Locus 8577

Sequence ID	X_DroMel_CAF1
Location	21,275,608 – 21,275,899
Length	291
Max. P	0.886650

overview

Window 5

Location	21,275,608 – 21,275,725
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	75.21
Mean single sequence MFE	-35.04
Consensus MFE	-16.53
Energy contribution	-17.32
Covariance contribution	0.79
Combinations/Pair	1.29
Mean z-score	-1.79
Structure conservation index	0.47
SVM decision value	0.15
SVM RNA-class probability	0.606509
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21275608 117 + 22224390
UUACAUUAGCGGUGGGUGCGUGAGUGGAUUUUAAUUUUCAAUAAGAAGACUUCAAAAUCACUCUAU--UUGCGCUGCAAGCCCGACUUGGGCUCAG-UACUCAAGCUGAGCAAAUUGCUU
.....(((((..((((((((.((((((.(((.(((((((.....))))).)).))).))))))...--.)))((((..(((((.....))))))))-)))))).)))))((.....)).. ( -35.30)
>DroSec_CAF1 16753 117 + 1
UCACAUCAGCGGUGGGUGCGUGAGUGGAUUUUAAUUUUCAAUAAGAAGACUUCAAAAUCACUUAAU--UUGCGCUGCAAGCCCGACUUGUGCUCAA-UACUCAAGCUGAGCAAGUUGCUU
.....(((((..((((((((..(((.(((((((((((((.....))))).)).)))))).....))--)..))).(((((.....)))))......-.))))).)))))((.....)).. ( -31.00)
>DroSim_CAF1 28273 117 + 1
UUACAUCAGCGGUGGGUGCGUGAGUGGAUUUUAAUUUUCAAUAAGAAGACUUCAAAAUCACUUAAU--UUGCGCUGCAAGCCCGGCUUGGGCUCAG-UACUCAAGCUGAGCAAGUUGCUU
.....(((((..(((((((.(((((((.(((.(((((((.....))))).)).))).)))))))..--.((.(((.(((((...)))))))).)))-)))))).)))))((.....)).. ( -36.10)
>DroEre_CAF1 16772 102 + 1
UUACAUCAGCGGUGGGAGCGUGAGUGGAGUC----------------GGCUUCCGAAUCACUCCGC--UCACGGUGCAAGCCCGACUUGGGCGCAGCUACUCCGGCUAAGCAAAUUGAUU
........(((((.(((((((((((((((((----------------((...))))....))))))--)))))..((..((((.....))))...))..)))).)))..))......... ( -43.30)
>DroYak_CAF1 18629 102 + 1
UUACAUCAGCGGUGGGAGCGUGAGUGGAUUUUAAUUUCCAAUAAACGGGCUUCGAAAGCACUCCACUCUCACGAUGCUAGCCCGACUUGGGAACA------------AAGCAGA------
...........(((((((.(.(((((..(((..(..(((.......)))..)..))).)))))).)))))))..((((..(((.....)))....------------.))))..------ ( -29.50)
>consensus
UUACAUCAGCGGUGGGUGCGUGAGUGGAUUUUAAUUUUCAAUAAGAAGACUUCAAAAUCACUCAAU__UUGCGCUGCAAGCCCGACUUGGGCUCAG_UACUCAAGCUGAGCAAAUUGCUU
........((((((.(...(((((((.(((((..(((((.....)))))....)))))))))).))...).))))))..((((.....))))............................ (-16.53 = -17.32 +   0.79)

alignment

secondary structure

dotplot

Window 6

Location	21,275,725 – 21,275,837
Length	112
Sequences	3
Columns	113
Reading direction	reverse
Mean pairwise identity	81.10
Mean single sequence MFE	-28.64
Consensus MFE	-21.39
Energy contribution	-21.50
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-1.67
Structure conservation index	0.75
SVM decision value	0.34
SVM RNA-class probability	0.696643
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21275725 112 - 22224390
CGGAGAUGAGUGCGUGACUUCUCUGAGAAGUCAGCAUUCAUGCUAACCAACUCUCUUUCUCUUUCUCCAGAAAUAUAUUU-UUUCGCAGGGUCCCGUCUCUGUUUUGUUUCGG
.((((((((((((.(((((((.....))))))))))))))((.....))..............))))).((((((.....-....((((((......))))))..)))))).. ( -33.20)
>DroSec_CAF1 16870 102 - 1
CGGAGAUGAGUGCGUGACUUCUCUGAGAAGUCAGCAUUCACGCUAAUCAACUCUCU---------UCCAGGAAUAUAUUUCUUUCGUAGGGCCCAGU--CUGUUUUGUUUCGG
(((((.(((((((.(((((((.....))))))))))))))....(((..(((((((---------...(((((.....)))))....))))...)))--..)))...))))). ( -26.30)
>DroSim_CAF1 28390 88 - 1
CGGAGAUGAGUGCGUGACUUCUCUGAGAAGUCAGCAUU--------------CUCU---------UCCAGGAAUAUAUUUCUUUCGUAGGGCCCAGU--CUGUUUUGUUUCGG
.((((..((((((.(((((((.....))))))))))))--------------)..)---------))).((((((.............((((...))--))....)))))).. ( -26.43)
>consensus
CGGAGAUGAGUGCGUGACUUCUCUGAGAAGUCAGCAUUCA_GCUAA_CAACUCUCU_________UCCAGGAAUAUAUUUCUUUCGUAGGGCCCAGU__CUGUUUUGUUUCGG
..(((((((((((.(((((((.....)))))))))))))..........................(((.((((........))))...)))...............))))).. (-21.39 = -21.50 +   0.11)

alignment

secondary structure

dotplot

Window 7

Location	21,275,797 – 21,275,899
Length	102
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	87.75
Mean single sequence MFE	-31.28
Consensus MFE	-23.05
Energy contribution	-23.49
Covariance contribution	0.44
Combinations/Pair	1.14
Mean z-score	-2.25
Structure conservation index	0.74
SVM decision value	0.94
SVM RNA-class probability	0.886650
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21275797 102 - 22224390
UCCUGCUCAAAGGGUUUUCCCCGACCCGCAAAG--CUCUGUGAUGUACAUGUAUUUACAUUUUUCGGAGAUGAGUGCGUGACUUCUCUGAGAAGUCAGCAUUCA
...........(((((......)))))......--(((((.((((((........))))))...))))).(((((((.(((((((.....)))))))))))))) ( -34.90)
>DroSec_CAF1 16932 96 - 1
UCCUGCUCAAAGGGUUUUCCCCGACCCUCGAAG--CUCUGUGAUG------UAUUUACAUGUUUCGGAGAUGAGUGCGUGACUUCUCUGAGAAGUCAGCAUUCA
.....(((..((((((......))))))(((((--(..(((((..------...))))).))))))))).(((((((.(((((((.....)))))))))))))) ( -37.80)
>DroSim_CAF1 28440 94 - 1
UCCUGCUCAAAGGGUUUUCCCCGACCCUCGAAG--CUCUGUGAUG------UAUUUACAUGUUUCGGAGAUGAGUGCGUGACUUCUCUGAGAAGUCAGCAUU--
....(((((.((((((......))))))(((((--(..(((((..------...))))).))))))....)))))((.(((((((.....)))))))))...-- ( -33.70)
>DroEre_CAF1 16921 96 - 1
UCCUGCUCAAAGGGUUUUCCCCGACCCCCGACGUAUUCCUUGAUG------UAUUUACAUGUUUCGGAGAUGAGUGCGUGACUUCCUUGGGG-CCCAGCACCC-
...((((....(((....((((((......(((((((((((((..------(((....)))..)).)))..)))))))).......))))))-)))))))...- ( -23.12)
>DroYak_CAF1 18769 94 - 1
UCCUGCUCAAAGGGUUUUCCCCGACCCUCGCAG--UUCUGUGAUG------UAUUUACAUGUUUCGGAGAUGAGUGCGUGACUUCUCUGAGG-CUCAGCAUUC-
..((((....((((((......)))))).))))--...(((((..------...))))).((((((((((..(((.....))))))))))))-).........- ( -26.90)
>consensus
UCCUGCUCAAAGGGUUUUCCCCGACCCUCGAAG__CUCUGUGAUG______UAUUUACAUGUUUCGGAGAUGAGUGCGUGACUUCUCUGAGAAGUCAGCAUUC_
....(((((..(((((......)))))........(((((.(((................))).))))).)))))((.((((((((...))))))))))..... (-23.05 = -23.49 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:07:38 2006