Locus 3908

Sequence ID	2R_DroMel_CAF1
Location	12,878,362 – 12,878,572
Length	210
Max. P	0.881214

overview

Window 8

Location	12,878,362 – 12,878,452
Length	90
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	72.16
Mean single sequence MFE	-40.97
Consensus MFE	-17.32
Energy contribution	-18.83
Covariance contribution	1.50
Combinations/Pair	1.33
Mean z-score	-1.84
Structure conservation index	0.42
SVM decision value	0.28
SVM RNA-class probability	0.665719
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12878362 90 - 20766785
UGAGCCUGCAUUUGCAGUAGUGUUGCCAUGGAAACGGCUUGA---UGCUGGGCGGGCUGAACAGGCUG------------------UGCACCAGCUGCUGCGGCCACAUAG
(.(((((((.....(((((.....(((..(....))))....---))))).))))))).)...(((((------------------((((.....))).))))))...... ( -35.40)
>DroPse_CAF1 1542 90 - 1
UGAGCCUGCAUCUGCAGCAGGGUGGCCAUGGAGACGGCCUGC---GGCUGUGGCGCCUGGACGGGCUG------------------CGGGGCAGCUGCAGCGGCCACGAAU
....(((((.......)))))((((((.((....))((.(((---((((((.((((((....)))).)------------------)...))))))))))))))))).... ( -48.70)
>DroSec_CAF1 1506 90 - 1
UGAGCCUGCAUUUGCAGUAGUGUUGCCAUGGAAACGGCUUGA---UGAUGGGCGGCCUGAACAGGCUG------------------UGCACCAGCUGCUGCGGCCACAUAG
((.(((.......((((((((...(((..(....))))....---((.((.(((((((....))))))------------------).)).)))))))))))))))..... ( -35.31)
>DroEre_CAF1 1593 90 - 1
UGCGCCUGCAUUUGCAGUAAUGUGGCCAUGGAAACGGCCUGA---GGCUGGGCGGCCUGAACCGGCUG------------------CGCACCAGCUGCUGCGGCCACAUAG
.....((((....))))..((((((((.((....))((....---((((((((((((......)))))------------------)...))))))...)))))))))).. ( -44.10)
>DroWil_CAF1 1680 107 - 1
-GGCUCUGCAUUUGCAAGAGGGCAGCCAUUGACAUGGUCUGUCCGGGCAUGGGAGGUUGCACGGGUUGCGGCACUGGGGCUGGCGGUGGGGCAGCUGGAUUGGC---AAAG
-.(((((((....)))...((((((((((....)))).))))))))))........((((.(.((((((..(((((.......)))))..)))))).)....))---)).. ( -40.60)
>DroYak_CAF1 1602 90 - 1
UGUGCCUGCAUUUGCAUCAAUGUGGCCAUGGAAACGGCUUGA---GGCUGGGCGGCCUGAACGGGCUG------------------GGCACCAGCUGCUGCGGCCACAUAG
......(((....)))...((((((((.((....))((....---(((((((((((((....))))).------------------.)).))))))...)))))))))).. ( -41.70)
>consensus
UGAGCCUGCAUUUGCAGUAGUGUGGCCAUGGAAACGGCCUGA___GGCUGGGCGGCCUGAACGGGCUG__________________UGCACCAGCUGCUGCGGCCACAUAG
...((.(((....))))).((((.(((.......(((((......))))).(((((.......(((((.......................))))))))))))).)))).. (-17.32 = -18.83 +   1.50)

alignment

secondary structure

dotplot

Window 9

Location	12,878,412 – 12,878,532
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	80.57
Mean single sequence MFE	-42.62
Consensus MFE	-26.78
Energy contribution	-27.59
Covariance contribution	0.81
Combinations/Pair	1.14
Mean z-score	-2.16
Structure conservation index	0.63
SVM decision value	0.92
SVM RNA-class probability	0.881214
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12878412 120 + 20766785
AAGCCGUUUCCAUGGCAACACUACUGCAAAUGCAGGCUCAGGCCCAGGCGCAGGCAGCACAAGUUCAGGCCCAAGCUCAGGCUCAAGCUCAAGCUCAAGCUCAGGCCCAGGCUCAGGCCC
..(((((....))))).......((((...(((.(((....)))...)))...))))..........((((..((((..((((..((((........))))..))))..))))..)))). ( -43.60)
>DroSec_CAF1 1556 120 + 1
AAGCCGUUUCCAUGGCAACACUACUGCAAAUGCAGGCUCAGGCCCAGGCGCAGGCGGCACAAGUCCAGGCCCAAGCUCAGGCUCAAGCUCAAGCUCAGGCCCAGGCCCAGGCUCAGGCCC
..(((((....))))).......((((....)))).....((((..(((...((((((....)))..((((..((((..(((....)))..))))..))))...)))...)))..)))). ( -46.10)
>DroEre_CAF1 1643 105 + 1
AGGCCGUUUCCAUGGCCACAUUACUGCAAAUGCAGGCGCAGGCACAGGCCCAGGCG---------CAGGCACAAGUUCAGGCUCAGGCCCAGGCUCAA------GCCCAGGCUCAGGCCC
.((((((....))))))......((((....))))((((.(((....)))...)))---------).(((...((((..((((..(((....)))..)------)))..))))...))). ( -46.00)
>DroYak_CAF1 1652 99 + 1
AAGCCGUUUCCAUGGCCACAUUGAUGCAAAUGCAGGCACAGGCACAAGUCCAGG---------------CCCAAGCUCAGGCUCAGGCUCAAGCUCAA------GCCCAGGCUCAGGCCC
..(((...((.(((....))).))(((....))))))...(((....)))..((---------------((..((((..((((..(((....)))..)------)))..))))..)))). ( -34.80)
>consensus
AAGCCGUUUCCAUGGCAACACUACUGCAAAUGCAGGCUCAGGCACAGGCCCAGGCG_________CAGGCCCAAGCUCAGGCUCAAGCUCAAGCUCAA______GCCCAGGCUCAGGCCC
..(((((....)))))........(((....)))((((..((((..(((...(((.............)))..((((..(((....)))..)))).........)))..))))..)))). (-26.78 = -27.59 +   0.81)

alignment

secondary structure

dotplot

Window 0

Location	12,878,412 – 12,878,532
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	80.57
Mean single sequence MFE	-50.90
Consensus MFE	-32.22
Energy contribution	-34.91
Covariance contribution	2.69
Combinations/Pair	1.06
Mean z-score	-1.93
Structure conservation index	0.63
SVM decision value	0.48
SVM RNA-class probability	0.751320
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12878412 120 - 20766785
GGGCCUGAGCCUGGGCCUGAGCUUGAGCUUGAGCUUGAGCCUGAGCUUGGGCCUGAACUUGUGCUGCCUGCGCCUGGGCCUGAGCCUGCAUUUGCAGUAGUGUUGCCAUGGAAACGGCUU
(((((..(((..((((..((((((......))))))..))))..)))..))))).(((...((((((.(((....((((....)))))))...))))))..)))(((..(....)))).. ( -54.40)
>DroSec_CAF1 1556 120 - 1
GGGCCUGAGCCUGGGCCUGGGCCUGAGCUUGAGCUUGAGCCUGAGCUUGGGCCUGGACUUGUGCCGCCUGCGCCUGGGCCUGAGCCUGCAUUUGCAGUAGUGUUGCCAUGGAAACGGCUU
((((((..((.(((((..(((((..(((((..((....))..)))))..)))))((.(....)))))))).))..))))))((((((((....))).............(....)))))) ( -56.60)
>DroEre_CAF1 1643 105 - 1
GGGCCUGAGCCUGGGC------UUGAGCCUGGGCCUGAGCCUGAACUUGUGCCUG---------CGCCUGGGCCUGUGCCUGCGCCUGCAUUUGCAGUAAUGUGGCCAUGGAAACGGCCU
(((((.(.(((..(((------....)))..)))).).))))......((((..(---------(((..((((....))))))))..))))..(((....)))((((..(....))))). ( -46.70)
>DroYak_CAF1 1652 99 - 1
GGGCCUGAGCCUGGGC------UUGAGCUUGAGCCUGAGCCUGAGCUUGGG---------------CCUGGACUUGUGCCUGUGCCUGCAUUUGCAUCAAUGUGGCCAUGGAAACGGCUU
(((((..(((..((((------((..((....))..))))))..)))..))---------------)))........(((((.(((.(((((......)))))))))).(....)))).. ( -45.90)
>consensus
GGGCCUGAGCCUGGGC______UUGAGCUUGAGCCUGAGCCUGAGCUUGGGCCUG_________CGCCUGCGCCUGGGCCUGAGCCUGCAUUUGCAGUAAUGUGGCCAUGGAAACGGCUU
((((((..((((((((....((((((((((..((....))..)))))))))).............))))))))..))))))..(((.(((((......)))))......(....)))).. (-32.22 = -34.91 +   2.69)

alignment

secondary structure

dotplot

Window 1

Location	12,878,452 – 12,878,572
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.56
Mean single sequence MFE	-45.22
Consensus MFE	-27.34
Energy contribution	-27.10
Covariance contribution	-0.25
Combinations/Pair	1.25
Mean z-score	-1.90
Structure conservation index	0.60
SVM decision value	0.17
SVM RNA-class probability	0.618418
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12878452 120 + 20766785
GGCCCAGGCGCAGGCAGCACAAGUUCAGGCCCAAGCUCAGGCUCAAGCUCAAGCUCAAGCUCAGGCCCAGGCUCAGGCCCAAAUGCGCCAGUUGGGUUCCCUGCCCAGUUCAGGACUAGC
((.((.((((((.(.(((....)))).((((..((((..((((..((((........))))..))))..))))..))))....))))))..((((((.....))))))....)).))... ( -46.30)
>DroSec_CAF1 1596 120 + 1
GGCCCAGGCGCAGGCGGCACAAGUCCAGGCCCAAGCUCAGGCUCAAGCUCAAGCUCAGGCCCAGGCCCAGGCUCAGGCCCAAAUGCGCCAGUUGGGUUCCCUGCCCAGUUCAGGUCUAGC
((((..((((((((((((....)))..((((..((((..(((....)))..))))..))))...)))..(((....)))....))))))..((((((.....))))))....)))).... ( -51.20)
>DroEre_CAF1 1683 105 + 1
GGCACAGGCCCAGGCG---------CAGGCACAAGUUCAGGCUCAGGCCCAGGCUCAA------GCCCAGGCUCAGGCCCAAAUGCGCCAGUUGGGAUCCCUGCCCAGUUCAGGACUAAC
((((..((((((((((---------(((((...((((..((((..(((....)))..)------)))..))))...)))....))))))...)))).))..))))............... ( -42.10)
>DroYak_CAF1 1692 99 + 1
GGCACAAGUCCAGG---------------CCCAAGCUCAGGCUCAGGCUCAAGCUCAA------GCCCAGGCUCAGGCCCAAAUGCGUCAGUUGGGCUCCCUGCCCAGUUCAGGACUAAC
......(((((.((---------------((..((((..((((..(((....)))..)------)))..))))..))))............((((((.....))))))....)))))... ( -41.30)
>consensus
GGCACAGGCCCAGGCG_________CAGGCCCAAGCUCAGGCUCAAGCUCAAGCUCAA______GCCCAGGCUCAGGCCCAAAUGCGCCAGUUGGGUUCCCUGCCCAGUUCAGGACUAAC
(((.(((((...(((.............)))...)))..((((..((((...(((........)))...))))..))))....)).)))..((((((.....))))))............ (-27.34 = -27.10 +  -0.25)

alignment

secondary structure

dotplot

Window 2

Location	12,878,452 – 12,878,572
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	81.56
Mean single sequence MFE	-53.23
Consensus MFE	-31.73
Energy contribution	-34.48
Covariance contribution	2.75
Combinations/Pair	1.09
Mean z-score	-2.05
Structure conservation index	0.60
SVM decision value	0.36
SVM RNA-class probability	0.703337
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12878452 120 - 20766785
GCUAGUCCUGAACUGGGCAGGGAACCCAACUGGCGCAUUUGGGCCUGAGCCUGGGCCUGAGCUUGAGCUUGAGCUUGAGCCUGAGCUUGGGCCUGAACUUGUGCUGCCUGCGCCUGGGCC
....((((......((((.((....))....((((((((..((((..(((..((((..((((((......))))))..))))..)))..))))..))..))))))))))......)))). ( -59.00)
>DroSec_CAF1 1596 120 - 1
GCUAGACCUGAACUGGGCAGGGAACCCAACUGGCGCAUUUGGGCCUGAGCCUGGGCCUGGGCCUGAGCUUGAGCUUGAGCCUGAGCUUGGGCCUGGACUUGUGCCGCCUGCGCCUGGGCC
............(..(((.((....))....((((((((..((((..(((..((((..(((((.......).))))..))))..)))..))))..))..))))))......)))..)... ( -56.60)
>DroEre_CAF1 1683 105 - 1
GUUAGUCCUGAACUGGGCAGGGAUCCCAACUGGCGCAUUUGGGCCUGAGCCUGGGC------UUGAGCCUGGGCCUGAGCCUGAACUUGUGCCUG---------CGCCUGGGCCUGUGCC
....(..(.(..(..(((.((....))....((((((((..((((.(.(((..(((------....)))..)))).).)))..))..))))))..---------.)))..)..).)..). ( -47.60)
>DroYak_CAF1 1692 99 - 1
GUUAGUCCUGAACUGGGCAGGGAGCCCAACUGACGCAUUUGGGCCUGAGCCUGGGC------UUGAGCUUGAGCCUGAGCCUGAGCUUGGG---------------CCUGGACUUGUGCC
((((((.......(((((.....)))))))))))(((((..((((..(((..((((------((..((....))..))))))..)))..))---------------))..)....)))). ( -49.71)
>consensus
GCUAGUCCUGAACUGGGCAGGGAACCCAACUGGCGCAUUUGGGCCUGAGCCUGGGC______UUGAGCUUGAGCCUGAGCCUGAGCUUGGGCCUG_________CGCCUGCGCCUGGGCC
((((((((......)))).((....))...)))).......(((((..((((((((....((((((((((..((....))..)))))))))).............))))))))..))))) (-31.73 = -34.48 +   2.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:03 2006