Locus 5453

Sequence ID	3R_DroMel_CAF1
Location	14,402,658 – 14,402,785
Length	127
Max. P	0.972991

overview

Window 2

Location	14,402,658 – 14,402,772
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	81.00
Mean single sequence MFE	-24.70
Consensus MFE	-16.12
Energy contribution	-15.40
Covariance contribution	-0.72
Combinations/Pair	1.22
Mean z-score	-1.59
Structure conservation index	0.65
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14402658 114 + 27905053
UGGUUAGAAAUUAGUCGACCUAUUUGGC------CAUUUUAAUAUUCCUGUACGCCAUUCGCUUAAUUGGUGGCAACAGGUGCCACACCUGCGCCUCUCUCUCGCCCCCCCCCCUUCUAC
.(((.(((((((((.(((......((((------...................)))).))).))))))((.(((..((((((...)))))).))).)).))).))).............. ( -24.01)
>DroSec_CAF1 181307 102 + 1
UGGAUUGAAAUUAGCCGACCUAUUUGGC------CAUUUUAAUAUUUCUAAACGCCAUUCGCUUAAUUGGUGGCAACAGGUGCCACACCUGCGUCUC-------CCC-----CCUUCUAC
.((((((((((..(((((.....)))))------.))))))))..........((((((.........))))))..((((((...))))))......-------...-----))...... ( -22.70)
>DroSim_CAF1 173367 107 + 1
UGGAUAGAAAUUAGCCGACCUAUUUGGC------CAUUUUAAUAUUUCUAAACGCCAUUCGCUUAAUUGGUGGCAACAGGUGCCACACCUGCGCCUC-------CCCCCUCCCCUUCUAC
.((((((((((..(((((.....)))))------.........)))))))..................((.(((..((((((...)))))).))).)-------)....)))........ ( -24.70)
>DroEre_CAF1 188586 95 + 1
UGGGUAAAAAUGUCCCAACCUAUC-GGC------CGUUUUAAUAUUUCUAAACGCCAUUCGCUUAAUUGGUGGCAACAGGUGCCACACCUGCGCC------------------CCGCCAC
((((.........)))).......-(((------.((((..........)))))))...........((((((...((((((...))))))....------------------)))))). ( -25.90)
>DroYak_CAF1 202278 101 + 1
UGGGUAGAAACUAGCCAACCUAUU-GGUCGGUCCCAUUUUAAUAUUUCUAAACGCCAUUCGCUUAAUUGGUGGCAACAGGUGCCACACCUGCGCC------------------CUUCCAC
.((((.(..((..(((((....))-)))..))..)..................((((((.........))))))..((((((...)))))).)))------------------)...... ( -26.20)
>consensus
UGGAUAGAAAUUAGCCGACCUAUUUGGC______CAUUUUAAUAUUUCUAAACGCCAUUCGCUUAAUUGGUGGCAACAGGUGCCACACCUGCGCCUC_______CCC_____CCUUCUAC
(((...........)))........(((.........................((((((.........))))))..((((((...)))))).)))......................... (-16.12 = -15.40 +  -0.72)

alignment

secondary structure

dotplot

Window 3

Location	14,402,658 – 14,402,772
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.00
Mean single sequence MFE	-32.16
Consensus MFE	-20.92
Energy contribution	-21.52
Covariance contribution	0.60
Combinations/Pair	1.17
Mean z-score	-1.83
Structure conservation index	0.65
SVM decision value	0.38
SVM RNA-class probability	0.710889
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14402658 114 - 27905053
GUAGAAGGGGGGGGGGCGAGAGAGAGGCGCAGGUGUGGCACCUGUUGCCACCAAUUAAGCGAAUGGCGUACAGGAAUAUUAAAAUG------GCCAAAUAGGUCGACUAAUUUCUAACCA
......((..((..(...((.....((((((((((...)))))).)))).((......((.....)).....))..........((------(((.....))))).))..)..))..)). ( -31.20)
>DroSec_CAF1 181307 102 - 1
GUAGAAGG-----GGG-------GAGACGCAGGUGUGGCACCUGUUGCCACCAAUUAAGCGAAUGGCGUUUAGAAAUAUUAAAAUG------GCCAAAUAGGUCGGCUAAUUUCAAUCCA
......((-----(..-------((((.(((((((...))))))).(((.....(((((((.....)))))))............(------(((.....)))))))...))))..))). ( -30.20)
>DroSim_CAF1 173367 107 - 1
GUAGAAGGGGAGGGGG-------GAGGCGCAGGUGUGGCACCUGUUGCCACCAAUUAAGCGAAUGGCGUUUAGAAAUAUUAAAAUG------GCCAAAUAGGUCGGCUAAUUUCUAUCCA
......((..((..((-------(.((((((((((...)))))).)))).))..(((((((.....)))))))...........((------(((.........))))).)..))..)). ( -33.90)
>DroEre_CAF1 188586 95 - 1
GUGGCGG------------------GGCGCAGGUGUGGCACCUGUUGCCACCAAUUAAGCGAAUGGCGUUUAGAAAUAUUAAAACG------GCC-GAUAGGUUGGGACAUUUUUACCCA
.((((((------------------((((((((((...)))))).)))).))..(((((((.....))))))).............------)))-)......((((.........)))) ( -31.10)
>DroYak_CAF1 202278 101 - 1
GUGGAAG------------------GGCGCAGGUGUGGCACCUGUUGCCACCAAUUAAGCGAAUGGCGUUUAGAAAUAUUAAAAUGGGACCGACC-AAUAGGUUGGCUAGUUUCUACCCA
(((((((------------------((((((((((...)))))).)))).....(((((((.....))))))).............((.((((((-....))))))))..)))))))... ( -34.40)
>consensus
GUAGAAGG_____GGG_______GAGGCGCAGGUGUGGCACCUGUUGCCACCAAUUAAGCGAAUGGCGUUUAGAAAUAUUAAAAUG______GCCAAAUAGGUCGGCUAAUUUCUACCCA
(((((((..................((((((((((...)))))).)))).((..(((((((.....)))))))...................(((.....))).))....)))))))... (-20.92 = -21.52 +   0.60)

alignment

secondary structure

dotplot

Window 4

Location	14,402,692 – 14,402,785
Length	93
Sequences	4
Columns	97
Reading direction	forward
Mean pairwise identity	81.25
Mean single sequence MFE	-17.52
Consensus MFE	-14.89
Energy contribution	-15.20
Covariance contribution	0.31
Combinations/Pair	1.06
Mean z-score	-2.19
Structure conservation index	0.85
SVM decision value	1.70
SVM RNA-class probability	0.972991
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14402692 93 + 27905053
AAUAUUCCUGUACGCCAUUCGCUUAAUUGGUGGCAACAGGUGCCACACCUGCGCCUCUCUCUCGCCCCCCCCCCUUCUACCGCCAAAAGAAAA----
....(((......((.....))....(((((((...((((((...)))))).((.........))..............)))))))..)))..---- ( -16.90)
>DroSec_CAF1 181341 81 + 1
AAUAUUUCUAAACGCCAUUCGCUUAAUUGGUGGCAACAGGUGCCACACCUGCGUCUC-------CCC-----CCUUCUACCGCCAAAAGAAAA----
....(((((....((.....))....(((((((...((((((...)))))).(....-------...-----.).....))))))).))))).---- ( -17.30)
>DroSim_CAF1 173401 86 + 1
AAUAUUUCUAAACGCCAUUCGCUUAAUUGGUGGCAACAGGUGCCACACCUGCGCCUC-------CCCCCUCCCCUUCUACCGCCAAAAGAAAA----
....(((((....((.....))......((.(((..((((((...)))))).))).)-------)......................))))).---- ( -17.90)
>DroYak_CAF1 202317 79 + 1
AAUAUUUCUAAACGCCAUUCGCUUAAUUGGUGGCAACAGGUGCCACACCUGCGCC------------------CUUCCACCACGUAAAGAACCCCCA
.....((((..((((.....)).....((((((.....(((((.......)))))------------------...)))))).))..))))...... ( -18.00)
>consensus
AAUAUUUCUAAACGCCAUUCGCUUAAUUGGUGGCAACAGGUGCCACACCUGCGCCUC_______CCC_____CCUUCUACCGCCAAAAGAAAA____
....(((((....((((..........))))(((..((((((...)))))).)))................................)))))..... (-14.89 = -15.20 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:04 2006