Locus 4691

Sequence ID	2L_DroMel_CAF1
Location	13,484,526 – 13,484,658
Length	132
Max. P	0.999405

overview

Window 5

Location	13,484,526 – 13,484,631
Length	105
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	81.18
Mean single sequence MFE	-23.98
Consensus MFE	-17.19
Energy contribution	-17.52
Covariance contribution	0.33
Combinations/Pair	1.11
Mean z-score	-1.19
Structure conservation index	0.72
SVM decision value	-0.04
SVM RNA-class probability	0.512217
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13484526 105 + 22407834
AGAAAAG--CAGCCGACCACUGGCGAU-CAACGCAGCCCAUCCUCAGCCCGCCACUCAACUGCGCCAGCCCUUCGACUUCGAGGCUGACGCAGUUUUUCAAACGCCAC
.((((((--(.((.((.....(((...-.......))).....)).))..))......((((((.(((((..(((....)))))))).)))))))))))......... ( -30.80)
>DroVir_CAF1 133979 97 + 1
AGA-AAGUAGAGCCGACCACUUGCGAUUCAACGCAGCACAUCCUCCGCCCGCCACUCAACUGCGCCAGGA------CCACAACACUGACGCAGUUCCUCAAC----AC
...-..((.(((........(((((......))))).....................(((((((.(((..------........))).))))))).))).))----.. ( -20.60)
>DroPse_CAF1 126248 94 + 1
AGAUACG--CAGCCGACCACUGGCGAU-CAACGCAGCCCAUCCUCAGCCCGCCACUCAGCUGCGCCAGCCC--------CCGCGCUGACGCAGUUUUUCAA---CCAC
.((...(--(.((.((.....(((...-.......))).....)).))..))...))(((((((.((((..--------....)))).)))))))......---.... ( -23.60)
>DroGri_CAF1 92463 96 + 1
AGA-AAGCACAGCCGACCACUGGCAAU-CAACGCAGCACAUCCUCAGCCCGCCACUCAGCUGCGCCAGGA------CCUAAUCACUGACGCAGUUGCUCAAC----AC
.((-..((...((((.....))))...-.......((.........))..))....((((((((.(((((------.....)).))).)))))))).))...----.. ( -22.20)
>DroAna_CAF1 147290 98 + 1
AGAUAAG--CAGCCGACCACUGGCGAU-CAACGCAGCCCAUCCUCAGCCCGCCACUCAACUGCGCCAGUC-----ACUUC-CGGCUGACGCAGUUUUCCAACAACCA-
.((...(--(.((.((.....(((...-.......))).....)).))..))...))(((((((.(((((-----.....-.))))).)))))))............- ( -24.80)
>DroPer_CAF1 100813 94 + 1
AGAUACG--CAGCCGACCACUAGCGAU-CAACGCAGCCCAUCCUCAGCCCGCCACUCAGCUGCGCCAGCCC--------CCGCGCUGACGCAGUUUUUCAA---CCAC
.(((.((--(((.......)).)))))-)...((.((.........))..)).....(((((((.((((..--------....)))).)))))))......---.... ( -21.90)
>consensus
AGAUAAG__CAGCCGACCACUGGCGAU_CAACGCAGCCCAUCCUCAGCCCGCCACUCAACUGCGCCAGCC______C_UCAACGCUGACGCAGUUUUUCAAC__CCAC
...........((((.....))))........((.((.........))..)).....(((((((.((((..............)))).)))))))............. (-17.19 = -17.52 +   0.33)

alignment

secondary structure

dotplot

Window 6

Location	13,484,526 – 13,484,631
Length	105
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	81.18
Mean single sequence MFE	-39.33
Consensus MFE	-25.69
Energy contribution	-25.72
Covariance contribution	0.03
Combinations/Pair	1.05
Mean z-score	-1.68
Structure conservation index	0.65
SVM decision value	0.25
SVM RNA-class probability	0.652579
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13484526 105 - 22407834
GUGGCGUUUGAAAAACUGCGUCAGCCUCGAAGUCGAAGGGCUGGCGCAGUUGAGUGGCGGGCUGAGGAUGGGCUGCGUUG-AUCGCCAGUGGUCGGCUG--CUUUUCU
.(((((.(..(..((((((((((((((((....)))..))))))))))))).....((((.((......)).)))).)..-).)))))(..(....)..--)...... ( -46.50)
>DroVir_CAF1 133979 97 - 1
GU----GUUGAGGAACUGCGUCAGUGUUGUGG------UCCUGGCGCAGUUGAGUGGCGGGCGGAGGAUGUGCUGCGUUGAAUCGCAAGUGGUCGGCUCUACUU-UCU
..----.......(((((((((((..(....)------..)))))))))))((((((...((((........))))(((((..(....)...))))).))))))-... ( -32.80)
>DroPse_CAF1 126248 94 - 1
GUGG---UUGAAAAACUGCGUCAGCGCGG--------GGGCUGGCGCAGCUGAGUGGCGGGCUGAGGAUGGGCUGCGUUG-AUCGCCAGUGGUCGGCUG--CGUAUCU
(..(---((....)))..)((((((....--------..))))))((((((((.(.((.(((.((.((((.....)))).-.))))).)).))))))))--)...... ( -40.60)
>DroGri_CAF1 92463 96 - 1
GU----GUUGAGCAACUGCGUCAGUGAUUAGG------UCCUGGCGCAGCUGAGUGGCGGGCUGAGGAUGUGCUGCGUUG-AUUGCCAGUGGUCGGCUGUGCUU-UCU
..----...(((((...(((((((.(((...)------)))))))))((((((.(.((.(((....((((.....)))).-...))).)).))))))).)))))-... ( -34.50)
>DroAna_CAF1 147290 98 - 1
-UGGUUGUUGGAAAACUGCGUCAGCCG-GAAGU-----GACUGGCGCAGUUGAGUGGCGGGCUGAGGAUGGGCUGCGUUG-AUCGCCAGUGGUCGGCUG--CUUAUCU
-.(.((((((...(((((((((((((.-...).-----).)))))))))))...)))))).)...((((((((...((((-((((....)))))))).)--))))))) ( -41.90)
>DroPer_CAF1 100813 94 - 1
GUGG---UUGAAAAACUGCGUCAGCGCGG--------GGGCUGGCGCAGCUGAGUGGCGGGCUGAGGAUGGGCUGCGUUG-AUCGCUAGUGGUCGGCUG--CGUAUCU
(..(---((....)))..)((((((....--------..))))))((((((.....((((.((......)).))))...(-((((....))))))))))--)...... ( -39.70)
>consensus
GUGG__GUUGAAAAACUGCGUCAGCGCGGA_G______GGCUGGCGCAGCUGAGUGGCGGGCUGAGGAUGGGCUGCGUUG_AUCGCCAGUGGUCGGCUG__CUUAUCU
...............(((((((((................)))))))))......(((.((((........((((((......))).))))))).))).......... (-25.69 = -25.72 +   0.03)

alignment

secondary structure

dotplot

Window 7

Location	13,484,563 – 13,484,658
Length	95
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	91.50
Mean single sequence MFE	-22.38
Consensus MFE	-20.10
Energy contribution	-20.50
Covariance contribution	0.40
Combinations/Pair	1.05
Mean z-score	-3.35
Structure conservation index	0.90
SVM decision value	3.57
SVM RNA-class probability	0.999405
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13484563 95 + 22407834
UCCUCAGCCCGCCACUCAACUGCGCCAGCCCUUCGACUUCGAGGCUGACGCAGUUUUUCAAACGCCACAGCUACAGAAAAACCCCCCAAAAAACC
.....(((..((.....(((((((.(((((..(((....)))))))).)))))))........))....)))....................... ( -23.02)
>DroSec_CAF1 83336 94 + 1
UCCUCAGCCCGCCACUCAACUGCGCCAGCCCUUCGACUUCGAGGCUGACGCAGUUUUUCAAACGCCACAGCUACAGAAAAACCC-CCAAAAAACC
.....(((..((.....(((((((.(((((..(((....)))))))).)))))))........))....)))............-.......... ( -23.02)
>DroSim_CAF1 84899 95 + 1
UCCUCAGCCCGCCACUCAACUGCGCCAGCCCUUCGACUUCGAGGCUGACGCAGUUUUUCAAACGCCACAGCUACAGAAAAACCCCCCAAAAAACC
.....(((..((.....(((((((.(((((..(((....)))))))).)))))))........))....)))....................... ( -23.02)
>DroEre_CAF1 88040 95 + 1
UCCUCAGCCCGCCACUCAACUGCGCCAGCCCUUCGAUUCCGAGGCUGACGCAGUUUUUCAAACGCCACAGCUACAGAAAAACCCCCCAAAAAACC
.....(((..((.....(((((((.(((((..(((....)))))))).)))))))........))....)))....................... ( -22.42)
>DroYak_CAF1 85304 95 + 1
UCCUCAGCCCGCCACUCAACUGCGCCAGCCCUUCGACUCCGAGGCUGACGCAGUUUUUCAAACGCCACAGCUACAGAAAAACCCCCCAAAAAACC
.....(((..((.....(((((((.(((((..(((....)))))))).)))))))........))....)))....................... ( -22.42)
>DroAna_CAF1 147327 85 + 1
UCCUCAGCCCGCCACUCAACUGCGCCAGUC-----ACUUC-CGGCUGACGCAGUUUUCCAACAACCA-GGCUACAGAAAGAA---AAAAAAAACC
.....((((........(((((((.(((((-----.....-.))))).)))))))............-))))..........---.......... ( -20.35)
>consensus
UCCUCAGCCCGCCACUCAACUGCGCCAGCCCUUCGACUUCGAGGCUGACGCAGUUUUUCAAACGCCACAGCUACAGAAAAACCCCCCAAAAAACC
.....(((..((.....(((((((.(((((..(((....)))))))).)))))))........))....)))....................... (-20.10 = -20.50 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	13,484,563 – 13,484,658
Length	95
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	91.50
Mean single sequence MFE	-35.45
Consensus MFE	-32.03
Energy contribution	-32.63
Covariance contribution	0.60
Combinations/Pair	1.07
Mean z-score	-2.86
Structure conservation index	0.90
SVM decision value	3.20
SVM RNA-class probability	0.998734
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13484563 95 - 22407834
GGUUUUUUGGGGGGUUUUUCUGUAGCUGUGGCGUUUGAAAAACUGCGUCAGCCUCGAAGUCGAAGGGCUGGCGCAGUUGAGUGGCGGGCUGAGGA
..................(((.(((((((.((........((((((((((((((((....)))..)))))))))))))..)).)).))))).))) ( -36.10)
>DroSec_CAF1 83336 94 - 1
GGUUUUUUGG-GGGUUUUUCUGUAGCUGUGGCGUUUGAAAAACUGCGUCAGCCUCGAAGUCGAAGGGCUGGCGCAGUUGAGUGGCGGGCUGAGGA
..........-.......(((.(((((((.((........((((((((((((((((....)))..)))))))))))))..)).)).))))).))) ( -36.10)
>DroSim_CAF1 84899 95 - 1
GGUUUUUUGGGGGGUUUUUCUGUAGCUGUGGCGUUUGAAAAACUGCGUCAGCCUCGAAGUCGAAGGGCUGGCGCAGUUGAGUGGCGGGCUGAGGA
..................(((.(((((((.((........((((((((((((((((....)))..)))))))))))))..)).)).))))).))) ( -36.10)
>DroEre_CAF1 88040 95 - 1
GGUUUUUUGGGGGGUUUUUCUGUAGCUGUGGCGUUUGAAAAACUGCGUCAGCCUCGGAAUCGAAGGGCUGGCGCAGUUGAGUGGCGGGCUGAGGA
..................(((.(((((((.((........((((((((((((((((....)))..)))))))))))))..)).)).))))).))) ( -35.20)
>DroYak_CAF1 85304 95 - 1
GGUUUUUUGGGGGGUUUUUCUGUAGCUGUGGCGUUUGAAAAACUGCGUCAGCCUCGGAGUCGAAGGGCUGGCGCAGUUGAGUGGCGGGCUGAGGA
..................(((.(((((((.((........((((((((((((((((....)))..)))))))))))))..)).)).))))).))) ( -35.20)
>DroAna_CAF1 147327 85 - 1
GGUUUUUUUU---UUCUUUCUGUAGCC-UGGUUGUUGGAAAACUGCGUCAGCCG-GAAGU-----GACUGGCGCAGUUGAGUGGCGGGCUGAGGA
..........---.....(((.(((((-((.(..((....(((((((((((((.-...).-----).))))))))))).))..)))))))).))) ( -34.00)
>consensus
GGUUUUUUGGGGGGUUUUUCUGUAGCUGUGGCGUUUGAAAAACUGCGUCAGCCUCGAAGUCGAAGGGCUGGCGCAGUUGAGUGGCGGGCUGAGGA
..................(((.(((((....((((.....((((((((((((((((....)))..)))))))))))))....))))))))).))) (-32.03 = -32.63 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:44 2006