Locus 2824

Sequence ID	2R_DroMel_CAF1
Location	9,823,737 – 9,823,898
Length	161
Max. P	0.925028

overview

Window 9

Location	9,823,737 – 9,823,828
Length	91
Sequences	5
Columns	91
Reading direction	forward
Mean pairwise identity	94.07
Mean single sequence MFE	-22.97
Consensus MFE	-20.14
Energy contribution	-20.68
Covariance contribution	0.54
Combinations/Pair	1.12
Mean z-score	-1.55
Structure conservation index	0.88
SVM decision value	1.17
SVM RNA-class probability	0.925028
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9823737 91 + 20766785
AAGGUGGAGCUCAAGAGCAGCUGCACAUUUGGCAUGGGUCAGUUUAAAAGACGAAACCAUACUGAUCUCGUUUGCAUUUCUACACUUAUAA
((((((.(((((....).)))).))).....(((.((((((((.................))))))))....))).........))).... ( -20.23)
>DroSec_CAF1 61471 91 + 1
AAGGUGGAGCUCAAGAGCAGCUGCAAAUUUGGCAUGUGUCAGUUUAAAAGACGAAACCAUACUGAUCUCUUUUGCAUUUCUACACUUAUAA
(((((((((((....)))...((((((.(..(.(((.((..(((.....)))...))))).)..).....))))))..))))).))).... ( -18.80)
>DroSim_CAF1 63011 91 + 1
AAGGUGGAGCUCAAGAGCAGCUGCAAAUUUGGCAUGGGUCAGUUUAAAAGAUGAAACCAUACUGAUCUCGUUUGAAUUUCUACACUUAUAA
(((((((((((....))).......((((..(.((((((((((.................))))))).))))..))))))))).))).... ( -20.23)
>DroEre_CAF1 66201 91 + 1
AAGGUGGAGCUCAAGAGCAGCUGCAAAUUUGGCAUGGGUCAGUUUAAAAGACGAAACCAUACCGAUCUCGUUUGCAUUUCUACACCUUUAA
((((((..(((....)))...(((((((((((.((((....(((.....)))....)))).))))....)))))))......))))))... ( -26.60)
>DroYak_CAF1 63297 91 + 1
AAGGUGGAGCUGAAAAGCAGCUGCAAAUUUGGCAUGGGUCAGUUUAGAAGACGAAACCAUACCGAUCUCGUUUGCAUUUCCACACCUUUAA
((((((.(((((.....)))))((((((((((.((((....(((.....)))....)))).))))....)))))).......))))))... ( -29.00)
>consensus
AAGGUGGAGCUCAAGAGCAGCUGCAAAUUUGGCAUGGGUCAGUUUAAAAGACGAAACCAUACUGAUCUCGUUUGCAUUUCUACACUUAUAA
...((((((((....)))...(((((((((((.((((....(((.....)))....)))).))))....)))))))..)))))........ (-20.14 = -20.68 +   0.54)

alignment

secondary structure

dotplot

Window 0

Location	9,823,792 – 9,823,898
Length	106
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	84.81
Mean single sequence MFE	-27.74
Consensus MFE	-22.48
Energy contribution	-23.00
Covariance contribution	0.52
Combinations/Pair	1.11
Mean z-score	-1.81
Structure conservation index	0.81
SVM decision value	0.65
SVM RNA-class probability	0.812143
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9823792 106 - 20766785
GUACCGACAUGCCCCACACCUAUUU-UUUAAUGGGGGAGGUUGGGGGAUUUUUG-----UAAGCCAGGUUUUAUGGUUAUAAGUGUAGAAAUGCAAACGAGAUCAGUAUGGU
..((((((...((((((.((((((.-...))))))....).)))))((((((.(-----(.(((((.......))))).....((((....)))).)))))))).)).)))) ( -29.90)
>DroSec_CAF1 61526 98 - 1
---------UGCCCGACACCUAUUUUUUUAAUGGGUGAGGUUGGGGGAUUUUAG-----UAAGCCAGGUUUUAUGGUUAUAAGUGUAGAAAUGCAAAAGAGAUCAGUAUGGU
---------..(((((((((((((.....)))))))...)))))).((((((..-----..(((((.......))))).....((((....))))...))))))........ ( -27.20)
>DroSim_CAF1 63066 98 - 1
---------UGCCCGACACCUAUUUUUUUAAUGGGGGAGGUUGGGGGAUUUUCG-----UAAGCCAGGUUUUAUGGUUAUAAGUGUAGAAAUUCAAACGAGAUCAGUAUGGU
---------..((((((.((((((.....))))))....)))))).(((((.((-----(.(((((.......))))).....((.(....).)).))))))))........ ( -24.90)
>DroEre_CAF1 66256 104 - 1
GUAC-----UGCCCGACACCUAUUUUU---AUGGGGGAAGUUGGGGGGUUUUUAUUUUGUAAGCUAGGUUUUAUGGUUAAAGGUGUAGAAAUGCAAACGAGAUCGGUAUGGU
((((-----((((((((.(((((....---)))))....))))))........(((((((.(((((.......))))).....((((....)))).)))))))))))))... ( -27.10)
>DroYak_CAF1 63352 99 - 1
GCAC-----UGCCCGACACCUAUUUUU---AUGGGGGAGGUUGGGGGAUUUUCA-----UACGCCAAGUUUUAUGGUUAAAGGUGUGGAAAUGCAAACGAGAUCGGUAUGGU
..((-----((((((((.(((((....---)))))....))))))(.(((((((-----(((((((.......)))).....)))))))))).).........))))..... ( -29.60)
>consensus
G_AC_____UGCCCGACACCUAUUUUUUUAAUGGGGGAGGUUGGGGGAUUUUCG_____UAAGCCAGGUUUUAUGGUUAUAAGUGUAGAAAUGCAAACGAGAUCAGUAUGGU
...........((((((.((((((.....))))))....)))))).((((((.........(((((.......))))).....((((....))))...))))))........ (-22.48 = -23.00 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:23 2006