Locus 7168

Sequence ID	X_DroMel_CAF1
Location	17,977,819 – 17,977,967
Length	148
Max. P	0.996438

overview

Window 1

Location	17,977,819 – 17,977,927
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.17
Mean single sequence MFE	-40.68
Consensus MFE	-33.94
Energy contribution	-35.10
Covariance contribution	1.16
Combinations/Pair	1.06
Mean z-score	-1.70
Structure conservation index	0.83
SVM decision value	1.04
SVM RNA-class probability	0.905134
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17977819 108 - 22224390
CCCGCGCAUGUGGACAAAUGUCCAAACAAUUCGCACACAACAAAUUCAUUUGCCACCCAAAUGGGCGGUGGG------------GCGUGGCCAUGCCGCUGGCAUCAUUUGUAUUCCAUA
...(((.((.(((((....)))))....)).))).....((((((.....(((((.((....))(((((..(------------((...)))..))))))))))..))))))........ ( -34.80)
>DroSec_CAF1 8729 120 - 1
CCCGCGCAUGUGGACAAAUGUCCAACCAAUUCGCACACAACAAAUUCAUUUGCCACCCAAAGGGGCGGUGGGGCGCGUGUUGGGGCGUGGCCAUGCCGCAGGCAUCAUUUGUAUUGCAUA
...(((.((.(((((....)))))....)).))).....((((((.....((((.(((...)))((((((((.(((((......))))).)).)))))).))))..))))))........ ( -44.00)
>DroSim_CAF1 8426 120 - 1
CCCGCGCAUGUGGACAAAUGUCCAACCAAUUCGCACACAACAAAUUCAUUUGCCACCCAAAGGGGCGGUGGGGCGCGUGUUGGGGCGUGGCCAUGCCGCAGGCAUCAUUUGUAUUGCAUA
...(((.((.(((((....)))))....)).))).....((((((.....((((.(((...)))((((((((.(((((......))))).)).)))))).))))..))))))........ ( -44.00)
>DroEre_CAF1 10074 119 - 1
CCCGCGCAUGUGGACAAAUGUCCAAACAAUUCGCACACAACAAAUUCAUUAGACACCCAAAUGGGCGGUGG-CCACGGGUUAGGGCGUGGUCAUGCCGCAGCCAUCAUUUGUAUUGCAUA
...(((.((.(((((....)))))....)).))).....((((((...........((....))(((((((-(((((........)))))))..))))).......))))))........ ( -35.40)
>DroYak_CAF1 7737 120 - 1
CCCGCGCAUGUGGACAAAUGUCCAAACAAUUCGCACACAACAAAUUCAUUUGCCACCCAAAUGGGCGGUGGGGCGCGGGUUAGGGCGUGGUCAUGCCGCUGGCAUCAUUUGUAUUGCAUA
(((((((...(((((....)))))........................((..((.(((....))).))..)))))))))....(((((....)))))((..(((.....)))...))... ( -45.20)
>consensus
CCCGCGCAUGUGGACAAAUGUCCAAACAAUUCGCACACAACAAAUUCAUUUGCCACCCAAAUGGGCGGUGGGGCGCGGGUUAGGGCGUGGCCAUGCCGCAGGCAUCAUUUGUAUUGCAUA
...(((.((.(((((....)))))....)).))).....((((((.....((((.((.....))((((((((.((((........)))).)).)))))).))))..))))))........ (-33.94 = -35.10 +   1.16)

alignment

secondary structure

dotplot

Window 2

Location	17,977,855 – 17,977,967
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.83
Mean single sequence MFE	-39.50
Consensus MFE	-37.34
Energy contribution	-37.38
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.78
Structure conservation index	0.95
SVM decision value	2.70
SVM RNA-class probability	0.996438
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17977855 112 + 22224390
--------CCCACCGCCCAUUUGGGUGGCAAAUGAAUUUGUUGUGUGCGAAUUGUUUGGACAUUUGUCCACAUGCGCGGGCAGAUUUAUGAGACAGCCGUCUUCCAUUUACACAGCAUAC
--------....((((((....))))))..........(((((((((((...(((..((((....)))))))..)))(((.((((...((...))...)))))))....))))))))... ( -36.50)
>DroSec_CAF1 8769 120 + 1
ACACGCGCCCCACCGCCCCUUUGGGUGGCAAAUGAAUUUGUUGUGUGCGAAUUGGUUGGACAUUUGUCCACAUGCGCGGGCAGAUUUAUGAGACAGCCGUCUCCCAUUUACACAGCAUAC
....(((((((..(((((....)))))((((((.(((((((.....))))))).)))((((....))))...)))).))))........(((((....)))))...........)).... ( -40.20)
>DroSim_CAF1 8466 120 + 1
ACACGCGCCCCACCGCCCCUUUGGGUGGCAAAUGAAUUUGUUGUGUGCGAAUUGGUUGGACAUUUGUCCACAUGCGCGGGCAGAUUUAUGAGACAGCCGUCUCCCAUUUACACAGCAUAC
....(((((((..(((((....)))))((((((.(((((((.....))))))).)))((((....))))...)))).))))........(((((....)))))...........)).... ( -40.20)
>DroEre_CAF1 10114 119 + 1
ACCCGUGG-CCACCGCCCAUUUGGGUGUCUAAUGAAUUUGUUGUGUGCGAAUUGUUUGGACAUUUGUCCACAUGCGCGGGCAGAUUUAUGAGGCAGCCGUCUCCCAUUUACACAGCAUAC
(((((.((-(....)))....)))))............(((((((((((...(((..((((....)))))))..)))(((.((((...((...))...)))))))....))))))))... ( -37.60)
>DroYak_CAF1 7777 120 + 1
ACCCGCGCCCCACCGCCCAUUUGGGUGGCAAAUGAAUUUGUUGUGUGCGAAUUGUUUGGACAUUUGUCCACAUGCGCGGGCAGAUUUAUGAGACAGCCGUCUCCCAUUUACACAGCAUAC
.(((((((....((((((....))))))...((((((((((.....)))))))...(((((....))))))))))))))).........(((((....)))))................. ( -43.00)
>consensus
ACACGCGCCCCACCGCCCAUUUGGGUGGCAAAUGAAUUUGUUGUGUGCGAAUUGUUUGGACAUUUGUCCACAUGCGCGGGCAGAUUUAUGAGACAGCCGUCUCCCAUUUACACAGCAUAC
............((((((....))))))..........(((((((((((...((..(((((....)))))))..)))(((.((((...((...))...)))))))....))))))))... (-37.34 = -37.38 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:52 2006