Locus 746

Sequence ID	X_DroMel_CAF1
Location	2,037,308 – 2,037,435
Length	127
Max. P	0.997359

overview

Window 7

Location	2,037,308 – 2,037,407
Length	99
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	88.92
Mean single sequence MFE	-26.64
Consensus MFE	-22.40
Energy contribution	-24.00
Covariance contribution	1.60
Combinations/Pair	1.15
Mean z-score	-2.45
Structure conservation index	0.84
SVM decision value	2.53
SVM RNA-class probability	0.994951
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2037308 99 + 22224390
----U-UAAAGCAUU-AUCUUUGUAAUUUAUUUAUUUCAGUUUCGCGCUGAUCAAUCGAUAAAUGUCACAUCGAAUCGAUACGCGCAACUGUUGAAAUAUAUGGA
----.-(((((....-..)))))...(((((.((((((((....((((..(((..(((((.........)))))...)))..)))).....)))))))).))))) ( -18.10)
>DroSec_CAF1 3999 101 + 1
----UAUAGAGCAUUUGGCUUUGUAAGCUAUUUAUUUCAGUUUUGCGCUGGUCAAUCGAUAAAUGUCACAUCGAAUCGAUACGCGCAACUGUUGAAAUAUAUGGA
----((((((((.....))))))))..((((.((((((((..((((((..(((..(((((.........)))))...)))..))))))...)))))))).)))). ( -30.00)
>DroSim_CAF1 3990 97 + 1
----UAUAGAGCAUUUGGCUUUGUAAGCUAUUUAUUUCAGUUUUGCG----UCAAUCGAUAAAUGUCACAUCGAAUCGAUACGCGCAACUGUUGAAAUAUAUGGA
----((((((((.....))))))))..((((.((((((((..(((((----(..((((((..(((...)))...))))))..))))))...)))))))).)))). ( -27.90)
>DroEre_CAF1 4020 105 + 1
UGCUUAUAGAGCAUUUGGCUUCAUAAGCUAUUUUUGUCAGUUUUGCGCUCGUCAAUCGAUAAAUUUCACAUCGAAUCGAUACGCGCAACUGUUGAAUUAUAUGGA
.((((((..(((.....)))..))))))....((((.((((..(((((..(((..(((((.........)))))...)))..))))))))).))))......... ( -27.20)
>DroYak_CAF1 3989 105 + 1
UGCUUAUGGAGCAUUUGGCUUUAUAAGCUAUUUUUGUCAGUUUUGCGCUCGUCAAUCGAUAAAUGUCACAUCGAAUCGAUACGCGCAACUGUUGAAUUAUAUGGA
.(((((((((((.....)))))))))))....((((.((((..(((((..(((..(((((.........)))))...)))..))))))))).))))......... ( -30.00)
>consensus
____UAUAGAGCAUUUGGCUUUGUAAGCUAUUUAUUUCAGUUUUGCGCUCGUCAAUCGAUAAAUGUCACAUCGAAUCGAUACGCGCAACUGUUGAAAUAUAUGGA
....((((((((.....))))))))..((((.((((((((..((((((..(((..(((((.........)))))...)))..))))))...)))))))).)))). (-22.40 = -24.00 +   1.60)

alignment

secondary structure

dotplot

Window 8

Location	2,037,308 – 2,037,407
Length	99
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	88.92
Mean single sequence MFE	-26.20
Consensus MFE	-19.88
Energy contribution	-21.12
Covariance contribution	1.24
Combinations/Pair	1.04
Mean z-score	-3.42
Structure conservation index	0.76
SVM decision value	2.45
SVM RNA-class probability	0.994094
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2037308 99 - 22224390
UCCAUAUAUUUCAACAGUUGCGCGUAUCGAUUCGAUGUGACAUUUAUCGAUUGAUCAGCGCGAAACUGAAAUAAAUAAAUUACAAAGAU-AAUGCUUUA-A----
......(((((((....((((((..((((((.(((((.......)))))))))))..))))))...)))))))..........((((..-....)))).-.---- ( -24.80)
>DroSec_CAF1 3999 101 - 1
UCCAUAUAUUUCAACAGUUGCGCGUAUCGAUUCGAUGUGACAUUUAUCGAUUGACCAGCGCAAAACUGAAAUAAAUAGCUUACAAAGCCAAAUGCUCUAUA----
......(((((((....((((((...(((((.(((((.......))))))))))...))))))...)))))))....(((.....))).............---- ( -25.00)
>DroSim_CAF1 3990 97 - 1
UCCAUAUAUUUCAACAGUUGCGCGUAUCGAUUCGAUGUGACAUUUAUCGAUUGA----CGCAAAACUGAAAUAAAUAGCUUACAAAGCCAAAUGCUCUAUA----
......(((((((....(((((((.((((((..((((...)))).)))))))).----)))))...)))))))....(((.....))).............---- ( -19.80)
>DroEre_CAF1 4020 105 - 1
UCCAUAUAAUUCAACAGUUGCGCGUAUCGAUUCGAUGUGAAAUUUAUCGAUUGACGAGCGCAAAACUGACAAAAAUAGCUUAUGAAGCCAAAUGCUCUAUAAGCA
..............(((((((((...(((((.(((((.......))))))))))...)))))..)))).........(((((((.(((.....))).))))))). ( -31.50)
>DroYak_CAF1 3989 105 - 1
UCCAUAUAAUUCAACAGUUGCGCGUAUCGAUUCGAUGUGACAUUUAUCGAUUGACGAGCGCAAAACUGACAAAAAUAGCUUAUAAAGCCAAAUGCUCCAUAAGCA
..............(((((((((...(((((.(((((.......))))))))))...)))))..)))).........((((((..(((.....)))..)))))). ( -29.90)
>consensus
UCCAUAUAUUUCAACAGUUGCGCGUAUCGAUUCGAUGUGACAUUUAUCGAUUGACCAGCGCAAAACUGAAAUAAAUAGCUUACAAAGCCAAAUGCUCUAUA____
......(((((((....((((((...(((((.(((((.......))))))))))...))))))...)))))))................................ (-19.88 = -21.12 +   1.24)

alignment

secondary structure

dotplot

Window 9

Location	2,037,330 – 2,037,435
Length	105
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	90.54
Mean single sequence MFE	-25.68
Consensus MFE	-21.80
Energy contribution	-22.84
Covariance contribution	1.04
Combinations/Pair	1.11
Mean z-score	-2.47
Structure conservation index	0.85
SVM decision value	2.84
SVM RNA-class probability	0.997359
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2037330 105 - 22224390
AAGCUGGGAAAACAAACGGCUGAUAGCUUCCAUAUAUUUCAACAGUUGCGCGUAUCGAUUCGAUGUGACAUUUAUCGAUUGAUCAGCGCGAAACUGAAAUAAAUA
.(((((..........))))).............(((((((....((((((..((((((.(((((.......)))))))))))..))))))...))))))).... ( -29.90)
>DroSec_CAF1 4023 105 - 1
AAGCUGGGAAAACAAACGGCGUAUAGCUUCCAUAUAUUUCAACAGUUGCGCGUAUCGAUUCGAUGUGACAUUUAUCGAUUGACCAGCGCAAAACUGAAAUAAAUA
..((((..........))))..............(((((((....((((((...(((((.(((((.......))))))))))...))))))...))))))).... ( -28.50)
>DroSim_CAF1 4014 101 - 1
AAGCUGGGAAAACAAACGUCGUAUAGCUUCCAUAUAUUUCAACAGUUGCGCGUAUCGAUUCGAUGUGACAUUUAUCGAUUGA----CGCAAAACUGAAAUAAAUA
((((((..(..((....))..).)))))).....(((((((....(((((((.((((((..((((...)))).)))))))).----)))))...))))))).... ( -22.80)
>DroEre_CAF1 4048 102 - 1
AAACUGAUAAAACAAACGGU---UAGCUUCCAUAUAAUUCAACAGUUGCGCGUAUCGAUUCGAUGUGAAAUUUAUCGAUUGACGAGCGCAAAACUGACAAAAAUA
.(((((..........))))---)..................(((((((((...(((((.(((((.......))))))))))...)))))..))))......... ( -22.50)
>DroYak_CAF1 4017 102 - 1
AAGCUGAGAAAAUAAACGGU---UAGCUUCCAUAUAAUUCAACAGUUGCGCGUAUCGAUUCGAUGUGACAUUUAUCGAUUGACGAGCGCAAAACUGACAAAAAUA
(((((((............)---)))))).............(((((((((...(((((.(((((.......))))))))))...)))))..))))......... ( -24.70)
>consensus
AAGCUGGGAAAACAAACGGC__AUAGCUUCCAUAUAUUUCAACAGUUGCGCGUAUCGAUUCGAUGUGACAUUUAUCGAUUGACCAGCGCAAAACUGAAAUAAAUA
..((((..........))))..............(((((((....((((((...(((((.(((((.......))))))))))...))))))...))))))).... (-21.80 = -22.84 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:48 2006