Locus 1070

Sequence ID	3R_DroMel_CAF1
Location	3,292,671 – 3,292,809
Length	138
Max. P	0.998663

overview

Window 9

Location	3,292,671 – 3,292,769
Length	98
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	91.94
Mean single sequence MFE	-21.62
Consensus MFE	-21.14
Energy contribution	-21.02
Covariance contribution	-0.12
Combinations/Pair	1.08
Mean z-score	-1.87
Structure conservation index	0.98
SVM decision value	3.18
SVM RNA-class probability	0.998663
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3292671 98 - 27905053
UCAUUCUCAAUGCGCUCGCUGUAGUUUUUGCAAUUUUUCAACUGAUUGCAGAAAUGCGAAAGAAAUGAAUGCAUAAAAAUGCUCUUAUUGACAGUUUC
.................(((((.((((((((((((........)))))))))))).(....).(((((..((((....))))..))))).)))))... ( -22.30)
>DroSec_CAF1 45556 98 - 1
UCAUUCUCAAUGCGCUCGCUGUAGUUUUUGCAAUUUUUCAACUGAUUGCAGAAAUGCAAAAGAAAUGAAUGCAUAAAAAUGCUCUUAUUGACAGUUUC
.................(((((.((((((((((((........))))))))))))........(((((..((((....))))..))))).)))))... ( -21.80)
>DroSim_CAF1 46732 98 - 1
UCAUUCUCAAUGCGCUCGCUGUAGUUUUUGCAAUUUUUCAACUGAUUGCAGAAAUGCGAAAGAAAUGAAUGCAUAAAAAUGCUCUUAUUGACAGUUUC
.................(((((.((((((((((((........)))))))))))).(....).(((((..((((....))))..))))).)))))... ( -22.30)
>DroEre_CAF1 47354 83 - 1
---------------UCGCUGUAGUUUGUGCAGUUUUUCAACUGAUUGCAGAAAUGCGAAAGAAAUGAAUGCAUAAAAAUGCUCUUAUUGACAGUUUC
---------------..(((((.((((.(((((((........))))))).)))).(....).(((((..((((....))))..))))).)))))... ( -20.80)
>DroYak_CAF1 64992 98 - 1
UCAUUCUCAAUGCGUUCGCUGUAGUUUUUGUAAUUUUUCAACUGAUUGCAGAAAUGCGAAAGAAAUGAAUGCAUAAAAAUGCUCUUAUUGACAGUUUC
.........(((((((((.....((((((((((((........)))))))))))).(....)...)))))))))........................ ( -20.90)
>consensus
UCAUUCUCAAUGCGCUCGCUGUAGUUUUUGCAAUUUUUCAACUGAUUGCAGAAAUGCGAAAGAAAUGAAUGCAUAAAAAUGCUCUUAUUGACAGUUUC
.................(((((.((((((((((((........))))))))))))........(((((..((((....))))..))))).)))))... (-21.14 = -21.02 +  -0.12)

alignment

secondary structure

dotplot

Window 0

Location	3,292,708 – 3,292,809
Length	101
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	89.80
Mean single sequence MFE	-20.31
Consensus MFE	-17.93
Energy contribution	-18.21
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-1.33
Structure conservation index	0.88
SVM decision value	0.28
SVM RNA-class probability	0.665201
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3292708 101 - 27905053
UUUUCGGAGAAAGCAAAUGCAUUAACAUUUCUCAAACUUUUCAUUCUCAAUGCGCUCGCUGUAGUUUUUGCAAUUUUUCAACUGAUUGCAGAAAUGCGAAA
......((((((((....)).......))))))......................((((....((((((((((((........)))))))))))))))).. ( -20.61)
>DroSec_CAF1 45593 101 - 1
UUUUCGGAGCAAGCAAUUGCAUUAACAUUUCUCAAAGUUUUCAUUCUCAAUGCGCUCGCUGUAGUUUUUGCAAUUUUUCAACUGAUUGCAGAAAUGCAAAA
......((((((....))(((((.........................)))))))))..((((.(((((((((((........)))))))))))))))... ( -20.51)
>DroSim_CAF1 46769 101 - 1
UUUUCGGAGAAAGCAAUUGCAUUAACAUUUCUCAAAGUUUUCAUUCUCAAUGCGCUCGCUGUAGUUUUUGCAAUUUUUCAACUGAUUGCAGAAAUGCGAAA
......((((((((....)).......))))))......................((((....((((((((((((........)))))))))))))))).. ( -20.61)
>DroEre_CAF1 47391 84 - 1
CUUUCGGAGAAAGCAAUUGCAUUAACAUUUCUCAAAGU-----------------UCGCUGUAGUUUGUGCAGUUUUUCAACUGAUUGCAGAAAUGCGAAA
......((((((((....)).......))))))....(-----------------((((....((((.(((((((........))))))).))))))))). ( -20.11)
>DroYak_CAF1 65029 101 - 1
UUUUCGGAGAAAGCAAUUGCAUUAACAUUUCUCAAAGUUUUCAUUCUCAAUGCGUUCGCUGUAGUUUUUGUAAUUUUUCAACUGAUUGCAGAAAUGCGAAA
.((((.((((((((....)).......))))))..................(((((..((((((((.(((........)))..)))))))).))))))))) ( -19.71)
>consensus
UUUUCGGAGAAAGCAAUUGCAUUAACAUUUCUCAAAGUUUUCAUUCUCAAUGCGCUCGCUGUAGUUUUUGCAAUUUUUCAACUGAUUGCAGAAAUGCGAAA
......((((((((....)).......))))))......................((((....((((((((((((........)))))))))))))))).. (-17.93 = -18.21 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:47 2006