Locus 215

Sequence ID	3R_DroMel_CAF1
Location	881,536 – 881,748
Length	212
Max. P	0.985418

overview

Window 3

Location	881,536 – 881,631
Length	95
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	80.78
Mean single sequence MFE	-32.88
Consensus MFE	-22.80
Energy contribution	-23.93
Covariance contribution	1.13
Combinations/Pair	1.04
Mean z-score	-1.54
Structure conservation index	0.69
SVM decision value	-0.03
SVM RNA-class probability	0.518196
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 881536 95 - 27905053
GGCCGUUCCCAGGCCUUCCUUCAUUCUGCUCGG-------------------------UCUGGUACACAAGCUCCGGGCUCAAAAUCAGGCCCGGCUCAUUCGUUAUGCGCGCACAAUGA
((((.......)))).....(((((.(((.(((-------------------------..((.....))..).(((((((........))))))).............)).))).))))) ( -31.00)
>DroSec_CAF1 49577 95 - 1
GGCCUUUCCCAGGCCUUCCUUCAAUCUGCUCGG-------------------------UCUGGUCCACAAGCUCCGGGCUCAAAAUCAGGCCCGGCUCAUUCGUUAUGCGCGCACAAUGA
(((((.....)))))............(((.((-------------------------((((((.....(((.....)))....)))))))).)))....(((((.((....)).))))) ( -28.20)
>DroSim_CAF1 48780 95 - 1
GGCCUUUCCCAGGCCUUCCUUCAUUCUGCUCGG-------------------------UCUGGUCCACAAGCUCCGGGCUCAAAAUCAGGCCCGGCUCAUUCGUUAUGCGCGCACAAUGA
(((((.....))))).....(((((.(((.(((-------------------------..((.....))..).(((((((........))))))).............)).))).))))) ( -31.30)
>DroEre_CAF1 48538 116 - 1
GGCCAUUCCCAGGCCUUCG----UUCUGUUCGGUCUUCGUUCGGUCUGGUGUCUGUUGUCUGGUGCACAAGCUCCGGACUCGAAAUCAGGCCCGGCUCAUUCGCCAUGCACACACAAUGA
((((.......)))).(((----((.(((..(((((...((((((((((.(..(((.((.....)))))..).)))))).))))...))))).(((......)))......))).))))) ( -41.00)
>consensus
GGCCUUUCCCAGGCCUUCCUUCAUUCUGCUCGG_________________________UCUGGUCCACAAGCUCCGGGCUCAAAAUCAGGCCCGGCUCAUUCGUUAUGCGCGCACAAUGA
((((.......)))).....(((((.(((.((............................((.....)).(..(((((((........)))))))..)..........)).))).))))) (-22.80 = -23.93 +   1.13)

alignment

secondary structure

dotplot

Window 4

Location	881,576 – 881,668
Length	92
Sequences	3
Columns	92
Reading direction	forward
Mean pairwise identity	96.01
Mean single sequence MFE	-44.03
Consensus MFE	-40.90
Energy contribution	-41.57
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-4.37
Structure conservation index	0.93
SVM decision value	1.68
SVM RNA-class probability	0.971989
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 881576 92 + 27905053
AGCCCGGAGCUUGUGUACCAGACCGAGCAGAAUGAAGGAAGGCCUGGGAACGGCCGGGCAGACUGGUGGUCUGGAGCGGAGGGUCGGGCAUG
.((((((..(((.(((.((((((((..(((..((......((((.(....)))))...))..))).)))))))).))).))).))))))... ( -45.90)
>DroSec_CAF1 49617 92 + 1
AGCCCGGAGCUUGUGGACCAGACCGAGCAGAUUGAAGGAAGGCCUGGGAAAGGCCGUGCAGACUCGUGGUCUGGAGCGGAGGGUCGGGCAUG
.((((((..(((.((..((((((((.(.((.(((......(((((.....)))))...))).))).))))))))..)).))).))))))... ( -41.80)
>DroSim_CAF1 48820 92 + 1
AGCCCGGAGCUUGUGGACCAGACCGAGCAGAAUGAAGGAAGGCCUGGGAAAGGCCGAGCAGACUGGUGGUCUGGAGCGGAGGGUCGGGCAUG
.((((((..(((.((..((((((((..(((..((......(((((.....)))))...))..))).))))))))..)).))).))))))... ( -44.40)
>consensus
AGCCCGGAGCUUGUGGACCAGACCGAGCAGAAUGAAGGAAGGCCUGGGAAAGGCCGAGCAGACUGGUGGUCUGGAGCGGAGGGUCGGGCAUG
.((((((..(((.((..((((((((..(((..((......(((((.....)))))...))..))).))))))))..)).))).))))))... (-40.90 = -41.57 +   0.67)

alignment

secondary structure

dotplot

Window 5

Location	881,576 – 881,668
Length	92
Sequences	3
Columns	92
Reading direction	reverse
Mean pairwise identity	96.01
Mean single sequence MFE	-31.27
Consensus MFE	-29.87
Energy contribution	-30.20
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-3.01
Structure conservation index	0.96
SVM decision value	2.01
SVM RNA-class probability	0.985418
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 881576 92 - 27905053
CAUGCCCGACCCUCCGCUCCAGACCACCAGUCUGCCCGGCCGUUCCCAGGCCUUCCUUCAUUCUGCUCGGUCUGGUACACAAGCUCCGGGCU
...(((((...((.....(((((((..(((..((...((((.......))))......))..)))...)))))))......))...))))). ( -31.60)
>DroSec_CAF1 49617 92 - 1
CAUGCCCGACCCUCCGCUCCAGACCACGAGUCUGCACGGCCUUUCCCAGGCCUUCCUUCAAUCUGCUCGGUCUGGUCCACAAGCUCCGGGCU
...(((((...((.....(((((((..((((.((...(((((.....)))))......))....)))))))))))......))...))))). ( -30.30)
>DroSim_CAF1 48820 92 - 1
CAUGCCCGACCCUCCGCUCCAGACCACCAGUCUGCUCGGCCUUUCCCAGGCCUUCCUUCAUUCUGCUCGGUCUGGUCCACAAGCUCCGGGCU
...(((((...((.....(((((((..(((..((...(((((.....)))))......))..)))...)))))))......))...))))). ( -31.90)
>consensus
CAUGCCCGACCCUCCGCUCCAGACCACCAGUCUGCACGGCCUUUCCCAGGCCUUCCUUCAUUCUGCUCGGUCUGGUCCACAAGCUCCGGGCU
...(((((...((.....(((((((..(((..((...((((.......))))......))..)))...)))))))......))...))))). (-29.87 = -30.20 +   0.33)

alignment

secondary structure

dotplot

Window 6

Location	881,598 – 881,708
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.42
Mean single sequence MFE	-35.62
Consensus MFE	-28.39
Energy contribution	-28.45
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-2.62
Structure conservation index	0.80
SVM decision value	1.51
SVM RNA-class probability	0.960322
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 881598 110 + 27905053
-------CCGAGCAGAAUGAAGGAAGGCCUGGGAACGGCCG--GGCAGACUGGUGGUCUGGAGCGGAGGG-UCGGGCAUGCCAAGUGGAAAUAAAGUAAUUUAAAUAUGAUGGCAGCACA
-------((((.(............((((.(....))))).--..(((((.....)))))........).-))))((.(((((.(((....((((....))))..)))..)))))))... ( -33.80)
>DroSec_CAF1 49639 110 + 1
-------CCGAGCAGAUUGAAGGAAGGCCUGGGAAAGGCCG--UGCAGACUCGUGGUCUGGAGCGGAGGG-UCGGGCAUGCCAAGUGGAAAUAAAGUAAUUUAAAUAUGAUGGCAGCACA
-------((((.(............(((((.....)))))(--(.(((((.....)))))..))....).-))))((.(((((.(((....((((....))))..)))..)))))))... ( -36.20)
>DroSim_CAF1 48842 110 + 1
-------CCGAGCAGAAUGAAGGAAGGCCUGGGAAAGGCCG--AGCAGACUGGUGGUCUGGAGCGGAGGG-UCGGGCAUGCCAAGUGGAAAUAAAGUAAUUUAAAUAUGAUGGCAGCACA
-------((((.(............(((((.....))))).--..(((((.....)))))........).-))))((.(((((.(((....((((....))))..)))..)))))))... ( -34.80)
>DroEre_CAF1 48618 116 + 1
ACGAAGACCGAACAGAA----CGAAGGCCUGGGAAUGGCCACCAGUAGACUGGUGGUCUGGAGCGGAGGGUUCGGGCACGCCAAGUGGAAAUAAAGUAAUUUAAAUAUGAUGGCAGCACA
.......((((((....----((....((.......(((((((((....))))))))).))..))....))))))((..((((.(((....((((....))))..)))..)))).))... ( -37.70)
>consensus
_______CCGAGCAGAAUGAAGGAAGGCCUGGGAAAGGCCG__AGCAGACUGGUGGUCUGGAGCGGAGGG_UCGGGCAUGCCAAGUGGAAAUAAAGUAAUUUAAAUAUGAUGGCAGCACA
.......((((.(............((((.......)))).....(((((.....))))).........).))))((.(((((.(((.((((......))))...)))..)))))))... (-28.39 = -28.45 +   0.06)

alignment

secondary structure

dotplot

Window 7

Location	881,598 – 881,708
Length	110
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	89.42
Mean single sequence MFE	-26.08
Consensus MFE	-22.67
Energy contribution	-22.73
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-2.16
Structure conservation index	0.87
SVM decision value	1.47
SVM RNA-class probability	0.956852
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 881598 110 - 27905053
UGUGCUGCCAUCAUAUUUAAAUUACUUUAUUUCCACUUGGCAUGCCCGA-CCCUCCGCUCCAGACCACCAGUCUGCC--CGGCCGUUCCCAGGCCUUCCUUCAUUCUGCUCGG-------
...(((((((.......((((....))))........))))).))((((-..........(((((.....)))))..--.((((.......))))..............))))------- ( -24.36)
>DroSec_CAF1 49639 110 - 1
UGUGCUGCCAUCAUAUUUAAAUUACUUUAUUUCCACUUGGCAUGCCCGA-CCCUCCGCUCCAGACCACGAGUCUGCA--CGGCCUUUCCCAGGCCUUCCUUCAAUCUGCUCGG-------
...(((((((.......((((....))))........))))).))((((-..........(((((.....)))))..--.(((((.....)))))..............))))------- ( -24.66)
>DroSim_CAF1 48842 110 - 1
UGUGCUGCCAUCAUAUUUAAAUUACUUUAUUUCCACUUGGCAUGCCCGA-CCCUCCGCUCCAGACCACCAGUCUGCU--CGGCCUUUCCCAGGCCUUCCUUCAUUCUGCUCGG-------
...(((((((.......((((....))))........))))).))((((-..........(((((.....)))))..--.(((((.....)))))..............))))------- ( -24.66)
>DroEre_CAF1 48618 116 - 1
UGUGCUGCCAUCAUAUUUAAAUUACUUUAUUUCCACUUGGCGUGCCCGAACCCUCCGCUCCAGACCACCAGUCUACUGGUGGCCAUUCCCAGGCCUUCG----UUCUGUUCGGUCUUCGU
.(..(.((((.......((((....))))........)))))..).((((....(((...((((.((((((....)))))((((.......))))...)----.))))..)))..)))). ( -30.66)
>consensus
UGUGCUGCCAUCAUAUUUAAAUUACUUUAUUUCCACUUGGCAUGCCCGA_CCCUCCGCUCCAGACCACCAGUCUGCU__CGGCCUUUCCCAGGCCUUCCUUCAUUCUGCUCGG_______
...(((((((.......((((....))))........))))).))((((...........(((((.....))))).....((((.......))))..............))))....... (-22.67 = -22.73 +   0.06)

alignment

secondary structure

dotplot

Window 8

Location	881,631 – 881,748
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.50
Mean single sequence MFE	-27.84
Consensus MFE	-24.58
Energy contribution	-24.46
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-1.67
Structure conservation index	0.88
SVM decision value	0.25
SVM RNA-class probability	0.653327
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 881631 117 - 27905053
CCUUGUCGGCAAUGGCUGUUAUUCAAAGCUGCGGCCCCUUUGUGCUGCCAUCAUAUUUAAAUUACUUUAUUUCCACUUGGCAUGCCCGA-CCCUCCGCUCCAGACCACCAGUCUGCC--C
....((((((((.((((((...........))))))...))).(((((((.......((((....))))........))))).))))))-).........(((((.....)))))..--. ( -27.86)
>DroSec_CAF1 49672 117 - 1
CCUUGUCGGCAAUGGCUGUUAUUCAAAGCUGCGGCCCCUUUGUGCUGCCAUCAUAUUUAAAUUACUUUAUUUCCACUUGGCAUGCCCGA-CCCUCCGCUCCAGACCACGAGUCUGCA--C
....((((((((.((((((...........))))))...))).(((((((.......((((....))))........))))).))))))-).........(((((.....)))))..--. ( -27.86)
>DroSim_CAF1 48875 117 - 1
CCUUGUCGGCAAUGGCUGUUAUUCAAAGCUGCGGCCCCUUUGUGCUGCCAUCAUAUUUAAAUUACUUUAUUUCCACUUGGCAUGCCCGA-CCCUCCGCUCCAGACCACCAGUCUGCU--C
....((((((((.((((((...........))))))...))).(((((((.......((((....))))........))))).))))))-).........(((((.....)))))..--. ( -27.86)
>DroEre_CAF1 48654 120 - 1
CCUUGUCAGCAAUUGCUGUUAUUCAAAGCUGCGGCCCCUUUGUGCUGCCAUCAUAUUUAAAUUACUUUAUUUCCACUUGGCGUGCCCGAACCCUCCGCUCCAGACCACCAGUCUACUGGU
....((((((....)))..........(..((((....((((.(((((((.......((((....))))........))))).)).))))....))))..).))).(((((....))))) ( -27.76)
>consensus
CCUUGUCGGCAAUGGCUGUUAUUCAAAGCUGCGGCCCCUUUGUGCUGCCAUCAUAUUUAAAUUACUUUAUUUCCACUUGGCAUGCCCGA_CCCUCCGCUCCAGACCACCAGUCUGCU__C
..(((.((((....)))).....)))....((((.....(((.(((((((.......((((....))))........))))).)).))).....))))..(((((.....)))))..... (-24.58 = -24.46 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:50 2006