Locus 4246

Sequence ID	X_DroMel_CAF1
Location	11,139,925 – 11,140,083
Length	158
Max. P	0.773515

overview

Window 6

Location	11,139,925 – 11,140,045
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.86
Mean single sequence MFE	-32.84
Consensus MFE	-24.68
Energy contribution	-24.68
Covariance contribution	-0.00
Combinations/Pair	1.14
Mean z-score	-1.93
Structure conservation index	0.75
SVM decision value	0.14
SVM RNA-class probability	0.605118
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11139925 120 + 22224390
GCUGGUAUUCGAAUUGCUGACUGCAAUUGAUUCGACUACCGGGCGCAAUGCCCACACUCGAAUGCUAUCAAUCGGUAGCUCAUUUACAUGUGAAUUUGCCGAAUGUCAUUUGGAUAUUUU
...((((.(((((((((.....)))....)))))).))))((((.....))))....(((((((....((.(((((((.((((......))))..))))))).)).)))))))....... ( -37.10)
>DroSec_CAF1 54652 118 + 1
GCUAGUAUCCGAAUUACUGACUGCAAUUGAUGCGACUACCG-GCGCAAUGCCCACACUCGAAUGCUAUCA-UCGGUAACUCAUUUACAUGCGAAUUUGCCGAAUGUCAUUUGGAUAUUUU
...(((((((((((.(((((..(((.((((((((.(.....-)))))..........)))).)))..)))-((((((((.(((....))).)...)))))))..)).))))))))))).. ( -29.30)
>DroSim_CAF1 20295 118 + 1
GCUGGUAUCCGAAUUACUGACUGCAAUUGAUUCGACUACCG-GCGCAAUGCCCACACUCGAAUGCUAUCA-UCGGUAGCUCAUUUACAUGUGAAUUUGCCGAAUGUCAUUUGGAUAUUUU
...(((((((((((.(((((..(((.....(((((.....(-((.....))).....))))))))..)))-(((((((.((((......))))..)))))))..)).))))))))))).. ( -33.40)
>DroEre_CAF1 55038 118 + 1
GCUGGUAUCCGAAUCACCGACUGCAAUUGAUUCGACUACCG-GCGUAUUGCCCCCACUCGAAUGCUAUCA-UCAGUAGCUCAUUUACAUGUGAAUUUGCCGAAUGUCAUUUGGAUAUUUU
(((((((..(((((((...........)))))))..)))))-))..............((((((((((..-...)))))((((......)))))))))..(((((((.....))))))). ( -29.40)
>DroYak_CAF1 58124 118 + 1
GCUGGUAUCCGAAUGACUGACUGCAAUUGAUUCGACUACCG-GCGUAUUGCCCCCACUUGAAUGCUAUCA-UCGGGAGCUCAUUUACAUGUGAAUUUGCCGAAUGUCAUUUGGAUAUUUU
...(((((((((((((((((..(((.....(((((.....(-((.....))).....))))))))..)))-(((((((.((((......)))).))).))))..)))))))))))))).. ( -35.00)
>consensus
GCUGGUAUCCGAAUUACUGACUGCAAUUGAUUCGACUACCG_GCGCAAUGCCCACACUCGAAUGCUAUCA_UCGGUAGCUCAUUUACAUGUGAAUUUGCCGAAUGUCAUUUGGAUAUUUU
...(((((((((((.((.((..(((.....(((((.....(.((.....))).....))))))))..))..(((((((.((((......))))..)))))))..)).))))))))))).. (-24.68 = -24.68 +  -0.00)

alignment

secondary structure

dotplot

Window 7

Location	11,139,965 – 11,140,083
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.52
Mean single sequence MFE	-33.02
Consensus MFE	-25.66
Energy contribution	-26.94
Covariance contribution	1.28
Combinations/Pair	1.06
Mean z-score	-1.81
Structure conservation index	0.78
SVM decision value	0.54
SVM RNA-class probability	0.773515
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11139965 118 + 22224390
GGGCGCAAUGCCCACACUCGAAUGCUAUCAAUCGGUAGCUCAUUUACAUGUGAAUUUGCCGAAUGUCAUUUGGAUAUUUUGACAGUC--GAAGGCAACUCAAGUGGGCAUACGAAAACAA
...((..((((((((..((((..........(((((((.((((......))))..))))))).(((((...........))))).))--))((....))...)))))))).))....... ( -34.70)
>DroSec_CAF1 54692 118 + 1
G-GCGCAAUGCCCACACUCGAAUGCUAUCA-UCGGUAACUCAUUUACAUGCGAAUUUGCCGAAUGUCAUUUGGAUAUUUUGACAGUCUUGCCUUCGACUCAAGUGGGCAUACGAAAACAA
.-.((..((((((((..(((((.((.....-((((((((.(((....))).)...))))))).(((((...........))))).....)).))))).....)))))))).))....... ( -31.90)
>DroSim_CAF1 20335 116 + 1
G-GCGCAAUGCCCACACUCGAAUGCUAUCA-UCGGUAGCUCAUUUACAUGUGAAUUUGCCGAAUGUCAUUUGGAUAUUUUGACAGUC--GAAGGCAACUCAAGUGGGCAUACGAAAACAA
.-.((..((((((((..((((.........-(((((((.((((......))))..))))))).(((((...........))))).))--))((....))...)))))))).))....... ( -34.70)
>DroEre_CAF1 55078 116 + 1
G-GCGUAUUGCCCCCACUCGAAUGCUAUCA-UCAGUAGCUCAUUUACAUGUGAAUUUGCCGAAUGUCAUUUGGAUAUUUUGACAGUC--GAAGGCAACUUAAGUGGGCAUACGAAAACAG
.-.(((((.((((.(...((((((((((..-...)))))((((......))))))))).(((.(((((...........))))).))--)(((....)))..).)))))))))....... ( -30.50)
>DroYak_CAF1 58164 116 + 1
G-GCGUAUUGCCCCCACUUGAAUGCUAUCA-UCGGGAGCUCAUUUACAUGUGAAUUUGCCGAAUGUCAUUUGGAUAUUUUGACAGUC--GAAGGCAACCUAAGUGGGCAUACGAAAACAA
.-.(((((.((((..(((((..((((.((.-(((((((.((((......)))).))).)))).(((((...........)))))...--)).))))...))))))))))))))....... ( -33.30)
>consensus
G_GCGCAAUGCCCACACUCGAAUGCUAUCA_UCGGUAGCUCAUUUACAUGUGAAUUUGCCGAAUGUCAUUUGGAUAUUUUGACAGUC__GAAGGCAACUCAAGUGGGCAUACGAAAACAA
...((...(((((((.......((((.((..(((((((.((((......))))..))))))).(((((...........))))).....)).))))......)))))))..))....... (-25.66 = -26.94 +   1.28)

alignment

secondary structure

dotplot

Window 8

Location	11,139,965 – 11,140,083
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.52
Mean single sequence MFE	-31.52
Consensus MFE	-26.14
Energy contribution	-26.62
Covariance contribution	0.48
Combinations/Pair	1.11
Mean z-score	-1.43
Structure conservation index	0.83
SVM decision value	0.35
SVM RNA-class probability	0.699515
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11139965 118 - 22224390
UUGUUUUCGUAUGCCCACUUGAGUUGCCUUC--GACUGUCAAAAUAUCCAAAUGACAUUCGGCAAAUUCACAUGUAAAUGAGCUACCGAUUGAUAGCAUUCGAGUGUGGGCAUUGCGCCC
.......(((((((((((.....(((((...--((.(((((...........))))).)))))))((((.(((....))).((((........))))....))))))))))).))))... ( -33.00)
>DroSec_CAF1 54692 118 - 1
UUGUUUUCGUAUGCCCACUUGAGUCGAAGGCAAGACUGUCAAAAUAUCCAAAUGACAUUCGGCAAAUUCGCAUGUAAAUGAGUUACCGA-UGAUAGCAUUCGAGUGUGGGCAUUGCGC-C
.......(((((((((((...(.(((((.((.....(((((...........))))).((((..((((((........)))))).))))-.....)).))))).)))))))).)))).-. ( -33.90)
>DroSim_CAF1 20335 116 - 1
UUGUUUUCGUAUGCCCACUUGAGUUGCCUUC--GACUGUCAAAAUAUCCAAAUGACAUUCGGCAAAUUCACAUGUAAAUGAGCUACCGA-UGAUAGCAUUCGAGUGUGGGCAUUGCGC-C
.......(((((((((((.....(((((...--((.(((((...........))))).)))))))((((.(((....))).((((....-...))))....))))))))))).)))).-. ( -32.70)
>DroEre_CAF1 55078 116 - 1
CUGUUUUCGUAUGCCCACUUAAGUUGCCUUC--GACUGUCAAAAUAUCCAAAUGACAUUCGGCAAAUUCACAUGUAAAUGAGCUACUGA-UGAUAGCAUUCGAGUGGGGGCAAUACGC-C
.......(((((((((.......(((((...--((.(((((...........))))).)))))))((((.(((....))).(((((...-.).))))....))))..)))).))))).-. ( -29.50)
>DroYak_CAF1 58164 116 - 1
UUGUUUUCGUAUGCCCACUUAGGUUGCCUUC--GACUGUCAAAAUAUCCAAAUGACAUUCGGCAAAUUCACAUGUAAAUGAGCUCCCGA-UGAUAGCAUUCAAGUGGGGGCAAUACGC-C
.......(((((.(((((((.(..(((..((--(..(((((...........))))).((((....((((........))))...))))-)))..)))..))))))))....))))).-. ( -28.50)
>consensus
UUGUUUUCGUAUGCCCACUUGAGUUGCCUUC__GACUGUCAAAAUAUCCAAAUGACAUUCGGCAAAUUCACAUGUAAAUGAGCUACCGA_UGAUAGCAUUCGAGUGUGGGCAUUGCGC_C
.......(((((((((((((((((((((.....((.(((((...........))))).))))))).....(((....))).((((........)))).)))))))..))))).))))... (-26.14 = -26.62 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:09 2006