Locus 5601

Sequence ID	2L_DroMel_CAF1
Location	15,876,640 – 15,876,770
Length	130
Max. P	0.914768

overview

Window 4

Location	15,876,640 – 15,876,744
Length	104
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	85.69
Mean single sequence MFE	-33.73
Consensus MFE	-24.89
Energy contribution	-25.50
Covariance contribution	0.61
Combinations/Pair	1.03
Mean z-score	-2.48
Structure conservation index	0.74
SVM decision value	0.13
SVM RNA-class probability	0.599299
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15876640 104 + 22407834
GAUGUGAGCGCUUAAAUUAUGUGCAAAAUGCUCGCAAAAGCCUCGGUGGCUUUUGGAGGCUAG----CAAACUUUUGCUCAAAAGUUUGCCACCAGCCCCGCCUCGAA
((.(((.((((.........)))).......((.((((((((.....))))))))))((((.(----(((((((((....))))))))))....)))).))).))... ( -36.10)
>DroPse_CAF1 43124 105 + 1
GAUGUGUGCGCUUAAAUUAUGUGCAAAAUGCUCGCAAAAGCCGCCCGGGCUUUUGG-GGCUAAAAAAUAAACUUUUCCAGAAAACUUUUU--CCGGCCCCCUCCCAAA
......(((((.........)))))....((((.((((((((.....)))))))))-)))................((.((((....)))--).))............ ( -25.10)
>DroSim_CAF1 50189 104 + 1
GAUGUGAGCGCUUAAAUUAUGUGCAAAAUGCUCGCAAAAGCCUCGGUGGCUUUUGGAGGCUAG----CAAACUUUUGCUCAAAAGUUUGCCACCAGCCCCGCCUCGAA
((.(((.((((.........)))).......((.((((((((.....))))))))))((((.(----(((((((((....))))))))))....)))).))).))... ( -36.10)
>DroEre_CAF1 40204 104 + 1
GAUGUGAGCGCUUAAAUUAUGUGCAAAAUGCUCGCAAAAGCCUCGGUGGCUUUUGGGGGCUGG----CAAACUUUUGCUCAAAAGUUUGCCACCAGCCCCGCCUUGCA
..((..((.((.........(.((.....)).).((((((((.....))))))))((((((((----(((((((((....)))))))))))...))))))))))..)) ( -47.00)
>DroYak_CAF1 26373 104 + 1
GAUGUGAGCGCUUAAAUUAUGUGCAAAAUGCUCGCAAAAGCCUCGGUGGCUUUUGGGGGCUAG----CAAACUUUUGCUUAAAAGUUUUCCACCAGCCCCGCCUCGAA
....((((.((.........(.((.....)).).((((((((.....))))))))((((((.(----.((((((((....))))))))....).)))))))))))).. ( -34.30)
>DroPer_CAF1 69037 105 + 1
GAUGUGUGCGCUUAAAUUAUGUGCAAAAUGCUCGCAAAAGCCGCCCGGGCUUUUGG-GGCUAAAAAAUAAACUUUUCCAGAAAACUUUUU--CCGCCCCCCUCCCAAA
...((((((((.........)))))....((((.((((((((.....)))))))))-)))..............................--.)))............ ( -23.80)
>consensus
GAUGUGAGCGCUUAAAUUAUGUGCAAAAUGCUCGCAAAAGCCUCGGUGGCUUUUGG_GGCUAG____CAAACUUUUGCUCAAAAGUUUGCCACCAGCCCCGCCUCGAA
...((((((((...........)).....))))))(((((((.....)))))))((.((((.......((((((((....))))))))......))))))........ (-24.89 = -25.50 +   0.61)

alignment

secondary structure

dotplot

Window 5

Location	15,876,640 – 15,876,744
Length	104
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	85.69
Mean single sequence MFE	-36.53
Consensus MFE	-25.82
Energy contribution	-26.85
Covariance contribution	1.03
Combinations/Pair	1.10
Mean z-score	-2.78
Structure conservation index	0.71
SVM decision value	0.08
SVM RNA-class probability	0.574901
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15876640 104 - 22407834
UUCGAGGCGGGGCUGGUGGCAAACUUUUGAGCAAAAGUUUG----CUAGCCUCCAAAAGCCACCGAGGCUUUUGCGAGCAUUUUGCACAUAAUUUAAGCGCUCACAUC
...(((((((((((...(((((((((((....)))))))))----))))))))((((((((.....))))))))...((.....))...........)).)))..... ( -39.30)
>DroPse_CAF1 43124 105 - 1
UUUGGGAGGGGGCCGG--AAAAAGUUUUCUGGAAAAGUUUAUUUUUUAGCC-CCAAAAGCCCGGGCGGCUUUUGCGAGCAUUUUGCACAUAAUUUAAGCGCACACAUC
.(((((..((((((((--(((....))))))((((((....)))))).)))-)).....)))))(((((....))..((.....))............)))....... ( -28.50)
>DroSim_CAF1 50189 104 - 1
UUCGAGGCGGGGCUGGUGGCAAACUUUUGAGCAAAAGUUUG----CUAGCCUCCAAAAGCCACCGAGGCUUUUGCGAGCAUUUUGCACAUAAUUUAAGCGCUCACAUC
...(((((((((((...(((((((((((....)))))))))----))))))))((((((((.....))))))))...((.....))...........)).)))..... ( -39.30)
>DroEre_CAF1 40204 104 - 1
UGCAAGGCGGGGCUGGUGGCAAACUUUUGAGCAAAAGUUUG----CCAGCCCCCAAAAGCCACCGAGGCUUUUGCGAGCAUUUUGCACAUAAUUUAAGCGCUCACAUC
(((((.((((((((...(((((((((((....)))))))))----))))))))((((((((.....))))))))...))...)))))..................... ( -43.10)
>DroYak_CAF1 26373 104 - 1
UUCGAGGCGGGGCUGGUGGAAAACUUUUAAGCAAAAGUUUG----CUAGCCCCCAAAAGCCACCGAGGCUUUUGCGAGCAUUUUGCACAUAAUUUAAGCGCUCACAUC
...((((((((((((((...((((((((....)))))))))----))))))))((((((((.....))))))))...((.....))...........)).)))..... ( -39.40)
>DroPer_CAF1 69037 105 - 1
UUUGGGAGGGGGGCGG--AAAAAGUUUUCUGGAAAAGUUUAUUUUUUAGCC-CCAAAAGCCCGGGCGGCUUUUGCGAGCAUUUUGCACAUAAUUUAAGCGCACACAUC
.(((((...(((((..--(((((((...((.....))...))))))).)))-)).....)))))(((((....))..((.....))............)))....... ( -29.60)
>consensus
UUCGAGGCGGGGCUGGUGGAAAACUUUUGAGCAAAAGUUUG____CUAGCC_CCAAAAGCCACCGAGGCUUUUGCGAGCAUUUUGCACAUAAUUUAAGCGCUCACAUC
........((((((((....((((((((....)))))))).....))))))))((((((((.....)))))))).((((.(((............))).))))..... (-25.82 = -26.85 +   1.03)

alignment

secondary structure

dotplot

Window 6

Location	15,876,680 – 15,876,770
Length	90
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	81.82
Mean single sequence MFE	-29.33
Consensus MFE	-22.94
Energy contribution	-22.47
Covariance contribution	-0.47
Combinations/Pair	1.21
Mean z-score	-2.49
Structure conservation index	0.78
SVM decision value	1.10
SVM RNA-class probability	0.914768
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15876680 90 + 22407834
CCUCGGUGGCUUUUGGAGGCUAG----CAAACUUUUGCUCAAAAGUUUGCCACCAGCCCCGCCUCGAAUA---------UCAA--AAUAUUGGCAGUCACGUGUG
.....((((((...((.((((.(----(((((((((....))))))))))....))))))(((...((((---------(...--.))))))))))))))..... ( -30.60)
>DroPse_CAF1 43164 102 + 1
CCGCCCGGGCUUUUGG-GGCUAAAAAAUAAACUUUUCCAGAAAACUUUUU--CCGGCCCCCUCCCAAAAAAUGUGAGUCCCAAAUACUAUUGACAGUCCGAUAUU
.....((((((.((((-((((..((((...................))))--..))))))(((.((.....)).)))..............)).))))))..... ( -20.81)
>DroSec_CAF1 50176 90 + 1
CCUCGGUGGCUUUUGGAGGCUAG----CAAACUUUUGCUCAAAAGUUUGCCACCAGCCCCGCCUCGAAUA---------UCAA--AAUAUUGGCAGUCACGUGUG
.....((((((...((.((((.(----(((((((((....))))))))))....))))))(((...((((---------(...--.))))))))))))))..... ( -30.60)
>DroSim_CAF1 50229 90 + 1
CCUCGGUGGCUUUUGGAGGCUAG----CAAACUUUUGCUCAAAAGUUUGCCACCAGCCCCGCCUCGAAUA---------UCAA--AAUAUUGGCAGUCACGUGUG
.....((((((...((.((((.(----(((((((((....))))))))))....))))))(((...((((---------(...--.))))))))))))))..... ( -30.60)
>DroEre_CAF1 40244 90 + 1
CCUCGGUGGCUUUUGGGGGCUGG----CAAACUUUUGCUCAAAAGUUUGCCACCAGCCCCGCCUUGCAUA---------UCAA--AAUAUUGGUAGUCACGUGUG
.....(((((.....((((((((----(((((((((....)))))))))))...))))))........((---------((((--....)))))))))))..... ( -35.90)
>DroYak_CAF1 26413 90 + 1
CCUCGGUGGCUUUUGGGGGCUAG----CAAACUUUUGCUUAAAAGUUUUCCACCAGCCCCGCCUCGAAUA---------CCAA--AAUAUUGGUAGUCACGUGUG
...(((.((((..(((..(((((----(((....)))))....)).)..)))..)))))))....((.((---------((((--....)))))).))....... ( -27.50)
>consensus
CCUCGGUGGCUUUUGGAGGCUAG____CAAACUUUUGCUCAAAAGUUUGCCACCAGCCCCGCCUCGAAUA_________UCAA__AAUAUUGGCAGUCACGUGUG
.....((((((...((.((((......(((((((((....))))))))).....))))))(((............................)))))))))..... (-22.94 = -22.47 +  -0.47)

alignment

secondary structure

dotplot

Window 7

Location	15,876,680 – 15,876,770
Length	90
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	81.82
Mean single sequence MFE	-29.07
Consensus MFE	-21.15
Energy contribution	-20.98
Covariance contribution	-0.16
Combinations/Pair	1.20
Mean z-score	-1.82
Structure conservation index	0.73
SVM decision value	0.49
SVM RNA-class probability	0.756852
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15876680 90 - 22407834
CACACGUGACUGCCAAUAUU--UUGA---------UAUUCGAGGCGGGGCUGGUGGCAAACUUUUGAGCAAAAGUUUG----CUAGCCUCCAAAAGCCACCGAGG
.....(((.((((((((((.--...)---------))))...)))((((((...(((((((((((....)))))))))----)))))).))...)).)))..... ( -28.40)
>DroPse_CAF1 43164 102 - 1
AAUAUCGGACUGUCAAUAGUAUUUGGGACUCACAUUUUUUGGGAGGGGGCCGG--AAAAAGUUUUCUGGAAAAGUUUAUUUUUUAGCC-CCAAAAGCCCGGGCGG
.........(((((.........((((.(((.((.....)).)))((((((((--(((....))))))((((((....)))))).)))-)).....))))))))) ( -26.20)
>DroSec_CAF1 50176 90 - 1
CACACGUGACUGCCAAUAUU--UUGA---------UAUUCGAGGCGGGGCUGGUGGCAAACUUUUGAGCAAAAGUUUG----CUAGCCUCCAAAAGCCACCGAGG
.....(((.((((((((((.--...)---------))))...)))((((((...(((((((((((....)))))))))----)))))).))...)).)))..... ( -28.40)
>DroSim_CAF1 50229 90 - 1
CACACGUGACUGCCAAUAUU--UUGA---------UAUUCGAGGCGGGGCUGGUGGCAAACUUUUGAGCAAAAGUUUG----CUAGCCUCCAAAAGCCACCGAGG
.....(((.((((((((((.--...)---------))))...)))((((((...(((((((((((....)))))))))----)))))).))...)).)))..... ( -28.40)
>DroEre_CAF1 40244 90 - 1
CACACGUGACUACCAAUAUU--UUGA---------UAUGCAAGGCGGGGCUGGUGGCAAACUUUUGAGCAAAAGUUUG----CCAGCCCCCAAAAGCCACCGAGG
....((.(.....(((....--))).---------.......(((((((((...(((((((((((....)))))))))----)))))))).....))).)))... ( -29.90)
>DroYak_CAF1 26413 90 - 1
CACACGUGACUACCAAUAUU--UUGG---------UAUUCGAGGCGGGGCUGGUGGAAAACUUUUAAGCAAAAGUUUG----CUAGCCCCCAAAAGCCACCGAGG
....(((((.((((((....--))))---------)).))).((((((((((((...((((((((....)))))))))----)))))))).....)))..))... ( -33.10)
>consensus
CACACGUGACUGCCAAUAUU__UUGA_________UAUUCGAGGCGGGGCUGGUGGCAAACUUUUGAGCAAAAGUUUG____CUAGCCUCCAAAAGCCACCGAGG
.....(((.((..(((......)))....................((((((((...(((((((((....)))))))))....))))))))....)).)))..... (-21.15 = -20.98 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:22 2006