Locus 892

Sequence ID	2R_DroMel_CAF1
Location	4,041,814 – 4,041,960
Length	146
Max. P	0.765494

overview

Window 7

Location	4,041,814 – 4,041,934
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.48
Mean single sequence MFE	-38.65
Consensus MFE	-34.64
Energy contribution	-35.08
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.30
Structure conservation index	0.90
SVM decision value	0.49
SVM RNA-class probability	0.758311
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4041814 120 - 20766785
CAGGAGCUUUAAGGAUAUUAGGAUGGGUAGUGAGGCGUGGCCACGGGAACGCCUUGCUGUCACUGGAUAUGCAUGAUUGAUGCUGGACCCUAUCAUAAAUUGAAUUCGCCCCAAAACGAA
..((.((....((((((((.((...(..((..((((((..(....)..))))))..))..).)).)))))((((.....)))).....))).(((.....)))....)).))........ ( -33.80)
>DroSec_CAF1 24500 119 - 1
CGGGAGCUUUAAGGAUAUUAGGAUGGGCAGUGAGGCGUGGCCACGGGAACGCCUUGCUGUCACUGGAUAUGCAUGAUUGAUGCUGGACCCUAUCAUAAAUUGAAUUCGCCCCA-AACGAA
.(((.((....((((((((.((...(((((..((((((..(....)..))))))..))))).)).)))))((((.....)))).....))).(((.....)))....))))).-...... ( -40.90)
>DroSim_CAF1 26653 119 - 1
CGGGAGCUUUAAGGAUAUUAGGAUGGGCAGUGAGGCGUGGCCACGGGAACGCCUUGCUGUCACUGGAUAUGCAUGAUUGAUGCUGGACCCUAUCAUAAAUUGAAUUCGCCCCA-AACGAA
.(((.((....((((((((.((...(((((..((((((..(....)..))))))..))))).)).)))))((((.....)))).....))).(((.....)))....))))).-...... ( -40.90)
>DroEre_CAF1 23790 119 - 1
CGGGAGCCGUAAGGAUAUUAGGAUGGGCAGUGAGGCGUGGCCACGGGAACGCCUUGCUGUCACUGGAUAUGCAUGAUUGAUGCUGGACCCUAUCAUAAAUUGAAUUCGCCCCA-AGCGAA
.(((..((....))(((((.((...(((((..((((((..(....)..))))))..))))).)).)))))((((.....))))....)))..(((.....))).(((((....-.))))) ( -42.00)
>DroYak_CAF1 27719 119 - 1
CAGGAGCUUUAAGGACAUUAGAAUGGGCAGUGAGGCGUGUCCCUGAGAACGCCUUGCUGUCACUGGAUAUGCAUGAUUGAUGCUGGGCCCUAUCAUAAAUUGAAUUCGCCCCA-AACGAA
....(((.((((.(.(((.......(((((..((((((..........))))))..))))).......))))....)))).)))((((....(((.....)))....))))..-...... ( -35.64)
>consensus
CGGGAGCUUUAAGGAUAUUAGGAUGGGCAGUGAGGCGUGGCCACGGGAACGCCUUGCUGUCACUGGAUAUGCAUGAUUGAUGCUGGACCCUAUCAUAAAUUGAAUUCGCCCCA_AACGAA
.(((.((....(((...((((....(((((..((((((..(....)..))))))..))))).))))....((((.....)))).....))).(((.....)))....)))))........ (-34.64 = -35.08 +   0.44)

alignment

secondary structure

dotplot

Window 8

Location	4,041,854 – 4,041,960
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.16
Mean single sequence MFE	-38.24
Consensus MFE	-28.38
Energy contribution	-29.50
Covariance contribution	1.12
Combinations/Pair	1.08
Mean z-score	-1.68
Structure conservation index	0.74
SVM decision value	0.51
SVM RNA-class probability	0.765494
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4041854 106 - 20766785
UGGAUGCG---GGGU------GC-----UUGGUGCGGGAGCAGGAGCUUUAAGGAUAUUAGGAUGGGUAGUGAGGCGUGGCCACGGGAACGCCUUGCUGUCACUGGAUAUGCAUGAUUGA
...((((.---....------((-----((..(((....))).)))).......(((((.((...(..((..((((((..(....)..))))))..))..).)).)))))))))...... ( -34.60)
>DroSec_CAF1 24539 111 - 1
CGGAUGCG---GGGU------GCGGUUGCGGGUGCGGGAGCGGGAGCUUUAAGGAUAUUAGGAUGGGCAGUGAGGCGUGGCCACGGGAACGCCUUGCUGUCACUGGAUAUGCAUGAUUGA
((.((.((---.((.------....)).)).)).))(((((....)))))..(.(((((.((...(((((..((((((..(....)..))))))..))))).)).))))).)........ ( -40.40)
>DroSim_CAF1 26692 117 - 1
CGGAUGCG---GGGUGUGGGUGCGGGUGCGGGUGCGGGAGCGGGAGCUUUAAGGAUAUUAGGAUGGGCAGUGAGGCGUGGCCACGGGAACGCCUUGCUGUCACUGGAUAUGCAUGAUUGA
((.((.((---.....)).)).)).(((((.((.(((((((....))))................(((((..((((((..(....)..))))))..))))).))).)).)))))...... ( -42.20)
>DroEre_CAF1 23829 87 - 1
---------------------------------GCGGGUGCGGGAGCCGUAAGGAUAUUAGGAUGGGCAGUGAGGCGUGGCCACGGGAACGCCUUGCUGUCACUGGAUAUGCAUGAUUGA
---------------------------------(((.((.(((...((....))...........(((((..((((((..(....)..))))))..))))).))).)).)))........ ( -34.90)
>DroYak_CAF1 27758 120 - 1
UGGGUGCGCAUGGGUGCGGUUGCCGGUGAGGAUGAGGGUGCAGGAGCUUUAAGGACAUUAGAAUGGGCAGUGAGGCGUGUCCCUGAGAACGCCUUGCUGUCACUGGAUAUGCAUGAUUGA
...(((((((....))).....(((((((.(..((((((.((((.((((((..(.(((....)))..)..)))))).....))))...)).))))..).)))))))....))))...... ( -39.10)
>consensus
CGGAUGCG___GGGU______GC_G_UGCGGGUGCGGGAGCGGGAGCUUUAAGGAUAUUAGGAUGGGCAGUGAGGCGUGGCCACGGGAACGCCUUGCUGUCACUGGAUAUGCAUGAUUGA
...............................((((((((((....))))).......((((....(((((..((((((..(....)..))))))..))))).))))...)))))...... (-28.38 = -29.50 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:17 2006