Locus 6209

Sequence ID	2R_DroMel_CAF1
Location	19,541,408 – 19,541,533
Length	125
Max. P	0.962041

overview

Window 3

Location	19,541,408 – 19,541,508
Length	100
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.87
Mean single sequence MFE	-23.48
Consensus MFE	-19.90
Energy contribution	-19.86
Covariance contribution	-0.04
Combinations/Pair	1.13
Mean z-score	-1.47
Structure conservation index	0.85
SVM decision value	0.06
SVM RNA-class probability	0.564417
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19541408 100 - 20766785
UGGAGGCCAAUCAGUUUUCUUAAAUUGUAGAUACAUUUAUAUGUGUUUGUGCUUUAAGAAUUAAAAUAUUGUAUGCCUUUUGCA-AGGUGCGUAUACGGGA-------------------
......((........((((((((.(..((((((((....))))))))..).)))))))).........((((((((((.....-))).))))))).))..------------------- ( -22.40)
>DroPse_CAF1 3722 120 - 1
CAGGGGCCAAUCCGUUUUCUUGAAAUGUAGAUACAUUUAUAUGUGUUUGUGGCUUAAGAAUUGAAAUAUUGUAUGCCUUUUGCAAAGGUAAAUAUAGGCAACAUCCAAGUCAAAUUAAAC
...((((((...((((((...))))))(((((((((....))))))))))))))).....((((.....(((.((((((((((....)))))...))))))))......))))....... ( -27.20)
>DroSim_CAF1 272 100 - 1
UGGAGGCCAAUCAGUUUUCUUAAAUUGUAGAUACAUUUAUAUGUGUUUGUGCUUUAAGAAUUAAAAUAUUGUAUGCCUUUUGCA-AGGUGCGUAUACGGGA-------------------
......((........((((((((.(..((((((((....))))))))..).)))))))).........((((((((((.....-))).))))))).))..------------------- ( -22.40)
>DroYak_CAF1 268 100 - 1
UGGAGGCCAAUCAGUUUUCUUAAAUUGUAGAUACAUUUAUAUGUGUUUGUGCUUUAAGAAUUAAAAUAUUGUAUGCCUUUUGCA-AGGUGCGUAUACGAAA-------------------
.((((((....((((.((((((((.(..((((((((....))))))))..).)))))))).......))))...)))))).((.-....))..........------------------- ( -21.40)
>DroAna_CAF1 257 101 - 1
UGGAGGCCAAUCAGUUUUCUUAAAUUGUAGAUACAUUUAUAUGUGUUUGUGCUUUAAGAAUUGAAAUAUUGUAUGCCUUUUGCAAAGGUGCGUAUUCGGGA-------------------
......((..(((((..(((((((.(..((((((((....))))))))..).))))))))))))......((((((((((....)))).))))))..))..------------------- ( -24.00)
>consensus
UGGAGGCCAAUCAGUUUUCUUAAAUUGUAGAUACAUUUAUAUGUGUUUGUGCUUUAAGAAUUAAAAUAUUGUAUGCCUUUUGCA_AGGUGCGUAUACGGGA___________________
.((((((((((.....((((((((.(..((((((((....))))))))..).)))))))).......))))...))))))((((....))))............................ (-19.90 = -19.86 +  -0.04)

alignment

secondary structure

dotplot

Window 4

Location	19,541,428 – 19,541,533
Length	105
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.93
Mean single sequence MFE	-19.17
Consensus MFE	-15.19
Energy contribution	-15.83
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-2.26
Structure conservation index	0.79
SVM decision value	1.53
SVM RNA-class probability	0.962041
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19541428 105 + 20766785
AAAGGCAUACAAUAUUUUAAUUCUUAAAGCACAAACACAUAUAAAUGUAUCUACAAUUUAAGAAAACUGAUUGGCCUCCACCGAUAGUUUUGCCAUCGCUUUCCA---------------
...((((.............((((((((........((((....))))........))))))))(((((.((((......))))))))).))))...........--------------- ( -18.79)
>DroPse_CAF1 3762 119 + 1
AAAGGCAUACAAUAUUUCAAUUCUUAAGCCACAAACACAUAUAAAUGUAUCUACAUUUCAAGAAAACGGAUUGGCCCCUGCCGAUAGUU-UGCCAUCGCUUUCUGUGCGACCCUGUGCGA
...((((.((..................((......((((....)))).(((........)))....))((((((....)))))).)).-)))).((((.......)))).......... ( -22.40)
>DroSim_CAF1 292 105 + 1
AAAGGCAUACAAUAUUUUAAUUCUUAAAGCACAAACACAUAUAAAUGUAUCUACAAUUUAAGAAAACUGAUUGGCCUCCACCGAUAGUUUUGCCAUCGCUUUCCA---------------
...((((.............((((((((........((((....))))........))))))))(((((.((((......))))))))).))))...........--------------- ( -18.79)
>DroYak_CAF1 288 105 + 1
AAAGGCAUACAAUAUUUUAAUUCUUAAAGCACAAACACAUAUAAAUGUAUCUACAAUUUAAGAAAACUGAUUGGCCUCCACCGAUAGUUUUGCCAUCGCUUUCCA---------------
...((((.............((((((((........((((....))))........))))))))(((((.((((......))))))))).))))...........--------------- ( -18.79)
>DroAna_CAF1 278 99 + 1
AAAGGCAUACAAUAUUUCAAUUCUUAAAGCACAAACACAUAUAAAUGUAUCUACAAUUUAAGAAAACUGAUUGGCCUCCACCGAUAGUUUUG------CUUUCCA---------------
.((((((.............((((((((........((((....))))........))))))))(((((.((((......))))))))).))------))))...--------------- ( -17.09)
>consensus
AAAGGCAUACAAUAUUUUAAUUCUUAAAGCACAAACACAUAUAAAUGUAUCUACAAUUUAAGAAAACUGAUUGGCCUCCACCGAUAGUUUUGCCAUCGCUUUCCA_______________
...((((.............((((((((........((((....))))........))))))))(((((.((((......))))))))).)))).......................... (-15.19 = -15.83 +   0.64)

alignment

secondary structure

dotplot

Window 5

Location	19,541,428 – 19,541,533
Length	105
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.93
Mean single sequence MFE	-26.06
Consensus MFE	-22.08
Energy contribution	-23.00
Covariance contribution	0.92
Combinations/Pair	1.09
Mean z-score	-1.79
Structure conservation index	0.85
SVM decision value	1.06
SVM RNA-class probability	0.909451
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19541428 105 - 20766785
---------------UGGAAAGCGAUGGCAAAACUAUCGGUGGAGGCCAAUCAGUUUUCUUAAAUUGUAGAUACAUUUAUAUGUGUUUGUGCUUUAAGAAUUAAAAUAUUGUAUGCCUUU
---------------.......((((((.....))))))..((((((....((((.((((((((.(..((((((((....))))))))..).)))))))).......))))...)))))) ( -26.00)
>DroPse_CAF1 3762 119 - 1
UCGCACAGGGUCGCACAGAAAGCGAUGGCA-AACUAUCGGCAGGGGCCAAUCCGUUUUCUUGAAAUGUAGAUACAUUUAUAUGUGUUUGUGGCUUAAGAAUUGAAAUAUUGUAUGCCUUU
.........(((((.......)))))((((-.((....(((....)))........(((((((..(..((((((((....))))))))..)..)))))))..........)).))))... ( -30.10)
>DroSim_CAF1 292 105 - 1
---------------UGGAAAGCGAUGGCAAAACUAUCGGUGGAGGCCAAUCAGUUUUCUUAAAUUGUAGAUACAUUUAUAUGUGUUUGUGCUUUAAGAAUUAAAAUAUUGUAUGCCUUU
---------------.......((((((.....))))))..((((((....((((.((((((((.(..((((((((....))))))))..).)))))))).......))))...)))))) ( -26.00)
>DroYak_CAF1 288 105 - 1
---------------UGGAAAGCGAUGGCAAAACUAUCGGUGGAGGCCAAUCAGUUUUCUUAAAUUGUAGAUACAUUUAUAUGUGUUUGUGCUUUAAGAAUUAAAAUAUUGUAUGCCUUU
---------------.......((((((.....))))))..((((((....((((.((((((((.(..((((((((....))))))))..).)))))))).......))))...)))))) ( -26.00)
>DroAna_CAF1 278 99 - 1
---------------UGGAAAG------CAAAACUAUCGGUGGAGGCCAAUCAGUUUUCUUAAAUUGUAGAUACAUUUAUAUGUGUUUGUGCUUUAAGAAUUGAAAUAUUGUAUGCCUUU
---------------.((...(------(((.......(((....)))..(((((..(((((((.(..((((((((....))))))))..).))))))))))))....))))...))... ( -22.20)
>consensus
_______________UGGAAAGCGAUGGCAAAACUAUCGGUGGAGGCCAAUCAGUUUUCUUAAAUUGUAGAUACAUUUAUAUGUGUUUGUGCUUUAAGAAUUAAAAUAUUGUAUGCCUUU
......................((((((.....))))))..((((((((((.....((((((((.(..((((((((....))))))))..).)))))))).......))))...)))))) (-22.08 = -23.00 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:36 2006