Locus 5178

Sequence ID	2L_DroMel_CAF1
Location	14,665,342 – 14,665,487
Length	145
Max. P	0.996804

overview

Window 4

Location	14,665,342 – 14,665,447
Length	105
Sequences	4
Columns	106
Reading direction	reverse
Mean pairwise identity	82.64
Mean single sequence MFE	-26.45
Consensus MFE	-18.40
Energy contribution	-19.90
Covariance contribution	1.50
Combinations/Pair	1.07
Mean z-score	-3.34
Structure conservation index	0.70
SVM decision value	2.75
SVM RNA-class probability	0.996804
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14665342 105 - 22407834
CCUCUGGCUCUCUGUUUUUUUUUUUCUGUUUUAUUUUUCCUUACAGAAAAGUAAGAAAAAAAA-AACAAAACAGCUAAAAACUGGAACUGCCACCGGGCCAAGUGG
((.(((((((.(((((((.((((((...(((((((((((......)))))))))))...))))-)).)))))))........(((.....)))..))))).)).)) ( -29.30)
>DroSec_CAF1 19950 93 - 1
CCUCUGGCUCUCUGUUUUU-----------GUAUUUUUUCUUGCAGAAAAGUAAGAAAAAAA--AAAAAAACAGCUAAAAACUGGAACUGCCACCGGGCCAAGUGG
((.(((((((.((((((((-----------...(((((((((((......))))))))))).--..))))))))........(((.....)))..))))).)).)) ( -30.10)
>DroSim_CAF1 21620 95 - 1
CCUCUGGCUCUCUGUUUUU-----------GUAUUUUUUCUUGCAGAAAAGUAAGAAAAAAAAAAAAAAAACAGCUAAAAACUGGAACUGCCACCGGGCCAAGUGG
((.(((((((.((((((((-----------.(.(((((((((((......))))))))))).)...))))))))........(((.....)))..))))).)).)) ( -28.80)
>DroEre_CAF1 20007 80 - 1
CUUCUGGCUCUCCGUU--------------------UUCCUGGCGGAAAAGUAAGAAAA------ACAAAACAGCUAAAAACUGGAACUGCCACCGGGCCAAGUGG
....((((((((((((--------------------.....))))))............------......(((.......)))...........))))))..... ( -17.60)
>consensus
CCUCUGGCUCUCUGUUUUU___________GUAUUUUUCCUUGCAGAAAAGUAAGAAAAAAA__AAAAAAACAGCUAAAAACUGGAACUGCCACCGGGCCAAGUGG
((.(((((((...((((((..............(((((((((((......)))))))))))...............))))))(((.....)))..))))).)).)) (-18.40 = -19.90 +   1.50)

alignment

secondary structure

dotplot

Window 5

Location	14,665,374 – 14,665,487
Length	113
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	82.32
Mean single sequence MFE	-25.28
Consensus MFE	-17.56
Energy contribution	-17.88
Covariance contribution	0.32
Combinations/Pair	1.14
Mean z-score	-1.76
Structure conservation index	0.69
SVM decision value	0.30
SVM RNA-class probability	0.677765
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14665374 113 - 22407834
GUAGCGGUUACCUGUCAAUUGAUGAGCGGAGACUACAGUUCCUCUGGCUCUCUGUUUUUUUUUUUCUGUUUUAUUUUUCCUUACAGAAAAGUAAGAAAAAAAA-AACAAAACAG
...((((....))))........(((((....)..(((.....))))))).(((((((.((((((...(((((((((((......)))))))))))...))))-)).))))))) ( -27.20)
>DroSec_CAF1 19982 101 - 1
GUAGCGGUUACCUGUCAAUUGAUGAGCGGAGACUACAGUUCCUCUGGCUCUCUGUUUUU-----------GUAUUUUUUCUUGCAGAAAAGUAAGAAAAAAA--AAAAAAACAG
...((((....))))........(((((....)..(((.....))))))).((((((((-----------...(((((((((((......))))))))))).--..)))))))) ( -28.00)
>DroSim_CAF1 21652 103 - 1
GUAGCGGUUACCUGUCAAUUGAUGAGCGGAGACUACAGUUCCUCUGGCUCUCUGUUUUU-----------GUAUUUUUUCUUGCAGAAAAGUAAGAAAAAAAAAAAAAAAACAG
...((((....))))........(((((....)..(((.....))))))).((((((((-----------.(.(((((((((((......))))))))))).)...)))))))) ( -26.70)
>DroEre_CAF1 20039 88 - 1
GUAGCGGUUACCUGUCAAUUGAUCGGCGGAGACUACAGUUCUUCUGGCUCUCCGUU--------------------UUCCUGGCGGAAAAGUAAGAAAA------ACAAAACAG
(((((..(..((.(((....))).))..).).)))).(((.((((.(((.((((((--------------------.....))))))..))).)))).)------))....... ( -22.90)
>DroYak_CAF1 20451 88 - 1
GUAGCGGUUACCUGUCAAUUGAUGAGCGGAGACUACAGUUCUUCUGGCUCUCUGUU--------------------UUCCUGGCAGUGAAGUAAGAAAA------ACAAAACAG
...((..((((.(((((...((.(((((((((...(((.....)))..))))))))--------------------))).))))))))).)).......------......... ( -21.60)
>consensus
GUAGCGGUUACCUGUCAAUUGAUGAGCGGAGACUACAGUUCCUCUGGCUCUCUGUUUUU____________UAUUUUUCCUUGCAGAAAAGUAAGAAAAAAA__AACAAAACAG
...........((((........(((((((((...(((.....)))..)))))))))......................(((((......)))))...............)))) (-17.56 = -17.88 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:58 2006