Locus 5006

Sequence ID	3L_DroMel_CAF1
Location	13,761,349 – 13,761,517
Length	168
Max. P	0.999835

overview

Window 9

Location	13,761,349 – 13,761,465
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.56
Mean single sequence MFE	-36.40
Consensus MFE	-23.67
Energy contribution	-25.28
Covariance contribution	1.62
Combinations/Pair	1.23
Mean z-score	-1.81
Structure conservation index	0.65
SVM decision value	0.49
SVM RNA-class probability	0.757506
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13761349 116 + 23771897
UUUAGUUAGACU--CUCAGUAAGUUUGACUGCGCAACUGUGUGGCAUUUCCGCUUCCGCAACGGAAGCUAAUGGAAAUGGAAGGGAGCAAUUGCGAGG--GUCCAAAUGACUUGGAAAUU
...(((((((((--(((.((((((((..(..(((....)))..)((((((((((((((...)))))))....))))))).....))))..))))))))--)))....)))))........ ( -37.90)
>DroGri_CAF1 14621 108 + 1
UUUA---GGACUCAGUGAGUAUGUCUGACUGCGCGACUGUGUAGCACUUCCGCUUCCGUAACGGAAGCUAAUGAACGUAGU--CGAGUAGCAGCGACGCGAACAAAAUGGC-----AG--
....---..((((...)))).((.(((.((((.(((((((((..((.....(((((((...)))))))...)).)))))))--)).)))))))))..((.(......).))-----..-- ( -30.90)
>DroSec_CAF1 7887 116 + 1
UUUAGUUAGACU--CUGAGUAAGUUUGACUGCGCAACUGUGUGGCAUUUCCGCUUCCGCAACGGAAGCUAAUGGAAAUGGAAGGGAGCAAUUGCGAGG--GUCCAAAUGACUUGGAAAUU
...........(--(..(((...((.((((.(((((.(((....((((((((((((((...)))))))....))))))).......))).)))))..)--))).))...)))..)).... ( -38.20)
>DroEre_CAF1 7145 116 + 1
UUUAGUUAGACU--CUCAGUAAGUUUGACUGCGCAACUGUGUGGCAUUUCCGCUUCCGCAACGGAAGCUAAUGGAAAUGGAAGGGAGCAAUUGCGAGG--GUCCAAAUGACUUGGAAAUU
...(((((((((--(((.((((((((..(..(((....)))..)((((((((((((((...)))))))....))))))).....))))..))))))))--)))....)))))........ ( -37.90)
>DroYak_CAF1 5158 116 + 1
UUUAGUUAGACU--CUCAGUAAGUUUGACUGCGCAACUGUGUGGCAUUUCCGCUUCCGUAACGGAAGCUAAUGGAAAUGGAAGGGAACAAUUGCGAGG--GUCCAAAUGACUUGGAAAUU
...(((((((((--(((.((((((((..(..(((....)))..)((((((((((((((...)))))))....))))))).....))))..))))))))--)))....)))))........ ( -37.90)
>DroMoj_CAF1 17698 108 + 1
UGUG---GGGCUCACUGAGUGUGUCUGACUGCGCGACUGUGUAGCACUUCCGCUUCCGCAACGGAAGCUAAUGAACAUAGC--CGAGCAGCAGCGACGCGAACAAAAUGGC-----AA--
....---..(((...((..((((((((.((((.((.((((((..((.....(((((((...)))))))...)).)))))).--)).))))))..))))))..))....)))-----..-- ( -35.60)
>consensus
UUUAGUUAGACU__CUCAGUAAGUUUGACUGCGCAACUGUGUGGCAUUUCCGCUUCCGCAACGGAAGCUAAUGGAAAUGGAAGGGAGCAAUUGCGAGG__GUCCAAAUGACUUGGAAAUU
..(((((((((...........)))))))))(((((.(((....((((((((((((((...)))))))....))))))).......))).)))))......................... (-23.67 = -25.28 +   1.62)

alignment

secondary structure

dotplot

Window 0

Location	13,761,349 – 13,761,465
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.56
Mean single sequence MFE	-33.13
Consensus MFE	-23.09
Energy contribution	-22.79
Covariance contribution	-0.30
Combinations/Pair	1.28
Mean z-score	-2.56
Structure conservation index	0.70
SVM decision value	1.24
SVM RNA-class probability	0.934601
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13761349 116 - 23771897
AAUUUCCAAGUCAUUUGGAC--CCUCGCAAUUGCUCCCUUCCAUUUCCAUUAGCUUCCGUUGCGGAAGCGGAAAUGCCACACAGUUGCGCAGUCAAACUUACUGAG--AGUCUAACUAAA
..............((((((--.((((((((((........(((((((....(((((((...)))))))))))))).....)))))))..(((.......))))))--.))))))..... ( -33.12)
>DroGri_CAF1 14621 108 - 1
--CU-----GCCAUUUUGUUCGCGUCGCUGCUACUCG--ACUACGUUCAUUAGCUUCCGUUACGGAAGCGGAAGUGCUACACAGUCGCGCAGUCAGACAUACUCACUGAGUCC---UAAA
--..-----..............((((((((....((--(((..((.((((.(((((((...)))))))...))))..))..))))).)))))..)))..((((...))))..---.... ( -28.30)
>DroSec_CAF1 7887 116 - 1
AAUUUCCAAGUCAUUUGGAC--CCUCGCAAUUGCUCCCUUCCAUUUCCAUUAGCUUCCGUUGCGGAAGCGGAAAUGCCACACAGUUGCGCAGUCAAACUUACUCAG--AGUCUAACUAAA
...(((..(((......(((--...((((((((........(((((((....(((((((...)))))))))))))).....))))))))..)))......)))..)--)).......... ( -30.62)
>DroEre_CAF1 7145 116 - 1
AAUUUCCAAGUCAUUUGGAC--CCUCGCAAUUGCUCCCUUCCAUUUCCAUUAGCUUCCGUUGCGGAAGCGGAAAUGCCACACAGUUGCGCAGUCAAACUUACUGAG--AGUCUAACUAAA
..............((((((--.((((((((((........(((((((....(((((((...)))))))))))))).....)))))))..(((.......))))))--.))))))..... ( -33.12)
>DroYak_CAF1 5158 116 - 1
AAUUUCCAAGUCAUUUGGAC--CCUCGCAAUUGUUCCCUUCCAUUUCCAUUAGCUUCCGUUACGGAAGCGGAAAUGCCACACAGUUGCGCAGUCAAACUUACUGAG--AGUCUAACUAAA
..............((((((--.(((((((((((.......(((((((....(((((((...))))))))))))))....))))))))..(((.......))))))--.))))))..... ( -34.80)
>DroMoj_CAF1 17698 108 - 1
--UU-----GCCAUUUUGUUCGCGUCGCUGCUGCUCG--GCUAUGUUCAUUAGCUUCCGUUGCGGAAGCGGAAGUGCUACACAGUCGCGCAGUCAGACACACUCAGUGAGCCC---CACA
--..-----((((((..((..(.(((...(((((.((--(((.(((......(((((((((.....)))))))))...))).))))).)))))..))).)))..)))).))..---.... ( -38.80)
>consensus
AAUUUCCAAGUCAUUUGGAC__CCUCGCAAUUGCUCCCUUCCAUUUCCAUUAGCUUCCGUUGCGGAAGCGGAAAUGCCACACAGUUGCGCAGUCAAACUUACUCAG__AGUCUAACUAAA
.................(((.....((((((((........(((((((....(((((((...)))))))))))))).....))))))))..))).......................... (-23.09 = -22.79 +  -0.30)

alignment

secondary structure

dotplot

Window 1

Location	13,761,387 – 13,761,505
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	86.74
Mean single sequence MFE	-32.57
Consensus MFE	-26.19
Energy contribution	-26.82
Covariance contribution	0.63
Combinations/Pair	1.24
Mean z-score	-3.09
Structure conservation index	0.80
SVM decision value	1.14
SVM RNA-class probability	0.921130
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13761387 118 - 23771897
UUAAAAAUUGCUUGUACAUUGUUUUUCAAUUCCAGCUUGGAAUUUCCAAGUCAUUUGGAC--CCUCGCAAUUGCUCCCUUCCAUUUCCAUUAGCUUCCGUUGCGGAAGCGGAAAUGCCAC
.....((((((......((((.....))))((((((((((.....))))))....)))).--....)))))).........(((((((....(((((((...)))))))))))))).... ( -33.10)
>DroSec_CAF1 7925 118 - 1
UUAAAAAUUGCUUGUGCAUUGUUUUUCAAUUCCAGCUUGGAAUUUCCAAGUCAUUUGGAC--CCUCGCAAUUGCUCCCUUCCAUUUCCAUUAGCUUCCGUUGCGGAAGCGGAAAUGCCAC
.........((...(((((((.....))))((((((((((.....))))))....)))).--....)))...)).......(((((((....(((((((...)))))))))))))).... ( -33.90)
>DroSim_CAF1 4505 118 - 1
UUAAAAAUUGCUUGUGCAUUGUUUUUCAAUUCCAGCUUGGAAUUUCCAAGUCAUUUGGAC--CCUCGCAAUUGCUCCCUUCCAUUUCCAUUAGCUUCCGUUGCGGAAGCGGAAAUGCCAC
.........((...(((((((.....))))((((((((((.....))))))....)))).--....)))...)).......(((((((....(((((((...)))))))))))))).... ( -33.90)
>DroEre_CAF1 7183 118 - 1
UUAAAAAUUGCUUCUACAUUGUUUUUCAAUUCCAGCUCGGAAUUUCCAAGUCAUUUGGAC--CCUCGCAAUUGCUCCCUUCCAUUUCCAUUAGCUUCCGUUGCGGAAGCGGAAAUGCCAC
.....((((((................((((((.....))))))((((((...)))))).--....)))))).........(((((((....(((((((...)))))))))))))).... ( -30.10)
>DroYak_CAF1 5196 118 - 1
UUAAAAAUUGCUUGUGCAUUGUUUUUCAAUUCCAGCUUGGAAUUUCCAAGUCAUUUGGAC--CCUCGCAAUUGUUCCCUUCCAUUUCCAUUAGCUUCCGUUACGGAAGCGGAAAUGCCAC
.....((((((......((((.....))))((((((((((.....))))))....)))).--....)))))).........(((((((....(((((((...)))))))))))))).... ( -33.10)
>DroMoj_CAF1 17735 109 - 1
UUAACAUUUGCCUG-GCAUUUUCUUAGAGUCUCGAGUCG---UU-----GCCAUUUUGUUCGCGUCGCUGCUGCUCG--GCUAUGUUCAUUAGCUUCCGUUGCGGAAGCGGAAGUGCUAC
............((-((((((((....(((..(((((.(---(.-----((.....((....))..)).)).)))))--)))..........(((((((...))))))))))))))))). ( -31.30)
>consensus
UUAAAAAUUGCUUGUGCAUUGUUUUUCAAUUCCAGCUUGGAAUUUCCAAGUCAUUUGGAC__CCUCGCAAUUGCUCCCUUCCAUUUCCAUUAGCUUCCGUUGCGGAAGCGGAAAUGCCAC
.....((((((......((((.....))))((((((((((.....))))))....)))).......)))))).........(((((((....(((((((...)))))))))))))).... (-26.19 = -26.82 +   0.63)

alignment

secondary structure

dotplot

Window 2

Location	13,761,427 – 13,761,517
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	98.00
Mean single sequence MFE	-16.22
Consensus MFE	-15.70
Energy contribution	-15.90
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.71
Structure conservation index	0.97
SVM decision value	4.20
SVM RNA-class probability	0.999835
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13761427 90 - 23771897
CCCUUUAUUUAUUUAAAAAUUGCUUGUACAUUGUUUUUCAAUUCCAGCUUGGAAUUUCCAAGUCAUUUGGACCCUCGCAAUUGCUCCCUU
.................((((((......((((.....))))((((((((((.....))))))....)))).....))))))........ ( -16.50)
>DroSec_CAF1 7965 90 - 1
CCCUUUAUUUAUUUAAAAAUUGCUUGUGCAUUGUUUUUCAAUUCCAGCUUGGAAUUUCCAAGUCAUUUGGACCCUCGCAAUUGCUCCCUU
.....................((...(((((((.....))))((((((((((.....))))))....)))).....)))...))...... ( -17.30)
>DroSim_CAF1 4545 90 - 1
CCCUUUAUUUAUUUAAAAAUUGCUUGUGCAUUGUUUUUCAAUUCCAGCUUGGAAUUUCCAAGUCAUUUGGACCCUCGCAAUUGCUCCCUU
.....................((...(((((((.....))))((((((((((.....))))))....)))).....)))...))...... ( -17.30)
>DroEre_CAF1 7223 90 - 1
CCCUUUAUUUAUUUAAAAAUUGCUUCUACAUUGUUUUUCAAUUCCAGCUCGGAAUUUCCAAGUCAUUUGGACCCUCGCAAUUGCUCCCUU
.................((((((................((((((.....))))))((((((...)))))).....))))))........ ( -13.50)
>DroYak_CAF1 5236 90 - 1
CCCUUUAUUUAUUUAAAAAUUGCUUGUGCAUUGUUUUUCAAUUCCAGCUUGGAAUUUCCAAGUCAUUUGGACCCUCGCAAUUGUUCCCUU
.................((((((......((((.....))))((((((((((.....))))))....)))).....))))))........ ( -16.50)
>consensus
CCCUUUAUUUAUUUAAAAAUUGCUUGUGCAUUGUUUUUCAAUUCCAGCUUGGAAUUUCCAAGUCAUUUGGACCCUCGCAAUUGCUCCCUU
.................((((((......((((.....))))((((((((((.....))))))....)))).....))))))........ (-15.70 = -15.90 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:27 2006