Locus 4978

Sequence ID	2L_DroMel_CAF1
Location	14,365,737 – 14,365,937
Length	200
Max. P	0.978231

overview

Window 3

Location	14,365,737 – 14,365,857
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.49
Mean single sequence MFE	-35.78
Consensus MFE	-29.73
Energy contribution	-30.24
Covariance contribution	0.51
Combinations/Pair	1.09
Mean z-score	-1.65
Structure conservation index	0.83
SVM decision value	0.87
SVM RNA-class probability	0.869890
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14365737 120 - 22407834
ACUGACGGCUGAGGUUAAAGCCCGGCCGAUUAAGCUGACAGUUUUUGUCGGGCUCGUAUUUUUCAGUUAAAAAGCGUGUUCAAUGUGACUUGGCACACCGCCGAAGAAAUACAUCGUGCU
.....((((((.(((....)))))))))......(((((((...)))))))((.((....((((.........((((.....))))...(((((.....))))).)))).....)).)). ( -34.50)
>DroSec_CAF1 13433 105 - 1
ACUGACGGCUGAGGUUAAAGCCCGGCCGAUUAAGCUGACAGUU--UGUCGGGCUCGUAUUUUUCAGUU---------UUUCAA----ACUUGGCACACAGGCGAAGAAAUACAUCGUGCU
.(((.((((((.(((....))))))))).....((..(..(((--((..(((((.(......).))))---------)..)))----)))..))...)))((((.(.....).))))... ( -29.90)
>DroSim_CAF1 15564 118 - 1
ACUGACGGCUGAGGUUAAAGCCCGGCCGAUUAAGCUGACAGUU--UGUCGGGCUCGUAUUUUUCAGUUAAAAAGCUUGUUCAAUGCGACUUGGCACACAGCCGAAGAAAUACAUCGUGCU
.((..((((((.((((((.(((((((.((((........))))--.)))))))(((((((...(((((....))).))...))))))).))))).).)))))).)).............. ( -36.50)
>DroEre_CAF1 14167 118 - 1
ACUGACGGCUGAGGUUAAAGCCCGGCCGAUUAAACUGACAGUU--UGUCGGGCUCGUAUUUUUCAGUUAAAAAGCGUGUUCAAUGUGACUUGGCACACAGCCGAAGAAAUACAUUGCGCU
(((((((((((.(((....)))))))))......(((((....--.)))))...........))))).....((((....(((((((.((((((.....))).)))...))))))))))) ( -38.60)
>DroYak_CAF1 13726 118 - 1
ACUGACGGCUGAGGUUAAAACCCGGCCGAUUAAACUGACAGUU--UGUCAGGCUCGUAUUUUUCAGUUAAAAAGCGUGUUCAAUGUGUCUUGGCACACAGCCGAACAAAUACAUAGCGCU
(((((((((((.(((....)))))))))......(((((....--.)))))...........))))).....(((((........(((.(((((.....))))))))........))))) ( -39.39)
>consensus
ACUGACGGCUGAGGUUAAAGCCCGGCCGAUUAAGCUGACAGUU__UGUCGGGCUCGUAUUUUUCAGUUAAAAAGCGUGUUCAAUGUGACUUGGCACACAGCCGAAGAAAUACAUCGUGCU
.....((((((.(((....)))))))))......((((((.....))))))....((((((((..........((((.....))))...(((((.....)))))))))))))........ (-29.73 = -30.24 +   0.51)

alignment

secondary structure

dotplot

Window 4

Location	14,365,777 – 14,365,897
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.26
Mean single sequence MFE	-34.85
Consensus MFE	-30.12
Energy contribution	-30.32
Covariance contribution	0.20
Combinations/Pair	1.06
Mean z-score	-1.20
Structure conservation index	0.86
SVM decision value	-0.01
SVM RNA-class probability	0.528845
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14365777 120 + 22407834
AACACGCUUUUUAACUGAAAAAUACGAGCCCGACAAAAACUGUCAGCUUAAUCGGCCGGGCUUUAACCUCAGCCGUCAGUUGGUCUAAAGCGCCGCCGUUUCGCCAGCCGAUCUUUAGCG
....((((......((((.......((((((((((.....)))).(((.....))).)))))).....))))..(((.((((((...(((((....))))).)))))).)))....)))) ( -33.10)
>DroSec_CAF1 13469 109 + 1
AAA---------AACUGAAAAAUACGAGCCCGACA--AACUGUCAGCUUAAUCGGCCGGGCUUUAACCUCAGCCGUCAGUUGGUCCAAAGCGCCGCCGUUUCGCCGGCCGAUCUUUAGCG
...---------..(((((......((((..(((.--....))).)))).((((((((((((((....(((((.....)))))...)))))..((......))))))))))).))))).. ( -32.00)
>DroSim_CAF1 15604 118 + 1
AACAAGCUUUUUAACUGAAAAAUACGAGCCCGACA--AACUGUCAGCUUAAUCGGCCGGGCUUUAACCUCAGCCGUCAGUUGGUCCAAAGCGCCGCCGUUUCGCAGGCCGAUCUUUAGCG
.....(((.................((((..(((.--....))).)))).((((((((((((((....(((((.....)))))...))))).))((......)).)))))))....))). ( -33.10)
>DroEre_CAF1 14207 118 + 1
AACACGCUUUUUAACUGAAAAAUACGAGCCCGACA--AACUGUCAGUUUAAUCGGCCGGGCUUUAACCUCAGCCGUCAGUUGGGCUAAAGCGCCGCCGCUUCGCCGGCCGAUCUUUAGCG
....((((....((((((......((....))...--.....))))))..(((((((((((((((.((.((((.....)))))).))))))((....))....)))))))))....)))) ( -39.14)
>DroYak_CAF1 13766 118 + 1
AACACGCUUUUUAACUGAAAAAUACGAGCCUGACA--AACUGUCAGUUUAAUCGGCCGGGUUUUAACCUCAGCCGUCAGUUGGGCUAAAGCGCCGCCGUUUCGCUGGCCGAUCUUUAGCG
..........((((((((.......((((.((((.--....))))))))...((((.((((....))).).))))))))))))(((((((..(.((((......)))).)..))))))). ( -36.90)
>consensus
AACACGCUUUUUAACUGAAAAAUACGAGCCCGACA__AACUGUCAGCUUAAUCGGCCGGGCUUUAACCUCAGCCGUCAGUUGGUCUAAAGCGCCGCCGUUUCGCCGGCCGAUCUUUAGCG
..............(((((......((((..((((.....)))).)))).(((((((((((((((...(((((.....)))))..)))))).))((......)).))))))).))))).. (-30.12 = -30.32 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	14,365,777 – 14,365,897
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.26
Mean single sequence MFE	-40.72
Consensus MFE	-38.92
Energy contribution	-38.60
Covariance contribution	-0.32
Combinations/Pair	1.12
Mean z-score	-1.52
Structure conservation index	0.96
SVM decision value	1.81
SVM RNA-class probability	0.978231
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14365777 120 - 22407834
CGCUAAAGAUCGGCUGGCGAAACGGCGGCGCUUUAGACCAACUGACGGCUGAGGUUAAAGCCCGGCCGAUUAAGCUGACAGUUUUUGUCGGGCUCGUAUUUUUCAGUUAAAAAGCGUGUU
((((((((..(.((((......)))).)..)))))....((((((((((((.(((....)))))))))....(((((((((...))))).))))........)))))).....))).... ( -39.70)
>DroSec_CAF1 13469 109 - 1
CGCUAAAGAUCGGCCGGCGAAACGGCGGCGCUUUGGACCAACUGACGGCUGAGGUUAAAGCCCGGCCGAUUAAGCUGACAGUU--UGUCGGGCUCGUAUUUUUCAGUU---------UUU
..((((((..(.((((......)))).)..))))))...((((((((((((.(((....)))))))))....(((((((....--.))).))))........))))))---------... ( -40.50)
>DroSim_CAF1 15604 118 - 1
CGCUAAAGAUCGGCCUGCGAAACGGCGGCGCUUUGGACCAACUGACGGCUGAGGUUAAAGCCCGGCCGAUUAAGCUGACAGUU--UGUCGGGCUCGUAUUUUUCAGUUAAAAAGCUUGUU
.((((((((((((((((((((....((((...(..(.....)..)((((((.(((....))))))))).....))))....))--)).))))).)).)))))).)))............. ( -37.80)
>DroEre_CAF1 14207 118 - 1
CGCUAAAGAUCGGCCGGCGAAGCGGCGGCGCUUUAGCCCAACUGACGGCUGAGGUUAAAGCCCGGCCGAUUAAACUGACAGUU--UGUCGGGCUCGUAUUUUUCAGUUAAAAAGCGUGUU
((((...(((((((((((......))((((((((((((........)))))))))....))))))))))))...(((((....--.))))).....................)))).... ( -44.20)
>DroYak_CAF1 13766 118 - 1
CGCUAAAGAUCGGCCAGCGAAACGGCGGCGCUUUAGCCCAACUGACGGCUGAGGUUAAAACCCGGCCGAUUAAACUGACAGUU--UGUCAGGCUCGUAUUUUUCAGUUAAAAAGCGUGUU
.(((((((..(.(((........))).)..)))))))..((((((((((((.(((....)))))))))......(((((....--.)))))...........))))))............ ( -41.40)
>consensus
CGCUAAAGAUCGGCCGGCGAAACGGCGGCGCUUUAGACCAACUGACGGCUGAGGUUAAAGCCCGGCCGAUUAAGCUGACAGUU__UGUCGGGCUCGUAUUUUUCAGUUAAAAAGCGUGUU
..((((((..(.((((......)))).)..))))))...((((((((((((.(((....)))))))))......((((((.....))))))...........))))))............ (-38.92 = -38.60 +  -0.32)

alignment

secondary structure

dotplot

Window 6

Location	14,365,817 – 14,365,937
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.92
Mean single sequence MFE	-39.48
Consensus MFE	-36.88
Energy contribution	-36.48
Covariance contribution	-0.40
Combinations/Pair	1.12
Mean z-score	-1.31
Structure conservation index	0.93
SVM decision value	0.66
SVM RNA-class probability	0.814942
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14365817 120 - 22407834
CUUUUGACAGCACUUAAGUUGAAUUUGGUAAUGACAGUCGCGCUAAAGAUCGGCUGGCGAAACGGCGGCGCUUUAGACCAACUGACGGCUGAGGUUAAAGCCCGGCCGAUUAAGCUGACA
.......((((.......................((((....((((((..(.((((......)))).)..))))))....)))).((((((.(((....))))))))).....))))... ( -38.80)
>DroSec_CAF1 13498 120 - 1
CUUUUGACAGCACUUAAGUUGAAUUUGGUAAUGACAGUCGCGCUAAAGAUCGGCCGGCGAAACGGCGGCGCUUUGGACCAACUGACGGCUGAGGUUAAAGCCCGGCCGAUUAAGCUGACA
.......((((.......................((((....((((((..(.((((......)))).)..))))))....)))).((((((.(((....))))))))).....))))... ( -40.70)
>DroSim_CAF1 15642 120 - 1
CUUUUGACAGCACUUAAGUUGAAUUUGGUAAUGACAGUCGCGCUAAAGAUCGGCCUGCGAAACGGCGGCGCUUUGGACCAACUGACGGCUGAGGUUAAAGCCCGGCCGAUUAAGCUGACA
.......((((.......................((((....((((((..(.(((........))).)..))))))....)))).((((((.(((....))))))))).....))))... ( -37.10)
>DroEre_CAF1 14245 120 - 1
CUUUUGACAGCACUUAAGUUGAAUUUGGUAAUGACAGUCGCGCUAAAGAUCGGCCGGCGAAGCGGCGGCGCUUUAGCCCAACUGACGGCUGAGGUUAAAGCCCGGCCGAUUAAACUGACA
.......((((......))))...(..((.....((((.(.(((((((....((((.((...)).)))).))))))).).)))).((((((.(((....))))))))).....))..).. ( -42.00)
>DroYak_CAF1 13804 120 - 1
CUUUUGACAGCACUUAAGUUGAAUUUGGUAAUGACAGUCGCGCUAAAGAUCGGCCAGCGAAACGGCGGCGCUUUAGCCCAACUGACGGCUGAGGUUAAAACCCGGCCGAUUAAACUGACA
.......((((......))))...(..((.....((((.(.(((((((..(.(((........))).)..))))))).).)))).((((((.(((....))))))))).....))..).. ( -38.80)
>consensus
CUUUUGACAGCACUUAAGUUGAAUUUGGUAAUGACAGUCGCGCUAAAGAUCGGCCGGCGAAACGGCGGCGCUUUAGACCAACUGACGGCUGAGGUUAAAGCCCGGCCGAUUAAGCUGACA
.......((((......))))...(..((.....((((.(.(((((((..(.((((......)))).)..)))))).)).)))).((((((.(((....))))))))).....))..).. (-36.88 = -36.48 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:28 2006