Locus 9195

Sequence ID	3R_DroMel_CAF1
Location	24,523,551 – 24,523,678
Length	127
Max. P	0.836812

overview

Window 8

Location	24,523,551 – 24,523,642
Length	91
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	88.95
Mean single sequence MFE	-19.39
Consensus MFE	-14.76
Energy contribution	-15.80
Covariance contribution	1.04
Combinations/Pair	1.05
Mean z-score	-1.96
Structure conservation index	0.76
SVM decision value	0.74
SVM RNA-class probability	0.836812
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24523551 91 - 27905053
AGGUAUUUUUCAUGGAUUUGCGGCUUUUUAGAAUAUUAAAAAUAUUUUUUAGCUGCA-GAGCCAGCACGAACCUAACAAUAUAUGUAUAUAU
((((........(((.(((((((((....(((((((.....)))))))..)))))))-)).)))......)))).................. ( -22.34)
>DroSec_CAF1 21956 91 - 1
AGGUAUUUUUCAUGGAUUUGCGGCUUUUUAGAAUAUUAAAAAUAUUGUUUAGCUGCA-GAGCCAGCACGAACCUAACAAUAUAUGUAUAUAU
((((........(((.(((((((((....(.(((((.....))))).)..)))))))-)).)))......)))).................. ( -20.84)
>DroSim_CAF1 23957 91 - 1
AGGUAUUUUUCAUGGAUUUGCGGCUUUUUAGAAUAUUAAAAAUAUUUUUUAGCUGCA-GAGCCAGCACGAACCUAACAAUAUAUGUAUAUAU
((((........(((.(((((((((....(((((((.....)))))))..)))))))-)).)))......)))).................. ( -22.34)
>DroYak_CAF1 22345 91 - 1
AGGUAUUUUUCAUGGAUUUGCGGCUUUUUAGAAUAUUAAAAAUAUUUUUUAGCUGCA-GACCCAGCGCAGACCCAACAAUAUUUAUAUAUAU
.(((........(((.(((((((((....(((((((.....)))))))..)))))))-)).)))......)))................... ( -22.14)
>DroAna_CAF1 22762 86 - 1
UGGUAUUUUUCAUGGAUUUGCGGCUUUUUAGAAUAUUAAAAACAUUUUUUAGCCAACUACGCGAG--CUUACCUAACAAUAUAUGUA----U
.((((...(((.((.......((((....(((((.........)))))..)))).....)).)))--..))))..............----. (  -9.30)
>consensus
AGGUAUUUUUCAUGGAUUUGCGGCUUUUUAGAAUAUUAAAAAUAUUUUUUAGCUGCA_GAGCCAGCACGAACCUAACAAUAUAUGUAUAUAU
.(((........(((...(((((((....(((((((.....)))))))..)))))))....)))......)))................... (-14.76 = -15.80 +   1.04)

alignment

secondary structure

dotplot

Window 9

Location	24,523,566 – 24,523,678
Length	112
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	79.33
Mean single sequence MFE	-30.51
Consensus MFE	-10.69
Energy contribution	-11.25
Covariance contribution	0.56
Combinations/Pair	1.26
Mean z-score	-2.82
Structure conservation index	0.35
SVM decision value	0.19
SVM RNA-class probability	0.625366
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24523566 112 - 27905053
GCGUAGUUCGCAGUUCGAUGGCUU-UACAUUUUGGUAAGGUAUUUUUCAUGGAUUUGCGGCUUUUUAGAAUAUUAAA-AAUAUUUUUUAGCUGCA-GAGCCAGCACGAACCUAAC
(((.....))).(((((.((((((-(((......)))))))........(((.(((((((((....(((((((....-.)))))))..)))))))-)).))).)))))))..... ( -35.20)
>DroVir_CAF1 10841 97 - 1
GUAAAGUCCACAAUGCGCUGGGUUGUAUAUUUUGAAAUGGUAUUUUCAAUGGAUUUGUGGCUUUUUAGAAUAUUAAAAAAUAUUU--CAAAUGCA-CAC---------------A
...(((((((((((.(...).))))).....((((((......)))))).))))))(((((..(((..((((((....)))))).--.))).)).-)))---------------. ( -20.70)
>DroSec_CAF1 21971 112 - 1
GCGUAGUUUGCAGUUCGAUGGCUU-UACAUUUUGGUAAGGUAUUUUUCAUGGAUUUGCGGCUUUUUAGAAUAUUAAA-AAUAUUGUUUAGCUGCA-GAGCCAGCACGAACCUAAC
(((.....))).(((((.((((((-(((......)))))))........(((.(((((((((....(.(((((....-.))))).)..)))))))-)).))).)))))))..... ( -32.30)
>DroSim_CAF1 23972 112 - 1
GCGUAGUUCGCAGUUCGAUGGCUU-UACAUUUUGGUAAGGUAUUUUUCAUGGAUUUGCGGCUUUUUAGAAUAUUAAA-AAUAUUUUUUAGCUGCA-GAGCCAGCACGAACCUAAC
(((.....))).(((((.((((((-(((......)))))))........(((.(((((((((....(((((((....-.)))))))..)))))))-)).))).)))))))..... ( -35.20)
>DroYak_CAF1 22360 112 - 1
GCGUAGUUCGCAGUUCAAUGGCUU-UAUAUUUUGGUAAGGUAUUUUUCAUGGAUUUGCGGCUUUUUAGAAUAUUAAA-AAUAUUUUUUAGCUGCA-GACCCAGCGCAGACCCAAC
((((................((((-(((......)))))))........(((.(((((((((....(((((((....-.)))))))..)))))))-)).)))))))......... ( -29.80)
>DroAna_CAF1 22773 111 - 1
ACGUAGUUGGCGACUCAACGGUUU-UAUAUUCUAAAAUGGUAUUUUUCAUGGAUUUGCGGCUUUUUAGAAUAUUAAA-AACAUUUUUUAGCCAACUACGCGAG--CUUACCUAAC
.((((((((((.........((((-(((((((((((((.(((..((.....))..))).)..)))))))))))..))-)))........))))))))))....--.......... ( -29.83)
>consensus
GCGUAGUUCGCAGUUCGAUGGCUU_UACAUUUUGGUAAGGUAUUUUUCAUGGAUUUGCGGCUUUUUAGAAUAUUAAA_AAUAUUUUUUAGCUGCA_GAGCCAGCACGAACCUAAC
((.......((((.((.((((....(((...........)))....)))).)).))))((((....((((((((....))))))))..))))))..................... (-10.69 = -11.25 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:28:42 2006