Locus 3595

Sequence ID	3L_DroMel_CAF1
Location	10,579,754 – 10,579,975
Length	221
Max. P	0.868329

overview

Window 2

Location	10,579,754 – 10,579,845
Length	91
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.36
Mean single sequence MFE	-16.61
Consensus MFE	-11.14
Energy contribution	-11.00
Covariance contribution	-0.14
Combinations/Pair	1.10
Mean z-score	-1.08
Structure conservation index	0.67
SVM decision value	-0.04
SVM RNA-class probability	0.513644
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10579754 91 + 23771897
AGCUA---CUCUUUCCACAUUCUACUUACCAUUUG------------UGCUCC----G----------CUCCAGCUCGCUUAUCGUCUGCUGCACACGCAGCUGCAACGUUUUUGCAUGU
((((.---.......((((..............))------------))....----.----------....)))).((....(((..(((((....)))))....))).....)).... ( -15.97)
>DroSec_CAF1 459163 90 + 1
AG-UC---CUCUUUCCACAUUCAACUUACCAUUUG------------UGCUCC----G----------CUCCAGCUCGCUUAUCGUCUGCUGCACACGCAGCUGCAACGUUUUUGCAUGU
..-..---........((((.(((...((...(((------------((((.(----(----------...((((..((.....))..))))....)).))).)))).))..))).)))) ( -14.80)
>DroEre_CAF1 468489 101 + 1
AACUC---CGCUUUCCACAUUCAACUUACCAUUUG------------UGCUCC----GCUCCGGUCCGCUCCAGCUCGCUUAUCGUCUGCUGCACACGCAGCUGCAACAUUUUUGCAUGU
.....---.((....((((..............))------------))....----))..((((..((........))..))))...(((((....)))))(((((.....)))))... ( -18.24)
>DroYak_CAF1 470321 94 + 1
AGCUCCUCCUCUUUCCACAUUCAACUUACCAUUUG------------UGCUCC----G----------CUCCAGCUCGCUUAUCGUCUGCUGCACACGCAGCUGCAACGUUUUUGCAUGU
(((............((((..............))------------))....----(----------(....))..)))........(((((....)))))(((((.....)))))... ( -15.74)
>DroAna_CAF1 452390 70 + 1
-------------UCCACUUUCAACUU-CCAUUUG------------------------------------CAGCUCGCUUAUCGUCUGUUGCACACGCAGCUGCAACCUUUUUGCAUGU
-------------..............-....(((------------------------------------(((((.((..................))))))))))............. ( -12.27)
>DroPer_CAF1 525956 105 + 1
AG-UA---ACAGCUCCACUUUCAACUU-CCAUUUGCAGCUGCCUCUCUGCUUCUCUGG----------CUCCUUUUCGCUUAUCGGCUGCUGCACACGCAGCUGCAACGUUUUUGCAUGU
.(-((---(.(((..............-....((((((((((......((..((..((----------(........)))....))..)).......)))))))))).))).)))).... ( -22.63)
>consensus
AG_UC___CUCUUUCCACAUUCAACUUACCAUUUG____________UGCUCC____G__________CUCCAGCUCGCUUAUCGUCUGCUGCACACGCAGCUGCAACGUUUUUGCAUGU
........................................................................................(((((....)))))(((((.....)))))... (-11.14 = -11.00 +  -0.14)

alignment

secondary structure

dotplot

Window 3

Location	10,579,805 – 10,579,902
Length	97
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	72.39
Mean single sequence MFE	-25.40
Consensus MFE	-12.90
Energy contribution	-13.70
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.88
Structure conservation index	0.51
SVM decision value	0.86
SVM RNA-class probability	0.868329
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10579805 97 + 23771897
UAUCGUCUGCUGCACACGCAGCUGCAACGUUUUUGCAUGUUGCUGGCUUUUUUGCUAC--CAAUUCCGGGUGACCCCUCCGUCCACCGUCC------------UCCGC--CAA
........(((((....))))).(((((((......)))))))((((....(((....--)))...(((..(((......)))..)))...------------...))--)). ( -26.20)
>DroPse_CAF1 516769 91 + 1
UAUCGGCUGCUGCACACGCAGCUGCAACGUUUUUGCAUGUUUCUGACUUUUU-GCUCCAGCAACA---------GCACCCGUACCCGGGCC------------AGCACUCGCA
.....((.(((((....)))))(((........(((.((((.(((.......-....))).))))---------)))((((....))))..------------.)))...)). ( -25.50)
>DroSec_CAF1 459213 97 + 1
UAUCGUCUGCUGCACACGCAGCUGCAACGUUUUUGCAUGUUGCUGGCUUUUUUGCUAC--CAAUUCCGGGUGACCCCUCCGUCCUCCGUCC------------UCCGC--CAA
........(((((....))))).(((((((......)))))))((((....(((....--)))...((((.(((......))).))))...------------...))--)). ( -27.00)
>DroYak_CAF1 470375 100 + 1
UAUCGUCUGCUGCACACGCAGCUGCAACGUUUUUGCAUGUUGCUGGCUUU-UUGCUAC--CAAUUCCGUGUGACCCC--------CCUUCCCCCUUUCAUCCACCCCC--CUC
............(((((((((((((((.....))))).)))))((((...-..)))).--.......))))).....--------.......................--... ( -21.80)
>DroPer_CAF1 526021 91 + 1
UAUCGGCUGCUGCACACGCAGCUGCAACGUUUUUGCAUGUUUCUGACUUUUU-GCUCCAGCAACA---------GCACCCGUACCCGGGCC------------UGCACUCGCA
.....((.(((((....))))).))........(((.((((.(((.......-....))).))))---------(((((((....))))..------------)))....))) ( -26.50)
>consensus
UAUCGUCUGCUGCACACGCAGCUGCAACGUUUUUGCAUGUUGCUGGCUUUUUUGCUAC__CAAUUCCG_GUGACCCCCCCGUACCCCGUCC____________UCCAC__CAA
....(((.(((((....))))).(((((((......))))))).))).................................................................. (-12.90 = -13.70 +   0.80)

alignment

secondary structure

dotplot

Window 4

Location	10,579,876 – 10,579,975
Length	99
Sequences	4
Columns	112
Reading direction	forward
Mean pairwise identity	70.89
Mean single sequence MFE	-19.85
Consensus MFE	-14.15
Energy contribution	-14.40
Covariance contribution	0.25
Combinations/Pair	1.14
Mean z-score	-1.31
Structure conservation index	0.71
SVM decision value	0.56
SVM RNA-class probability	0.782396
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10579876 99 + 23771897
CCCCUCCGUCCACCGUCC------------UCCGCCAACCCGAUUCCCCUAAAGCUAUAUAGCUAUGUGUAUAUAUAGCU-UCAGUUGCAGCUAGUUGUGCUUGUGCCGCUG
..................------------...((((((..(......((.((((((((((((.....)).)))))))))-).))......)..)))).))........... ( -17.50)
>DroSec_CAF1 459284 93 + 1
CCCCUCCGUCCUCCGUCC------------UCCGCCAACCCGAUUC--CUAAAGCUAUAUAGCUAUGU----AUAUAGCU-UCAGUUGGAGCUAGUAGUGCUACUGCCGCUG
..................------------.........((((((.--...((((((((((......)----))))))))-).))))))(((..((((.....)))).))). ( -19.60)
>DroSim_CAF1 461648 93 + 1
NNNNNNNNNNNNNNNNNN------------NNNGCCAACCCGAUUC--CUAAAGCUAUAUAGCUAUGU----AUAUAGCU-UCAGUUGCAGCUAGUAGUGCUACUGCCGCUG
..................------------................--...((((((((((......)----))))))))-)((((.((((.(((.....))))))).)))) ( -21.00)
>DroYak_CAF1 470445 98 + 1
CCCC--------CCUUCCCCCUUUCAUCCACCCCCCUCCCCAAUUC--CCAAAGCUAUAUAGCUAUGC----AUAUAGCUUCUAGUUGCAGCUAGUAGUGCUGCUGCCGCUG
....--------..................................--...(((((((((.((...))----))))))))).((((.(((((.((.....))))))).)))) ( -21.30)
>consensus
CCCC________CCGUCC____________UCCGCCAACCCGAUUC__CUAAAGCUAUAUAGCUAUGU____AUAUAGCU_UCAGUUGCAGCUAGUAGUGCUACUGCCGCUG
....................................................((((((((.((...))....))))))))..((((.((((.(((.....))))))).)))) (-14.15 = -14.40 +   0.25)

alignment

secondary structure

dotplot

Window 5

Location	10,579,876 – 10,579,975
Length	99
Sequences	4
Columns	112
Reading direction	reverse
Mean pairwise identity	70.89
Mean single sequence MFE	-27.47
Consensus MFE	-15.31
Energy contribution	-16.00
Covariance contribution	0.69
Combinations/Pair	1.14
Mean z-score	-1.79
Structure conservation index	0.56
SVM decision value	0.81
SVM RNA-class probability	0.856142
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10579876 99 - 23771897
CAGCGGCACAAGCACAACUAGCUGCAACUGA-AGCUAUAUAUACACAUAGCUAUAUAGCUUUAGGGGAAUCGGGUUGGCGGA------------GGACGGUGGACGGAGGGG
((.((.(....((.(((((.....(..((((-(((((((((..........)))))))))))))..).....)))))))...------------.).)).)).......... ( -29.90)
>DroSec_CAF1 459284 93 - 1
CAGCGGCAGUAGCACUACUAGCUCCAACUGA-AGCUAUAU----ACAUAGCUAUAUAGCUUUAG--GAAUCGGGUUGGCGGA------------GGACGGAGGACGGAGGGG
..((.......)).(..(((((((...((((-((((((((----(......)))))))))))))--.....)))))))..).------------...((.....))...... ( -27.20)
>DroSim_CAF1 461648 93 - 1
CAGCGGCAGUAGCACUACUAGCUGCAACUGA-AGCUAUAU----ACAUAGCUAUAUAGCUUUAG--GAAUCGGGUUGGCNNN------------NNNNNNNNNNNNNNNNNN
..(((((((((....)))).)))))..((((-((((((((----(......)))))))))))))--................------------.................. ( -27.30)
>DroYak_CAF1 470445 98 - 1
CAGCGGCAGCAGCACUACUAGCUGCAACUAGAAGCUAUAU----GCAUAGCUAUAUAGCUUUGG--GAAUUGGGGAGGGGGGUGGAUGAAAGGGGGAAGG--------GGGG
..((....))..(((..((..((.(((((.((((((((((----((...)).)))))))))).)--)..))).))..))..)))................--------.... ( -25.50)
>consensus
CAGCGGCAGUAGCACUACUAGCUGCAACUGA_AGCUAUAU____ACAUAGCUAUAUAGCUUUAG__GAAUCGGGUUGGCGGA____________GGACGG________GGGG
..(((((((((....)))).)))))..((((.((((((((............))))))))))))................................................ (-15.31 = -16.00 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:49 2006