Locus 6408

Sequence ID	2L_DroMel_CAF1
Location	17,990,931 – 17,991,038
Length	107
Max. P	0.828102

overview

Window 5

Location	17,990,931 – 17,991,038
Length	107
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.89
Mean single sequence MFE	-27.07
Consensus MFE	-18.67
Energy contribution	-18.64
Covariance contribution	-0.02
Combinations/Pair	1.17
Mean z-score	-1.62
Structure conservation index	0.69
SVM decision value	0.56
SVM RNA-class probability	0.782830
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17990931 107 + 22407834
AAAAAA---GA---------ACAGGAAACUUUCCGGGCUCUUGGCAAAACUUAUUU-UGCUGUAAGUUGAGAAAUUUAUUGAGCUUGCCGUUAAGCACUUAAAGUUGGGCUACGGCAAAC
......---((---------(.((....))))).((((((..(((((((....)))-))))(((((((....))))))).))))))(((((..(((.((.......)))))))))).... ( -29.40)
>DroSec_CAF1 207131 106 + 1
AAAAAA----A---------CAAGGAAACUUUCCCAGCUCUUGGCAAAACUUAUUU-UGCUGUAAGUUGAGAAAUUUAUUGAGCUUGCCGUUAAGCACUUAAAGUUGGGCUACGGCAAAC
......----.---------((((....)((((.(((((..((((((((....)))-)))))..))))).))))....)))...(((((((..(((.((.......)))))))))))).. ( -29.40)
>DroSim_CAF1 205695 102 + 1
AAAAC-----------------CGGAAACUUUCCCAGCUCUUGGCAAAACUUAUUU-UGCUGUAAGUUGAGAAAUUUAUUGAGCUUGCCGUUAAGCACUUAAAGUUGGGCUACGGCAAAC
.....-----------------.(....)((((.(((((..((((((((....)))-)))))..))))).))))..........(((((((..(((.((.......)))))))))))).. ( -28.90)
>DroEre_CAF1 197557 119 + 1
AAGAAAAAGAAACAGGAAAAAAGGAAAACUUUUCGAGCUCUUGGCAAAACUUAUUU-UGGUGUAAGUUGGGAAAUUUAUUGAGCUUGCCGUUAAGCACUUAAAGUUGGGCUACAGCAAAC
..........(((.((..(((((.....)))))(((((((....(..(((((((..-....)))))))..).........))))))))))))...........((((.....)))).... ( -21.52)
>DroYak_CAF1 212862 101 + 1
AA------------------ACAGAAAACUUUCCGAGCUCUUGGCAAAACUUAUUU-CGGUGUAAGUUGGGAAAUUUAUUGAGCUUGCCGUUAAGCACUUAAAGUUGGGCUACGGCAAAC
..------------------.(((.(((.(((((..((.....))..(((((((..-....)))))))))))).))).)))...(((((((..(((.((.......)))))))))))).. ( -25.90)
>DroAna_CAF1 197164 111 + 1
----UCCGGCCACAGGAAAAACA-----AGUUUCGAGUUCUUGGGGAAACUUCUUUGUGGUGUAAGUUGCGAAAUUUAUUGAGCUUGCUGCAAAGCACUUAAAGUUAGGCUUCGGCAAAC
----....(((((((((....((-----((.........))))((....)))).)))))))(((((((.(((......))))))))))(((.((((.((.......))))))..)))... ( -27.30)
>consensus
AAAAAA____A_________ACAGGAAACUUUCCGAGCUCUUGGCAAAACUUAUUU_UGCUGUAAGUUGAGAAAUUUAUUGAGCUUGCCGUUAAGCACUUAAAGUUGGGCUACGGCAAAC
...................................(((((.......(((((((.......)))))))............)))))((((((..(((.((.......)))))))))))... (-18.67 = -18.64 +  -0.02)

alignment

secondary structure

dotplot

Window 6

Location	17,990,931 – 17,991,038
Length	107
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.89
Mean single sequence MFE	-25.22
Consensus MFE	-15.72
Energy contribution	-16.00
Covariance contribution	0.28
Combinations/Pair	1.16
Mean z-score	-1.99
Structure conservation index	0.62
SVM decision value	0.70
SVM RNA-class probability	0.828102
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17990931 107 - 22407834
GUUUGCCGUAGCCCAACUUUAAGUGCUUAACGGCAAGCUCAAUAAAUUUCUCAACUUACAGCA-AAAUAAGUUUUGCCAAGAGCCCGGAAAGUUUCCUGU---------UC---UUUUUU
((((((((((((.(........).)))..)))))))))......................(((-(((....)))))).((((((..(((.....))).))---------))---)).... ( -26.50)
>DroSec_CAF1 207131 106 - 1
GUUUGCCGUAGCCCAACUUUAAGUGCUUAACGGCAAGCUCAAUAAAUUUCUCAACUUACAGCA-AAAUAAGUUUUGCCAAGAGCUGGGAAAGUUUCCUUG---------U----UUUUUU
((((((((((((.(........).)))..)))))))))........(((((((.(((...(((-(((....))))))...))).))))))).........---------.----...... ( -29.00)
>DroSim_CAF1 205695 102 - 1
GUUUGCCGUAGCCCAACUUUAAGUGCUUAACGGCAAGCUCAAUAAAUUUCUCAACUUACAGCA-AAAUAAGUUUUGCCAAGAGCUGGGAAAGUUUCCG-----------------GUUUU
((((((((((((.(........).)))..)))))))))........(((((((.(((...(((-(((....))))))...))).))))))).......-----------------..... ( -29.00)
>DroEre_CAF1 197557 119 - 1
GUUUGCUGUAGCCCAACUUUAAGUGCUUAACGGCAAGCUCAAUAAAUUUCCCAACUUACACCA-AAAUAAGUUUUGCCAAGAGCUCGAAAAGUUUUCCUUUUUUCCUGUUUCUUUUUCUU
((((((((((((.(........).)))..)))))))))..............((((((.....-...)))))).....((((((..((((((.......))))))..).)))))...... ( -20.20)
>DroYak_CAF1 212862 101 - 1
GUUUGCCGUAGCCCAACUUUAAGUGCUUAACGGCAAGCUCAAUAAAUUUCCCAACUUACACCG-AAAUAAGUUUUGCCAAGAGCUCGGAAAGUUUUCUGU------------------UU
((((((((((((.(........).)))..))))))))).((..((((((.((((((((.....-...))))))..((.....))..)).))))))..)).------------------.. ( -22.80)
>DroAna_CAF1 197164 111 - 1
GUUUGCCGAAGCCUAACUUUAAGUGCUUUGCAGCAAGCUCAAUAAAUUUCGCAACUUACACCACAAAGAAGUUUCCCCAAGAACUCGAAACU-----UGUUUUUCCUGUGGCCGGA----
((((((((((((((.......)).))))))..))))))......................(((((((.(((((((...........))))))-----).)).....))))).....---- ( -23.80)
>consensus
GUUUGCCGUAGCCCAACUUUAAGUGCUUAACGGCAAGCUCAAUAAAUUUCUCAACUUACACCA_AAAUAAGUUUUGCCAAGAGCUCGGAAAGUUUCCUGU_________U____UUUUUU
((((((((((((.(........).)))..)))))))))...............................((((((....))))))................................... (-15.72 = -16.00 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:16 2006