Locus 2200

Sequence ID	2R_DroMel_CAF1
Location	8,125,426 – 8,125,553
Length	127
Max. P	0.966621

overview

Window 8

Location	8,125,426 – 8,125,528
Length	102
Sequences	4
Columns	102
Reading direction	forward
Mean pairwise identity	98.53
Mean single sequence MFE	-35.23
Consensus MFE	-33.00
Energy contribution	-33.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.16
Structure conservation index	0.94
SVM decision value	0.66
SVM RNA-class probability	0.815355
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8125426 102 + 20766785
AGGAAGGUGGCAAACAGCCCAAGGAACUGCCAUCUACCACAUCCAAUGCAGAAGCUGCUGCCGAGGCGGCGGCCAACAAUGGCAAUUCCAUCGAGGAGCACA
.((.((((((((.....((...))...)))))))).))...(((.........((((((((....))))))))...(.((((.....)))).).)))..... ( -35.70)
>DroSec_CAF1 11725 102 + 1
AGGACGGUGGCAAACAGCCCAAGGAACUGCCAUCCACCACAUCCAAUGCAGAAGCUGCUGCCGAGGCGGCGGCCAACAAUGGCAAUUCCAUCGAGGAGCACA
....(((((((.....)))...((((.((((((........((.......)).((((((((....)))))))).....)))))).))))))))......... ( -33.90)
>DroSim_CAF1 2589 102 + 1
AGGAAGGUGGCAAACAGCCCAAGGAACUGCCAUCCACCACAUCCAAUGCAGAAGCUGCUGCCGAGGCGGCGGCCAACAAUGGCAAUUCCAUCGAGGAGCACA
.((..(((((((.....((...))...)))))))..))...(((.........((((((((....))))))))...(.((((.....)))).).)))..... ( -33.40)
>DroYak_CAF1 12123 102 + 1
AGGAAGGUGGCAAACAGCCCAAGGAGCUGCCAUCCACCACAUCCAAUGCAGAAGCUGCUGCCGAGGCGGCGGCCAACAAUGGCAAUUCCAUCGAGGAGCACA
.(((.(((((....(((((....).))))....)))))...)))..(((....((((((((....)))))))).............(((.....)))))).. ( -37.90)
>consensus
AGGAAGGUGGCAAACAGCCCAAGGAACUGCCAUCCACCACAUCCAAUGCAGAAGCUGCUGCCGAGGCGGCGGCCAACAAUGGCAAUUCCAUCGAGGAGCACA
.((..(((((((.....((...))...)))))))..))...(((.........((((((((....))))))))...(.((((.....)))).).)))..... (-33.00 = -33.00 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	8,125,426 – 8,125,528
Length	102
Sequences	4
Columns	102
Reading direction	reverse
Mean pairwise identity	98.53
Mean single sequence MFE	-40.23
Consensus MFE	-38.62
Energy contribution	-38.88
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.94
Structure conservation index	0.96
SVM decision value	0.48
SVM RNA-class probability	0.753221
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8125426 102 - 20766785
UGUGCUCCUCGAUGGAAUUGCCAUUGUUGGCCGCCGCCUCGGCAGCAGCUUCUGCAUUGGAUGUGGUAGAUGGCAGUUCCUUGGGCUGUUUGCCACCUUCCU
.........(((.((((((((((((....(((((..((...((((......))))...))..))))).)))))))))))))))(((.....)))........ ( -41.10)
>DroSec_CAF1 11725 102 - 1
UGUGCUCCUCGAUGGAAUUGCCAUUGUUGGCCGCCGCCUCGGCAGCAGCUUCUGCAUUGGAUGUGGUGGAUGGCAGUUCCUUGGGCUGUUUGCCACCGUCCU
.........(((.(((((((((((......(((((((.((.(..((((...))))..).)).)))))))))))))))))))))(((.....)))........ ( -39.20)
>DroSim_CAF1 2589 102 - 1
UGUGCUCCUCGAUGGAAUUGCCAUUGUUGGCCGCCGCCUCGGCAGCAGCUUCUGCAUUGGAUGUGGUGGAUGGCAGUUCCUUGGGCUGUUUGCCACCUUCCU
.........(((.(((((((((((......(((((((.((.(..((((...))))..).)).)))))))))))))))))))))(((.....)))........ ( -39.20)
>DroYak_CAF1 12123 102 - 1
UGUGCUCCUCGAUGGAAUUGCCAUUGUUGGCCGCCGCCUCGGCAGCAGCUUCUGCAUUGGAUGUGGUGGAUGGCAGCUCCUUGGGCUGUUUGCCACCUUCCU
.(.(((...((((((.....))))))..))))((((...)))).((((...))))...(((...(((((..(((((((.....)))))))..))))).))). ( -41.40)
>consensus
UGUGCUCCUCGAUGGAAUUGCCAUUGUUGGCCGCCGCCUCGGCAGCAGCUUCUGCAUUGGAUGUGGUGGAUGGCAGUUCCUUGGGCUGUUUGCCACCUUCCU
.........(((.((((((((((((....(((((..((...((((......))))...))..))))).)))))))))))))))(((.....)))........ (-38.62 = -38.88 +   0.25)

alignment

secondary structure

dotplot

Window 0

Location	8,125,460 – 8,125,553
Length	93
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	98.49
Mean single sequence MFE	-26.00
Consensus MFE	-25.48
Energy contribution	-25.48
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.60
Structure conservation index	0.98
SVM decision value	1.60
SVM RNA-class probability	0.966621
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8125460 93 + 20766785
UACCACAUCCAAUGCAGAAGCUGCUGCCGAGGCGGCGGCCAACAAUGGCAAUUCCAUCGAGGAGCACAAGCAGAAGAAACUAGGUAAUGACAC
((((...(((.........((((((((....))))))))...(.((((.....)))).).)))((....))...........))))....... ( -26.60)
>DroSec_CAF1 11759 93 + 1
CACCACAUCCAAUGCAGAAGCUGCUGCCGAGGCGGCGGCCAACAAUGGCAAUUCCAUCGAGGAGCACAAGCAGAAGAAACUAGGUAAUGACAC
.(((...(((.........((((((((....))))))))...(.((((.....)))).).)))((....))...........)))........ ( -25.50)
>DroSim_CAF1 2623 93 + 1
CACCACAUCCAAUGCAGAAGCUGCUGCCGAGGCGGCGGCCAACAAUGGCAAUUCCAUCGAGGAGCACAAGCAGAAGAAACUAGGUAAUGACAC
.(((...(((.........((((((((....))))))))...(.((((.....)))).).)))((....))...........)))........ ( -25.50)
>DroEre_CAF1 2761 93 + 1
CACCACAUCCAAUGCAGAAGCUGCUGCCGAGGCGGCGGCCAACAAUGGCAACUCCAUCGAGGAGCACAAGCAGAAGAAAUUAGGUAAUGACAC
.(((........(((....((((((((....))))))))......((((..(((....)))..)).)).))).((....)).)))........ ( -26.90)
>DroYak_CAF1 12157 93 + 1
CACCACAUCCAAUGCAGAAGCUGCUGCCGAGGCGGCGGCCAACAAUGGCAAUUCCAUCGAGGAGCACAAGCAGAAGAAAUUAGGUAAUGACAC
.(((...(((.........((((((((....))))))))...(.((((.....)))).).)))((....))...........)))........ ( -25.50)
>consensus
CACCACAUCCAAUGCAGAAGCUGCUGCCGAGGCGGCGGCCAACAAUGGCAAUUCCAUCGAGGAGCACAAGCAGAAGAAACUAGGUAAUGACAC
.(((...(((.........((((((((....))))))))...(.((((.....)))).).)))((....))...........)))........ (-25.48 = -25.48 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:42 2006