Locus 1909

Sequence ID	3L_DroMel_CAF1
Location	5,346,799 – 5,346,956
Length	157
Max. P	0.965500

overview

Window 7

Location	5,346,799 – 5,346,917
Length	118
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.43
Mean single sequence MFE	-33.28
Consensus MFE	-22.74
Energy contribution	-23.80
Covariance contribution	1.06
Combinations/Pair	1.08
Mean z-score	-2.66
Structure conservation index	0.68
SVM decision value	1.56
SVM RNA-class probability	0.963810
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5346799 118 + 23771897
UUACCAUGGGGGCGUAUACGUGUUAAGCGUAGGCAAAAGAUAAAUAUUGUCCUUUGGACAAUAUUUGCUCAGUUGCCCGACAGUUUUUAC--CCCAGUCCAUAGACCACAGCAACAUCUC
......(((((.....(((((.....)))))(((((..((((((((((((((...)))))))))))).))..)))))............)--))))(((....))).............. ( -36.40)
>DroSec_CAF1 94720 111 + 1
UUACCAUGGGGGCGUAUACGUGUUAAGCGUAGGCAAAAGUUAAAUAUUGUCCUUUGGACAAUAUUGGCUCAGUUGCCCGGCUGUUUUUCC--CCCAGUCC-------ACAGCAACAUCUC
......((((((....(((((.....)))))(((((.((((((.((((((((...))))))))))))))...)))))...........))--))))....-------............. ( -35.60)
>DroSim_CAF1 96483 111 + 1
UUACCAUGGGGGCGUAUACGUGUUAAGCGUAGGCAAAAGAUAAAUAUUGUCCUUUGGACAAUAUUUGCUCAGUUGCCCGGCUGUUUUUCC--CUCAGUCC-------ACAGCAACAUCUC
......((((((....(((((.....)))))(((((..((((((((((((((...)))))))))))).))..)))))...........))--))))....-------............. ( -34.40)
>DroEre_CAF1 94808 120 + 1
UUACCAUGGGGGCGUAUACGUGUUAAGCGUAGGCAAGAGAUAAAUAUUGUCCUUUGGACAAUAUUUGCUCAGUUGCCCGGCUUUUUUGCCAGCUCUGUCCGACAUCUACAGCUACAUCUC
......(((((((((.(((((.....))))).))..(((.((((((((((((...)))))))))))))))....))))(((......)))........)))................... ( -39.20)
>DroYak_CAF1 103520 90 + 1
UUACCAUGGGGGCGUAUACGUGUUAAGCGUAGGCAAAAGAUAAAUAUUGUCCUUUGGACAAUAUUUACCCAGUUGCCCGGCUUUUUU------------------------------CCC
.......((((((...(((((.....)))))(((((..(.((((((((((((...)))))))))))).)...)))))..))).....------------------------------))) ( -28.40)
>DroAna_CAF1 96909 93 + 1
UUACCAUGGGGGCGUAUACGUGUUAAGCGUAGGCAGAAGACAAAUAUUGUCCCUUCAACAAUAUUUGCUCGGCU------CUGUUUUCCC-----AC----------------UCAUCUC
......((((((....(((((.....)))))((((((.((((((((((((.......)))))))))).))...)------))))))))))-----).----------------....... ( -25.70)
>consensus
UUACCAUGGGGGCGUAUACGUGUUAAGCGUAGGCAAAAGAUAAAUAUUGUCCUUUGGACAAUAUUUGCUCAGUUGCCCGGCUGUUUUUCC__C_CAGUCC_______ACAGCAACAUCUC
.........((((((.(((((.....))))).))....(((((((((((((.....))))))))))).))....)))).......................................... (-22.74 = -23.80 +   1.06)

alignment

secondary structure

dotplot

Window 8

Location	5,346,799 – 5,346,917
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.43
Mean single sequence MFE	-33.95
Consensus MFE	-18.77
Energy contribution	-18.92
Covariance contribution	0.14
Combinations/Pair	1.13
Mean z-score	-2.77
Structure conservation index	0.55
SVM decision value	1.41
SVM RNA-class probability	0.950889
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5346799 118 - 23771897
GAGAUGUUGCUGUGGUCUAUGGACUGGG--GUAAAAACUGUCGGGCAACUGAGCAAAUAUUGUCCAAAGGACAAUAUUUAUCUUUUGCCUACGCUUAACACGUAUACGCCCCCAUGGUAA
......(((((((((((....))).(((--((..........((((((..((..(((((((((((...))))))))))).))..))))))(((.......)))....))))))))))))) ( -39.90)
>DroSec_CAF1 94720 111 - 1
GAGAUGUUGCUGU-------GGACUGGG--GGAAAAACAGCCGGGCAACUGAGCCAAUAUUGUCCAAAGGACAAUAUUUAACUUUUGCCUACGCUUAACACGUAUACGCCCCCAUGGUAA
......(((((((-------((...(((--.(..........((((((..(((..((((((((((...))))))))))...)))))))))(((.......)))...).)))))))))))) ( -33.50)
>DroSim_CAF1 96483 111 - 1
GAGAUGUUGCUGU-------GGACUGAG--GGAAAAACAGCCGGGCAACUGAGCAAAUAUUGUCCAAAGGACAAUAUUUAUCUUUUGCCUACGCUUAACACGUAUACGCCCCCAUGGUAA
......(((((((-------((.....(--((......(((.((((((..((..(((((((((((...))))))))))).))..))))))..))).....((....)))))))))))))) ( -35.70)
>DroEre_CAF1 94808 120 - 1
GAGAUGUAGCUGUAGAUGUCGGACAGAGCUGGCAAAAAAGCCGGGCAACUGAGCAAAUAUUGUCCAAAGGACAAUAUUUAUCUCUUGCCUACGCUUAACACGUAUACGCCCCCAUGGUAA
...(((..(.((((.((((.(....((((.(((......)))((((((..((..(((((((((((...))))))))))).))..))))))..))))..))))).)))).)..)))..... ( -37.00)
>DroYak_CAF1 103520 90 - 1
GGG------------------------------AAAAAAGCCGGGCAACUGGGUAAAUAUUGUCCAAAGGACAAUAUUUAUCUUUUGCCUACGCUUAACACGUAUACGCCCCCAUGGUAA
(((------------------------------....((((.((((((..(((((((((((((((...))))))))))))))).))))))..))))....((....))..)))....... ( -34.40)
>DroAna_CAF1 96909 93 - 1
GAGAUGA----------------GU-----GGGAAAACAG------AGCCGAGCAAAUAUUGUUGAAGGGACAAUAUUUGUCUUCUGCCUACGCUUAACACGUAUACGCCCCCAUGGUAA
.......----------------((-----(((....(((------((....((((((((((((.....)))))))))))).)))))..((((.......))))......)))))..... ( -23.20)
>consensus
GAGAUGUUGCUGU_______GGACUG_G__GGAAAAACAGCCGGGCAACUGAGCAAAUAUUGUCCAAAGGACAAUAUUUAUCUUUUGCCUACGCUUAACACGUAUACGCCCCCAUGGUAA
...........................................(((((..((...(((((((((.....)))))))))..))..)))))((((.......))))...(((.....))).. (-18.77 = -18.92 +   0.14)

alignment

secondary structure

dotplot

Window 9

Location	5,346,839 – 5,346,956
Length	117
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	83.60
Mean single sequence MFE	-25.52
Consensus MFE	-15.36
Energy contribution	-17.18
Covariance contribution	1.81
Combinations/Pair	1.04
Mean z-score	-2.26
Structure conservation index	0.60
SVM decision value	0.50
SVM RNA-class probability	0.760162
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5346839 117 + 23771897
UAAAUAUUGUCCUUUGGACAAUAUUUGCUCAGUUGCCCGACAGUUUUUAC--CCCAGUCCAUAGACCACAGCAACAUCUCCGCAGCGAGAAGACAAAAACUUUGCCAUAAGCGCACAAC
.(((((((((((...)))))))))))(((..(((((......((....))--....(((....)))....))))).((((......))))...................)))....... ( -22.70)
>DroSec_CAF1 94760 108 + 1
UAAAUAUUGUCCUUUGGACAAUAUUGGCUCAGUUGCCCGGCUGUUUUUCC--CCCAGUCC-------ACAGCAACAUCUCCGCAGCGAGAAGACAAAAACUUUGCCAUAAG--CACAAC
..((((((((((...))))))))))(((...(((((..(((((.......--..))))).-------...))))).((((......)))).............))).....--...... ( -28.40)
>DroSim_CAF1 96523 98 + 1
UAAAUAUUGUCCUUUGGACAAUAUUUGCUCAGUUGCCCGGCUGUUUUUCC--CUCAGUCC-------ACAGCAACAUCUCCG----------ACAAAAACUUUGCCAUAAG--CACAAC
.(((((((((((...)))))))))))(((..(((((..(((((.......--..))))).-------...)))))......(----------.(((.....))).)...))--)..... ( -23.50)
>DroEre_CAF1 94848 117 + 1
UAAAUAUUGUCCUUUGGACAAUAUUUGCUCAGUUGCCCGGCUUUUUUGCCAGCUCUGUCCGACAUCUACAGCUACAUCUCCAAUGCGAGAAGACAAAAACUUGGCCAUAAG--CACAAC
.(((((((((((...)))))))))))(((..((.(((.(((......))).....((((.(....)..........((((......)))).)))).......))).)).))--)..... ( -27.50)
>consensus
UAAAUAUUGUCCUUUGGACAAUAUUUGCUCAGUUGCCCGGCUGUUUUUCC__CCCAGUCC_______ACAGCAACAUCUCCGCAGCGAGAAGACAAAAACUUUGCCAUAAG__CACAAC
.(((((((((((...)))))))))))((..((((....(((((...........))))).................((((......)))).......))))..)).............. (-15.36 = -17.18 +   1.81)

alignment

secondary structure

dotplot

Window 0

Location	5,346,839 – 5,346,956
Length	117
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	83.60
Mean single sequence MFE	-35.12
Consensus MFE	-25.99
Energy contribution	-26.12
Covariance contribution	0.13
Combinations/Pair	1.06
Mean z-score	-2.43
Structure conservation index	0.74
SVM decision value	1.58
SVM RNA-class probability	0.965500
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5346839 117 - 23771897
GUUGUGCGCUUAUGGCAAAGUUUUUGUCUUCUCGCUGCGGAGAUGUUGCUGUGGUCUAUGGACUGGG--GUAAAAACUGUCGGGCAACUGAGCAAAUAUUGUCCAAAGGACAAUAUUUA
.....((((.....))..(((((((((((((.......))))))...(((.(((((....))))).)--))))))))).((((....))))))(((((((((((...))))))))))). ( -37.10)
>DroSec_CAF1 94760 108 - 1
GUUGUG--CUUAUGGCAAAGUUUUUGUCUUCUCGCUGCGGAGAUGUUGCUGU-------GGACUGGG--GGAAAAACAGCCGGGCAACUGAGCCAAUAUUGUCCAAAGGACAAUAUUUA
......--....((((...((((((.(((((...(..(((........))).-------.)...)))--))))))))...(((....))).))))(((((((((...)))))))))... ( -33.70)
>DroSim_CAF1 96523 98 - 1
GUUGUG--CUUAUGGCAAAGUUUUUGU----------CGGAGAUGUUGCUGU-------GGACUGAG--GGAAAAACAGCCGGGCAACUGAGCAAAUAUUGUCCAAAGGACAAUAUUUA
.....(--((((((((((.....))))----------)).....((((((.(-------((.(((..--.......)))))))))))))))))(((((((((((...))))))))))). ( -31.60)
>DroEre_CAF1 94848 117 - 1
GUUGUG--CUUAUGGCCAAGUUUUUGUCUUCUCGCAUUGGAGAUGUAGCUGUAGAUGUCGGACAGAGCUGGCAAAAAAGCCGGGCAACUGAGCAAAUAUUGUCCAAAGGACAAUAUUUA
.....(--((((..(((..((((((((((((.......))))))...........((((((......)))))).))))))..)))...)))))(((((((((((...))))))))))). ( -38.10)
>consensus
GUUGUG__CUUAUGGCAAAGUUUUUGUCUUCUCGCUGCGGAGAUGUUGCUGU_______GGACUGAG__GGAAAAACAGCCGGGCAACUGAGCAAAUAUUGUCCAAAGGACAAUAUUUA
(((........(((((((.(((((((...........))))))).)))))))........)))...............(((((....))).))(((((((((((...))))))))))). (-25.99 = -26.12 +   0.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:46 2006