Locus 7736

Sequence ID	3L_DroMel_CAF1
Location	20,637,585 – 20,637,678
Length	93
Max. P	0.863998

overview

Window 8

Location	20,637,585 – 20,637,678
Length	93
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	86.63
Mean single sequence MFE	-31.94
Consensus MFE	-21.54
Energy contribution	-21.38
Covariance contribution	-0.16
Combinations/Pair	1.22
Mean z-score	-2.60
Structure conservation index	0.67
SVM decision value	0.84
SVM RNA-class probability	0.863998
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20637585 93 + 23771897
UCAUUAGCCGCGCUGGCUAUAAAUAUUUUGAUUUGUGGCAAACGCAGUUUUCCGCUGCAACAAAUGCA-GUACGAAGUGCACAUGCGAUGGCCG-----
......((((((((((((((((((......)))))))))....(((.(((...((((((.....))))-))..))).))).)).))).))))..----- ( -33.20)
>DroSec_CAF1 10836 93 + 1
UCAUUAGCCGCGCUGGCCAUAAAUAUUUUGAUUUGUGGCAAACGCAGUUUUCCGCUGCAUCAAAUGCA-GCACGAAGUGCACAUGCAAUGGCCG-----
......((((.(((((((((((((......)))))))))....(((.(((...(((((((...)))))-))..))).))).)).))..))))..----- ( -33.10)
>DroSim_CAF1 14177 92 + 1
UCAUUAGCCGCGCUGGCCAUAAAUAUUUUGAUUUGUGGCAAACGCAGUU-UCCGCUGCAACAAAUGCA-GCACGAAGUGCACAUACGAUGGCCG-----
......((((((...(((((((((......)))))))))....(((.((-(..((((((.....))))-))..))).))).....)).))))..----- ( -33.00)
>DroEre_CAF1 68 97 + 1
UCAUUAGCCGCGCUGGCAAUAAAUAUUUUGAUUUGUGGCAAAUGCACUUUUCCGCGCCAACAAAUGCGGGUACGAAGUGCACAUGCGU--GCCACACAU
......(((.....)))................(((((((..((((((((((((((........))))))...))))))))......)--))))))... ( -31.30)
>DroYak_CAF1 190689 99 + 1
UCAUUAGCCGCGCUGGCUAUAAAUAUUUUGAUUUGUGGCAAAUGCAGAUUUCCGCUCGAGCAAAUGCAGGUACGAAGUGGGCAUGCGAUGGCCCCACUG
......(((((((..(((((((((......)))))))))..((((......(((((((.((........)).)).)))))))))))).))))....... ( -29.10)
>consensus
UCAUUAGCCGCGCUGGCCAUAAAUAUUUUGAUUUGUGGCAAACGCAGUUUUCCGCUGCAACAAAUGCA_GUACGAAGUGCACAUGCGAUGGCCG_____
......((((((...(((((((((......)))))))))...)))...................((((.((((...))))...))))..)))....... (-21.54 = -21.38 +  -0.16)

alignment

secondary structure

dotplot

Window 9

Location	20,637,585 – 20,637,678
Length	93
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	86.63
Mean single sequence MFE	-29.94
Consensus MFE	-19.36
Energy contribution	-19.88
Covariance contribution	0.52
Combinations/Pair	1.16
Mean z-score	-2.10
Structure conservation index	0.65
SVM decision value	0.08
SVM RNA-class probability	0.573441
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20637585 93 - 23771897
-----CGGCCAUCGCAUGUGCACUUCGUAC-UGCAUUUGUUGCAGCGGAAAACUGCGUUUGCCACAAAUCAAAAUAUUUAUAGCCAGCGCGGCUAAUGA
-----.(((...((((.((....((((..(-((((.....)))))))))..))))))...))).................(((((.....))))).... ( -26.70)
>DroSec_CAF1 10836 93 - 1
-----CGGCCAUUGCAUGUGCACUUCGUGC-UGCAUUUGAUGCAGCGGAAAACUGCGUUUGCCACAAAUCAAAAUAUUUAUGGCCAGCGCGGCUAAUGA
-----.((((..(((....))).(((.(((-(((((...)))))))))))....(((((.((((.((((......)))).)))).)))))))))..... ( -33.70)
>DroSim_CAF1 14177 92 - 1
-----CGGCCAUCGUAUGUGCACUUCGUGC-UGCAUUUGUUGCAGCGGA-AACUGCGUUUGCCACAAAUCAAAAUAUUUAUGGCCAGCGCGGCUAAUGA
-----.((((.............(((.(((-((((.....)))))))))-)...(((((.((((.((((......)))).)))).)))))))))..... ( -32.80)
>DroEre_CAF1 68 97 - 1
AUGUGUGGC--ACGCAUGUGCACUUCGUACCCGCAUUUGUUGGCGCGGAAAAGUGCAUUUGCCACAAAUCAAAAUAUUUAUUGCCAGCGCGGCUAAUGA
...((((((--(.....((((((((((..((.((....)).))..)))...))))))).)))))))...........((((((((.....))).))))) ( -31.70)
>DroYak_CAF1 190689 99 - 1
CAGUGGGGCCAUCGCAUGCCCACUUCGUACCUGCAUUUGCUCGAGCGGAAAUCUGCAUUUGCCACAAAUCAAAAUAUUUAUAGCCAGCGCGGCUAAUGA
..(((((((........)))).....(((..(((((((((....)))))....))))..))))))...............(((((.....))))).... ( -24.80)
>consensus
_____CGGCCAUCGCAUGUGCACUUCGUAC_UGCAUUUGUUGCAGCGGAAAACUGCGUUUGCCACAAAUCAAAAUAUUUAUAGCCAGCGCGGCUAAUGA
......(((....(((.((((.....)))).)))..........((((....))))....))).................(((((.....))))).... (-19.36 = -19.88 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:55:33 2006