Locus 6279

Sequence ID	2L_DroMel_CAF1
Location	17,480,411 – 17,480,589
Length	178
Max. P	0.998822

overview

Window 1

Location	17,480,411 – 17,480,520
Length	109
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	85.10
Mean single sequence MFE	-29.73
Consensus MFE	-25.23
Energy contribution	-24.90
Covariance contribution	-0.33
Combinations/Pair	1.10
Mean z-score	-1.61
Structure conservation index	0.85
SVM decision value	0.22
SVM RNA-class probability	0.638169
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17480411 109 + 22407834
-----------UGACCAACUGUCUUUUCGGCAGUGUGGCAACGCUGCCAAAUCAGCUGCCGGUUUGUUAUUUAACAAAAGUGGAGGAUCAUAGAGCCCAUAAAAUAAUGGAGUUCCUGAC
-----------(((((.(((......((((((((.(((((....))))).....))))))))((((((....)))))))))...)).)))..((((((((......)))).))))..... ( -34.40)
>DroSim_CAF1 1 109 + 1
-----------UGAACCACUGUCUUUUCAGCAAUGUGGCAACGCUGCCAAAUCAGCUGCCGGUUUGUUAUUUAACAAAAGUAGAGGAUCAAAUAGCCCAUAAAACAAUGGAGUUCCUGAC
-----------(((.((.(((.(((((.(((((..(((((..((((......)))))))))..))))).......)))))))).)).)))...(((((((......)))).)))...... ( -24.20)
>DroYak_CAF1 81 120 + 1
CCAAGCACUGUUAACCCAUAUUCUAUUCAGCAAUGUGGCAACGCUGCCAAAUCAGCUGCCGGUUUGUUAUUUAACAAAAGUAGAGGACCAAAGAGCCCAUGAAAUAAUGGAGUUCCUGAC
....(((.((((...(((((((((....)).))))))).)))).)))....((((.....((((..((((((.....))))))..))))...((((((((......)))).)))))))). ( -30.60)
>consensus
___________UGACCCACUGUCUUUUCAGCAAUGUGGCAACGCUGCCAAAUCAGCUGCCGGUUUGUUAUUUAACAAAAGUAGAGGAUCAAAGAGCCCAUAAAAUAAUGGAGUUCCUGAC
..........................((((......((((..((((......))))))))((((..((((((.....))))))..))))...((((((((......)))).)))))))). (-25.23 = -24.90 +  -0.33)

alignment

secondary structure

dotplot

Window 2

Location	17,480,440 – 17,480,554
Length	114
Sequences	3
Columns	114
Reading direction	forward
Mean pairwise identity	93.57
Mean single sequence MFE	-31.96
Consensus MFE	-29.45
Energy contribution	-28.79
Covariance contribution	-0.66
Combinations/Pair	1.11
Mean z-score	-1.54
Structure conservation index	0.92
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17480440 114 + 22407834
ACGCUGCCAAAUCAGCUGCCGGUUUGUUAUUUAACAAAAGUGGAGGAUCAUAGAGCCCAUAAAAUAAUGGAGUUCCUGACUAAAGUGUGGGCCAAAGAGGCAACAGCGCCCGAG
.((((((((.....(((.(((.((((((....))))))..))).((.(((..((((((((......)))).)))).)))))..))).)))(((.....)))..)))))...... ( -30.10)
>DroSim_CAF1 30 114 + 1
ACGCUGCCAAAUCAGCUGCCGGUUUGUUAUUUAACAAAAGUAGAGGAUCAAAUAGCCCAUAAAACAAUGGAGUUCCUGACUAAAGUGUGGGCCAAAGAGGCAACUGCGCCCGAG
.(((((((..(((..((((...((((((....)))))).))))..)))......(((((((.......((....)).........)))))))......))))...)))...... ( -30.79)
>DroYak_CAF1 121 114 + 1
ACGCUGCCAAAUCAGCUGCCGGUUUGUUAUUUAACAAAAGUAGAGGACCAAAGAGCCCAUGAAAUAAUGGAGUUCCUGACUAAAGUGUGGGCCAAAGAGGCAACUACGCCGGUA
..((((......))))((((((((((((....)))))..((((....(((..((((((((......)))).))))((......))..)))(((.....)))..))))))))))) ( -35.00)
>consensus
ACGCUGCCAAAUCAGCUGCCGGUUUGUUAUUUAACAAAAGUAGAGGAUCAAAGAGCCCAUAAAAUAAUGGAGUUCCUGACUAAAGUGUGGGCCAAAGAGGCAACUGCGCCCGAG
..((((......))))((((((((..((((((.....))))))..)))).....(((((((.......((....)).........)))))))......))))............ (-29.45 = -28.79 +  -0.66)

alignment

secondary structure

dotplot

Window 3

Location	17,480,480 – 17,480,589
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	78.10
Mean single sequence MFE	-29.44
Consensus MFE	-18.28
Energy contribution	-20.28
Covariance contribution	2.00
Combinations/Pair	1.00
Mean z-score	-2.05
Structure conservation index	0.62
SVM decision value	1.11
SVM RNA-class probability	0.916671
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17480480 109 + 22407834
UGGAGGAUCAUAGAGCCCAUAAAAUAAUGGAGUUCCUGACUAAAGUGUGGGCCAAAGAGGCAACAGCGCCCGAGGCAAUAGAAGCCAUCACCGGCGCAGCGCAAGAAAA
....((.(((..((((((((......)))).)))).)))))...((((..(((.....)))....(((((.(((((.......))).))...))))).))))....... ( -32.00)
>DroSec_CAF1 1 83 + 1
--------------------------AUGGAAUUCCUGACUAAAGUGUGGGCCAAAGAGGCAACUGCGCCCGAGGCAAUAGAAGACAUCACCGGCGCAGCGCAGGAAAA
--------------------------......((((((............(((.....)))..(((((((.((..(.......)...))...)))))))..)))))).. ( -24.50)
>DroSim_CAF1 70 109 + 1
UAGAGGAUCAAAUAGCCCAUAAAACAAUGGAGUUCCUGACUAAAGUGUGGGCCAAAGAGGCAACUGCGCCCGAGGCAAUAGAAGCCAUCACCGGCGCAGCGCAGGAAAA
................((((......))))..((((((............(((.....)))..(((((((.(((((.......))).))...)))))))..)))))).. ( -33.20)
>DroEre_CAF1 1 83 + 1
--------------------------AUGGAGUUCCUGACUAAAGUGUGGGCCAAAGAGGCAACUACGCCGGAAGCAUUAGAAGCCGUCACCGGCGCAGCUCAGAAAAA
--------------------------...(((((.(...((((.(((((((((.....)))..))))))(....)..))))..((((....))))).)))))....... ( -23.70)
>DroYak_CAF1 161 109 + 1
UAGAGGACCAAAGAGCCCAUGAAAUAAUGGAGUUCCUGACUAAAGUGUGGGCCAAAGAGGCAACUACGCCGGUAGCAAUAGAAGCAGUCACCGGCGCAGCCCAGAAAAA
............((((((((......)))).))))..........(.(((((.....((....)).(((((((..(..........)..)))))))..))))).).... ( -33.80)
>consensus
U_GAGGA_CA_A_AGCCCAU_AAA_AAUGGAGUUCCUGACUAAAGUGUGGGCCAAAGAGGCAACUGCGCCCGAGGCAAUAGAAGCCAUCACCGGCGCAGCGCAGGAAAA
................................((((((............(((.....)))..(((((((.(((((.......))).))...)))))))..)))))).. (-18.28 = -20.28 +   2.00)

alignment

secondary structure

dotplot

Window 4

Location	17,480,480 – 17,480,589
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	78.10
Mean single sequence MFE	-33.50
Consensus MFE	-25.98
Energy contribution	-26.30
Covariance contribution	0.32
Combinations/Pair	1.16
Mean z-score	-3.07
Structure conservation index	0.78
SVM decision value	3.24
SVM RNA-class probability	0.998822
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17480480 109 - 22407834
UUUUCUUGCGCUGCGCCGGUGAUGGCUUCUAUUGCCUCGGGCGCUGUUGCCUCUUUGGCCCACACUUUAGUCAGGAACUCCAUUAUUUUAUGGGCUCUAUGAUCCUCCA
..((((((.((((((((((..((((...))))..))...)))))(((.(((.....)))..)))....))))))))).(((((......)))))............... ( -30.60)
>DroSec_CAF1 1 83 - 1
UUUUCCUGCGCUGCGCCGGUGAUGUCUUCUAUUGCCUCGGGCGCAGUUGCCUCUUUGGCCCACACUUUAGUCAGGAAUUCCAU--------------------------
..(((((((((((((((((..(((.....)))..))...)))))))).(((.....)))..........).))))))......-------------------------- ( -31.80)
>DroSim_CAF1 70 109 - 1
UUUUCCUGCGCUGCGCCGGUGAUGGCUUCUAUUGCCUCGGGCGCAGUUGCCUCUUUGGCCCACACUUUAGUCAGGAACUCCAUUGUUUUAUGGGCUAUUUGAUCCUCUA
..(((((((((((((((((..((((...))))..))...)))))))).(((.....)))..........).)))))).(((((......)))))............... ( -36.90)
>DroEre_CAF1 1 83 - 1
UUUUUCUGAGCUGCGCCGGUGACGGCUUCUAAUGCUUCCGGCGUAGUUGCCUCUUUGGCCCACACUUUAGUCAGGAACUCCAU--------------------------
..(((((((((((((((((....(((.......))).)))))))))).(((.....)))...........)))))))......-------------------------- ( -31.40)
>DroYak_CAF1 161 109 - 1
UUUUUCUGGGCUGCGCCGGUGACUGCUUCUAUUGCUACCGGCGUAGUUGCCUCUUUGGCCCACACUUUAGUCAGGAACUCCAUUAUUUCAUGGGCUCUUUGGUCCUCUA
..(((((((((((((((((((...((.......)))))))))))))))(((.....)))............))))))..............(((((....))))).... ( -36.80)
>consensus
UUUUCCUGCGCUGCGCCGGUGAUGGCUUCUAUUGCCUCGGGCGCAGUUGCCUCUUUGGCCCACACUUUAGUCAGGAACUCCAUU_UUU_AUGGGCU_U_UG_UCCUC_A
..((((((.((((((((((((((((...))))))))...)))))))).(((.....)))............))))))................................ (-25.98 = -26.30 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:07 2006