Locus 6638

Sequence ID	X_DroMel_CAF1
Location	16,556,776 – 16,556,883
Length	107
Max. P	0.950978

overview

Window 1

Location	16,556,776 – 16,556,883
Length	107
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	79.28
Mean single sequence MFE	-37.30
Consensus MFE	-23.94
Energy contribution	-24.47
Covariance contribution	0.53
Combinations/Pair	1.19
Mean z-score	-1.40
Structure conservation index	0.64
SVM decision value	0.12
SVM RNA-class probability	0.592827
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16556776 107 + 22224390
ACCGAGCAGCACGACAAGGGCAUCGUGGAUAUGGUG---GCCACCACCGGAGACUCCAACCGGGACGCCAUGCUCAUGCUGCUCCAGAUGAUGUGAGUAUACA------CAUUUGA
...((((((((.((((..(((.((.(((....((((---(...)))))((.....))..))).)).))).)).)).))))))))((((((.((((....))))------)))))). ( -44.00)
>DroSec_CAF1 12308 110 + 1
ACCGAGCAGCACGACAAGGGCAUCGUGGAUAUGAUG---GGCACCACCGGAGACUC---CCGGGACGCCAUGCUCAUGCUGCUCCAGAUUAUGUGAGUAUGCAUAACAACAUUUGA
...((((((((.((((....((((((....))))))---(((..(.((((......---)))))..))).)).)).))))))))((((((((((......))))).....))))). ( -36.70)
>DroSim_CAF1 9656 110 + 1
ACCGAGCAGCACGACAAGGGCAUCGUGGAUAUGAUG---GGCACCACCGGAGACUC---CCGGGACGCCAUGCUCAUGCUGCUCCAGAUGAUGUGAGUAUACAUGACACCAUUUUA
...((((((((.((((....((((((....))))))---(((..(.((((......---)))))..))).)).)).)))))))).(((((.(((.(.......).))).))))).. ( -36.70)
>DroEre_CAF1 10873 99 + 1
AGCGAACAGCACGACAAGGGCAUUGUGGAUAUGGUG---GGCGCCACCGGGGACUCCACCCGGGACACCAUGCUCAUGCUGCUCCAGAUGAUGUGAGUACAC--------------
.((.....)).......((((((.(((....((((.---...))))(((((.......)))))..))).)))))).((.(((((((.....)).))))))).-------------- ( -34.70)
>DroYak_CAF1 12245 99 + 1
AGCGAGCAGCACGACAAGGGCAUCGUGGAUAUGGUG---GGCGCCACUGGAGACGCCUCCCGGGACACCAUGCUCAUGCUGCUCCAGAUGAUGUGAGUAUAU--------------
.(.((((((((......((((((.(((....(((..---((((.(......).))))..)))...))).)))))).))))))))).................-------------- ( -36.90)
>DroAna_CAF1 16907 110 + 1
GCAGAUCAGCACGACAAGGGCAUCGUGGACAUUGUGCGGGGAGUGACGGGGGAUGCGCCACGGGACACCAUACUCAUGAUGCUCCAAAUGCUGUAAGUAUGCAUA------UUUCA
(((...(((((......(((((((((((.((((.(.((........)).).))))..))))((....))........)))))))....)))))......)))...------..... ( -34.80)
>consensus
ACCGAGCAGCACGACAAGGGCAUCGUGGAUAUGGUG___GGCACCACCGGAGACUCC_CCCGGGACACCAUGCUCAUGCUGCUCCAGAUGAUGUGAGUAUACA________UUU_A
...((((((((......((((((.(((....(((((.....)))))((((.........))))..))).)))))).))))))))................................ (-23.94 = -24.47 +   0.53)

alignment

secondary structure

dotplot

Window 2

Location	16,556,776 – 16,556,883
Length	107
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	79.28
Mean single sequence MFE	-40.35
Consensus MFE	-28.11
Energy contribution	-28.94
Covariance contribution	0.83
Combinations/Pair	1.12
Mean z-score	-2.35
Structure conservation index	0.70
SVM decision value	1.41
SVM RNA-class probability	0.950978
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16556776 107 - 22224390
UCAAAUG------UGUAUACUCACAUCAUCUGGAGCAGCAUGAGCAUGGCGUCCCGGUUGGAGUCUCCGGUGGUGGC---CACCAUAUCCACGAUGCCCUUGUCGUGCUGCUCGGU
....(((------((......)))))......(((((((((((.((.((((((..((..((.....))(((((...)---))))....))..))))))..)))))))))))))... ( -44.60)
>DroSec_CAF1 12308 110 - 1
UCAAAUGUUGUUAUGCAUACUCACAUAAUCUGGAGCAGCAUGAGCAUGGCGUCCCGG---GAGUCUCCGGUGGUGCC---CAUCAUAUCCACGAUGCCCUUGUCGUGCUGCUCGGU
.........((((((........))))))...(((((((((((.((.((((((.(((---(....))))((((....---........))))))))))..)))))))))))))... ( -41.20)
>DroSim_CAF1 9656 110 - 1
UAAAAUGGUGUCAUGUAUACUCACAUCAUCUGGAGCAGCAUGAGCAUGGCGUCCCGG---GAGUCUCCGGUGGUGCC---CAUCAUAUCCACGAUGCCCUUGUCGUGCUGCUCGGU
....(((((((...(....)..)))))))...(((((((((((.((.((((((.(((---(....))))((((....---........))))))))))..)))))))))))))... ( -43.40)
>DroEre_CAF1 10873 99 - 1
--------------GUGUACUCACAUCAUCUGGAGCAGCAUGAGCAUGGUGUCCCGGGUGGAGUCCCCGGUGGCGCC---CACCAUAUCCACAAUGCCCUUGUCGUGCUGUUCGCU
--------------(((....)))........((((((((((((((((((((((((((.......))))).))))))---.............)))).....)))))))))))... ( -38.51)
>DroYak_CAF1 12245 99 - 1
--------------AUAUACUCACAUCAUCUGGAGCAGCAUGAGCAUGGUGUCCCGGGAGGCGUCUCCAGUGGCGCC---CACCAUAUCCACGAUGCCCUUGUCGUGCUGCUCGCU
--------------..................(((((((((((((((.(((....((..((((((......))))))---..)).....))).)))).....)))))))))))... ( -42.70)
>DroAna_CAF1 16907 110 - 1
UGAAA------UAUGCAUACUUACAGCAUUUGGAGCAUCAUGAGUAUGGUGUCCCGUGGCGCAUCCCCCGUCACUCCCCGCACAAUGUCCACGAUGCCCUUGUCGUGCUGAUCUGC
.....------............((((((..((.(((((.((..(((.((((...((((((.......)))))).....)))).)))..)).))))))).....))))))...... ( -31.70)
>consensus
U_AAA________UGUAUACUCACAUCAUCUGGAGCAGCAUGAGCAUGGCGUCCCGGG_GGAGUCUCCGGUGGCGCC___CACCAUAUCCACGAUGCCCUUGUCGUGCUGCUCGGU
................................(((((((((((.((.((((((.(((.........)))((((...............))))))))))..)))))))))))))... (-28.11 = -28.94 +   0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:18:53 2006