Locus 5461

Sequence ID	3R_DroMel_CAF1
Location	14,444,439 – 14,444,578
Length	139
Max. P	0.835238

overview

Window 6

Location	14,444,439 – 14,444,550
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.88
Mean single sequence MFE	-20.96
Consensus MFE	-14.81
Energy contribution	-15.09
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-1.76
Structure conservation index	0.71
SVM decision value	0.37
SVM RNA-class probability	0.710828
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14444439 111 - 27905053
GAUUUUUCACUUCCCAUACGGAAUGUAAGUAGAAAAAAAGCAGCAAAAGAGCGGGAGUUUUAAGUUUGGGGCGUGAAAGGAAAAAGUAAAAUGUUUGCCAAAA---------AAAAAAGU
..((((((((.(((((.((.........((.(........).))...(((((....)))))..)).))))).)))))))).....((((.....)))).....---------........ ( -20.00)
>DroSec_CAF1 1607 113 - 1
GAUUUUUCACUUCCCAUGUGCAGCGUAAG----AAAAAAGCAGCAAAAGAGCGGGAGUUUUGGGUUUGGGGCGUGAAAGGAAAAAGUAAAAUGUUUGCCAAAAUAAAA---AACAAAAGU
..((((((((.(((((..(((.((.....----......)).)))..(((((....))))).....))))).))))))))...........(((((...........)---))))..... ( -24.00)
>DroSim_CAF1 1678 116 - 1
GAUUUUUCACUUCCCAUAUGCAGCGUAAG----AAAAAAGCAGCAAAAGAGCGGGAGUUUUGGGUUUGGGGCGUGAAAGGAAAAAGUAAAAUGUUUGCCAAAAUAAAAAGAAAAAAAAGU
..((((((((.(((((..(((.((.....----......)).)))..(((((....))))).....))))).))))))))...........(((((....)))))............... ( -23.20)
>DroEre_CAF1 1593 97 - 1
GAUUUUUCACUUCCCGUGUGGAG---AGG----AAAAAAGCAGCAAAGGAGCGGGAGUU-UGAGUUUGGGGCGUGAAAGGAAAAAGUAAAAUGCUUGCCAAAAAA---------------
....(((((((((((.......)---.))----))....((..((((.((((....)))-)...))))..))))))))((...((((.....)))).))......--------------- ( -20.70)
>DroYak_CAF1 1705 105 - 1
GAUUUUUCACUUCCAAU--AAAG---AGA----AAAAAAUCAGCCAAAGAGCGGGAGUU-UGAGUUUGGGGCGUGAAAGGAA-AAGUAAAAUGUUUGCCAAAAAA-AA---AACAAAAAU
..((((((((((((((.--...(---(..----......)).......((((....)))-)....)))))).))))))))..-........(((((.........-.)---))))..... ( -16.90)
>consensus
GAUUUUUCACUUCCCAUAUGCAG_GUAAG____AAAAAAGCAGCAAAAGAGCGGGAGUUUUGAGUUUGGGGCGUGAAAGGAAAAAGUAAAAUGUUUGCCAAAAAA_AA___AAAAAAAGU
..((((((((.(((((.........................(((...(((((....)))))..)))))))).)))))))).....((((.....))))...................... (-14.81 = -15.09 +   0.28)

alignment

secondary structure

dotplot

Window 7

Location	14,444,470 – 14,444,578
Length	108
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	71.52
Mean single sequence MFE	-16.50
Consensus MFE	-10.38
Energy contribution	-10.57
Covariance contribution	0.19
Combinations/Pair	1.20
Mean z-score	-1.60
Structure conservation index	0.63
SVM decision value	0.73
SVM RNA-class probability	0.835238
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14444470 108 + 27905053
CCUUUCACGCCCCAAACUUAAAACUCCCGCUCUUUUGCUGCUUUUUUUCUACUUACAUUCCGUAUGGGAAGUGAAAAAUCUUGUUUUCUUG------------UAUAUAUGUAUGUAUGC
..((((((..((((..............((......))...............(((.....)))))))..))))))..............(------------((((((....))))))) ( -17.10)
>DroSec_CAF1 1644 85 + 1
CCUUUCACGCCCCAAACCCAAAACUCCCGCUCUUUUGCUGCUUUUUU----CUUACGCUGCACAUGGGAAGUGAAAAAUCUUGUUUUC-------------------------------C
..((((((..((((..............((......))(((......----........)))..))))..))))))............-------------------------------. ( -15.14)
>DroSim_CAF1 1718 85 + 1
CCUUUCACGCCCCAAACCCAAAACUCCCGCUCUUUUGCUGCUUUUUU----CUUACGCUGCAUAUGGGAAGUGAAAAAUCUUGUUUUC-------------------------------C
..((((((..((((..............((......))(((......----........)))..))))..))))))............-------------------------------. ( -15.24)
>DroYak_CAF1 1740 110 + 1
CCUUUCACGCCCCAAACUCA-AACUCCCGCUCUUUGGCUGAUUUUUU----UCU---CUUU--AUUGGAAGUGAAAAAUCUUGUUUUCCCGAGCAUAUAUAUGUAUAUAUGUAUAUCCGC
........((..........-.......((((...((..(((.((((----((.---((((--....)))).))))))....)))..)).))))(((((((((....)))))))))..)) ( -18.50)
>consensus
CCUUUCACGCCCCAAACCCAAAACUCCCGCUCUUUUGCUGCUUUUUU____CUUACGCUGCAUAUGGGAAGUGAAAAAUCUUGUUUUC_______________________________C
..((((((..((((..............((......))(((..................)))..))))..))))))............................................ (-10.38 = -10.57 +   0.19)

alignment

secondary structure

dotplot

Window 8

Location	14,444,470 – 14,444,578
Length	108
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	71.52
Mean single sequence MFE	-20.65
Consensus MFE	-14.06
Energy contribution	-14.56
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.28
Structure conservation index	0.68
SVM decision value	0.12
SVM RNA-class probability	0.593511
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14444470 108 - 27905053
GCAUACAUACAUAUAUA------------CAAGAAAACAAGAUUUUUCACUUCCCAUACGGAAUGUAAGUAGAAAAAAAGCAGCAAAAGAGCGGGAGUUUUAAGUUUGGGGCGUGAAAGG
.................------------..............(((((((.(((((.((.........((.(........).))...(((((....)))))..)).))))).))))))). ( -19.30)
>DroSec_CAF1 1644 85 - 1
G-------------------------------GAAAACAAGAUUUUUCACUUCCCAUGUGCAGCGUAAG----AAAAAAGCAGCAAAAGAGCGGGAGUUUUGGGUUUGGGGCGUGAAAGG
.-------------------------------...........(((((((.(((((..(((.((.....----......)).)))..(((((....))))).....))))).))))))). ( -21.90)
>DroSim_CAF1 1718 85 - 1
G-------------------------------GAAAACAAGAUUUUUCACUUCCCAUAUGCAGCGUAAG----AAAAAAGCAGCAAAAGAGCGGGAGUUUUGGGUUUGGGGCGUGAAAGG
.-------------------------------...........(((((((.(((((..(((.((.....----......)).)))..(((((....))))).....))))).))))))). ( -22.00)
>DroYak_CAF1 1740 110 - 1
GCGGAUAUACAUAUAUACAUAUAUAUGCUCGGGAAAACAAGAUUUUUCACUUCCAAU--AAAG---AGA----AAAAAAUCAGCCAAAGAGCGGGAGUU-UGAGUUUGGGGCGUGAAAGG
.......................(((((((.(((...(((((....))((((((...--...(---(..----......)).((......)))))))))-))..))).)))))))..... ( -19.40)
>consensus
G_______________________________GAAAACAAGAUUUUUCACUUCCCAUAUGCAGCGUAAG____AAAAAAGCAGCAAAAGAGCGGGAGUUUUGAGUUUGGGGCGUGAAAGG
...........................................(((((((.(((((.........................(((...(((((....)))))..)))))))).))))))). (-14.06 = -14.56 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:17 2006