Locus 5318

Sequence ID	2R_DroMel_CAF1
Location	17,241,767 – 17,241,964
Length	197
Max. P	0.995566

overview

Window 3

Location	17,241,767 – 17,241,873
Length	106
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	81.30
Mean single sequence MFE	-18.34
Consensus MFE	-14.20
Energy contribution	-14.45
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.67
Structure conservation index	0.77
SVM decision value	0.41
SVM RNA-class probability	0.724996
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17241767 106 - 20766785
AACAACGAGCAAUAACAACAAAAGGCGCCACAAGUUGGCAGCCUUUUC-GCUCCGCCGUUUUCAUACUUCAUUCGCUUUGUGCACUUUCUUCCCCCU----------ACCCCUUUCC---
...((((.((.........(((((((((((.....)))).))))))).-.....))))))..............((.....))..............----------..........--- ( -18.46)
>DroSim_CAF1 44444 106 - 1
AACAACGAGUAAUAACAACAAAAGGCGCCACAAGUUGGCAGCCUUUUC-GCUCCGCCGUUUUCAUACUUCAUUCGCUUUGUGCACUUUCUUCCCCCU----------ACCCCUUCCC---
.(((((((((.........(((((((((((.....)))).))))))).-........((......))...)))))..))))................----------..........--- ( -17.60)
>DroEre_CAF1 43622 111 - 1
AACAACGAGUAAUAACAACAAAAGGCGCCACAAGUUGGCAGCCUUUUU-GCUCCGCCGUUUUCAUACUUCAUUCGCUUUGUGCAUUUUCUUCCC-CCA----CACUCACCCUUCACC---
......((((.........(((((((((((.....)))).))))))).-.........................((.....))...........-...----.))))..........--- ( -19.80)
>DroAna_CAF1 39308 113 - 1
AACAAC-------UACAACAAAAGGCGCCACAAGUUGGCAGCCCUUUCGGCUCUACAAUUUUCAUACUUCAUUCGCUUUGUGCAUAUUCUUCUGCCCAUUUCCCCUUGCCCCUUGCCCCC
......-------.....(((..((((....((((.(((((((.....))).......................((.....)).........)))).)))).....))))..)))..... ( -17.50)
>consensus
AACAACGAGUAAUAACAACAAAAGGCGCCACAAGUUGGCAGCCUUUUC_GCUCCGCCGUUUUCAUACUUCAUUCGCUUUGUGCACUUUCUUCCCCCC__________ACCCCUUACC___
...................(((((((((((.....)))).)))))))...........................((.....))..................................... (-14.20 = -14.45 +   0.25)

alignment

secondary structure

dotplot

Window 4

Location	17,241,794 – 17,241,907
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.77
Mean single sequence MFE	-24.95
Consensus MFE	-17.99
Energy contribution	-18.48
Covariance contribution	0.49
Combinations/Pair	1.04
Mean z-score	-2.06
Structure conservation index	0.72
SVM decision value	0.47
SVM RNA-class probability	0.747523
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17241794 113 - 20766785
AAAAGUGCAAUAACAAACAGGAA------ACAGCAACAGCAACAACGAGCAAUAACAACAAAAGGCGCCACAAGUUGGCAGCCUUUUC-GCUCCGCCGUUUUCAUACUUCAUUCGCUUUG
.((((((.(((........((((------((.((....((........)).........(((((((((((.....)))).))))))).-.....)).)))))).......))))))))). ( -26.56)
>DroSec_CAF1 41417 113 - 1
AAAAGUGCAAUAACAAACAGGAA------ACAGCAACAGCAACAACGAGUAAUAACAACAAAAGGCGCCACAAGUUGGCAGCCUUUUC-GCUCCGCCGUUUUCAUACUUCAUUCGCUUUG
.((((((.(((........((((------((.((...(((........((....))...(((((((((((.....)))).))))))).-)))..)).)))))).......))))))))). ( -26.86)
>DroSim_CAF1 44471 113 - 1
AAAAGUGCAAUAACAAACAGGAA------ACAGCAACAGCAACAACGAGUAAUAACAACAAAAGGCGCCACAAGUUGGCAGCCUUUUC-GCUCCGCCGUUUUCAUACUUCAUUCGCUUUG
.((((((.(((........((((------((.((...(((........((....))...(((((((((((.....)))).))))))).-)))..)).)))))).......))))))))). ( -26.86)
>DroEre_CAF1 43654 119 - 1
AAAAGUGCAAUAACAAACAGGAAGCAGCAACAGCAAAAGCAACAACGAGUAAUAACAACAAAAGGCGCCACAAGUUGGCAGCCUUUUU-GCUCCGCCGUUUUCAUACUUCAUUCGCUUUG
.((((((.(((........((((((.((....((....))......((((((........((((((((((.....)))).))))))))-)))).)).)))))).......))))))))). ( -30.06)
>DroAna_CAF1 39348 97 - 1
AAAAGUGCAAUAACAAACAGGAA----------------CAACAAC-------UACAACAAAAGGCGCCACAAGUUGGCAGCCCUUUCGGCUCUACAAUUUUCAUACUUCAUUCGCUUUG
....((......)).........----------------.......-------........(((((((((.....))))((((.....))))......................))))). ( -14.40)
>consensus
AAAAGUGCAAUAACAAACAGGAA______ACAGCAACAGCAACAACGAGUAAUAACAACAAAAGGCGCCACAAGUUGGCAGCCUUUUC_GCUCCGCCGUUUUCAUACUUCAUUCGCUUUG
.((((((.(((........(((..........((....))...................(((((((((((.....)))).)))))))....)))...((......))...))))))))). (-17.99 = -18.48 +   0.49)

alignment

secondary structure

dotplot

Window 5

Location	17,241,833 – 17,241,947
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.30
Mean single sequence MFE	-23.16
Consensus MFE	-22.00
Energy contribution	-22.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.82
Structure conservation index	0.95
SVM decision value	1.10
SVM RNA-class probability	0.915736
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17241833 114 - 20766785
CCCUUUCGCACACCUCUGCCUUUGUCUCUUUUCAGCACGCAAAAGUGCAAUAACAAACAGGAA------ACAGCAACAGCAACAACGAGCAAUAACAACAAAAGGCGCCACAAGUUGGCA
.................(((((((((((......((((......))))...........(...------.).((....))......)))........)).))))))((((.....)))). ( -23.30)
>DroSec_CAF1 41456 114 - 1
CCUUUUCCCACACCUCUGCCUUUGUCUCUUUCCAGCACGCAAAAGUGCAAUAACAAACAGGAA------ACAGCAACAGCAACAACGAGUAAUAACAACAAAAGGCGCCACAAGUUGGCA
.................((((((..(((......((((......))))...........(...------.).((....))......)))...........))))))((((.....)))). ( -23.32)
>DroSim_CAF1 44510 114 - 1
CCCUUUCCCACACCUCUGCCUUUGUCUCUUUUCAGCACGCAAAAGUGCAAUAACAAACAGGAA------ACAGCAACAGCAACAACGAGUAAUAACAACAAAAGGCGCCACAAGUUGGCA
.................((((((..(((......((((......))))...........(...------.).((....))......)))...........))))))((((.....)))). ( -23.32)
>DroEre_CAF1 43693 120 - 1
CUUUUUCCCGCACCUCUGCCUUUGUCUCUUUUCAGCACGCAAAAGUGCAAUAACAAACAGGAAGCAGCAACAGCAAAAGCAACAACGAGUAAUAACAACAAAAGGCGCCACAAGUUGGCA
.................((((((((..(((((..((((......))))..................((....)))))))..)).....((....))....))))))((((.....)))). ( -22.70)
>consensus
CCCUUUCCCACACCUCUGCCUUUGUCUCUUUUCAGCACGCAAAAGUGCAAUAACAAACAGGAA______ACAGCAACAGCAACAACGAGUAAUAACAACAAAAGGCGCCACAAGUUGGCA
.................(((((((((((......((((......))))........................((....))......)))........)).))))))((((.....)))). (-22.00 = -22.00 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	17,241,873 – 17,241,964
Length	91
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	83.02
Mean single sequence MFE	-36.98
Consensus MFE	-24.97
Energy contribution	-24.66
Covariance contribution	-0.31
Combinations/Pair	1.14
Mean z-score	-3.45
Structure conservation index	0.68
SVM decision value	2.59
SVM RNA-class probability	0.995566
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17241873 91 + 20766785
GCUGUUGCUGU------UUCCUGUUUGUUAUUGCACUUUUGCGUGCUGAAAAGAGACAAAGGCAGAGGUGUGCGAAAGGGAGGGGU------------------GGGCAGCCAAA
(((((..((.(------(((((.(((((....((((((((((.(.((....))......).))))))))))))))))))))).)).------------------.).)))).... ( -35.00)
>DroSec_CAF1 41496 104 + 1
GCUGUUGCUGU------UUCCUGUUUGUUAUUGCACUUUUGCGUGCUGGAAAGAGACAAAGGCAGAGGUGUGGGAAAAGGAGGGGUGU-----GCGGCGGAGCAGGGCAGCCAAA
(((.(((((((------..(((.(((....(..(((((((((.(..((........)).).)))))))))..).....))).)))...-----)))))))))).((....))... ( -37.00)
>DroSim_CAF1 44550 96 + 1
GCUGUUGCUGU------UUCCUGUUUGUUAUUGCACUUUUGCGUGCUGAAAAGAGACAAAGGCAGAGGUGUGGGAAAGGGAGGGGCGU-----G--------CAGGGCAGCCAAA
((((((.((((------..(((.(((.((.(..(((((((((.(.((....))......).)))))))))..)..)).))).)))...-----)--------))))))))).... ( -35.40)
>DroEre_CAF1 43733 108 + 1
GCUUUUGCUGUUGCUGCUUCCUGUUUGUUAUUGCACUUUUGCGUGCUGAAAAGAGACAAAGGCAGAGGUGCGGGAAAAAGAGAGAGGUGGUGGGGG-------GGGGCAGCCAAA
((((((.((.(..(..((((((.(((....((((((((((((.(.((....))......).))))))))))))...))).)).))))..)..).))-------.))).))).... ( -40.50)
>consensus
GCUGUUGCUGU______UUCCUGUUUGUUAUUGCACUUUUGCGUGCUGAAAAGAGACAAAGGCAGAGGUGUGGGAAAAGGAGGGGUGU_____G_________AGGGCAGCCAAA
......(((((......(((((.(((....((((((((((((.(..((........)).).))))))))))))...))).))))).....................))))).... (-24.97 = -24.66 +  -0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:58 2006