Locus 6438

Sequence ID	2L_DroMel_CAF1
Location	18,086,653 – 18,086,813
Length	160
Max. P	0.727065

overview

Window 3

Location	18,086,653 – 18,086,773
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.67
Mean single sequence MFE	-30.50
Consensus MFE	-27.92
Energy contribution	-28.93
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.77
Structure conservation index	0.92
SVM decision value	0.41
SVM RNA-class probability	0.727065
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18086653 120 - 22407834
AACCAGGACAUUCCAUGGCCACGGAUUUGCCUUAAUUAAAUGCCCGGCUCCGGCAUUAAGUCACAUGUAUCUAUAUAUGCAAAUAAAUUAUGGAAAGCCCAGUGGCAUAUAUGGCAUGUG
.......((((.((((((((((((..((.((.(((((.((((((.(....)))))))......((((((....))))))......))))).)).))..)).)))))...))))).)))). ( -33.00)
>DroSec_CAF1 293909 118 - 1
AACCAGGACAUUCCAUGGCCACGGAUUUGCCUUAAUUAAAUGCCCGGCUCCGGCAUUAAGUCACAUGUAUCUAUAUAUGCAAAUAAAUUAUGGAAAGCCCAGUGGCAUAAAUG--AUAUU
...((((.....)).))(((((((..((.((.(((((.((((((.(....)))))))......((((((....))))))......))))).)).))..)).))))).......--..... ( -27.80)
>DroSim_CAF1 295996 120 - 1
AACCAGGACAUUCCAUGGCCACGGAUUUGCCUUAAUUAAAUGCCCGGCUCCGGCAUUAAGUCACAUGUAUCUAUAUAUGCAAAUAAAUUAUGGAAAGCCCAGUGGCAUAAAUGGCAUGUG
.......((((.((((.(((((((..((.((.(((((.((((((.(....)))))))......((((((....))))))......))))).)).))..)).)))))....)))).)))). ( -33.90)
>DroYak_CAF1 311393 120 - 1
AACCAGGACAUUCCCUAGCCACGGAUUUGCCUUAAUUAAAUGCCCGGCUCCGGCAUUAAGUCACAUGUAUCUAUAUAUGCAAAUAAAUUAUGGAAAGCCCACUGGCAUAAAUGGCAUGUG
....(((.((.(((........)))..)))))......((((((.(....)))))))....(((((((.((((((.............))))))..(((....))).......))))))) ( -27.32)
>consensus
AACCAGGACAUUCCAUGGCCACGGAUUUGCCUUAAUUAAAUGCCCGGCUCCGGCAUUAAGUCACAUGUAUCUAUAUAUGCAAAUAAAUUAUGGAAAGCCCAGUGGCAUAAAUGGCAUGUG
.......((((.((((.(((((((..((.((.(((((.((((((.(....)))))))......((((((....))))))......))))).)).))..)).)))))....)))).)))). (-27.92 = -28.93 +   1.00)

alignment

secondary structure

dotplot

Window 4

Location	18,086,693 – 18,086,813
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	98.75
Mean single sequence MFE	-31.33
Consensus MFE	-30.17
Energy contribution	-30.68
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.76
Structure conservation index	0.96
SVM decision value	0.14
SVM RNA-class probability	0.603399
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18086693 120 - 22407834
AAUUGACAUUAUUAAAUGCAGCAGUGAUACUGGCACUGUGAACCAGGACAUUCCAUGGCCACGGAUUUGCCUUAAUUAAAUGCCCGGCUCCGGCAUUAAGUCACAUGUAUCUAUAUAUGC
......(((...((.(((((...(((((...(((((((((..(((((.....)).))).)))))...)))).......((((((.(....)))))))..))))).))))).))...))). ( -32.60)
>DroSec_CAF1 293947 120 - 1
AAUUGACAUUAUUAAAUGCAGCAGUGAUACUGGCACUGUGAACCAGGACAUUCCAUGGCCACGGAUUUGCCUUAAUUAAAUGCCCGGCUCCGGCAUUAAGUCACAUGUAUCUAUAUAUGC
......(((...((.(((((...(((((...(((((((((..(((((.....)).))).)))))...)))).......((((((.(....)))))))..))))).))))).))...))). ( -32.60)
>DroSim_CAF1 296036 120 - 1
AAUUGACAUUAUUAAAUGCAGCAGUGAUACUGGCACUGUGAACCAGGACAUUCCAUGGCCACGGAUUUGCCUUAAUUAAAUGCCCGGCUCCGGCAUUAAGUCACAUGUAUCUAUAUAUGC
......(((...((.(((((...(((((...(((((((((..(((((.....)).))).)))))...)))).......((((((.(....)))))))..))))).))))).))...))). ( -32.60)
>DroYak_CAF1 311433 120 - 1
AAUUGACAUUAUUAAAUGCUGCAGUGAUACUGGCACUGUGAACCAGGACAUUCCCUAGCCACGGAUUUGCCUUAAUUAAAUGCCCGGCUCCGGCAUUAAGUCACAUGUAUCUAUAUAUGC
...................(((((((((...(((((((((..(.(((......))).).)))))...)))).......((((((.(....)))))))..))))).))))........... ( -27.50)
>consensus
AAUUGACAUUAUUAAAUGCAGCAGUGAUACUGGCACUGUGAACCAGGACAUUCCAUGGCCACGGAUUUGCCUUAAUUAAAUGCCCGGCUCCGGCAUUAAGUCACAUGUAUCUAUAUAUGC
......(((...((.(((((...(((((...(((((((((..(((((.....)).))).)))))...)))).......((((((.(....)))))))..))))).))))).))...))). (-30.17 = -30.68 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:14 2006