Locus 6323

Sequence ID	X_DroMel_CAF1
Location	15,982,100 – 15,982,241
Length	141
Max. P	0.999538

overview

Window 7

Location	15,982,100 – 15,982,201
Length	101
Sequences	4
Columns	106
Reading direction	forward
Mean pairwise identity	96.49
Mean single sequence MFE	-18.50
Consensus MFE	-18.75
Energy contribution	-18.50
Covariance contribution	-0.25
Combinations/Pair	1.05
Mean z-score	-1.42
Structure conservation index	1.01
SVM decision value	0.09
SVM RNA-class probability	0.578034
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15982100 101 + 22224390
---AAAAA--GCAGAAAAAAUAUAUCAAAGAGAAAAAGGAGCGCGUACAUGUGUAUAUGUAAUCCAAUCCAAGCAGUGGGCGUGGGUGGGUGUAAAAAACGAAGGC
---.....--..........((((((...........((((((..(((....)))..)))..))).(((((.((.....)).))))).))))))............ ( -18.50)
>DroSec_CAF1 49974 103 + 1
---AAAAAAGUCAGAAAAAAUAUAUCAAAGAGAAAAAGGAGCGCGUGCAUGUGUAUAUGUAAUCCAAUCCAAGCAGUGGGCGUGGGUGGGUGUAAAAAACGAAGGC
---.................((((((...........((((((..(((....)))..)))..))).(((((.((.....)).))))).))))))............ ( -18.50)
>DroSim_CAF1 40743 103 + 1
---AAAAAAGGCAGAAAAAAUAUAUCAAAGAGAAAAAGGAGCGCGUACAUGUGUAUAUGUAAUCCAAUCCAAGCAGUGGGCGUGGGUGGGUGUAAAAAACGAAGGC
---.................((((((...........((((((..(((....)))..)))..))).(((((.((.....)).))))).))))))............ ( -18.50)
>DroEre_CAF1 48680 106 + 1
GAAAAAAAAGGCAGAAAAAAUAUAUCAAAGAGAAAAAGGAGCGCGUGCAUGUGUAUAUGUAAUCCAAUCCAAGCAGUGGGCGUGGGUGGGUGUAAAAAACGAAGGC
....................((((((...........((((((..(((....)))..)))..))).(((((.((.....)).))))).))))))............ ( -18.50)
>consensus
___AAAAAAGGCAGAAAAAAUAUAUCAAAGAGAAAAAGGAGCGCGUACAUGUGUAUAUGUAAUCCAAUCCAAGCAGUGGGCGUGGGUGGGUGUAAAAAACGAAGGC
....................((((((...........((((((..(((....)))..)))..))).(((((.((.....)).))))).))))))............ (-18.75 = -18.50 +  -0.25)

alignment

secondary structure

dotplot

Window 8

Location	15,982,127 – 15,982,241
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.39
Mean single sequence MFE	-33.13
Consensus MFE	-30.77
Energy contribution	-30.45
Covariance contribution	-0.32
Combinations/Pair	1.07
Mean z-score	-2.37
Structure conservation index	0.93
SVM decision value	3.70
SVM RNA-class probability	0.999538
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15982127 114 + 22224390
AAAAAGGAGCGCGUACAUGUGUAUA------UGUAAUCCAAUCCAAGCAGUGGGCGUGGGUGGGUGUAAAAAACGAAGGCGCAACGCACUUUGUGUGUGUGCAAAAAGCAAGGAAGCCAA
.....((.((((.((((((....))------))))(((((.((((.((.....)).))))))))).............)))).((((((.....))))))((.....)).......)).. ( -32.30)
>DroSec_CAF1 50003 114 + 1
AAAAAGGAGCGCGUGCAUGUGUAUA------UGUAAUCCAAUCCAAGCAGUGGGCGUGGGUGGGUGUAAAAAACGAAGGCGCAACGCACUUUGUGUGUGUGCAAAAAGCAAGGAAGCCAA
.....((......(((...((((((------..(.(((((.((((.((.....)).))))))))).......(((((((((...))).)))))))..))))))....)))......)).. ( -32.50)
>DroSim_CAF1 40772 114 + 1
AAAAAGGAGCGCGUACAUGUGUAUA------UGUAAUCCAAUCCAAGCAGUGGGCGUGGGUGGGUGUAAAAAACGAAGGCGCAACGCACUUUGUGUGUGUGCAAAAAGCAAGGAAGCCAA
.....((.((((.((((((....))------))))(((((.((((.((.....)).))))))))).............)))).((((((.....))))))((.....)).......)).. ( -32.30)
>DroEre_CAF1 48712 114 + 1
AAAAAGGAGCGCGUGCAUGUGUAUA------UGUAAUCCAAUCCAAGCAGUGGGCGUGGGUGGGUGUAAAAAACGAAGGCGCAACGCACUUUGUGUGUGUGCAAAAAACAAGGAAGCCAA
.....((.((((.((((((....))------))))(((((.((((.((.....)).))))))))).............)))).((((((.....))))))................)).. ( -31.70)
>DroYak_CAF1 32715 120 + 1
AAAAAGGAGCGCGUGCAUGUGUAUAUGUGUAUGUAAUCCAAUCCAAGCAGUGGGCGUGGGUGGGUGUAAAAAACGAAGGCACAACGCACUUUGUGUGUGUGCAAAAAGCAAGGAAACCAA
.....(((..((((((((((....))))))))))..))).(((((.((.....)).))))).(((.............(((((.(((((...)))))))))).............))).. ( -36.87)
>consensus
AAAAAGGAGCGCGUGCAUGUGUAUA______UGUAAUCCAAUCCAAGCAGUGGGCGUGGGUGGGUGUAAAAAACGAAGGCGCAACGCACUUUGUGUGUGUGCAAAAAGCAAGGAAGCCAA
.....((...((((...(((((.............(((((.((((.((.....)).))))))))).............))))))))).((((((.((....))....))))))...)).. (-30.77 = -30.45 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:37 2006