Locus 3135

Sequence ID	X_DroMel_CAF1
Location	8,352,223 – 8,352,321
Length	98
Max. P	0.874107

overview

Window 5

Location	8,352,223 – 8,352,321
Length	98
Sequences	4
Columns	106
Reading direction	forward
Mean pairwise identity	76.28
Mean single sequence MFE	-32.75
Consensus MFE	-18.42
Energy contribution	-18.18
Covariance contribution	-0.25
Combinations/Pair	1.35
Mean z-score	-2.12
Structure conservation index	0.56
SVM decision value	0.88
SVM RNA-class probability	0.874107
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8352223 98 + 22224390
-UCGAU---CGAUUGUGUU----UUGGAUUGCCGGCGAAUUUUUGCGCCGGCGGCUGAUCCACUAAUCAAGUUGCAUUUAUAUGCCCCACCGAUCCGUCGGCUAUA
-..(((---((((((((..----(..(.(((((((((........))))))))))..)..))).)))).....((((....))))......))))........... ( -34.20)
>DroPse_CAF1 14261 97 + 1
---GAUUGCCGAUUGUGUCGUUUGUCGUUUGUCGUCG----UCUACGGCGGCAUCUGAUCCACUAAUCAAGGUGCAUUUAUAUGCCCAGCGGAUCCGAUGGCGA--
---..(((((.((((..((((..((((..((((((((----....))))))))..))))..)).......((.((((....))))))....))..)))))))))-- ( -34.00)
>DroSec_CAF1 17673 99 + 1
AUCGAU---CGAUUGUGUU----UUGGAUUGCCGGCGAAUUUUUGCGCCGACGGCUGAUCCACUAAUCAAGGUGCAUUUAUAUGCCCCACCGAUCCGCCGGCCAUA
...(((---((((((((..----(..(.(((.(((((........))))).))))..)..))).))))..((.((((....)))).))...))))........... ( -31.00)
>DroYak_CAF1 15794 86 + 1
---GAU---CGAUUGUGUU----UUGGAUUGCCGGCGG----------UGGCGGCUGAUCCACUAAUCAAGGUGCAUUUAUAUGCCCCACCGAUCCGGCGACUUUA
---(((---(.(.......----.).))))((((((((----------(((.(((.(((.((((......)))).))).....)))))))))..)))))....... ( -31.80)
>consensus
___GAU___CGAUUGUGUU____UUGGAUUGCCGGCGA___UUUGCGCCGGCGGCUGAUCCACUAAUCAAGGUGCAUUUAUAUGCCCCACCGAUCCGACGGCUAUA
........................(((...(((((((........)))))))(((.((((..((.....))..((((....))))......)))).)))..))).. (-18.42 = -18.18 +  -0.25)

alignment

secondary structure

dotplot

Window 6

Location	8,352,223 – 8,352,321
Length	98
Sequences	4
Columns	106
Reading direction	reverse
Mean pairwise identity	76.28
Mean single sequence MFE	-29.44
Consensus MFE	-18.45
Energy contribution	-20.95
Covariance contribution	2.50
Combinations/Pair	1.19
Mean z-score	-1.86
Structure conservation index	0.63
SVM decision value	0.69
SVM RNA-class probability	0.824240
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8352223 98 - 22224390
UAUAGCCGACGGAUCGGUGGGGCAUAUAAAUGCAACUUGAUUAGUGGAUCAGCCGCCGGCGCAAAAAUUCGCCGGCAAUCCAA----AACACAAUCG---AUCGA-
...........(((((((.((((((....))))...((((((....))))))))(((((((........))))))).......----......))))---)))..- ( -31.60)
>DroPse_CAF1 14261 97 - 1
--UCGCCAUCGGAUCCGCUGGGCAUAUAAAUGCACCUUGAUUAGUGGAUCAGAUGCCGCCGUAGA----CGACGACAAACGACAAACGACACAAUCGGCAAUC---
--..(.((((.((((((((((((((....)))).))......)))))))).)))).)((((....----...((............)).......))))....--- ( -27.14)
>DroSec_CAF1 17673 99 - 1
UAUGGCCGGCGGAUCGGUGGGGCAUAUAAAUGCACCUUGAUUAGUGGAUCAGCCGUCGGCGCAAAAAUUCGCCGGCAAUCCAA----AACACAAUCG---AUCGAU
....(((((((((((((((((((((....)))).)))(((((....)))))))))...........)))))))))).......----..........---...... ( -31.00)
>DroYak_CAF1 15794 86 - 1
UAAAGUCGCCGGAUCGGUGGGGCAUAUAAAUGCACCUUGAUUAGUGGAUCAGCCGCCA----------CCGCCGGCAAUCCAA----AACACAAUCG---AUC---
.......(((((..(((((((((((....)))).)).......((((.....))))))----------)))))))).......----..........---...--- ( -28.00)
>consensus
UAUAGCCGACGGAUCGGUGGGGCAUAUAAAUGCACCUUGAUUAGUGGAUCAGCCGCCGGCGCAAA___UCGCCGGCAAUCCAA____AACACAAUCG___AUC___
....((((((((((((((((.((((....))))...((((((....))))))))))))........)))))))))).............................. (-18.45 = -20.95 +   2.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:47 2006