Locus 5199

Sequence ID	2L_DroMel_CAF1
Location	14,710,629 – 14,710,758
Length	129
Max. P	0.998099

overview

Window 2

Location	14,710,629 – 14,710,725
Length	96
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	73.22
Mean single sequence MFE	-24.45
Consensus MFE	-12.96
Energy contribution	-12.77
Covariance contribution	-0.19
Combinations/Pair	1.21
Mean z-score	-1.99
Structure conservation index	0.53
SVM decision value	1.29
SVM RNA-class probability	0.938546
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14710629 96 + 22407834
UGAAAUUCAUAUGGAUGGAAAU--GGAACCACCCACACGCCACCCCACAUAUUCAGCUCCAGGAAUUUGCACCCACCUGCA--GGUGGGGCAUAACAUUC
..((((((...(((((((...(--((......)))....)))...............)))).))))))((.((((((....--))))))))......... ( -26.56)
>DroSec_CAF1 67393 96 + 1
UGAAAUUCAUAUGGAUGGAAAU--GGAACCACCCGCACGCCGCCCCACAUAUUCAGCUCCCGGAAUUUGCACCCAACUGCA--GGUGGGGCAUAACAUAC
.........((((...((...(--((......)))....))(((((((..((((........))))(((((......))))--))))))))....)))). ( -25.70)
>DroSim_CAF1 67617 96 + 1
UGAAAUUCAUAUGGAUGGAAAU--GGAACCACCCGCACGCCGCCCCACAAAUUCAGCUCCCGGAAUUUGCACCCAACUGCA--GGUGGGGCAUAACAUAC
.........((((...((...(--((......)))....))(((((((((((((........))))))(((......))).--.)))))))....)))). ( -26.70)
>DroEre_CAF1 66847 76 + 1
UGAAAUUCAUAUGGAUGGAAAU--GGCAACACCCACAUGCCGCCCCACCUAUG--------------------CACCUGCA--GGUGGGGCAUAAGAUAC
............(((((....(--(....))....))).))(((((((((..(--------------------(....)))--))))))))......... ( -27.60)
>DroYak_CAF1 66634 81 + 1
UGAAAUUCAUGUGGAUGGAUAU--GGAGCCACCCACUCGCCGCCCCACAAAUUCAGC--------------CCCACCUGCA---GUGGGGCAUAAAAUAC
.........(((((.(((...(--((......)))....)))..)))))......((--------------(((((.....---)))))))......... ( -26.60)
>DroPer_CAF1 93443 89 + 1
UGAAAUUCAUAUGGAUGGGAAGACAGACAUAUCUACACACAACCCCCCUUC--UAACCCC-----UUUU----UACCUGGAUAAGGGUGGCAUAAAAUAC
........(((((..((......))..)))))..........((.((((((--((.....-----....----....))))..)))).)).......... ( -13.52)
>consensus
UGAAAUUCAUAUGGAUGGAAAU__GGAACCACCCACACGCCGCCCCACAUAUUCAGCUCC_____UUUG__CCCACCUGCA__GGUGGGGCAUAACAUAC
.....(((((....))))).....((......)).......(((((((....................................)))))))......... (-12.96 = -12.77 +  -0.19)

alignment

secondary structure

dotplot

Window 3

Location	14,710,629 – 14,710,725
Length	96
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	73.22
Mean single sequence MFE	-32.30
Consensus MFE	-22.25
Energy contribution	-23.08
Covariance contribution	0.84
Combinations/Pair	1.33
Mean z-score	-2.46
Structure conservation index	0.69
SVM decision value	2.44
SVM RNA-class probability	0.994016
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14710629 96 - 22407834
GAAUGUUAUGCCCCACC--UGCAGGUGGGUGCAAAUUCCUGGAGCUGAAUAUGUGGGGUGGCGUGUGGGUGGUUCC--AUUUCCAUCCAUAUGAAUUUCA
((((....(((((((((--....)))))).))).))))...............((..((..(((((((((((....--....))))))))))).))..)) ( -37.20)
>DroSec_CAF1 67393 96 - 1
GUAUGUUAUGCCCCACC--UGCAGUUGGGUGCAAAUUCCGGGAGCUGAAUAUGUGGGGCGGCGUGCGGGUGGUUCC--AUUUCCAUCCAUAUGAAUUUCA
((((((..((((((((.--..((((((((.......))))...)))).....))))))))))))))((((((....--....))))))............ ( -36.90)
>DroSim_CAF1 67617 96 - 1
GUAUGUUAUGCCCCACC--UGCAGUUGGGUGCAAAUUCCGGGAGCUGAAUUUGUGGGGCGGCGUGCGGGUGGUUCC--AUUUCCAUCCAUAUGAAUUUCA
((((((..(((((((((--(......))))((((((((.(....).))))))))))))))))))))((((((....--....))))))............ ( -39.50)
>DroEre_CAF1 66847 76 - 1
GUAUCUUAUGCCCCACC--UGCAGGUG--------------------CAUAGGUGGGGCGGCAUGUGGGUGUUGCC--AUUUCCAUCCAUAUGAAUUUCA
........(((((((((--(((....)--------------------)..)))))))))).((((((((((..(..--..)..))))))))))....... ( -33.20)
>DroYak_CAF1 66634 81 - 1
GUAUUUUAUGCCCCAC---UGCAGGUGGG--------------GCUGAAUUUGUGGGGCGGCGAGUGGGUGGCUCC--AUAUCCAUCCACAUGAAUUUCA
(...((((((((((((---..(((.....--------------.))).....))))))).....((((((((....--....)))))))))))))...). ( -30.90)
>DroPer_CAF1 93443 89 - 1
GUAUUUUAUGCCACCCUUAUCCAGGUA----AAAA-----GGGGUUA--GAAGGGGGGUUGUGUGUAGAUAUGUCUGUCUUCCCAUCCAUAUGAAUUUCA
(...((((((((.(((((((((.....----....-----.))))..--.)))))))..((..((.(((((....)))))...))..))))))))...). ( -16.10)
>consensus
GUAUGUUAUGCCCCACC__UGCAGGUGGG__CAAA_____GGAGCUGAAUAUGUGGGGCGGCGUGUGGGUGGUUCC__AUUUCCAUCCAUAUGAAUUUCA
.........(((((((.....(((....................))).....)))))))..(((((((((((..........)))))))))))....... (-22.25 = -23.08 +   0.84)

alignment

secondary structure

dotplot

Window 4

Location	14,710,667 – 14,710,758
Length	91
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	71.96
Mean single sequence MFE	-25.54
Consensus MFE	-12.32
Energy contribution	-12.32
Covariance contribution	0.00
Combinations/Pair	1.20
Mean z-score	-2.91
Structure conservation index	0.48
SVM decision value	3.01
SVM RNA-class probability	0.998099
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14710667 91 + 22407834
CACCCCACAUAUUCAGCUCCAGGAAUUUGCACCCACCUGCA--GGUGGGGCAUAACAUUCUGACUGGGCUAAUGCAUUGCU-------AGCCACCCAAAU
.............(((...(((((...(((.((((((....--))))))))).....))))).)))(((((..((...)))-------))))........ ( -27.40)
>DroPse_CAF1 94452 89 + 1
AACCCCCCUUC--UAACCCC-----UUUU----UACCUGGAUAAGGGUGGCAUAAAAUACAGCUACGGCUAAUGCAUUGCCUUUCAGAAGGAACCCUAAU
......(((((--(...(((-----((.(----(.....)).))))).((((........(((....))).......))))....))))))......... ( -23.46)
>DroSec_CAF1 67431 91 + 1
CGCCCCACAUAUUCAGCUCCCGGAAUUUGCACCCAACUGCA--GGUGGGGCAUAACAUACUGACUGGGCUAAUGCAUUGCU-------AGCCACCCAAAU
.(((((((..((((........))))(((((......))))--))))))))...............(((((..((...)))-------))))........ ( -26.40)
>DroSim_CAF1 67655 91 + 1
CGCCCCACAAAUUCAGCUCCCGGAAUUUGCACCCAACUGCA--GGUGGGGCAUAACAUACUGACUGGGCUAAUGCAUUGCU-------AGCCACCUAAAU
.(((((((((((((........))))))(((......))).--.)))))))...............(((((..((...)))-------))))........ ( -27.40)
>DroEre_CAF1 66885 71 + 1
CGCCCCACCUAUG--------------------CACCUGCA--GGUGGGGCAUAAGAUACUGCCAAGGCUAAUGCAUUGCU-------AGCCACCCAAAU
.(((((((((..(--------------------(....)))--))))))))...............(((((..((...)))-------))))........ ( -27.70)
>DroYak_CAF1 66672 76 + 1
CGCCCCACAAAUUCAGC--------------CCCACCUGCA---GUGGGGCAUAAAAUACUGCCUGGGCUAAUGCAUUGCC-------AGCCACCCAAAU
.(((((((.....(((.--------------.....)))..---))))))).........((.((((((....))....))-------)).))....... ( -20.90)
>consensus
CGCCCCACAUAUUCAGCUCC_____UUUG__CCCACCUGCA__GGUGGGGCAUAACAUACUGACUGGGCUAAUGCAUUGCU_______AGCCACCCAAAU
.(((((((....................................)))))))...............(((.........)))................... (-12.32 = -12.32 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	14,710,667 – 14,710,758
Length	91
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	71.96
Mean single sequence MFE	-28.89
Consensus MFE	-17.84
Energy contribution	-18.29
Covariance contribution	0.45
Combinations/Pair	1.33
Mean z-score	-1.65
Structure conservation index	0.62
SVM decision value	1.22
SVM RNA-class probability	0.932035
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14710667 91 - 22407834
AUUUGGGUGGCU-------AGCAAUGCAUUAGCCCAGUCAGAAUGUUAUGCCCCACC--UGCAGGUGGGUGCAAAUUCCUGGAGCUGAAUAUGUGGGGUG
............-------.((..(((((((((((((...((((....(((((((((--....)))))).))).)))))))).)))))...))))..)). ( -31.00)
>DroPse_CAF1 94452 89 - 1
AUUAGGGUUCCUUCUGAAAGGCAAUGCAUUAGCCGUAGCUGUAUUUUAUGCCACCCUUAUCCAGGUA----AAAA-----GGGGUUA--GAAGGGGGGUU
.......((((((((((..((((......((((....)))).......)))).(((((.........----..))-----))).)))--))))))).... ( -25.42)
>DroSec_CAF1 67431 91 - 1
AUUUGGGUGGCU-------AGCAAUGCAUUAGCCCAGUCAGUAUGUUAUGCCCCACC--UGCAGUUGGGUGCAAAUUCCGGGAGCUGAAUAUGUGGGGCG
..((((((.((.-------......))....))))))............(((((((.--..((((((((.......))))...)))).....))))))). ( -30.80)
>DroSim_CAF1 67655 91 - 1
AUUUAGGUGGCU-------AGCAAUGCAUUAGCCCAGUCAGUAUGUUAUGCCCCACC--UGCAGUUGGGUGCAAAUUCCGGGAGCUGAAUUUGUGGGGCG
......(.((((-------((.......)))))))..............((((((((--(......))))((((((((.(....).))))))))))))). ( -29.70)
>DroEre_CAF1 66885 71 - 1
AUUUGGGUGGCU-------AGCAAUGCAUUAGCCUUGGCAGUAUCUUAUGCCCCACC--UGCAGGUG--------------------CAUAGGUGGGGCG
........((((-------((.......))))))...............((((((((--(((....)--------------------)..))))))))). ( -27.10)
>DroYak_CAF1 66672 76 - 1
AUUUGGGUGGCU-------GGCAAUGCAUUAGCCCAGGCAGUAUUUUAUGCCCCAC---UGCAGGUGGG--------------GCUGAAUUUGUGGGGCG
.........((.-------......))....((((..((((.((((...(((((((---.....)))))--------------)).)))))))).)))). ( -29.30)
>consensus
AUUUGGGUGGCU_______AGCAAUGCAUUAGCCCAGGCAGUAUGUUAUGCCCCACC__UGCAGGUGGG__CAAA_____GGAGCUGAAUAUGUGGGGCG
..((((((.((..............))....))))))............(((((((.....(((....................))).....))))))). (-17.84 = -18.29 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:25 2006