Locus 6206

Sequence ID	2R_DroMel_CAF1
Location	19,537,295 – 19,537,433
Length	138
Max. P	0.956789

overview

Window 6

Location	19,537,295 – 19,537,397
Length	102
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	67.68
Mean single sequence MFE	-39.42
Consensus MFE	-18.97
Energy contribution	-20.37
Covariance contribution	1.39
Combinations/Pair	1.43
Mean z-score	-1.98
Structure conservation index	0.48
SVM decision value	1.47
SVM RNA-class probability	0.956789
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19537295 102 - 20766785
CUUGUGCAGGCUCUCGGCGUCGGAAUACUCGUCGCCGUUCUCUGGCGCCCCUAGCUGCAUGGAGUUGUCCAGGCAGACCG---ACUGC---------------UCGCGCUUGAACUUCUU
(..((((..((..(((((((((((..((........))..))))))))).....((((.((((....)))).))))...)---)..))---------------..))))..)........ ( -38.70)
>DroPse_CAF1 4429 117 - 1
CUUUGGCAGACUCUCGGCAUCGGAUAGUUCUUCACAGUUUUCCGCCGGGAUUAAAGUUACAGUGCUCUCGGAAUAUUGUU---GCUGCAGCGGGGGGUUAUCGUGACGCUUUGUCUUUUU
.......((((....(((.((((((((..(((((((((.(((((..((.(((........))).))..))))).))))).---((....))))))..))))).))).)))..)))).... ( -32.90)
>DroSec_CAF1 2773 102 - 1
CUUGUGCAGGCUUUCGGCGUCGGAAUACUCGUCGCCGUUCUCUGGCGCCCCUAGCUGCAUGGAGUUGUCCAUGCAGACCG---ACUGC---------------UCGCGCUUACACUUCUU
...((((..((..(((((((((((..((........))..))))))))).....(((((((((....)))))))))...)---)..))---------------..))))........... ( -42.70)
>DroEre_CAF1 2969 102 - 1
CUUGGACAGGCUCUCGGCGUCGGAGAACUCGUCGCAGUUCUCUGGCGCCGCUAGCUGCCCAGAGUUCUCCAGGCAGACCG---ACUGU---------------UCGCGUUUGCACUUUUU
.((((...((((..(((((((((((((((......)))))))))))))))..))))..))))..........((((((((---(....---------------))).))))))....... ( -46.50)
>DroYak_CAF1 2871 105 - 1
CUUGGACAGGCUCUCGGCGUCGGAGAACUCGUCGCAGUUCUCUGGCGCCACUAGCUGCACGGAGCUCUCCAGGCAAACCGACGACUGU---------------UCGCGUUUGCACUUCUU
.(((((..((((((.((((((((((((((......))))))))))))))....(.....))))))).)))))(((((((((.......---------------))).))))))....... ( -45.10)
>DroAna_CAF1 2322 117 - 1
CUUUGGCAGGCUCUCCGCAUCGGAGAACUCGUCGCAAUUCUCCGCCUGAAUCAGUUGAACAGCGAUCUCUGCACAAUUUU---GCUGUUGUCCCGCGUUUUCGUCGCGCUUGCACUUCUU
.....((((((((((((...))))))...((.(((.((((.......))))......((((((((.............))---)))))).....)))....))....))))))....... ( -30.62)
>consensus
CUUGGGCAGGCUCUCGGCGUCGGAGAACUCGUCGCAGUUCUCUGGCGCCACUAGCUGCACAGAGUUCUCCAGGCAGACCG___ACUGC_______________UCGCGCUUGCACUUCUU
.....((((......(((((((((.(((........))).))))))))).....((((.(((......))).))))........))))................................ (-18.97 = -20.37 +   1.39)

alignment

secondary structure

dotplot

Window 7

Location	19,537,317 – 19,537,433
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	69.34
Mean single sequence MFE	-46.38
Consensus MFE	-17.05
Energy contribution	-19.25
Covariance contribution	2.20
Combinations/Pair	1.31
Mean z-score	-2.00
Structure conservation index	0.37
SVM decision value	0.73
SVM RNA-class probability	0.836385
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19537317 116 - 20766785
UGACAUCUUGAUCGAGUCUGCCGUCGGCUUU----GGGGGCUUGUGCAGGCUCUCGGCGUCGGAAUACUCGUCGCCGUUCUCUGGCGCCCCUAGCUGCAUGGAGUUGUCCAGGCAGACCG
............((.((((((((.(((((..----((((((..((.((((....(((((.(((.....))).)))))...)))))))))))))))))).((((....))))))))))))) ( -51.40)
>DroSec_CAF1 2795 116 - 1
UGACAUCUUGAUCGAGUCUGCCGACGGCUUU----GGGGGCUUGUGCAGGCUUUCGGCGUCGGAAUACUCGUCGCCGUUCUCUGGCGCCCCUAGCUGCAUGGAGUUGUCCAUGCAGACCG
.........((.(((((...((((((.(...----(..(((((....)))))..)).))))))...)))))))((((.....))))........(((((((((....))))))))).... ( -48.20)
>DroEre_CAF1 2991 116 - 1
UGACAGCUUGCUCAGAUCUGCCGACGACUUC----GGGGGCUUGGACAGGCUCUCGGCGUCGGAGAACUCGUCGCAGUUCUCUGGCGCCGCUAGCUGCCCAGAGUUCUCCAGGCAGACCG
..............(.((((((...(((.((----((((((((....)))))))))).)))(((((((((...((((....(((((...)))))))))...))))))))).)))))).). ( -55.50)
>DroYak_CAF1 2896 116 - 1
UGACAGCUUGCUUGGAUCUACCGACGACUUC----GGUGGCUUGGACAGGCUCUCGGCGUCGGAGAACUCGUCGCAGUUCUCUGGCGCCACUAGCUGCACGGAGCUCUCCAGGCAAACCG
.......(((((((((..((((((.....))----))))((((.(...((((...((((((((((((((......))))))))))))))...))))...).))))..))))))))).... ( -54.90)
>DroAna_CAF1 2359 113 - 1
CGACAGUUUG-------CUGUUGUCGGCUUUGUUGGGCGGCUUUGGCAGGCUCUCCGCAUCGGAGAACUCGUCGCAAUUCUCCGCCUGAAUCAGUUGAACAGCGAUCUCUGCACAAUUUU
.(.(((.(((-------((((..((((((...(..(((((...((((..(.((((((...)))))).)..)))).......)))))..)...)))))))))))))...))))........ ( -42.10)
>DroPer_CAF1 4548 110 - 1
UGAUAACUUU--UGAUUAU-C---CGCUUUU----UGUGGCUUUGGCAGACUCUCGGCAUCGGAUAGUUCUUCACAGUUUUCCGCCGGGAUUAAAGUUACAGUGCUCUCGGAAUAUUGUU
..........--......(-(---((....(----(((((((((((.....(((((((...(((................))))))))))))))))))))))......))))........ ( -26.19)
>consensus
UGACAGCUUG_UCGAAUCUGCCGACGGCUUU____GGGGGCUUGGGCAGGCUCUCGGCGUCGGAGAACUCGUCGCAGUUCUCUGGCGCCACUAGCUGCACAGAGUUCUCCAGGCAGACCG
...................................((.(((((....))))).))(((((((((.(((........))).))))))))).....((((.(((......))).)))).... (-17.05 = -19.25 +   2.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:28 2006