Locus 6845

Sequence ID	X_DroMel_CAF1
Location	17,044,916 – 17,045,016
Length	100
Max. P	0.970877

overview

Window 6

Location	17,044,916 – 17,045,016
Length	100
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	83.41
Mean single sequence MFE	-21.87
Consensus MFE	-17.17
Energy contribution	-18.17
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.38
Structure conservation index	0.79
SVM decision value	1.67
SVM RNA-class probability	0.970877
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17044916 100 + 22224390
GUAGUUUUUAAAAAAACCCACAGCUCCAUGCGUCUGACA----------UACUCACCAAUAUUCC------CAUUCCCAACAAGAUAUGGGUGCUAUAUACUCCAUAUAUGGAGCA
((.(((((....)))))..)).((((((((....(((..----------...)))...((((.((------(((((.......)).)))))....))))........)))))))). ( -19.00)
>DroSec_CAF1 44607 99 + 1
GUAGUUUU-AAAAAAACCCACAGCUCCAUGCGUCUGACA----------UGCUCACCCAAAUUCC------CAUUCCCAACUAGAUAUGGGUGCUAUAUACUCCAUAUAUGGAGCG
((.((((.-....))))..)).(((((((((((.....)----------))).((((((.(((..------............))).))))))...............))))))). ( -21.64)
>DroSim_CAF1 37870 99 + 1
GUAGUUUU-CAAAAAACCCACAGCUCCAUGCGUCUGACA----------UGCUCACCCAUAUUCC------CAUUCCCAACUAGAUAUGGGUGCUAUAUACUCCAUAUAUGGAGCG
((.((((.-....))))..)).(((((((((((.....)----------))).((((((((((..------............))))))))))...............))))))). ( -25.74)
>DroYak_CAF1 46723 115 + 1
GUAUUUUC-CACAAAAUUCGCAGCUCCAUGCGUCUGACACACGACGACACACUCACCCAUAUUCCAAUUUCCAUUCCCAAACAGAUAUGAGUACUAUAUGCUCCAUAUAUGGAGCA
........-.............(((((((.((((........))))......................................(((((((((.....)))).)))))))))))). ( -21.10)
>consensus
GUAGUUUU_AAAAAAACCCACAGCUCCAUGCGUCUGACA__________UACUCACCCAUAUUCC______CAUUCCCAACUAGAUAUGGGUGCUAUAUACUCCAUAUAUGGAGCA
......................((((((((.(.....)...............((((((((((....................))))))))))..............)))))))). (-17.17 = -18.17 +   1.00)

alignment

secondary structure

dotplot

Window 7

Location	17,044,916 – 17,045,016
Length	100
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	83.41
Mean single sequence MFE	-28.73
Consensus MFE	-21.13
Energy contribution	-20.75
Covariance contribution	-0.37
Combinations/Pair	1.22
Mean z-score	-1.52
Structure conservation index	0.74
SVM decision value	0.06
SVM RNA-class probability	0.563064
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17044916 100 - 22224390
UGCUCCAUAUAUGGAGUAUAUAGCACCCAUAUCUUGUUGGGAAUG------GGAAUAUUGGUGAGUA----------UGUCAGACGCAUGGAGCUGUGGGUUUUUUUAAAAACUAC
(((((((....)))))))((((((.(((((.(((....))).)))------))....((.(((.((.----------......)).))).))))))))((((((....)))))).. ( -28.60)
>DroSec_CAF1 44607 99 - 1
CGCUCCAUAUAUGGAGUAUAUAGCACCCAUAUCUAGUUGGGAAUG------GGAAUUUGGGUGAGCA----------UGUCAGACGCAUGGAGCUGUGGGUUUUUUU-AAAACUAC
.((((((....)))))).((((((.(((((.(((....))).)))------))............((----------(((.....)))))..))))))(((((....-.))))).. ( -27.80)
>DroSim_CAF1 37870 99 - 1
CGCUCCAUAUAUGGAGUAUAUAGCACCCAUAUCUAGUUGGGAAUG------GGAAUAUGGGUGAGCA----------UGUCAGACGCAUGGAGCUGUGGGUUUUUUG-AAAACUAC
.((((((....)))))).(((((((((((((((((........))------)..))))))))...((----------(((.....)))))..))))))(((((....-.))))).. ( -29.80)
>DroYak_CAF1 46723 115 - 1
UGCUCCAUAUAUGGAGCAUAUAGUACUCAUAUCUGUUUGGGAAUGGAAAUUGGAAUAUGGGUGAGUGUGUCGUCGUGUGUCAGACGCAUGGAGCUGCGAAUUUUGUG-GAAAAUAC
.((((((....))))))(((((.(((((((((((((((........))).))).)))))))))..)))))..(((((((.....)))))))..(..(((...)))..-)....... ( -28.70)
>consensus
CGCUCCAUAUAUGGAGUAUAUAGCACCCAUAUCUAGUUGGGAAUG______GGAAUAUGGGUGAGCA__________UGUCAGACGCAUGGAGCUGUGGGUUUUUUG_AAAACUAC
.((((((....))))))......(((((((((((.................)).))))))))).....................((((......))))((((((....)))))).. (-21.13 = -20.75 +  -0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:18 2006