Locus 2801

Sequence ID	3L_DroMel_CAF1
Location	7,963,236 – 7,963,386
Length	150
Max. P	0.895930

overview

Window 4

Location	7,963,236 – 7,963,346
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.58
Mean single sequence MFE	-37.72
Consensus MFE	-27.98
Energy contribution	-28.06
Covariance contribution	0.08
Combinations/Pair	1.08
Mean z-score	-2.08
Structure conservation index	0.74
SVM decision value	0.67
SVM RNA-class probability	0.816290
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7963236 110 - 23771897
GUCUAUUUCAGUUUUCCAAUGCACUUUACGAGCAGCUCUAAGGUAGGAGC---AGCUCACCAGAACAGUUGAACUCCACUCAAUGGACGGGGAG-------AAACUGGGAAAACUGGGGA
.....(..(((((((((............((((.(((((......)))))---.)))).......(((((...((((..((....))...))))-------.))))))))))))))..). ( -40.80)
>DroSec_CAF1 6475 110 - 1
GUCUAUUUCAGUUUUCCAAUGCACUUUACGAGCAGCUCUAAGGUAGGAGC---AGCUCACCAGAACAGUUGAACUCCACUCAAUGGACGGGGGG-------AAACUGGGCAAACUGGGGA
.....(..((((((.((............((((.(((((......)))))---.)))).......(((((...((((..((....))..)))).-------.))))))).))))))..). ( -37.20)
>DroSim_CAF1 6419 112 - 1
GUCUAUUUCAGUUUUCCAAUGCACUUUACGAGCAGCUCUAAGGUAGGAGC---AGCUCACCAGAACAGUUGAACUCCACUCAAUGGACGGGGGG-----GAAAACUGGGCAAACUGGGGA
.....(..((((((.((............((((.(((((......)))))---.)))).......(((((...((((.(((.......))))))-----)..))))))).))))))..). ( -38.30)
>DroEre_CAF1 6512 110 - 1
GUCUAUUUCAGUUUUCCAAUGCACUUUACGAGCAGCUCUAAGGUAGGAGC---AGCUCACCAGAACAGUUGAACUCCACUCAACGGACGGGGAAACCUG-------GGGGGCACUGGGGG
............(..(((.(((.......((((.(((((......)))))---.)))).((......(((((.......)))))...((((....))))-------))..))).)))..) ( -38.10)
>DroYak_CAF1 6887 120 - 1
GUCUAUUUCAGUUUUCCAAUGCACUUUACGAGCAGCUCUAAGGUAGGAGCAGCAGCUCACCAGAACAGUUGAACUCCACUCAAUGGACGGGGAAACUGAGUAUACUGGGUAUACUGGGGA
.((((..((((((((((............((((.(((((......)))))....)))).(((....(((.(....).)))...)))...))))))))))((((((...)))))))))).. ( -34.20)
>consensus
GUCUAUUUCAGUUUUCCAAUGCACUUUACGAGCAGCUCUAAGGUAGGAGC___AGCUCACCAGAACAGUUGAACUCCACUCAAUGGACGGGGAG_______AAACUGGGCAAACUGGGGA
.....(..((((((.((............((((.(((((......)))))....)))).((......(((((.......)))))......))...............)).))))))..). (-27.98 = -28.06 +   0.08)

alignment

secondary structure

dotplot

Window 5

Location	7,963,269 – 7,963,386
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.65
Mean single sequence MFE	-30.82
Consensus MFE	-28.00
Energy contribution	-28.20
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.64
Structure conservation index	0.91
SVM decision value	0.99
SVM RNA-class probability	0.895930
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7963269 117 - 23771897
CAUCCAUUUCAGUGUUCGGUGUGUCCAACUGUCUCGACUUGUCUAUUUCAGUUUUCCAAUGCACUUUACGAGCAGCUCUAAGGUAGGAGC---AGCUCACCAGAACAGUUGAACUCCACU
.......(((((((((((((((((..(((((....((....)).....))))).....)))))))....((((.(((((......)))))---.))))....))))).)))))....... ( -30.80)
>DroSec_CAF1 6508 117 - 1
CAUCCAUUUCAGUGUUCGGUGUGUCCAACUGUCUCGACUUGUCUAUUUCAGUUUUCCAAUGCACUUUACGAGCAGCUCUAAGGUAGGAGC---AGCUCACCAGAACAGUUGAACUCCACU
.......(((((((((((((((((..(((((....((....)).....))))).....)))))))....((((.(((((......)))))---.))))....))))).)))))....... ( -30.80)
>DroSim_CAF1 6454 117 - 1
CAUCCAUUUCACUGUUCGGUGUGUCCAACUGUCUCGACUUGUCUAUUUCAGUUUUCCAAUGCACUUUACGAGCAGCUCUAAGGUAGGAGC---AGCUCACCAGAACAGUUGAACUCCACU
.......(((((((((((((((((..(((((....((....)).....))))).....)))))))....((((.(((((......)))))---.))))....)))))).))))....... ( -33.10)
>DroEre_CAF1 6545 117 - 1
CAUCCAUUUCAGUGUUCGGUGUGUCCAACUGUCUCGACUUGUCUAUUUCAGUUUUCCAAUGCACUUUACGAGCAGCUCUAAGGUAGGAGC---AGCUCACCAGAACAGUUGAACUCCACU
.......(((((((((((((((((..(((((....((....)).....))))).....)))))))....((((.(((((......)))))---.))))....))))).)))))....... ( -30.80)
>DroYak_CAF1 6927 120 - 1
CAUCCAUUUCAGUGUUCGGUGUGUCCAACUGUCUCGACUUGUCUAUUUCAGUUUUCCAAUGCACUUUACGAGCAGCUCUAAGGUAGGAGCAGCAGCUCACCAGAACAGUUGAACUCCACU
.......(((((((((((((((((..(((((....((....)).....))))).....)))))))....((((.(((((......)))))....))))....))))).)))))....... ( -28.60)
>consensus
CAUCCAUUUCAGUGUUCGGUGUGUCCAACUGUCUCGACUUGUCUAUUUCAGUUUUCCAAUGCACUUUACGAGCAGCUCUAAGGUAGGAGC___AGCUCACCAGAACAGUUGAACUCCACU
.......(((((((((((((((((..(((((....((....)).....))))).....)))))))....((((.(((((......)))))....))))....))))).)))))....... (-28.00 = -28.20 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:03 2006