Locus 5728

Sequence ID	3R_DroMel_CAF1
Location	14,944,765 – 14,945,079
Length	314
Max. P	0.992519

overview

Window 2

Location	14,944,765 – 14,944,885
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.80
Mean single sequence MFE	-30.60
Consensus MFE	-25.76
Energy contribution	-26.26
Covariance contribution	0.50
Combinations/Pair	1.15
Mean z-score	-1.53
Structure conservation index	0.84
SVM decision value	0.28
SVM RNA-class probability	0.667644
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14944765 120 + 27905053
CCCAACCAACGCCACCAACUUCUCCCUUCUUUUUUUUUUAUUUUCUUUGCAACACUAAGAGGCAGGAAGAUGUGGGCGCGCUCACAGGCAUAAAUUCACAGGCUUUGGUUGAUUAAGGCA
..(((((((.(((.....(((((..((((((.........................))))))..))))).((((((....))))))..............))).)))))))......... ( -32.31)
>DroSec_CAF1 80582 115 + 1
CC-AACCAACGCCACCAACUUCCCCCUUCUUUUUUUC----UUUCUUUGCAACACUAAGAGGCAGGAAGAUGUGGGCGCGCUCACAGGCAUAAAUUCACAGGCUUUGGUUGAUUAAGGCA
.(-((((((.(((.....(((((..((((((......----...............))))))..))))).((((((....))))))..............))).)))))))......... ( -34.10)
>DroSim_CAF1 73415 115 + 1
CC-CACCAACGCCACCAACUUCCCCCUUCUUUUUUUC----UUUCUUUGCAACACUAAGAGGCAGGAAGAUGUGGGCGCGCUCACAGGCAUAAAUUCACAGGCUUUGGUUGAUUAAGGCA
.(-.(((((.(((.....(((((..((((((......----...............))))))..))))).((((((....))))))..............))).))))).)......... ( -30.00)
>DroYak_CAF1 77528 107 + 1
CC-AGCCACCGCCACCCACUUCCCCCCUUAUUU------------CUUGCAACACCAAGAGGCAGUAAGAUGUGGGCGCGCUCACAGGCAUAAAUUUACAGGCUUUGCUUGAUUAAGGAG
..-.....(((((.............(((((((------------((((......)))))...)))))).((((((....))))))))).........(((((...))))).....)).. ( -26.00)
>consensus
CC_AACCAACGCCACCAACUUCCCCCUUCUUUUUUUC____UUUCUUUGCAACACUAAGAGGCAGGAAGAUGUGGGCGCGCUCACAGGCAUAAAUUCACAGGCUUUGGUUGAUUAAGGCA
...((((((.(((.....(((((..((((((.........................))))))..))))).((((((....))))))..............))).)))))).......... (-25.76 = -26.26 +   0.50)

alignment

secondary structure

dotplot

Window 3

Location	14,944,885 – 14,944,999
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.77
Mean single sequence MFE	-23.35
Consensus MFE	-18.59
Energy contribution	-18.40
Covariance contribution	-0.19
Combinations/Pair	1.05
Mean z-score	-1.71
Structure conservation index	0.80
SVM decision value	-0.01
SVM RNA-class probability	0.527146
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14944885 114 + 27905053
GCUCCCCCGCAGCUUUUGC------UGCUCCCCCCUCCGCAUUUUCCUGGAAUAUCCUUGGCGAAAAUGAACAUAAAACAUUUCUCCGUAAUCAACUGGGCUGCUAAAAAUAAACCCAAA
((..(((.(((((....))------)))...........(((((((((((.....))..)).)))))))............................)))..))................ ( -23.70)
>DroSec_CAF1 80697 116 + 1
GCUCCCCCGCAGCUCUGGC---UGCUGCUC-CUCCUUCGCAUUUUCCUGGAAUAUCCUUGGCGAAAAUGAACAUAAAACAUUUCUCCGUAAUCAACUGGGCUGCUAAAAAUAAACCCAAA
((..(((.(((((....))---))).....-........(((((((((((.....))..)).)))))))............................)))..))................ ( -23.50)
>DroSim_CAF1 73530 119 + 1
GCUCCCCCGCAGCUCUUGCUCUUGCUGCUC-CUCCUCCGCAUUUUCCUGGAAUAUCCUUGGCGAAAAUGAACAUAAAACAUUUCUCCGUAAUCAACUGGGCUGCUAAAAAUAAACCCAAA
((..(((.(((((..........)))))..-........(((((((((((.....))..)).)))))))............................)))..))................ ( -22.80)
>DroYak_CAF1 77635 111 + 1
GCUC--CCGCAGCUCUUG------CUGCUC-CUCCUCCGCAUUUUCCUGGAAUAUCCUUGGCGAAAAUGAACAUAAAACAUUUCUCCGUAAUCAACUGGGCUGCUAAAAAUAAACCCAAA
((.(--(((((((....)------))))..-........(((((((((((.....))..)).)))))))............................)))..))................ ( -23.40)
>consensus
GCUCCCCCGCAGCUCUUGC_____CUGCUC_CUCCUCCGCAUUUUCCUGGAAUAUCCUUGGCGAAAAUGAACAUAAAACAUUUCUCCGUAAUCAACUGGGCUGCUAAAAAUAAACCCAAA
........(((((((........................(((((((((((.....))..)).)))))))........((........))........)))))))................ (-18.59 = -18.40 +  -0.19)

alignment

secondary structure

dotplot

Window 4

Location	14,944,959 – 14,945,079
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.10
Mean single sequence MFE	-42.00
Consensus MFE	-40.06
Energy contribution	-40.25
Covariance contribution	0.19
Combinations/Pair	1.09
Mean z-score	-3.75
Structure conservation index	0.95
SVM decision value	2.33
SVM RNA-class probability	0.992519
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14944959 120 + 27905053
UUUCUCCGUAAUCAACUGGGCUGCUAAAAAUAAACCCAAACUUGGCCUGCGAGGCCUUGUGGGCUAAUGCUGUAAGGCCUUUUGGUUUAGCAGCUUAGCAAGUAUGGCAACUUCAAUUAA
.....(((((.....(((((((((((((.......(((....)))((...(((((((((..(.(....))..)))))))))..)))))))))))))))....)))))............. ( -42.30)
>DroSec_CAF1 80773 118 + 1
UUUCUCCGUAAUCAACUGGGCUGCUAAAAAUAAACCCAAACUUGGCCUGCGGGGCCUU--GGGCUAAUGCUGUAAGGCCUUUUGGUUUAGCGGCUUAGCAAGUAUGGCAACUUCAAUUAA
.....(((((.....(((((((((((((.......(((((...(((((((((((((..--.))))....)))).))))).))))))))))))))))))....)))))............. ( -40.31)
>DroSim_CAF1 73609 118 + 1
UUUCUCCGUAAUCAACUGGGCUGCUAAAAAUAAACCCAAACUUGGCCUGCGGGGCCUU--GGGCUAAUGCUCUAAGGCCUUUUGGUUUAGCGGCUUAGCAAGUAUGGCAACUUCAAUUAA
.....(((((.....(((((((((((((.......(((....)))((...((((((((--((((....)).))))))))))..)))))))))))))))....)))))............. ( -43.10)
>DroYak_CAF1 77706 116 + 1
UUUCUCCGUAAUCAACUGGGCUGCUAAAAAUAAACCCAAACUCGGCCUG--GGGCCUU--GGGCUAACGCCAAAAGGCCUUUUGGUUUAGCGGCUUAGCAAGUAUGGCAACUUCAAUUAA
.....(((((.....(((((((((((((.......((......))((.(--(((((((--.(((....)))..))))))))..)))))))))))))))....)))))............. ( -42.30)
>consensus
UUUCUCCGUAAUCAACUGGGCUGCUAAAAAUAAACCCAAACUUGGCCUGCGGGGCCUU__GGGCUAAUGCUGUAAGGCCUUUUGGUUUAGCGGCUUAGCAAGUAUGGCAACUUCAAUUAA
.....(((((.....(((((((((((((.......((......))((...((((((((...(((....)))..))))))))..)))))))))))))))....)))))............. (-40.06 = -40.25 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:01 2006