Locus 6321

Sequence ID	2L_DroMel_CAF1
Location	17,617,755 – 17,617,895
Length	140
Max. P	0.800692

overview

Window 5

Location	17,617,755 – 17,617,855
Length	100
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	92.07
Mean single sequence MFE	-17.92
Consensus MFE	-15.92
Energy contribution	-15.80
Covariance contribution	-0.12
Combinations/Pair	1.11
Mean z-score	-1.35
Structure conservation index	0.89
SVM decision value	0.62
SVM RNA-class probability	0.800692
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17617755 100 + 22407834
GCCACUUCCCCUU------CCACUUCCACAUCCGCAUCAUCGCCAAAAACAAAAAACACCGCCC-CUUUGGAGGUUGCAUGUGCAACCAAUUACAGUCGUUUCCGGC
.............------......................(((..((((........(((...-...))).((((((....))))))..........))))..))) ( -17.60)
>DroSec_CAF1 13146 101 + 1
GCCACUUCCCCUU------CCACUUCCACAUCCGCAUCGCCGCCAAAAACAAAAAACACCGCCCCCAUUGGAGGUUGCAUGUGCAACCAAUUACAGUCGUUUCCGGU
.............------...................((((..((..((........(((.......))).((((((....)))))).......))..))..)))) ( -16.00)
>DroSim_CAF1 3335 101 + 1
GCCACUUCCCCUU------CCACUUCCACAUCCGCAUCGCCGCCAAAAACAAAAAACACCGCCCCCAUUGGAGGUUGCAUGUGCAACCAAUUACAUUCGUUUCCGGC
.............------...................((((....((((........(((.......))).((((((....))))))..........)))).)))) ( -17.40)
>DroEre_CAF1 1565 100 + 1
GCCACUUCCCCUU------CCACUUCCACUUCCGCAUCCCAGCGAAAAACAAAAAACACCGCCCCCU-UGGAGGUUGCAUGUGCAACCAAUUACAGUCGUUUCCGGC
(((..........------.............(((......))).........((((.(((......-))).((((((....))))))..........))))..))) ( -19.80)
>DroYak_CAF1 13090 107 + 1
GCCACUUCCCCUUCUCAUGCCACUUCCACUUCCGCAUCCCCACGAAAAACAAAAAACACCACCCCCUUUGGAGGUUGCAUGUGCAACCAAUUACAGUCGUUUCCGGC
(((.............((((.............))))....((((.............(((.......))).((((((....))))))........))))....))) ( -18.82)
>consensus
GCCACUUCCCCUU______CCACUUCCACAUCCGCAUCCCCGCCAAAAACAAAAAACACCGCCCCCUUUGGAGGUUGCAUGUGCAACCAAUUACAGUCGUUUCCGGC
(((..............................((......))..........((((.(((.......))).((((((....))))))..........))))..))) (-15.92 = -15.80 +  -0.12)

alignment

secondary structure

dotplot

Window 6

Location	17,617,789 – 17,617,895
Length	106
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	92.80
Mean single sequence MFE	-34.68
Consensus MFE	-27.18
Energy contribution	-27.70
Covariance contribution	0.52
Combinations/Pair	1.09
Mean z-score	-1.50
Structure conservation index	0.78
SVM decision value	0.04
SVM RNA-class probability	0.553168
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17617789 106 - 22407834
ACCCGCGUGGAUGCGAAAUUUCAGGCGCUAAAAACUGAUUGCCGGAAACGACUGUAAUUGGUUGCACAUGCAACCUCCAAAG-GGGCGGUGUUUUUUGUUUUUGGCG
....((.((((........)))).))(((((((((.((..((((....))(((((....((((((....)))))).((....-)))))))))..)).))))))))). ( -37.40)
>DroSec_CAF1 13180 107 - 1
ACCCGCGUGGAUGCGAAAUCUCAGGCGCAAAAAACUGAUUACCGGAAACGACUGUAAUUGGUUGCACAUGCAACCUCCAAUGGGGGCGGUGUUUUUUGUUUUUGGCG
..((((.(((((.....))).)).))(((((((((.......((....))(((((....((((((....))))))(((....)))))))))))))))))....)).. ( -34.90)
>DroSim_CAF1 3369 107 - 1
ACCCGCGUGGAUGCGAAAUUUCAGGCGCUAAAAACUGAUUGCCGGAAACGAAUGUAAUUGGUUGCACAUGCAACCUCCAAUGGGGGCGGUGUUUUUUGUUUUUGGCG
....((.((((........)))).))(((((((((..(((((((....))...)))))..)))((((.(((..((......))..)))))))........)))))). ( -35.80)
>DroEre_CAF1 1599 105 - 1
ACUCGCGCGGUUGCGA-AUUUCAGGCGCUAAAAACUGAUUGCCGGAAACGACUGUAAUUGGUUGCACAUGCAACCUCCA-AGGGGGCGGUGUUUUUUGUUUUUCGCU
......((((..((((-(....(((((((...(((..(((((((....))...)))))..)))......((..((....-.))..))))))))))))))...)))). ( -31.20)
>DroYak_CAF1 13130 106 - 1
ACGCGCGUGGAAGCGA-AUUUCUGGCGCUAAAAACUGAUUGCCGGAAACGACUGUAAUUGGUUGCACAUGCAACCUCCAAAGGGGGUGGUGUUUUUUGUUUUUCGUG
...((((.((((((((-(.....((((((...(((..(((((((....))...)))))..)))((....)).((((((...)))))))))))).))))))))))))) ( -34.10)
>consensus
ACCCGCGUGGAUGCGAAAUUUCAGGCGCUAAAAACUGAUUGCCGGAAACGACUGUAAUUGGUUGCACAUGCAACCUCCAAAGGGGGCGGUGUUUUUUGUUUUUGGCG
....((.((((........)))).))((.((((((.((..((((....))(((((....((((((....)))))).((.....)))))))))..)).)))))).)). (-27.18 = -27.70 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:17 2006