Locus 6299

Sequence ID	2L_DroMel_CAF1
Location	17,542,999 – 17,543,128
Length	129
Max. P	0.967493

overview

Window 0

Location	17,542,999 – 17,543,103
Length	104
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	78.92
Mean single sequence MFE	-24.13
Consensus MFE	-14.51
Energy contribution	-14.48
Covariance contribution	-0.02
Combinations/Pair	1.29
Mean z-score	-1.56
Structure conservation index	0.60
SVM decision value	0.12
SVM RNA-class probability	0.594440
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17542999 104 - 22407834
CAAAGCAAUCAUCUGCCUUUUCAGUGAGCAUCACAGUUGAGGUUACCUGAUGACUCAGGUAACUUUCUGCAUAAGUCAGCCAAAAAGUUUCAUCGAUAUGA--GAC
............(((.(((....(((.....))).((.((((((((((((....))))))))))))..))..))).))).......(((((((....))))--))) ( -26.30)
>DroSec_CAF1 59930 104 - 1
CAAAGCAAUCAUCUGCCUUUUCAGUGAGCAUUACAGUUGAGGUUACCUGAUGACUCAGGUAACUUUCUGCAUAAGUCAGCCAAAAAGUUUCAUCGAUAUGA--GAC
....((..(((.(((......))))))......(((..((((((((((((....))))))))))))))).........))......(((((((....))))--))) ( -25.80)
>DroSim_CAF1 59365 104 - 1
CAAAGCAAUCAUCUGCCUUUUCAGUGAGCAUUACAGUUGAGGUUACCUGAUGACUCAGGUAACUUUCUGCAUAAGUCAGCCAAAAAGUUUCAUCGAUAUGA--GAC
....((..(((.(((......))))))......(((..((((((((((((....))))))))))))))).........))......(((((((....))))--))) ( -25.80)
>DroEre_CAF1 61082 94 - 1
CAAAACCAUCAUCCACCU-------GAACA-----GUUGAGGUUACCUGAUGAGUCAGGUAACUUUCUGCAAAAGUCAGCCAAAAAGUUUCGUCGAUAUGAGAGAC
................((-------((...-----((.((((((((((((....))))))))))))..)).....)))).......(((((.((.....))))))) ( -22.50)
>DroYak_CAF1 61359 104 - 1
CAAAGCCAUCAUCAACCUUUUCGGCGAGCAAUGCCGUUGAGCUUACCUGAUGAGUCAGGUAACUUUCUGCAAAAGUCAGCCAAAAAGUUUCAUCGAUAUGA--UAC
.......(((((.((.(((((.(((..((..(((.(..(((.((((((((....))))))))))).).)))...))..))).))))).)).)).)))....--... ( -25.00)
>DroAna_CAF1 69044 88 - 1
---------UAGCUACCUUUUCUGUUCCCAUUAAUAUUGAAGUUACCUGA-------GGUGGCUUUUUGUCAGAGUCAGCCAAAAAGUUGAAUUGAUAUGA--GGC
---------.(((((((((.........((.......)).........))-------)))))))...((((((..(((((......))))).))))))...--... ( -19.37)
>consensus
CAAAGCAAUCAUCUACCUUUUCAGUGAGCAUUACAGUUGAGGUUACCUGAUGACUCAGGUAACUUUCUGCAAAAGUCAGCCAAAAAGUUUCAUCGAUAUGA__GAC
...................................((.((((((((((((....))))))))))))..)).................................... (-14.51 = -14.48 +  -0.02)

alignment

secondary structure

dotplot

Window 1

Location	17,543,037 – 17,543,128
Length	91
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	82.03
Mean single sequence MFE	-29.73
Consensus MFE	-20.27
Energy contribution	-21.03
Covariance contribution	0.75
Combinations/Pair	1.07
Mean z-score	-2.47
Structure conservation index	0.68
SVM decision value	1.61
SVM RNA-class probability	0.967493
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17543037 91 + 22407834
AAAGUUACCUGAGUCAUCAGGUAACCUCAACUGUGAUGCUCACUGAAAAGGCAGAUGAUUGCUUUGAUUCGGUUU--------------AGAAUAGAGGGUAUAU
...(((((((((....)))))))))..........(((((((((((((((((((....)))))))..))))))..--------------........)))))).. ( -25.50)
>DroSec_CAF1 59968 105 + 1
AAAGUUACCUGAGUCAUCAGGUAACCUCAACUGUAAUGCUCACUGAAAAGGCAGAUGAUUGCUUUGCUUCGGUUUCGGUAUCCAUCUAUAGAUUAGAGGGUAUAU
...(((((((((....)))))))))..........((((((.((((......(((((..((((..((....))...))))..))))).....)))).)))))).. ( -32.50)
>DroSim_CAF1 59403 105 + 1
AAAGUUACCUGAGUCAUCAGGUAACCUCAACUGUAAUGCUCACUGAAAAGGCAGAUGAUUGCUUUGCUUCGGUUUCGGUACUCAUCUAUAGAUUAGAGGGUAUAU
...(((((((((....)))))))))..........((((((.((((......((((((.((((..((....))...)))).)))))).....)))).)))))).. ( -33.90)
>DroYak_CAF1 61397 99 + 1
AAAGUUACCUGACUCAUCAGGUAAGCUCAACGGCAUUGCUCGCCGAAAAGGUUGAUGAUGGCUUUGCUUC------GGUACUCGGCAAUAGAUUAUAGGGUACAU
....((((((((....))))))))(((....)))..((((((((((.((((((......))))))((...------.))..)))))..((.....)))))))... ( -27.00)
>consensus
AAAGUUACCUGAGUCAUCAGGUAACCUCAACUGUAAUGCUCACUGAAAAGGCAGAUGAUUGCUUUGCUUCGGUUU_GGUACUCAUCUAUAGAUUAGAGGGUAUAU
...(((((((((....)))))))))..........((((((((((((((((((......))))))..))))))...(.....)..............)))))).. (-20.27 = -21.03 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:35 2006