Locus 5525

Sequence ID	2R_DroMel_CAF1
Location	17,665,139 – 17,665,299
Length	160
Max. P	0.899261

overview

Window 5

Location	17,665,139 – 17,665,259
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	99.58
Mean single sequence MFE	-40.48
Consensus MFE	-38.72
Energy contribution	-38.98
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-3.30
Structure conservation index	0.96
SVM decision value	1.01
SVM RNA-class probability	0.899261
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17665139 120 + 20766785
AAUGGGUCUUCAUCGAUAUAAAAAUUGAUGAAGCGCUCUUCUCGGAGGCAAAACUUUGGCCUGUCCCAGCAUCCUGAGAGAUUGGAGCCAGCAAUUUUCCAAGGAAAUUGCUUUCGCCCC
...((((((((((((((......)))))))))).(((((((((((((((.........)))..)))(((....))).))))..))))).(((((((((.....)))))))))...)))). ( -41.30)
>DroSec_CAF1 18578 120 + 1
AAUGGGUCUUCAUCGAUAUAAAAAUUGAUGAAGCGCUCUUCUCGGAGGCAAAACUUUGGCCUGUCCCAGCAUCCUGAGAGAUUGCAGCCAGCAAUUUUCCAAGGAAAUUGCUUUCGCCCC
...((((((((((((((......)))))))))).))))....(((((((((....((((......))))..(((((..(((((((.....)))))))..).))))..))))))))).... ( -40.20)
>DroEre_CAF1 18927 120 + 1
AAUGGGUCUUCAUCGAUAUAAAAAUUGAUGAAGCGCUCUUCUCGGAGGCAAAACUUUGGCCUGUCCCAGCAUCCUGAGAGAUUGCAGCCAGCAAUUUUCCAAGGAAAUUGCUUUCGCCCC
...((((((((((((((......)))))))))).))))....(((((((((....((((......))))..(((((..(((((((.....)))))))..).))))..))))))))).... ( -40.20)
>DroYak_CAF1 30636 120 + 1
AAUGGGUCUUCAUCGAUAUAAAAAUUGAUGAAGCGCUCUUCUCGGAGGCAAAACUUUGGCCUGUCCCAGCAUCCUGAGAGAUUGCAGCCAGCAAUUUUCCAAGGAAAUUGCUUUCGCCCC
...((((((((((((((......)))))))))).))))....(((((((((....((((......))))..(((((..(((((((.....)))))))..).))))..))))))))).... ( -40.20)
>consensus
AAUGGGUCUUCAUCGAUAUAAAAAUUGAUGAAGCGCUCUUCUCGGAGGCAAAACUUUGGCCUGUCCCAGCAUCCUGAGAGAUUGCAGCCAGCAAUUUUCCAAGGAAAUUGCUUUCGCCCC
...((((((((((((((......)))))))))).))))....(((((((((....((((......))))..(((((..(((((((.....)))))))..).))))..))))))))).... (-38.72 = -38.98 +   0.25)

alignment

secondary structure

dotplot

Window 6

Location	17,665,139 – 17,665,259
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	99.58
Mean single sequence MFE	-38.93
Consensus MFE	-38.92
Energy contribution	-38.92
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.20
Structure conservation index	1.00
SVM decision value	0.67
SVM RNA-class probability	0.818214
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17665139 120 - 20766785
GGGGCGAAAGCAAUUUCCUUGGAAAAUUGCUGGCUCCAAUCUCUCAGGAUGCUGGGACAGGCCAAAGUUUUGCCUCCGAGAAGAGCGCUUCAUCAAUUUUUAUAUCGAUGAAGACCCAUU
(((((((((....))))(((((((((((..(((((......((((((....))))))..))))).)))))....))))))....)).(((((((.((......)).))))))).)))... ( -38.10)
>DroSec_CAF1 18578 120 - 1
GGGGCGAAAGCAAUUUCCUUGGAAAAUUGCUGGCUGCAAUCUCUCAGGAUGCUGGGACAGGCCAAAGUUUUGCCUCCGAGAAGAGCGCUUCAUCAAUUUUUAUAUCGAUGAAGACCCAUU
(((((((((....))))(((((((((((..(((((......((((((....))))))..))))).)))))....))))))....)).(((((((.((......)).))))))).)))... ( -39.20)
>DroEre_CAF1 18927 120 - 1
GGGGCGAAAGCAAUUUCCUUGGAAAAUUGCUGGCUGCAAUCUCUCAGGAUGCUGGGACAGGCCAAAGUUUUGCCUCCGAGAAGAGCGCUUCAUCAAUUUUUAUAUCGAUGAAGACCCAUU
(((((((((....))))(((((((((((..(((((......((((((....))))))..))))).)))))....))))))....)).(((((((.((......)).))))))).)))... ( -39.20)
>DroYak_CAF1 30636 120 - 1
GGGGCGAAAGCAAUUUCCUUGGAAAAUUGCUGGCUGCAAUCUCUCAGGAUGCUGGGACAGGCCAAAGUUUUGCCUCCGAGAAGAGCGCUUCAUCAAUUUUUAUAUCGAUGAAGACCCAUU
(((((((((....))))(((((((((((..(((((......((((((....))))))..))))).)))))....))))))....)).(((((((.((......)).))))))).)))... ( -39.20)
>consensus
GGGGCGAAAGCAAUUUCCUUGGAAAAUUGCUGGCUGCAAUCUCUCAGGAUGCUGGGACAGGCCAAAGUUUUGCCUCCGAGAAGAGCGCUUCAUCAAUUUUUAUAUCGAUGAAGACCCAUU
(((((((((....))))(((((((((((..(((((......((((((....))))))..))))).)))))....))))))....)).(((((((.((......)).))))))).)))... (-38.92 = -38.92 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	17,665,179 – 17,665,299
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.89
Mean single sequence MFE	-41.20
Consensus MFE	-40.73
Energy contribution	-40.73
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.99
SVM decision value	0.22
SVM RNA-class probability	0.638645
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17665179 120 - 20766785
AACAGCAGCAGACCCAGCGGCAGUACACGCACCAGCACUCGGGGCGAAAGCAAUUUCCUUGGAAAAUUGCUGGCUCCAAUCUCUCAGGAUGCUGGGACAGGCCAAAGUUUUGCCUCCGAG
....((.((.......)).)).......((....)).((((((((((((((((((((....).)))))))(((((......((((((....))))))..)))))...))))))).))))) ( -40.70)
>DroSec_CAF1 18618 120 - 1
AACAGCAGCAGACCCAGCGGCAGUACACGCACCAGCACUCGGGGCGAAAGCAAUUUCCUUGGAAAAUUGCUGGCUGCAAUCUCUCAGGAUGCUGGGACAGGCCAAAGUUUUGCCUCCGAG
....((.((.......)).)).......((....)).((((((((((((((((((((....).)))))))(((((......((((((....))))))..)))))...))))))).))))) ( -41.80)
>DroYak_CAF1 30676 120 - 1
AACAGCAGCAGACCCAGCGGCAGUACACGCACCAACACUCGGGGCGAAAGCAAUUUCCUUGGAAAAUUGCUGGCUGCAAUCUCUCAGGAUGCUGGGACAGGCCAAAGUUUUGCCUCCGAG
................(((........))).......((((((((((((((((((((....).)))))))(((((......((((((....))))))..)))))...))))))).))))) ( -41.10)
>consensus
AACAGCAGCAGACCCAGCGGCAGUACACGCACCAGCACUCGGGGCGAAAGCAAUUUCCUUGGAAAAUUGCUGGCUGCAAUCUCUCAGGAUGCUGGGACAGGCCAAAGUUUUGCCUCCGAG
................(((........))).......((((((((((((((((((((....).)))))))(((((......((((((....))))))..)))))...))))))).))))) (-40.73 = -40.73 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:46 2006