Locus 3067

Sequence ID	3R_DroMel_CAF1
Location	8,102,286 – 8,102,551
Length	265
Max. P	0.931382

overview

Window 7

Location	8,102,286 – 8,102,406
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.42
Mean single sequence MFE	-32.22
Consensus MFE	-25.83
Energy contribution	-26.59
Covariance contribution	0.76
Combinations/Pair	1.04
Mean z-score	-1.64
Structure conservation index	0.80
SVM decision value	0.48
SVM RNA-class probability	0.752047
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8102286 120 + 27905053
AUGGCUUCGGCCUGGACAGACACCCAUAAACAAGGCGGAGCGUAUAUUAUAGUAGCUCAUACUAAAAAACCCCAAAAGGGGGAGGUUCGCAUGUAAUUACGUGCACACGGACACAUACAC
..(((....)))((..(.((.((((.......((...((((.(((......)))))))...))......((((....))))).)))))((((((....))))))....)..))....... ( -34.60)
>DroSec_CAF1 53943 120 + 1
AUGGCUUCGGCCUGGACAGACACCCAUAAACAAGGCGGAGCGUAUAUUAUAGUAGCUCAUACUAAAAAACCCCAAAAGGGGGAGGUUCGCAUGUAAUUACGUGCACACGGACACAUACAC
..(((....)))((..(.((.((((.......((...((((.(((......)))))))...))......((((....))))).)))))((((((....))))))....)..))....... ( -34.60)
>DroSim_CAF1 26029 120 + 1
AUGGCUUCGGCCUGGACAGACACCCAUAAACAAGGCGGAGCGUAUAUUAUAGUAGCUCAUACUAAAAAACCCCAAAAGGGGGAGGUUCGCAUGUAAUUACGUGCACACGGACACAUACAC
..(((....)))((..(.((.((((.......((...((((.(((......)))))))...))......((((....))))).)))))((((((....))))))....)..))....... ( -34.60)
>DroEre_CAF1 28992 114 + 1
AUGGCUUCGGCCUGGAAAAACGCCCAUAAACAAGGCGGAGCGUAUAUUAUAGUAGCUCAUACUAAAAAACCCCCAAAGGGGCAGGUUCGCAUGUAAUUACGUACACACA------GCUAC
.(((((.(((((((......((((.........))))((((.(((......)))))))...........((((....)))))))).)))..((((......))))...)------)))). ( -29.50)
>DroYak_CAF1 22434 120 + 1
AUGGCUUCGGCCUGGACAGACACCCAUAAACAAGGCGGAGCGUAUAUUAUAGUAGCUCAUACUAAAAAACACCCAAAGGGGGAGGUUCGCAUGUAAUUACGUACACACGGACACGGAUAC
..(((....)))...........((.......((...((((.(((......)))))))...))........(((....)))...(((((..((((......))))..)))))..)).... ( -27.80)
>consensus
AUGGCUUCGGCCUGGACAGACACCCAUAAACAAGGCGGAGCGUAUAUUAUAGUAGCUCAUACUAAAAAACCCCAAAAGGGGGAGGUUCGCAUGUAAUUACGUGCACACGGACACAUACAC
...((((((.(((...................)))))))))........(((((.....))))).....((((....))))...(((((..((((......))))..)))))........ (-25.83 = -26.59 +   0.76)

alignment

secondary structure

dotplot

Window 8

Location	8,102,406 – 8,102,513
Length	107
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.45
Mean single sequence MFE	-35.04
Consensus MFE	-28.80
Energy contribution	-28.80
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.48
Structure conservation index	0.82
SVM decision value	0.38
SVM RNA-class probability	0.713845
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8102406 107 - 27905053
GGCCCAUGUGUUUGUGCUCCACUCGAAAUGUAUUUCGAGAGCGCAUGUCAAAGGUCAGCCACUGCUCACAUAUGUCAGUCGCUGUCGAAGUAUCUGUAUCUGUAG-------------CU
((((..((....(((((((...((((((....)))))))))))))...))..)))).......(((.(((.(((.(((..(((.....)))..)))))).)))))-------------). ( -32.20)
>DroSec_CAF1 54063 107 - 1
GGCCCAUGUGUUUGUGCUCCACUCGAAAUGUAUUUCGAGAGCGCAUGUCAAGGGUCAGCCACUGCUCACAUGUGUCAGUUGCUGUCGAAGUAUCUGUAUCUGUAA-------------CU
(((((.((....(((((((...((((((....)))))))))))))...)).)))))(((....))).(((.(((.(((.((((.....)))).)))))).)))..-------------.. ( -34.60)
>DroSim_CAF1 26149 107 - 1
GGCCCAUGUGUUUGUGCUCCACUCGAAAUGUAUUUCGAGAGCGCAUGUCAAAGGUCAGCCACUGCUCACAUGUGUCAGUCGCUGUCGAAGUAUCUGUAUCUGUAA-------------CU
((((..((....(((((((...((((((....)))))))))))))...))..))))(((....))).(((.(((.(((..(((.....)))..)))))).)))..-------------.. ( -29.40)
>DroEre_CAF1 29106 120 - 1
GGCCCAUGUGUUUGUGCUCCACUCGAAAUGUAUUUCGAGAGCGCAUGUCAAAGGUCAGCCACUGCUCACAUGUGUCAGUCGCUGUCGAAGUAUCUGUAUCUGUGUCUGUGUGCAGUGUAU
((((..((....(((((((...((((((....)))))))))))))...))..))))...((((((.((((.(..((((..(((.....)))..))).....)..).)))).))))))... ( -40.00)
>DroYak_CAF1 22554 114 - 1
GGCCCAUGUGUUUGUGCUCCACUCGAAAUGUAUUUCGAGAGCGCAUGUCAAAGGUCAGCCACUGCUCACAUGUGUCAGUCGCUGUCGAAGUAUCUGUAUCUG------UGUGUAGUAUCU
((((..((....(((((((...((((((....)))))))))))))...))..))))....(((((.((((.(((.(((..(((.....)))..)))))).))------)).))))).... ( -39.00)
>consensus
GGCCCAUGUGUUUGUGCUCCACUCGAAAUGUAUUUCGAGAGCGCAUGUCAAAGGUCAGCCACUGCUCACAUGUGUCAGUCGCUGUCGAAGUAUCUGUAUCUGUAA_____________CU
((((..((....(((((((...((((((....)))))))))))))...))..))))(((.((((..((....)).)))).)))..................................... (-28.80 = -28.80 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	8,102,433 – 8,102,551
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.62
Mean single sequence MFE	-29.20
Consensus MFE	-26.48
Energy contribution	-27.08
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.54
Structure conservation index	0.91
SVM decision value	1.21
SVM RNA-class probability	0.931382
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8102433 118 + 27905053
GACUGACAUAUGUGAGCAGUGGCUGACCUUUGACAUGCGCUCUCGAAAUACAUUUCGAGUGGAGCACAAACACAUGGGCCCUGCCACUUUCACCACCCACCACCCACCACCCUCC--AUC
...........(((((.((((((.(.(((.((...((.((((((((((....))))))...)))).))....)).))).)..)))))))))))......................--... ( -29.80)
>DroSec_CAF1 54090 118 + 1
AACUGACACAUGUGAGCAGUGGCUGACCCUUGACAUGCGCUCUCGAAAUACAUUUCGAGUGGAGCACAAACACAUGGGCCCUGCCACAUUCCCCAACCACCACCGACCACCCUCC--AUC
.........(((((.((((.((((.(.........(((.(((((((((....))))))).)).)))........).)))))))))))))..........................--... ( -29.43)
>DroSim_CAF1 26176 118 + 1
GACUGACACAUGUGAGCAGUGGCUGACCUUUGACAUGCGCUCUCGAAAUACAUUUCGAGUGGAGCACAAACACAUGGGCCCUGCCACAUUCCCCAGCCACCAUCCACCACCCUCC--AUC
(.(((....(((((.((((.((((.(..((((...(((.(((((((((....))))))).)).)))))))....).)))))))))))))....))).).................--... ( -32.80)
>DroEre_CAF1 29146 112 + 1
GACUGACACAUGUGAGCAGUGGCUGACCUUUGACAUGCGCUCUCGAAAUACAUUUCGAGUGGAGCACAAACACAUGGGCCCUGCC--UUUCCCCAC----CCUCCACCACCCACUUCC--
(.((.((....)).)))(((((.((.................((((((....))))))((((((...........((((...)))--)........----.)))))))).)))))...-- ( -25.65)
>DroYak_CAF1 22588 120 + 1
GACUGACACAUGUGAGCAGUGGCUGACCUUUGACAUGCGCUCUCGAAAUACAUUUCGAGUGGAGCACAAACACAUGGGCCCUGCCACUUUCCCCACCCACCCACCACCACCCACUUCCAC
...........(((.((((.((((.(..((((...(((.(((((((((....))))))).)).)))))))....).)))))))))))................................. ( -28.30)
>consensus
GACUGACACAUGUGAGCAGUGGCUGACCUUUGACAUGCGCUCUCGAAAUACAUUUCGAGUGGAGCACAAACACAUGGGCCCUGCCACUUUCCCCACCCACCACCCACCACCCUCC__AUC
...........(((.((((.((((.(..((((...(((.(((((((((....))))))).)).)))))))....).)))))))))))................................. (-26.48 = -27.08 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:16 2006