Locus 7650

Sequence ID	3L_DroMel_CAF1
Location	20,566,482 – 20,566,641
Length	159
Max. P	0.984266

overview

Window 8

Location	20,566,482 – 20,566,601
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.92
Mean single sequence MFE	-35.50
Consensus MFE	-26.10
Energy contribution	-26.18
Covariance contribution	0.08
Combinations/Pair	1.14
Mean z-score	-1.58
Structure conservation index	0.74
SVM decision value	0.03
SVM RNA-class probability	0.546381
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20566482 119 + 23771897
UUUUUUUUUUGGUUAAGGUGGGGGGUGGGGGCAUGGA-CUUUGCAGGCAACAAUUUUUUGGUCUCUAAACUGACCUUAGCCAGAGAUCUGGCUUUGGGAGCUGCAAACGCAUUUCUGAUA
.....((((((((((((((.((...(((((((.....-..(((....)))(((....))))))))))..)).)))))))))))))).......(..((((.(((....)))))))..).. ( -38.40)
>DroSec_CAF1 11288 116 + 1
UUUUUU--U-AGUUGUACUGGUGGGUGGGGGGAUGGA-CUUUGCAGGCAACAAUUUUUUGGUCUCUAAACUGACCUUAGCCAGAGAUCUGGCUUUGGGAGCUGCAAACGCAUUUCUGAUA
......--.-.........(((.(((..((((((.((-.......(....)......)).))))))..))).)))..((((((....))))))(..((((.(((....)))))))..).. ( -32.72)
>DroAna_CAF1 32486 110 + 1
CCUUUUUUUU---------GGG-GUUCGAGGGAGGGAGGCUUGUAGGCAACAAUUUUUCGGUCUCUAAACUGACCUUAGCCAGAGAUCUGGCUCUGGGAGCUGCAAACGCAUUUCUGAUA
.......(((---------(((-(..(((((((..(..(((....)))..)..)))))))..)))))))....((..((((((....))))))..))(((.(((....))).)))..... ( -35.20)
>DroSim_CAF1 4947 116 + 1
UUUUCU--UAAGUUGUAGUGGA-GUUGGGGGGAUGGA-CUUUGCAGGCAACAAUUUUUUGGUCUCUAAACUGACCUUAGCCAGAGAUCUGGCUUUGGGAGCUGCAAACGCAUUUCUGAUA
......--...(((((.(..((-(((.(.....).))-)))..)..)))))........((((........))))..((((((....))))))(..((((.(((....)))))))..).. ( -34.70)
>DroEre_CAF1 4866 107 + 1
UUUU-----U------GG-GGGGUUUGGGGGGCUGGA-CUUUGUGGGCAACAAUUUUUUGGUCUCUAAACUGACCUUAGCCAGAGAUCUGGCUUUGGGAGCUGCAAACGCAUUUCUGAUA
....-----.------((-..((((((((((.(..((-..((((.....))))..))..).))))))))))..))..((((((....))))))(..((((.(((....)))))))..).. ( -36.50)
>consensus
UUUUUU__UU_GUU__AGUGGGGGUUGGGGGGAUGGA_CUUUGCAGGCAACAAUUUUUUGGUCUCUAAACUGACCUUAGCCAGAGAUCUGGCUUUGGGAGCUGCAAACGCAUUUCUGAUA
............................(((((((....(((((((.(.........(((((......)))))((..((((((....))))))..))..))))))))..))))))).... (-26.10 = -26.18 +   0.08)

alignment

secondary structure

dotplot

Window 9

Location	20,566,482 – 20,566,601
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.92
Mean single sequence MFE	-24.68
Consensus MFE	-24.26
Energy contribution	-24.02
Covariance contribution	-0.24
Combinations/Pair	1.05
Mean z-score	-1.75
Structure conservation index	0.98
SVM decision value	1.33
SVM RNA-class probability	0.942865
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20566482 119 - 23771897
UAUCAGAAAUGCGUUUGCAGCUCCCAAAGCCAGAUCUCUGGCUAAGGUCAGUUUAGAGACCAAAAAAUUGUUGCCUGCAAAG-UCCAUGCCCCCACCCCCCACCUUAACCAAAAAAAAAA
..........((((((((((.(..(((((((((....))))))..((((........))))......)))..).))))))..-...)))).............................. ( -25.60)
>DroSec_CAF1 11288 116 - 1
UAUCAGAAAUGCGUUUGCAGCUCCCAAAGCCAGAUCUCUGGCUAAGGUCAGUUUAGAGACCAAAAAAUUGUUGCCUGCAAAG-UCCAUCCCCCCACCCACCAGUACAACU-A--AAAAAA
.....((...((.(((((((.(..(((((((((....))))))..((((........))))......)))..).))))))))-)...)).....................-.--...... ( -25.30)
>DroAna_CAF1 32486 110 - 1
UAUCAGAAAUGCGUUUGCAGCUCCCAGAGCCAGAUCUCUGGCUAAGGUCAGUUUAGAGACCGAAAAAUUGUUGCCUACAAGCCUCCCUCCCUCGAAC-CCC---------AAAAAAAAGG
...((....)).((..(((((......((((((....))))))..((((........))))........)))))..))...................-...---------.......... ( -24.10)
>DroSim_CAF1 4947 116 - 1
UAUCAGAAAUGCGUUUGCAGCUCCCAAAGCCAGAUCUCUGGCUAAGGUCAGUUUAGAGACCAAAAAAUUGUUGCCUGCAAAG-UCCAUCCCCCCAAC-UCCACUACAACUUA--AGAAAA
.....((...((.(((((((.(..(((((((((....))))))..((((........))))......)))..).))))))))-)...))........-..............--...... ( -25.30)
>DroEre_CAF1 4866 107 - 1
UAUCAGAAAUGCGUUUGCAGCUCCCAAAGCCAGAUCUCUGGCUAAGGUCAGUUUAGAGACCAAAAAAUUGUUGCCCACAAAG-UCCAGCCCCCCAAACCCC-CC------A-----AAAA
...((....)).((..(((((......((((((....))))))..((((........))))........)))))..))....-..................-..------.-----.... ( -23.10)
>consensus
UAUCAGAAAUGCGUUUGCAGCUCCCAAAGCCAGAUCUCUGGCUAAGGUCAGUUUAGAGACCAAAAAAUUGUUGCCUGCAAAG_UCCAUCCCCCCAACCCCCACC__AAC_AA__AAAAAA
...((....)).((..(((((......((((((....))))))..((((........))))........)))))..)).......................................... (-24.26 = -24.02 +  -0.24)

alignment

secondary structure

dotplot

Window 0

Location	20,566,521 – 20,566,641
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.17
Mean single sequence MFE	-35.00
Consensus MFE	-34.24
Energy contribution	-34.44
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.68
Structure conservation index	0.98
SVM decision value	1.97
SVM RNA-class probability	0.984266
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20566521 120 + 23771897
UUGCAGGCAACAAUUUUUUGGUCUCUAAACUGACCUUAGCCAGAGAUCUGGCUUUGGGAGCUGCAAACGCAUUUCUGAUAAUGAUGGACUGUAUUAACCGUUAGCCAAAGUUGAAGCCAG
.....(((..((((..((((((...........((..((((((....))))))..))(((.(((....))).)))......((((((..........))))))))))))))))..))).. ( -35.10)
>DroSec_CAF1 11324 120 + 1
UUGCAGGCAACAAUUUUUUGGUCUCUAAACUGACCUUAGCCAGAGAUCUGGCUUUGGGAGCUGCAAACGCAUUUCUGAUAAUGAUGGACUGUAUUAACCGUUAGCCAAAGUUGAAGCCAG
.....(((..((((..((((((...........((..((((((....))))))..))(((.(((....))).)))......((((((..........))))))))))))))))..))).. ( -35.10)
>DroAna_CAF1 32516 120 + 1
UUGUAGGCAACAAUUUUUCGGUCUCUAAACUGACCUUAGCCAGAGAUCUGGCUCUGGGAGCUGCAAACGCAUUUCUGAUAAUGAUGGACUGUAUUAACCGUUAGCCAAAGUUGAGGCCAG
.....(((..(((((((..((((........))))..((((((....))))))..(((((.(((....))).)))......((((((..........)))))).)))))))))..))).. ( -34.80)
>DroSim_CAF1 4983 120 + 1
UUGCAGGCAACAAUUUUUUGGUCUCUAAACUGACCUUAGCCAGAGAUCUGGCUUUGGGAGCUGCAAACGCAUUUCUGAUAAUGAUGGACUGUAUUAACCGUUAGCCAAAGUUGAAGCCAG
.....(((..((((..((((((...........((..((((((....))))))..))(((.(((....))).)))......((((((..........))))))))))))))))..))).. ( -35.10)
>DroEre_CAF1 4893 120 + 1
UUGUGGGCAACAAUUUUUUGGUCUCUAAACUGACCUUAGCCAGAGAUCUGGCUUUGGGAGCUGCAAACGCAUUUCUGAUAAUGAUGGACUGUAUUAACCGUUAGCCAAAGUUGAAGCCAG
.....(((..((((..((((((...........((..((((((....))))))..))(((.(((....))).)))......((((((..........))))))))))))))))..))).. ( -34.90)
>consensus
UUGCAGGCAACAAUUUUUUGGUCUCUAAACUGACCUUAGCCAGAGAUCUGGCUUUGGGAGCUGCAAACGCAUUUCUGAUAAUGAUGGACUGUAUUAACCGUUAGCCAAAGUUGAAGCCAG
.....(((..((((..((((((...........((..((((((....))))))..))(((.(((....))).)))......((((((..........))))))))))))))))..))).. (-34.24 = -34.44 +   0.20)

alignment

secondary structure

dotplot

Window 1

Location	20,566,521 – 20,566,641
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.17
Mean single sequence MFE	-29.58
Consensus MFE	-29.40
Energy contribution	-29.00
Covariance contribution	-0.40
Combinations/Pair	1.08
Mean z-score	-1.12
Structure conservation index	0.99
SVM decision value	0.08
SVM RNA-class probability	0.572830
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20566521 120 - 23771897
CUGGCUUCAACUUUGGCUAACGGUUAAUACAGUCCAUCAUUAUCAGAAAUGCGUUUGCAGCUCCCAAAGCCAGAUCUCUGGCUAAGGUCAGUUUAGAGACCAAAAAAUUGUUGCCUGCAA
.(((((........)))))..((..........))..............((((...(((((......((((((....))))))..((((........))))........))))).)))). ( -29.50)
>DroSec_CAF1 11324 120 - 1
CUGGCUUCAACUUUGGCUAACGGUUAAUACAGUCCAUCAUUAUCAGAAAUGCGUUUGCAGCUCCCAAAGCCAGAUCUCUGGCUAAGGUCAGUUUAGAGACCAAAAAAUUGUUGCCUGCAA
.(((((........)))))..((..........))..............((((...(((((......((((((....))))))..((((........))))........))))).)))). ( -29.50)
>DroAna_CAF1 32516 120 - 1
CUGGCCUCAACUUUGGCUAACGGUUAAUACAGUCCAUCAUUAUCAGAAAUGCGUUUGCAGCUCCCAGAGCCAGAUCUCUGGCUAAGGUCAGUUUAGAGACCGAAAAAUUGUUGCCUACAA
.(((((........)))))..(((....(((((...((.......((..(((....)))..))....((((((....))))))..((((........))))))...))))).)))..... ( -31.70)
>DroSim_CAF1 4983 120 - 1
CUGGCUUCAACUUUGGCUAACGGUUAAUACAGUCCAUCAUUAUCAGAAAUGCGUUUGCAGCUCCCAAAGCCAGAUCUCUGGCUAAGGUCAGUUUAGAGACCAAAAAAUUGUUGCCUGCAA
.(((((........)))))..((..........))..............((((...(((((......((((((....))))))..((((........))))........))))).)))). ( -29.50)
>DroEre_CAF1 4893 120 - 1
CUGGCUUCAACUUUGGCUAACGGUUAAUACAGUCCAUCAUUAUCAGAAAUGCGUUUGCAGCUCCCAAAGCCAGAUCUCUGGCUAAGGUCAGUUUAGAGACCAAAAAAUUGUUGCCCACAA
.(((((........)))))..(((....(((((............((..(((....)))..))....((((((....))))))..((((........)))).....))))).)))..... ( -27.70)
>consensus
CUGGCUUCAACUUUGGCUAACGGUUAAUACAGUCCAUCAUUAUCAGAAAUGCGUUUGCAGCUCCCAAAGCCAGAUCUCUGGCUAAGGUCAGUUUAGAGACCAAAAAAUUGUUGCCUGCAA
.(((((........)))))..((..........))........((....)).((..(((((......((((((....))))))..((((........))))........)))))..)).. (-29.40 = -29.00 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:52:43 2006