Locus 6114

Sequence ID	2L_DroMel_CAF1
Location	17,113,386 – 17,113,586
Length	200
Max. P	0.831875

overview

Window 6

Location	17,113,386 – 17,113,506
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.25
Mean single sequence MFE	-19.68
Consensus MFE	-17.40
Energy contribution	-17.44
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.30
Structure conservation index	0.88
SVM decision value	0.49
SVM RNA-class probability	0.756940
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17113386 120 + 22407834
AGAAAGCAGCGCAAACUGACAAAGUUUCUUGUGCUUUUCGCAACUUUCUUCUGCUCAUCCCGCCCACUUUUCCGCCUCCCUUCCCUUUUUCCUUUUGCGAAUGCCUUUUGCUGUUCGCCU
.((((..((((((((((.....)))...)))))))))))(((.........)))..........................................((((((((.....)).)))))).. ( -19.20)
>DroSec_CAF1 77393 120 + 1
AGAAAGCAGCGCAAACUGACAAAGUUUCUUGUGCUUUUCGCAACUUUCUUCUGCUCAUCCCGCCCACUUUUCCGCCGCCCUUCCCUUUUUCCUUUUGCGAAUGCCUUUUGCUGUUCGCCU
.(((.((((((((((((.....)))...)))))))....(((.........)))......................))..))).............((((((((.....)).)))))).. ( -19.40)
>DroSim_CAF1 91022 120 + 1
AGAAAGCAGCGCAAACUGACAAAGUUUCUUGUGCUUUUCGCAACUUUCUUCUGCUCAUCCCGCCCACUUUUCCGCCGCCCAUCCCGUUUUCCUUUUGCGAAUGCCUUUUGCUGUUCGCCU
.((((((((((((((((.....)))...)))))))....(((.........)))...............................)))))).....((((((((.....)).)))))).. ( -22.50)
>DroEre_CAF1 78782 120 + 1
AGAAAGCAGCGCAAACUGACAAAGUUUCUUGUGCUUUUCGCAACUUUCCCCUGCUCAUCCCGCCCACUUUUCCGCCUCCCUCCUCUUUUUCCUUUUGCGAACGCCUUUUGCUGUUCGCCU
.((((..((((((((((.....)))...)))))))))))(((.........)))..........................................((((((((.....)).)))))).. ( -21.00)
>DroYak_CAF1 79249 120 + 1
AGAAAGCCUUGCAAACUGACAAAGUUUCUUUUGCUUUUCGCAACUUUCUCCUGCUCAUCCCACCUUCUUUUCCACUUCCCUUCUCACUUUCCUUUUGCGAAUGCCUUUUGCUGUUCGCCU
((((((..((((.((..(.(((((....))))))..)).))))))))))...............................................((((((((.....)).)))))).. ( -16.30)
>consensus
AGAAAGCAGCGCAAACUGACAAAGUUUCUUGUGCUUUUCGCAACUUUCUUCUGCUCAUCCCGCCCACUUUUCCGCCUCCCUUCCCUUUUUCCUUUUGCGAAUGCCUUUUGCUGUUCGCCU
.(((((((....(((((.....)))))....))))))).(((.........)))..........................................((((((((.....)).)))))).. (-17.40 = -17.44 +   0.04)

alignment

secondary structure

dotplot

Window 7

Location	17,113,386 – 17,113,506
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.25
Mean single sequence MFE	-28.57
Consensus MFE	-23.38
Energy contribution	-23.70
Covariance contribution	0.32
Combinations/Pair	1.11
Mean z-score	-1.64
Structure conservation index	0.82
SVM decision value	0.72
SVM RNA-class probability	0.831875
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17113386 120 - 22407834
AGGCGAACAGCAAAAGGCAUUCGCAAAAGGAAAAAGGGAAGGGAGGCGGAAAAGUGGGCGGGAUGAGCAGAAGAAAGUUGCGAAAAGCACAAGAAACUUUGUCAGUUUGCGCUGCUUUCU
..(((((..((.....)).)))))................(((((((((....(..(((..((..((...........(((.....)))........))..)).)))..).))))))))) ( -28.31)
>DroSec_CAF1 77393 120 - 1
AGGCGAACAGCAAAAGGCAUUCGCAAAAGGAAAAAGGGAAGGGCGGCGGAAAAGUGGGCGGGAUGAGCAGAAGAAAGUUGCGAAAAGCACAAGAAACUUUGUCAGUUUGCGCUGCUUUCU
..(((((..((.....)).)))))............((((((.(((((.(((.....((.......)).((..((((((((.....)))......))))).))..))).))))))))))) ( -28.90)
>DroSim_CAF1 91022 120 - 1
AGGCGAACAGCAAAAGGCAUUCGCAAAAGGAAAACGGGAUGGGCGGCGGAAAAGUGGGCGGGAUGAGCAGAAGAAAGUUGCGAAAAGCACAAGAAACUUUGUCAGUUUGCGCUGCUUUCU
..(((((..((.....)).)))))............(((.((((((((.(((.....((.......)).((..((((((((.....)))......))))).))..))).))))))))))) ( -28.50)
>DroEre_CAF1 78782 120 - 1
AGGCGAACAGCAAAAGGCGUUCGCAAAAGGAAAAAGAGGAGGGAGGCGGAAAAGUGGGCGGGAUGAGCAGGGGAAAGUUGCGAAAAGCACAAGAAACUUUGUCAGUUUGCGCUGCUUUCU
..((((((.((.....))))))))................(((((((((....(..(((....(((.(((((......(((.....))).......)))))))))))..).))))))))) ( -34.22)
>DroYak_CAF1 79249 120 - 1
AGGCGAACAGCAAAAGGCAUUCGCAAAAGGAAAGUGAGAAGGGAAGUGGAAAAGAAGGUGGGAUGAGCAGGAGAAAGUUGCGAAAAGCAAAAGAAACUUUGUCAGUUUGCAAGGCUUUCU
..(((((..((.....)).)))))....(((((((.....(.(((.((..((((...((.......)).........((((.....))))......))))..)).))).)...))))))) ( -22.90)
>consensus
AGGCGAACAGCAAAAGGCAUUCGCAAAAGGAAAAAGGGAAGGGAGGCGGAAAAGUGGGCGGGAUGAGCAGAAGAAAGUUGCGAAAAGCACAAGAAACUUUGUCAGUUUGCGCUGCUUUCU
..(((((..((.....)).)))))................(((((((((....(..(((..((..(..((........(((.....))).......)))..)).)))..).))))))))) (-23.38 = -23.70 +   0.32)

alignment

secondary structure

dotplot

Window 8

Location	17,113,466 – 17,113,586
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.08
Mean single sequence MFE	-20.70
Consensus MFE	-20.22
Energy contribution	-20.62
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.13
Structure conservation index	0.98
SVM decision value	0.43
SVM RNA-class probability	0.732961
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17113466 120 + 22407834
UUCCCUUUUUCCUUUUGCGAAUGCCUUUUGCUGUUCGCCUUGGUUUUCCUAUUAUUUGCGCAUUUUAUUUCCAUUGAACAUUUCAUUGACACUUUGACAGCAGCAUUGACAUUUGCGUGA
................(((((((.(...((((((((((..((((......))))...)))...........((.(((.....))).))..........)))))))..).))))))).... ( -21.80)
>DroSec_CAF1 77473 120 + 1
UUCCCUUUUUCCUUUUGCGAAUGCCUUUUGCUGUUCGCCUUGGUUUUCCUAUUAUUUGCGCAUUUUAUUUCCAUUGAACAUUUCAUUGACACUUUGACAGCAGCAUUGACAUUUGCGUGA
................(((((((.(...((((((((((..((((......))))...)))...........((.(((.....))).))..........)))))))..).))))))).... ( -21.80)
>DroSim_CAF1 91102 120 + 1
AUCCCGUUUUCCUUUUGCGAAUGCCUUUUGCUGUUCGCCUUGGUUUUCCUAUUAUUUGCGCAUUUUAUUUCCAUUGAACAUUUCAUUGACACUUUGACAGCAGCAUUGACAUUUGCGUGA
................(((((((.(...((((((((((..((((......))))...)))...........((.(((.....))).))..........)))))))..).))))))).... ( -21.80)
>DroEre_CAF1 78862 120 + 1
UCCUCUUUUUCCUUUUGCGAACGCCUUUUGCUGUUCGCCUUGCUUCUCCUAUUAUUUGCGCAUUUUAUUUCCAUUGAACAUUUCAUUGACACUUUGACAGCAGCAUUGACAUUUGCGUGA
................((((((((.....)).)))))).................(..((((.........((.(((.....))).))...(..((.(....)))..).....))))..) ( -17.10)
>DroYak_CAF1 79329 120 + 1
UUCUCACUUUCCUUUUGCGAAUGCCUUUUGCUGUUCGCCUUGGUCCUUCUAUUAUUUGCGCAUUUUAUUUCCAUUGAACAUUUCAUUGACACUUUGACAGCAGCAUUGACAUUUGCGUGA
................(((((((.(...((((((((((..((((......))))...)))...........((.(((.....))).))..........)))))))..).))))))).... ( -21.00)
>consensus
UUCCCUUUUUCCUUUUGCGAAUGCCUUUUGCUGUUCGCCUUGGUUUUCCUAUUAUUUGCGCAUUUUAUUUCCAUUGAACAUUUCAUUGACACUUUGACAGCAGCAUUGACAUUUGCGUGA
................(((((((.(...((((((((((..((((......))))...)))...........((.(((.....))).))..........)))))))..).))))))).... (-20.22 = -20.62 +   0.40)

alignment

secondary structure

dotplot

Window 9

Location	17,113,466 – 17,113,586
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.08
Mean single sequence MFE	-21.52
Consensus MFE	-20.13
Energy contribution	-19.97
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.12
Structure conservation index	0.94
SVM decision value	0.10
SVM RNA-class probability	0.583234
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17113466 120 - 22407834
UCACGCAAAUGUCAAUGCUGCUGUCAAAGUGUCAAUGAAAUGUUCAAUGGAAAUAAAAUGCGCAAAUAAUAGGAAAACCAAGGCGAACAGCAAAAGGCAUUCGCAAAAGGAAAAAGGGAA
....((.((((((..(((((.((((...((((..........(((....))).......))))........((....))..))))..)))))...)))))).))................ ( -21.93)
>DroSec_CAF1 77473 120 - 1
UCACGCAAAUGUCAAUGCUGCUGUCAAAGUGUCAAUGAAAUGUUCAAUGGAAAUAAAAUGCGCAAAUAAUAGGAAAACCAAGGCGAACAGCAAAAGGCAUUCGCAAAAGGAAAAAGGGAA
....((.((((((..(((((.((((...((((..........(((....))).......))))........((....))..))))..)))))...)))))).))................ ( -21.93)
>DroSim_CAF1 91102 120 - 1
UCACGCAAAUGUCAAUGCUGCUGUCAAAGUGUCAAUGAAAUGUUCAAUGGAAAUAAAAUGCGCAAAUAAUAGGAAAACCAAGGCGAACAGCAAAAGGCAUUCGCAAAAGGAAAACGGGAU
....((.((((((..(((((.((((...((((..........(((....))).......))))........((....))..))))..)))))...)))))).))................ ( -21.93)
>DroEre_CAF1 78862 120 - 1
UCACGCAAAUGUCAAUGCUGCUGUCAAAGUGUCAAUGAAAUGUUCAAUGGAAAUAAAAUGCGCAAAUAAUAGGAGAAGCAAGGCGAACAGCAAAAGGCGUUCGCAAAAGGAAAAAGAGGA
....((.((((((..(((((.((((......(((.(((.....))).)))........(((................))).))))..)))))...)))))).))................ ( -21.19)
>DroYak_CAF1 79329 120 - 1
UCACGCAAAUGUCAAUGCUGCUGUCAAAGUGUCAAUGAAAUGUUCAAUGGAAAUAAAAUGCGCAAAUAAUAGAAGGACCAAGGCGAACAGCAAAAGGCAUUCGCAAAAGGAAAGUGAGAA
((((.(...(((.(((((((((((.......(((.(((.....))).)))..........(((...................))).)))))....)))))).)))....)...))))... ( -20.61)
>consensus
UCACGCAAAUGUCAAUGCUGCUGUCAAAGUGUCAAUGAAAUGUUCAAUGGAAAUAAAAUGCGCAAAUAAUAGGAAAACCAAGGCGAACAGCAAAAGGCAUUCGCAAAAGGAAAAAGGGAA
....((.((((((..(((((.((((...((((..........(((....))).......))))........(......)..))))..)))))...)))))).))................ (-20.13 = -19.97 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:15 2006