Locus 1210

Sequence ID	2R_DroMel_CAF1
Location	4,806,545 – 4,806,689
Length	144
Max. P	0.991165

overview

Window 2

Location	4,806,545 – 4,806,659
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	93.33
Mean single sequence MFE	-42.48
Consensus MFE	-35.18
Energy contribution	-36.38
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-2.11
Structure conservation index	0.83
SVM decision value	1.86
SVM RNA-class probability	0.980183
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4806545 114 + 20766785
GCAGCAGCAGAAGCAGCAGCUGCUACCGUAGUGAAAUCCGAUGCAGCAUCUCGUCGGGAAAACUCACAGUUUGCUCUGCCAGGCUGCCAGGCACACAGGCAGCUAAGGACGCUG
.((((.(((((.(((((.(((((....)))))....(((((((.((...)))))))))..........).)))))))))..(((((((.(.....).)))))))......)))) ( -41.60)
>DroSec_CAF1 17849 108 + 1
GC------AGAAGCAGCAGCUGCUGCCGUAGUGAAAUCCGAUGCAGCAUCUCGUCGGGAAAACUCACAGUUUGCUCUGCCAGGCUGCCAGGCACACAGGCAGCUAAGGACGCUG
((------(((.(((((....)))))....((((..(((((((.((...))))))))).....)))).......)))))..(((((((.(.....).))))))).......... ( -38.30)
>DroSim_CAF1 17813 114 + 1
GCAGCAGCAGAAGCAGCAGCUGCUGCCGUAGUGAAAUCCGAUGCAGCAUCUCGUCGGGAAAACUCACAGUUUGCUCUGCCAGGCUGCCAGGCACACAGGCAGCUAAGGACGCUG
((((.((((((.(((((....)))))....((((..(((((((.((...))))))))).....))))..))))))))))..(((((((.(.....).))))))).......... ( -44.10)
>DroEre_CAF1 17782 114 + 1
GAAACAGCAGCAGCAGCAGCUGCUGGCGUAGUGAAAUCCGAUGGAGCAUCUCGUCGGGAAAACUCACAGUUUGCUCUGCCAGGCUGCCAAGCACACAGGCAGCAAAAGACGCUG
....((((((((((....))))))((((.((..((..(((((((......)))))))((....))....))..)).))))..((((((.........)))))).......)))) ( -44.50)
>DroYak_CAF1 15508 114 + 1
GAAACAGCAGCAGCAGCAGCUGCUGCCAUAGUGAAAUCCGAUGCAGCAUCUCGUCGGGAACACUCACAGUUUGCUCUGCCAGGCUGCCAAGCACACAGGCAGCUAAAGACGCUG
.((((.((((((((....))))))))....((((..(((((((.((...))))))))).....)))).))))(((((....(((((((.........)))))))..))).)).. ( -43.90)
>consensus
GCAACAGCAGAAGCAGCAGCUGCUGCCGUAGUGAAAUCCGAUGCAGCAUCUCGUCGGGAAAACUCACAGUUUGCUCUGCCAGGCUGCCAGGCACACAGGCAGCUAAGGACGCUG
....((((....((((.(((.((((....(((....(((((((........)))))))...)))..))))..)))))))..(((((((.........)))))))......)))) (-35.18 = -36.38 +   1.20)

alignment

secondary structure

dotplot

Window 3

Location	4,806,579 – 4,806,689
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	96.36
Mean single sequence MFE	-38.30
Consensus MFE	-35.24
Energy contribution	-35.44
Covariance contribution	0.20
Combinations/Pair	1.06
Mean z-score	-1.82
Structure conservation index	0.92
SVM decision value	2.25
SVM RNA-class probability	0.991165
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4806579 110 + 20766785
AAUCCGAUGCAGCAUCUCGUCGGGAAAACUCACAGUUUGCUCUGCCAGGCUGCCAGGCACACAGGCAGCUAAGGACGCUGCUUUGGCCCGUGGAAACACCACGUUCCCAC
...((((.(((((.(((.((.(((.((((.....)))).))).))..(((((((.(.....).)))))))..))).))))).))))..(((((.....)))))....... ( -39.20)
>DroSec_CAF1 17877 110 + 1
AAUCCGAUGCAGCAUCUCGUCGGGAAAACUCACAGUUUGCUCUGCCAGGCUGCCAGGCACACAGGCAGCUAAGGACGCUGCUUUGGCCCGUGGAAACACCACGUUCCCAC
...((((.(((((.(((.((.(((.((((.....)))).))).))..(((((((.(.....).)))))))..))).))))).))))..(((((.....)))))....... ( -39.20)
>DroSim_CAF1 17847 110 + 1
AAUCCGAUGCAGCAUCUCGUCGGGAAAACUCACAGUUUGCUCUGCCAGGCUGCCAGGCACACAGGCAGCUAAGGACGCUGCUUUGGCCCGUGGAAACACCACGUUCCCAC
...((((.(((((.(((.((.(((.((((.....)))).))).))..(((((((.(.....).)))))))..))).))))).))))..(((((.....)))))....... ( -39.20)
>DroEre_CAF1 17816 110 + 1
AAUCCGAUGGAGCAUCUCGUCGGGAAAACUCACAGUUUGCUCUGCCAGGCUGCCAAGCACACAGGCAGCAAAAGACGCUGCUUUGGCCUGUGGAAAUACCAGGUUCCCAC
.....(((((......)))))((((.....((.(((..(((((.....((((((.........))))))...))).)).))).))(((((.(......)))))))))).. ( -35.40)
>DroYak_CAF1 15542 110 + 1
AAUCCGAUGCAGCAUCUCGUCGGGAACACUCACAGUUUGCUCUGCCAGGCUGCCAAGCACACAGGCAGCUAAAGACGCUGCUUUGGCCUGUGGAAACACCAGGUUCCCAC
...((((.(((((.(((.((.(((...((.....))...))).))..(((((((.........)))))))..))).))))).))))((((((....)).))))....... ( -38.50)
>consensus
AAUCCGAUGCAGCAUCUCGUCGGGAAAACUCACAGUUUGCUCUGCCAGGCUGCCAGGCACACAGGCAGCUAAGGACGCUGCUUUGGCCCGUGGAAACACCACGUUCCCAC
...((((.(((((.(((.((.(((.((((.....)))).))).))..(((((((.........)))))))..))).))))).))))...((((.(((.....))).)))) (-35.24 = -35.44 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	4,806,579 – 4,806,689
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	96.36
Mean single sequence MFE	-42.34
Consensus MFE	-40.50
Energy contribution	-40.90
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.24
Structure conservation index	0.96
SVM decision value	0.66
SVM RNA-class probability	0.815354
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4806579 110 - 20766785
GUGGGAACGUGGUGUUUCCACGGGCCAAAGCAGCGUCCUUAGCUGCCUGUGUGCCUGGCAGCCUGGCAGAGCAAACUGUGAGUUUUCCCGACGAGAUGCUGCAUCGGAUU
...((..(((((.....)))))..))...(((((((((...((((((.........))))))((.((((......)))).))..........).))))))))........ ( -44.00)
>DroSec_CAF1 17877 110 - 1
GUGGGAACGUGGUGUUUCCACGGGCCAAAGCAGCGUCCUUAGCUGCCUGUGUGCCUGGCAGCCUGGCAGAGCAAACUGUGAGUUUUCCCGACGAGAUGCUGCAUCGGAUU
...((..(((((.....)))))..))...(((((((((...((((((.........))))))((.((((......)))).))..........).))))))))........ ( -44.00)
>DroSim_CAF1 17847 110 - 1
GUGGGAACGUGGUGUUUCCACGGGCCAAAGCAGCGUCCUUAGCUGCCUGUGUGCCUGGCAGCCUGGCAGAGCAAACUGUGAGUUUUCCCGACGAGAUGCUGCAUCGGAUU
...((..(((((.....)))))..))...(((((((((...((((((.........))))))((.((((......)))).))..........).))))))))........ ( -44.00)
>DroEre_CAF1 17816 110 - 1
GUGGGAACCUGGUAUUUCCACAGGCCAAAGCAGCGUCUUUUGCUGCCUGUGUGCUUGGCAGCCUGGCAGAGCAAACUGUGAGUUUUCCCGACGAGAUGCUCCAUCGGAUU
(((((((.......))))))).((....((((.((((....((((((.........))))))((.((((......)))).)).......))))...))))))........ ( -35.10)
>DroYak_CAF1 15542 110 - 1
GUGGGAACCUGGUGUUUCCACAGGCCAAAGCAGCGUCUUUAGCUGCCUGUGUGCUUGGCAGCCUGGCAGAGCAAACUGUGAGUGUUCCCGACGAGAUGCUGCAUCGGAUU
((((((((.....))))))))...((...((((((((((..((((((.........))))))((.((((......)))).))..........))))))))))...))... ( -44.60)
>consensus
GUGGGAACGUGGUGUUUCCACGGGCCAAAGCAGCGUCCUUAGCUGCCUGUGUGCCUGGCAGCCUGGCAGAGCAAACUGUGAGUUUUCCCGACGAGAUGCUGCAUCGGAUU
((((((((.....))))))))...((...((((((((....((((((.........))))))((.((((......)))).))............))))))))...))... (-40.50 = -40.90 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:03 2006