUCUUCUCCAGCGUCGGGGAUCCAAUCA
...((((((((.....))))...))))........(((((((.(((((((.((((((...((......))..))))))..((((...))))...........)))))))))))))).... ( -37.90)
>consensus
UGGUCCUAAGGAAUCGCCUUUCAAGCAGAAGUCAAUGGAUCUGCCGAUGCCGACACUCCAGGCAAAGACCACAGUGUCUACAUCAUCGAUGAAUCUCCUUCAGCGUCGGGGAUCCAAUCA
.(((...((((.....))))...............(((((((.(((((((.((((((...((......))..))))))..((((...))))...........))))))))))))))))). (-31.28 = -31.68 +   0.40)

alignment

secondary structure

dotplot

Window 9

Location	17,130,326 – 17,130,446
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-46.04
Consensus MFE	-43.48
Energy contribution	-44.12
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-1.20
Structure conservation index	0.94
SVM decision value	0.04
SVM RNA-class probability	0.553295
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17130326 120 + 20766785
CCGCCAGAGGAGGAGAACUCCACCAGGGUAAGGCACUCGGGAAGCGUUUUUAAAUUUGUGCUGGACGAGUGCAGUAACUGAUUGUGCUUGUGGGCGCUUCUCGGCGCUAGGCUUGCGCCU
..(((...((((.....))))((....))..)))....(((((((((((...............(((((..((((.....))))..))))))))))))))))(((((.......))))). ( -47.56)
>DroSec_CAF1 66217 120 + 1
CCGCCAGAGGAGGAGAACUCCACCAGGGUAAGGCACUCCGGAAGCGUUUUUAAAUUUGUGCUGGACGAGUGCAGUAACUGAUUGUGCUUGUGGGCGCUUCUCGGCGCUAGGCUUGCACCU
........((((.....))))...((((((((.(.(.((((((((((((...............(((((..((((.....))))..)))))))))))))).))).)...).))))).))) ( -41.66)
>DroSim_CAF1 57062 120 + 1
CCGCCAGAGGAGGAGAACUCCACCAGGGUAAGGCACUCCGGAAGCGUUUUUAAAUUUGUGCUGGACGAGUGCAGUAACUGAUUGUGCUUGUGGGCGCUUCUCGGCGCUAGGCUUGCACCU
........((((.....))))...((((((((.(.(.((((((((((((...............(((((..((((.....))))..)))))))))))))).))).)...).))))).))) ( -41.66)
>DroEre_CAF1 71739 120 + 1
CCGCCAGUGGAGGAGAACUCCACCAGGGUAAGGCACUCGGGAAGCGUCUUUAAAUUUGUGCUGGACGAGUGCAGUAACUGAUUGUGCUUGUGGGCGCUUCUCGGCGCUAGGCUUGCGCCU
..(((.((((((.....))))))...)))..(((.(.((((((((((((...............(((((..((((.....))))..)))))))))))))))))).)))((((....)))) ( -51.76)
>DroYak_CAF1 73636 120 + 1
CCGCCAGAGGAGGAGAACUCCACCAGGGUAAGGCACUCGGGAAGCGUUUUUAAAUUUGUGCUGGACGAGUGCAGUAACUGAUUGUGCUUGUGGGCGCUUCUCGGCGCUAGGCUUGCGCCU
..(((...((((.....))))((....))..)))....(((((((((((...............(((((..((((.....))))..))))))))))))))))(((((.......))))). ( -47.56)
>consensus
CCGCCAGAGGAGGAGAACUCCACCAGGGUAAGGCACUCGGGAAGCGUUUUUAAAUUUGUGCUGGACGAGUGCAGUAACUGAUUGUGCUUGUGGGCGCUUCUCGGCGCUAGGCUUGCGCCU
..(((...((((.....))))((....))..)))....(((((((((((...............(((((..((((.....))))..))))))))))))))))(((((.......))))). (-43.48 = -44.12 +   0.64)

alignment

secondary structure

dotplot

Window 0

Location	17,130,326 – 17,130,446
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-37.80
Consensus MFE	-35.88
Energy contribution	-36.24
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-1.23
Structure conservation index	0.95
SVM decision value	0.19
SVM RNA-class probability	0.624514
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17130326 120 - 20766785
AGGCGCAAGCCUAGCGCCGAGAAGCGCCCACAAGCACAAUCAGUUACUGCACUCGUCCAGCACAAAUUUAAAAACGCUUCCCGAGUGCCUUACCCUGGUGGAGUUCUCCUCCUCUGGCGG
((((....))))..((((.(((.((........))...(((((.....(((((((...(((..............)))...)))))))......)))))((((.....))))))))))). ( -40.24)
>DroSec_CAF1 66217 120 - 1
AGGUGCAAGCCUAGCGCCGAGAAGCGCCCACAAGCACAAUCAGUUACUGCACUCGUCCAGCACAAAUUUAAAAACGCUUCCGGAGUGCCUUACCCUGGUGGAGUUCUCCUCCUCUGGCGG
.(((((.......)))))......((((..........(((((.....((((((....(((..............)))....))))))......)))))((((.....))))...)))). ( -33.14)
>DroSim_CAF1 57062 120 - 1
AGGUGCAAGCCUAGCGCCGAGAAGCGCCCACAAGCACAAUCAGUUACUGCACUCGUCCAGCACAAAUUUAAAAACGCUUCCGGAGUGCCUUACCCUGGUGGAGUUCUCCUCCUCUGGCGG
.(((((.......)))))......((((..........(((((.....((((((....(((..............)))....))))))......)))))((((.....))))...)))). ( -33.14)
>DroEre_CAF1 71739 120 - 1
AGGCGCAAGCCUAGCGCCGAGAAGCGCCCACAAGCACAAUCAGUUACUGCACUCGUCCAGCACAAAUUUAAAGACGCUUCCCGAGUGCCUUACCCUGGUGGAGUUCUCCUCCACUGGCGG
((((....)))).((((......)))).....................(((((((...(((..............)))...)))))))....(((..((((((.....))))))..).)) ( -42.24)
>DroYak_CAF1 73636 120 - 1
AGGCGCAAGCCUAGCGCCGAGAAGCGCCCACAAGCACAAUCAGUUACUGCACUCGUCCAGCACAAAUUUAAAAACGCUUCCCGAGUGCCUUACCCUGGUGGAGUUCUCCUCCUCUGGCGG
((((....))))..((((.(((.((........))...(((((.....(((((((...(((..............)))...)))))))......)))))((((.....))))))))))). ( -40.24)
>consensus
AGGCGCAAGCCUAGCGCCGAGAAGCGCCCACAAGCACAAUCAGUUACUGCACUCGUCCAGCACAAAUUUAAAAACGCUUCCCGAGUGCCUUACCCUGGUGGAGUUCUCCUCCUCUGGCGG
((((....))))..((((.(((.((........))...(((((.....(((((((...(((..............)))...)))))))......)))))((((.....))))))))))). (-35.88 = -36.24 +   0.36)

alignment

secondary structure

dotplot

Window 1

Location	17,130,406 – 17,130,526
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.50
Mean single sequence MFE	-46.76
Consensus MFE	-40.21
Energy contribution	-40.05
Covariance contribution	-0.16
Combinations/Pair	1.09
Mean z-score	-1.45
Structure conservation index	0.86
SVM decision value	0.55
SVM RNA-class probability	0.777945
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17130406 120 + 20766785
AUUGUGCUUGUGGGCGCUUCUCGGCGCUAGGCUUGCGCCUAUUCCAAACUUCGAGCCACCGUCCACGCUACAGGCGGACUUCAGUUCAAAGUCCCCCAAACUGGGGGUUAAACUGGCGUC
....((((((((((((((....)))))..((((((................))))))..........)))))))))(((.((((((......(((((.....)))))...)))))).))) ( -43.99)
>DroSec_CAF1 66297 120 + 1
AUUGUGCUUGUGGGCGCUUCUCGGCGCUAGGCUUGCACCUAUUCCAAACUUUGAGCCACCGUCCACGCUGCAGGCGGACUUCAGUUCAAAGUCCCCCAAACUGGGGGUUAAACUGGCGUC
...((((..((.((((((....))))))..))..)))).....(((.(((((((((....((((..((.....))))))....)))))))))(((((.....)))))......))).... ( -44.80)
>DroSim_CAF1 57142 120 + 1
AUUGUGCUUGUGGGCGCUUCUCGGCGCUAGGCUUGCACCUAUUCCAAACUUUGAGCCGCCGUCCACGCUGCAGGCGGACUUCAGUUCAAAGUCCCCCAAACUGGGGGUUAAACUGGCGUC
...((((..((.((((((....))))))..))..)))).....(((.(((((((((.(..((((..((.....))))))..).)))))))))(((((.....)))))......))).... ( -45.50)
>DroEre_CAF1 71819 120 + 1
AUUGUGCUUGUGGGCGCUUCUCGGCGCUAGGCUUGCGCCUAUUCCAAACUUGGAGCCGCCGUCCACGCUGCAGGCGGACUUCAGUUCAAAGUCCCCCAGGCUGGGGGUUAAGCUGGCGUC
....((((((..(.((.....(((((.(((((....)))))(((((....))))).)))))....)))..))))))(((.((((((......(((((.....)))))...)))))).))) ( -49.20)
>DroYak_CAF1 73716 120 + 1
AUUGUGCUUGUGGGCGCUUCUCGGCGCUAGGCUUGCGCCUAUUCCAAACUUGGAGCCGCCGUCCACGCUGCAGGCGGACUUCAGUUCAAAGUCCCCAAGGCUGGGGGUUAGGCUUGCGUC
.....((..(((((((.....((((..(((((....))))).((((....)))))))).))))))))).((((((((((....))))..(..(((((....)))))..)..))))))... ( -50.30)
>consensus
AUUGUGCUUGUGGGCGCUUCUCGGCGCUAGGCUUGCGCCUAUUCCAAACUUGGAGCCGCCGUCCACGCUGCAGGCGGACUUCAGUUCAAAGUCCCCCAAACUGGGGGUUAAACUGGCGUC
....((((((((((((((....)))))..(((((..................)))))..........)))))))))(((.((((((......(((((.....)))))...)))))).))) (-40.21 = -40.05 +  -0.16)

alignment

secondary structure

dotplot

Window 2

Location	17,130,406 – 17,130,526
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.50
Mean single sequence MFE	-48.66
Consensus MFE	-46.96
Energy contribution	-46.96
Covariance contribution	0.00
Combinations/Pair	1.11
Mean z-score	-2.32
Structure conservation index	0.97
SVM decision value	4.26
SVM RNA-class probability	0.999853
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17130406 120 - 20766785
GACGCCAGUUUAACCCCCAGUUUGGGGGACUUUGAACUGAAGUCCGCCUGUAGCGUGGACGGUGGCUCGAAGUUUGGAAUAGGCGCAAGCCUAGCGCCGAGAAGCGCCCACAAGCACAAU
...(((((((((((((((.....)))))...))))))))..(((((((....).)))))).((((..((...(((((..(((((....)))))...)))))...)).))))..))..... ( -52.80)
>DroSec_CAF1 66297 120 - 1
GACGCCAGUUUAACCCCCAGUUUGGGGGACUUUGAACUGAAGUCCGCCUGCAGCGUGGACGGUGGCUCAAAGUUUGGAAUAGGUGCAAGCCUAGCGCCGAGAAGCGCCCACAAGCACAAU
..((((((((((((((((.....)))))...)))))))...(((((((....).)))))))))).......(((((...(((((....)))))((((......))))...)))))..... ( -46.30)
>DroSim_CAF1 57142 120 - 1
GACGCCAGUUUAACCCCCAGUUUGGGGGACUUUGAACUGAAGUCCGCCUGCAGCGUGGACGGCGGCUCAAAGUUUGGAAUAGGUGCAAGCCUAGCGCCGAGAAGCGCCCACAAGCACAAU
..((((((((((((((((.....)))))...)))))))...(((((((....).)))))))))).......(((((...(((((....)))))((((......))))...)))))..... ( -48.20)
>DroEre_CAF1 71819 120 - 1
GACGCCAGCUUAACCCCCAGCCUGGGGGACUUUGAACUGAAGUCCGCCUGCAGCGUGGACGGCGGCUCCAAGUUUGGAAUAGGCGCAAGCCUAGCGCCGAGAAGCGCCCACAAGCACAAU
.......((((..(((((.....)))))((((.((.(((..(((((((....).))))))..))).)).)))).(((..(((((....)))))((((......))))))).))))..... ( -50.10)
>DroYak_CAF1 73716 120 - 1
GACGCAAGCCUAACCCCCAGCCUUGGGGACUUUGAACUGAAGUCCGCCUGCAGCGUGGACGGCGGCUCCAAGUUUGGAAUAGGCGCAAGCCUAGCGCCGAGAAGCGCCCACAAGCACAAU
...((..(((....((((......)))).............(((((((....).)))))))))(((.(....(((((..(((((....)))))...)))))..).))).....))..... ( -45.90)
>consensus
GACGCCAGUUUAACCCCCAGUUUGGGGGACUUUGAACUGAAGUCCGCCUGCAGCGUGGACGGCGGCUCAAAGUUUGGAAUAGGCGCAAGCCUAGCGCCGAGAAGCGCCCACAAGCACAAU
.......((((..(((((.....)))))(((((((.(((..(((((((....).))))))..))).))))))).(((..(((((....)))))((((......))))))).))))..... (-46.96 = -46.96 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:46 2006