Locus 8033

Sequence ID	3R_DroMel_CAF1
Location	21,575,671 – 21,575,805
Length	134
Max. P	0.999923

overview

Window 9

Location	21,575,671 – 21,575,770
Length	99
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	74.19
Mean single sequence MFE	-27.78
Consensus MFE	-16.10
Energy contribution	-16.66
Covariance contribution	0.56
Combinations/Pair	1.12
Mean z-score	-2.92
Structure conservation index	0.58
SVM decision value	3.63
SVM RNA-class probability	0.999466
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21575671 99 + 27905053
GUGAGUAUAUGUAUGUAUGUGUGGCCACGCCCACACGCC-CUGUUUAUAAACACACAC----ACUGCCACACACAUAUUUAUUUACACGCACUUGAGCACGUGC
(((((((...((((((..(((((((...((......)).-.((((....)))).....----...))))))))))))).)))))))..((((........)))) ( -26.90)
>DroSec_CAF1 63938 90 + 1
GUGAGUAUAUGUACGUAUGUGUGGCCACGCCCACACGUGUGUGUUUAUGAAC--------------ACACACACAUAUUUAUUUACUCGCACUUGAGCACGUGC
(((((((...(((.((((((((((......))))..(((((((((....)))--------------)))))))))))).))).))))))).............. ( -33.40)
>DroSim_CAF1 59051 103 + 1
GUGAGUAUAUGUACGUAUGUGUGGCCACGCCCACACGCC-CUGUUUAUAAACAUAUACGACCACACACACACACAUAUUUAUUUACACGCACUUGAGCACGUGC
((((((((((((..((.(((((((.(..((......)).-.((((....)))).....).))))))).))..)))))..)))))))..((((........)))) ( -25.40)
>DroYak_CAF1 58102 85 + 1
GUGAGUAUAU--------GUGUGGCCACGCCCACACGCC-CCGUUUAUAAACACACA----------CACACACAUAUGUAUUUACACGCACUUGAGCACGUGC
((((((((((--------(((((.....((......)).-..(((....))).....----------....)))))))))))))))..((((........)))) ( -22.60)
>DroAna_CAF1 45707 97 + 1
AUGAAUGCCUGUGUG--UGUGUGGAUGCGACCACACCCA-CCGCUCU-A---CUGUGCCCCCAAACACACAUACAUAGUUAUUUACACGCACUUGAGCACGUGC
.((((((.(((((((--((((((..((.(..((((....-.......-.---.))))..).))..))))))))))))).))))))...((((........)))) ( -30.62)
>consensus
GUGAGUAUAUGUACGUAUGUGUGGCCACGCCCACACGCC_CUGUUUAUAAACACACAC____A___ACACACACAUAUUUAUUUACACGCACUUGAGCACGUGC
(((((((.((((......((((((......))))))......(((....)))......................)))).)))))))..((((........)))) (-16.10 = -16.66 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	21,575,671 – 21,575,770
Length	99
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	74.19
Mean single sequence MFE	-36.56
Consensus MFE	-21.56
Energy contribution	-22.72
Covariance contribution	1.16
Combinations/Pair	1.13
Mean z-score	-3.80
Structure conservation index	0.59
SVM decision value	4.57
SVM RNA-class probability	0.999923
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21575671 99 - 27905053
GCACGUGCUCAAGUGCGUGUAAAUAAAUAUGUGUGUGGCAGU----GUGUGUGUUUAUAAACAG-GGCGUGUGGGCGUGGCCACACAUACAUACAUAUACUCAC
(((((..(....)..)))))......(((((((((((((..(----((.(((....))).))).-.))((((((......)))))).)))))))))))...... ( -36.70)
>DroSec_CAF1 63938 90 - 1
GCACGUGCUCAAGUGCGAGUAAAUAAAUAUGUGUGUGU--------------GUUCAUAAACACACACGUGUGGGCGUGGCCACACAUACGUACAUAUACUCAC
((((........))))(((((.((...(((((((((((--------------(..(((...((((....))))...)))..)))))))))))).)).))))).. ( -36.40)
>DroSim_CAF1 59051 103 - 1
GCACGUGCUCAAGUGCGUGUAAAUAAAUAUGUGUGUGUGUGUGGUCGUAUAUGUUUAUAAACAG-GGCGUGUGGGCGUGGCCACACAUACGUACAUAUACUCAC
(((((..(....)..)))))......((((((((((((((((((((((((((((((.......)-))))))))....)))))))))))))))))))))...... ( -43.50)
>DroYak_CAF1 58102 85 - 1
GCACGUGCUCAAGUGCGUGUAAAUACAUAUGUGUGUG----------UGUGUGUUUAUAAACGG-GGCGUGUGGGCGUGGCCACAC--------AUAUACUCAC
(((((..(....)..)))))((((((((((......)----------)))))))))......((-(..((((((((...))).)))--------))...))).. ( -30.40)
>DroAna_CAF1 45707 97 - 1
GCACGUGCUCAAGUGCGUGUAAAUAACUAUGUAUGUGUGUUUGGGGGCACAG---U-AGAGCGG-UGGGUGUGGUCGCAUCCACACA--CACACAGGCAUUCAU
(((((..(....)..)))))........((((.(((((((......((....---.-...)).(-(((((((....))))))))..)--)))))).)))).... ( -35.80)
>consensus
GCACGUGCUCAAGUGCGUGUAAAUAAAUAUGUGUGUGU___U____GUAUAUGUUUAUAAACAG_GGCGUGUGGGCGUGGCCACACAUACAUACAUAUACUCAC
(((((..(....)..))))).........((((((((...............(((....)))......((((((......)))))).....))))))))..... (-21.56 = -22.72 +   1.16)

alignment

secondary structure

dotplot

Window 1

Location	21,575,702 – 21,575,805
Length	103
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	79.56
Mean single sequence MFE	-18.42
Consensus MFE	-8.87
Energy contribution	-9.37
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.31
Structure conservation index	0.48
SVM decision value	0.32
SVM RNA-class probability	0.687969
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21575702 103 + 27905053
CACACGCC-CUGUUUAUAAACACACAC----ACUGCCACACACAUAUUUAUUUACACGCACUUGAGCACGUGCUGAGCAGGGAAAAUAC--CCCACAAGCACAAACAAAA
......((-(((((((...........----..((.....))...............((((........))))))))))))).......--................... ( -15.80)
>DroSec_CAF1 63969 94 + 1
CACACGUGUGUGUUUAUGAAC--------------ACACACACAUAUUUAUUUACUCGCACUUGAGCACGUGCUGAGCAGGGAAAAUAA--CCCACAAGCACAAACAAAA
.....(((((((((....)))--------------))))))................((......))..(((((.....(((.......--)))...)))))........ ( -25.10)
>DroSim_CAF1 59082 107 + 1
CACACGCC-CUGUUUAUAAACAUAUACGACCACACACACACACAUAUUUAUUUACACGCACUUGAGCACGUGCUGAGCAGGGAAAAUAC--CCCACAAGCACAAACAAAA
......((-(((((((....(......).............................((((........))))))))))))).......--................... ( -15.80)
>DroEre_CAF1 54326 95 + 1
CACACGCC-CCCUUCAUAAACACACA------------CACACAUGUGUAUUUACACGCACUUGAGCACGUGCUGAGCAGGGAAAAUUC--CCCACAAGCACAAACAAAA
........-.......((((.(((((------------......))))).))))...((......))..(((((.....((((....))--))....)))))........ ( -19.50)
>DroYak_CAF1 58125 97 + 1
CACACGCC-CCGUUUAUAAACACACA----------CACACACAUAUGUAUUUACACGCACUUGAGCACGUGCUGAGGAGGGAAAAUAC--CCCACAAGCACAAACAAAA
........-..((((...........----------......((..(((........)))..)).....(((((...(.(((......)--)))...))))))))).... ( -16.60)
>DroAna_CAF1 45736 103 + 1
CACACCCA-CCGCUCU-A---CUGUGCCCCCAAACACACAUACAUAGUUAUUUACACGCACUUGAGCACGUGCUGAGCAGGGAGAAUAUAUACCAUAA--ACAAACAAAA
....(((.-..((((.-(---(((((................)))))).........((((........)))).)))).)))................--.......... ( -17.69)
>consensus
CACACGCC_CCGUUUAUAAACACACA_________ACACACACAUAUUUAUUUACACGCACUUGAGCACGUGCUGAGCAGGGAAAAUAC__CCCACAAGCACAAACAAAA
.........................................................((......))..(((((.....(((.........)))...)))))........ ( -8.87 =  -9.37 +   0.50)

alignment

secondary structure

dotplot

Window 2

Location	21,575,702 – 21,575,805
Length	103
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	79.56
Mean single sequence MFE	-31.60
Consensus MFE	-14.62
Energy contribution	-14.90
Covariance contribution	0.28
Combinations/Pair	1.24
Mean z-score	-2.58
Structure conservation index	0.46
SVM decision value	0.63
SVM RNA-class probability	0.803750
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21575702 103 - 27905053
UUUUGUUUGUGCUUGUGGG--GUAUUUUCCCUGCUCAGCACGUGCUCAAGUGCGUGUAAAUAAAUAUGUGUGUGGCAGU----GUGUGUGUUUAUAAACAG-GGCGUGUG
.((((((((((...(..((--(......)))..)...(((((..(((..(..(((((......)))))..)...).)).----.)))))...)))))))))-)....... ( -30.90)
>DroSec_CAF1 63969 94 - 1
UUUUGUUUGUGCUUGUGGG--UUAUUUUCCCUGCUCAGCACGUGCUCAAGUGCGAGUAAAUAAAUAUGUGUGUGU--------------GUUCAUAAACACACACGUGUG
..(((((((((((.(..((--........))..)..)))))..((((......))))))))))((((((((((((--------------........)))))))))))). ( -33.60)
>DroSim_CAF1 59082 107 - 1
UUUUGUUUGUGCUUGUGGG--GUAUUUUCCCUGCUCAGCACGUGCUCAAGUGCGUGUAAAUAAAUAUGUGUGUGUGUGUGGUCGUAUAUGUUUAUAAACAG-GGCGUGUG
........(..(....(((--(......))))((((.(((((..(....)..)))))..(((((((((((((..........))))))))))))).....)-))))..). ( -29.40)
>DroEre_CAF1 54326 95 - 1
UUUUGUUUGUGCUUGUGGG--GAAUUUUCCCUGCUCAGCACGUGCUCAAGUGCGUGUAAAUACACAUGUGUG------------UGUGUGUUUAUGAAGGG-GGCGUGUG
........(((((.(..((--((....))))..)..)))))..((((.......(((((((((((((....)------------))))))))))))....)-)))..... ( -34.90)
>DroYak_CAF1 58125 97 - 1
UUUUGUUUGUGCUUGUGGG--GUAUUUUCCCUCCUCAGCACGUGCUCAAGUGCGUGUAAAUACAUAUGUGUGUG----------UGUGUGUUUAUAAACGG-GGCGUGUG
........(((((.(..((--(......)))..)..)))))..((((..((...(((((((((((((......)----------)))))))))))).)).)-)))..... ( -31.90)
>DroAna_CAF1 45736 103 - 1
UUUUGUUUGU--UUAUGGUAUAUAUUCUCCCUGCUCAGCACGUGCUCAAGUGCGUGUAAAUAACUAUGUAUGUGUGUUUGGGGGCACAG---U-AGAGCGG-UGGGUGUG
..........--........(((((((...((((((.(((((..(....)..)))))...............((((((....)))))).---.-.))))))-.))))))) ( -28.90)
>consensus
UUUUGUUUGUGCUUGUGGG__GUAUUUUCCCUGCUCAGCACGUGCUCAAGUGCGUGUAAAUAAAUAUGUGUGUGU_________UGUGUGUUUAUAAACAG_GGCGUGUG
...((((((((.....(((.........)))......(((((..(....)..)))))...................................)))))))).......... (-14.62 = -14.90 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:00:54 2006