Locus 8258

Sequence ID	3L_DroMel_CAF1
Location	21,703,815 – 21,703,908
Length	93
Max. P	0.974661

overview

Window 3

Location	21,703,815 – 21,703,908
Length	93
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	67.14
Mean single sequence MFE	-30.84
Consensus MFE	-13.17
Energy contribution	-13.09
Covariance contribution	-0.08
Combinations/Pair	1.24
Mean z-score	-2.14
Structure conservation index	0.43
SVM decision value	1.50
SVM RNA-class probability	0.959085
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21703815 93 + 23771897
UUGGCGCCUGCGCGUAAACACAC---------------ACCUACACUCACUGACACA----CACUGUGGCGCUCCCGUGAUCCAGUGCGUGCGUGUGUAUUAGGUAUUUUUU
...(((....)))..........---------------(((((.((.(((.(.(((.----(((((.(((((....))).))))))).))))))).))..)))))....... ( -27.60)
>DroVir_CAF1 38256 105 + 1
AUGGCGCAUGCGCUAAAACUGGCUGCACUGAAGCAUUUCUAUACACUCACGCACACAAUUACAGCACGCGACAUG------UCAGUGUGUGUGUAUGUACUAAGGAUUU-UC
.(((((....)))))......(((.......)))..((((.((((..(((((((((.......(....)((....------)).)))))))))..))))...))))...-.. ( -27.90)
>DroSec_CAF1 41801 93 + 1
UUGGCGCCUGCGCAUAAACACAC---------------ACCUACACUCACUGACACA----CACUGUGGCGCUCCCGUGAUCCAGUGUGUGCGUGUGUAUUAGGUAUUUUUU
...(((....)))..........---------------(((((.((.(((.(.((((----(((((.(((((....))).))))))))))))))).))..)))))....... ( -31.50)
>DroSim_CAF1 36459 93 + 1
UUGGCGCCUGCGCACAAACACAC---------------ACCUACACUCACUGACACA----CACUGUGGCGCUCCUGUGAUCCAGUGUGUGCGUGUGUAUUAGGUAUUUUUU
((((((....))).)))......---------------(((((.((.(((.(.((((----(((((.(((((....))).))))))))))))))).))..)))))....... ( -33.20)
>DroMoj_CAF1 44343 111 + 1
AAGGCGCAUGCGCUAAAACUUGCUGCACUGAAGCAUUUCUAUACACUCACGCACACAAUCACAGCACGCGACUUGUGCGUCUCUGUGUGAGUGUGUGUACUAAGGAUUU-UC
..((((....))))......((((.......)))).((((.(((((.(((.((((((...((.(((((.....)))))))...)))))).))).)))))...))))...-.. ( -34.00)
>consensus
UUGGCGCCUGCGCAAAAACACAC_______________ACCUACACUCACUGACACA____CACUGUGGCGCUCCCGUGAUCCAGUGUGUGCGUGUGUAUUAGGUAUUUUUU
...(((....))).........................(((((.((.(((..(((((.........(((.....)))........)))))..))).))..)))))....... (-13.17 = -13.09 +  -0.08)

alignment

secondary structure

dotplot

Window 4

Location	21,703,815 – 21,703,908
Length	93
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	67.14
Mean single sequence MFE	-32.72
Consensus MFE	-14.65
Energy contribution	-14.85
Covariance contribution	0.20
Combinations/Pair	1.25
Mean z-score	-2.18
Structure conservation index	0.45
SVM decision value	1.73
SVM RNA-class probability	0.974661
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21703815 93 - 23771897
AAAAAAUACCUAAUACACACGCACGCACUGGAUCACGGGAGCGCCACAGUG----UGUGUCAGUGAGUGUAGGU---------------GUGUGUUUACGCGCAGGCGCCAA
............((((.(((((((((((((...(.(....).)...)))))----)))))..))).)))).(((---------------((.(((......))).))))).. ( -33.80)
>DroVir_CAF1 38256 105 - 1
GA-AAAUCCUUAGUACAUACACACACACUGA------CAUGUCGCGUGCUGUAAUUGUGUGCGUGAGUGUAUAGAAAUGCUUCAGUGCAGCCAGUUUUAGCGCAUGCGCCAU
..-......(((((............)))))------.(((.(((((((((.(((((..((((((((.((((....)))))))).))))..))))).))))))..))).))) ( -26.20)
>DroSec_CAF1 41801 93 - 1
AAAAAAUACCUAAUACACACGCACACACUGGAUCACGGGAGCGCCACAGUG----UGUGUCAGUGAGUGUAGGU---------------GUGUGUUUAUGCGCAGGCGCCAA
............((((.(((((((((((((...(.(....).)...)))))----)))))..))).)))).(((---------------((.(((......))).))))).. ( -34.20)
>DroSim_CAF1 36459 93 - 1
AAAAAAUACCUAAUACACACGCACACACUGGAUCACAGGAGCGCCACAGUG----UGUGUCAGUGAGUGUAGGU---------------GUGUGUUUGUGCGCAGGCGCCAA
.....(((((((.(((.(((((((((((((..((....))......)))))----)))))..))).))))))))---------------))(((((((....)))))))... ( -35.20)
>DroMoj_CAF1 44343 111 - 1
GA-AAAUCCUUAGUACACACACUCACACAGAGACGCACAAGUCGCGUGCUGUGAUUGUGUGCGUGAGUGUAUAGAAAUGCUUCAGUGCAGCAAGUUUUAGCGCAUGCGCCUU
((-(.....((.((((((.(((.(((((((..((((((.......)))).))..))))))).))).)))))).)).....))).(((((((..........)).)))))... ( -34.20)
>consensus
AAAAAAUACCUAAUACACACGCACACACUGGAUCACAGGAGCGCCACAGUG____UGUGUCAGUGAGUGUAGGU_______________GUGUGUUUAAGCGCAGGCGCCAA
.......(((((.(((.(((((((((((((................)))))....)))))..))).)))))))).........................(((....)))... (-14.65 = -14.85 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:10:41 2006