Locus 6772

Sequence ID	2L_DroMel_CAF1
Location	18,926,447 – 18,926,562
Length	115
Max. P	0.649905

overview

Window 4

Location	18,926,447 – 18,926,544
Length	97
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.62
Mean single sequence MFE	-28.49
Consensus MFE	-19.60
Energy contribution	-19.05
Covariance contribution	-0.55
Combinations/Pair	1.24
Mean z-score	-1.33
Structure conservation index	0.69
SVM decision value	0.24
SVM RNA-class probability	0.649905
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18926447 97 - 22407834
------GGACCAAAAACUGGUGCAAAUUAACACGCUAAGCACUUGAAUCGGACCAAAUGUGGCAUGAGUAAUGCCCUCAAGUGG-----------------CCAACAGAUGGCGCACAUU
------(.((((.....)))).)..........((....(((((((.....((.....))(((((.....))))).)))))))(-----------------(((.....))))))..... ( -26.30)
>DroVir_CAF1 46230 101 - 1
UUCGAAGCACUGA-AACUGGUGCAAAUUAACACGCUAAGCACUUGAAU-GCGCCAAAUGUGGCGUGAGUAAUGCCCUCAAGUGG-----------------CCGACAGAUGGCGCACAUU
(((((.(((((..-....)))))..........((...))..)))))(-((((((..((((((.((((.......))))....)-----------------)).)))..))))))).... ( -32.20)
>DroPse_CAF1 53148 113 - 1
------GAUCUAG-AACUGGUGCAAAUUAACACGCUAAGCACUUGAAUCCGGCCAAAUGUGGCAUGAGUAAUGCCCUCAAGUGGCUUCGCCUCGCAUCGUUCCAACAGAUGGCGCACAUU
------.......-.....((((..........((.((((((((((.....((.....))(((((.....))))).)))))).)))).))...(((((.........))).))))))... ( -28.20)
>DroGri_CAF1 69534 89 - 1
------------A-AACUGGUGCAAAUUAACGCGCUAAGCACUUGAAU-GCGCCAAAUGUGGCGUGAGUAAUGCCCUCAAGUGG-----------------CCGACAGAUGGCGCACAUU
------------.-...((((((........))))))..........(-((((((..((((((.((((.......))))....)-----------------)).)))..))))))).... ( -30.30)
>DroMoj_CAF1 74395 89 - 1
------------A-AACUGGUGCAAAUUAACACGCUAAGCACUUGAAC-GCGCUAAAUGUGGCGUGAGUAAUGCCUCCAAGUGG-----------------ACAACAGAUGGCGUGCAUU
------------.-..(.(((((...............))))).)..(-((((((..((((((((.....)))))(((....))-----------------)..)))..))))))).... ( -25.76)
>DroPer_CAF1 55229 113 - 1
------GAUCUAG-AACUGGUGCAAAUUAACACGCUAAGCACUUGAAUCCGGCCAAAUGUGGCAUGAGUAAUGCCCUCAAGUGGCUUCGCCUCGCAUCGUUCCAACAGAUGGCGCACAUU
------.......-.....((((..........((.((((((((((.....((.....))(((((.....))))).)))))).)))).))...(((((.........))).))))))... ( -28.20)
>consensus
______G__CUAA_AACUGGUGCAAAUUAACACGCUAAGCACUUGAAU_GCGCCAAAUGUGGCAUGAGUAAUGCCCUCAAGUGG_________________CCAACAGAUGGCGCACAUU
...................((((................(((((((.....((.....))(((((.....))))).)))))))..................(((.....))).))))... (-19.60 = -19.05 +  -0.55)

alignment

secondary structure

dotplot

Window 5

Location	18,926,470 – 18,926,562
Length	92
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	77.71
Mean single sequence MFE	-23.06
Consensus MFE	-16.59
Energy contribution	-16.53
Covariance contribution	-0.05
Combinations/Pair	1.06
Mean z-score	-0.92
Structure conservation index	0.72
SVM decision value	-0.05
SVM RNA-class probability	0.510204
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18926470 92 + 22407834
UUGAGGGCAUUACUCAUGCCACAUUUGGUCCGAUUCAAGUGCUUAGCGUGUUAAUUUGCACCAGUUUUUGGUCCCAGUAUCGG-GA---UCUUU---AA
....(((((.....(((((..(((((((......)))))))....)))))......))).)).......((((((......))-))---))...---.. ( -26.60)
>DroPse_CAF1 53188 82 + 1
UUGAGGGCAUUACUCAUGCCACAUUUGGCCGGAUUCAAGUGCUUAGCGUGUUAAUUUGCACCAGUU-CUAGAUCCGA-------------CUUG---AG
(..(((((((.....))))).........((((((..((.(((..(.((((......)))))))).-)).)))))).-------------))..---). ( -20.90)
>DroGri_CAF1 69557 75 + 1
UUGAGGGCAUUACUCACGCCACAUUUGGCGC-AUUCAAGUGCUUAGCGCGUUAAUUUGCACCAGUU-U------CGA-------------CUCG---AA
((((((((.........)))....((((.((-(.....((((...)))).......))).))))..-.------...-------------))))---). ( -19.40)
>DroWil_CAF1 18795 91 + 1
UUGAGGGCAUUACUCACGCCACAUUUGGCGC-AUUCAAGUGCUUAGCGUGUUAAUUUGCACCAGUU-UCAGUUG--GUCUUGG-GUCGUCGUUG---AA
..((.(((((((..(((((.......(((((-......)))))..))))).)))).....((((..-((....)--)..))))-))).))....---.. ( -22.10)
>DroAna_CAF1 34465 95 + 1
UUGAGGGCAUUACUCAUGCCACAUUUGGCAGGAUUCAAGUGCUUAGCGUGUUAAUUUGCACCAGUU-CCUGCCGCAGCUCCUGAGC---CCUUUUCGAG
..((((((..................(((((((.....((((...............))))....)-)))))).(((...))).))---))))...... ( -28.46)
>DroPer_CAF1 55269 82 + 1
UUGAGGGCAUUACUCAUGCCACAUUUGGCCGGAUUCAAGUGCUUAGCGUGUUAAUUUGCACCAGUU-CUAGAUCCGA-------------CUUG---AG
(..(((((((.....))))).........((((((..((.(((..(.((((......)))))))).-)).)))))).-------------))..---). ( -20.90)
>consensus
UUGAGGGCAUUACUCAUGCCACAUUUGGCCCGAUUCAAGUGCUUAGCGUGUUAAUUUGCACCAGUU_CUAGAUCCGA_____________CUUG___AA
....(((((.....(((((..(((((((......)))))))....)))))......))).))..................................... (-16.59 = -16.53 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:19:38 2006