Locus 5710

Sequence ID	X_DroMel_CAF1
Location	14,784,211 – 14,784,315
Length	104
Max. P	0.973641

overview

Window 5

Location	14,784,211 – 14,784,315
Length	104
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	74.60
Mean single sequence MFE	-26.92
Consensus MFE	-14.92
Energy contribution	-15.45
Covariance contribution	0.53
Combinations/Pair	1.11
Mean z-score	-2.21
Structure conservation index	0.55
SVM decision value	1.71
SVM RNA-class probability	0.973641
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14784211 104 + 22224390
AAUCACUU-AAAUCACUUUCAAUCAUUGAUCACUGAUCACUUACCGCUGCAGUGCGUCGCUCCCACUUUUUGAAGUCGCGCCACACGUACUCAUG-CAGCGGUACG
........-.................(((((...)))))..(((((((((((((((((((....((((....)))).)))....))))))...))-)))))))).. ( -29.40)
>DroPse_CAF1 19116 79 + 1
----------------------UUAUU-GU---CAAGCACUUACCGCUGCCGUGCGGCUCUCCCACUUCUUGAAGUCCCGCCAGACGUACUCGUG-GAGCGGCACA
----------------------.....-..---..(((.......)))...((((.((((....((((....))))..(((.((.....)).)))-)))).)))). ( -19.90)
>DroSim_CAF1 19562 104 + 1
AAUCACUU-AAAUCACUUUCAAUCCUUGAUCACUGAUCACUUACCGCUGCCGUGCGUCGCUCCCACUUUUUGAAGUCGCGCCACACGUACUCAUG-CAGCGGUACG
........-.................(((((...)))))..(((((((((.(((((((((....((((....)))).)))....))))))....)-)))))))).. ( -27.70)
>DroEre_CAF1 13872 89 + 1
----------------UUUCAACACUUGAUCACUGAUCACUUACCGCUGCAGUGCGUCGCUCCCACUUCUUGAAGUCGCGCCACACGUACUCGUG-CAGCGGCACG
----------------..........(((((...)))))....(((((((((((((((((....((((....)))).)))....))))))...))-)))))).... ( -27.30)
>DroYak_CAF1 13827 105 + 1
AAUCACUUUCAAUCACAUUCAAUCAUUGAUCACUGAUCACUUACCGCUGCGGUGCGUCGCUCCCACUUUUUGAAGUCGCGCCACACGUACUCGUG-CAGCGGUAGA
..........................(((((...))))).((((((((((((((((.(..((.........)).).))))))..(((....))))-))))))))). ( -32.90)
>DroPer_CAF1 19666 81 + 1
----------------------UUAUUAGU---CAAGCACUUACCGCUGCCGUGCGGCUCUCCCACUUCUUGAAGUCUCGCCAGACGUACUCGUGGGAGCGGCANN
----------------------........---...((.....((((......))))(.(((((((........((((....))))......))))))).)))... ( -24.34)
>consensus
________________UUUCAAUCAUUGAUCACUGAUCACUUACCGCUGCCGUGCGUCGCUCCCACUUCUUGAAGUCGCGCCACACGUACUCGUG_CAGCGGCACG
...........................................((((((..(.((((..((..((.....)).))..))))).((((....)))).)))))).... (-14.92 = -15.45 +   0.53)

alignment

secondary structure

dotplot

Window 6

Location	14,784,211 – 14,784,315
Length	104
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	74.60
Mean single sequence MFE	-31.70
Consensus MFE	-19.06
Energy contribution	-19.25
Covariance contribution	0.19
Combinations/Pair	1.11
Mean z-score	-1.83
Structure conservation index	0.60
SVM decision value	1.23
SVM RNA-class probability	0.933199
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14784211 104 - 22224390
CGUACCGCUG-CAUGAGUACGUGUGGCGCGACUUCAAAAAGUGGGAGCGACGCACUGCAGCGGUAAGUGAUCAGUGAUCAAUGAUUGAAAGUGAUUU-AAGUGAUU
..((((((((-((.......(((((.(((..((.(.....).))..))).)))))))))))))))...(((((.((((((.(.......).))))).-.).))))) ( -33.81)
>DroPse_CAF1 19116 79 - 1
UGUGCCGCUC-CACGAGUACGUCUGGCGGGACUUCAAGAAGUGGGAGAGCCGCACGGCAGCGGUAAGUGCUUG---AC-AAUAA----------------------
..((((((((-((((....)))...((((..((((........))))..))))..)).)))))))........---..-.....---------------------- ( -24.90)
>DroSim_CAF1 19562 104 - 1
CGUACCGCUG-CAUGAGUACGUGUGGCGCGACUUCAAAAAGUGGGAGCGACGCACGGCAGCGGUAAGUGAUCAGUGAUCAAGGAUUGAAAGUGAUUU-AAGUGAUU
..((((((((-(.......((((((.(((..((.(.....).))..))).)))))))))))))))...(((((.(..(((.....))).).))))).-........ ( -34.51)
>DroEre_CAF1 13872 89 - 1
CGUGCCGCUG-CACGAGUACGUGUGGCGCGACUUCAAGAAGUGGGAGCGACGCACUGCAGCGGUAAGUGAUCAGUGAUCAAGUGUUGAAA----------------
..((((((((-((.......(((((.(((..((.(.....).))..))).)))))))))))))))..(((((...)))))..........---------------- ( -32.71)
>DroYak_CAF1 13827 105 - 1
UCUACCGCUG-CACGAGUACGUGUGGCGCGACUUCAAAAAGUGGGAGCGACGCACCGCAGCGGUAAGUGAUCAGUGAUCAAUGAUUGAAUGUGAUUGAAAGUGAUU
..((((((((-(..(....)(((((.(((..((.(.....).))..))).))))).)))))))))...(((((.(..(((((.((.....)).))))).).))))) ( -36.80)
>DroPer_CAF1 19666 81 - 1
NNUGCCGCUCCCACGAGUACGUCUGGCGAGACUUCAAGAAGUGGGAGAGCCGCACGGCAGCGGUAAGUGCUUG---ACUAAUAA----------------------
..((((((((((((......((((....))))........))))))..(((....))).))))))........---........---------------------- ( -27.44)
>consensus
CGUACCGCUG_CACGAGUACGUGUGGCGCGACUUCAAAAAGUGGGAGCGACGCACGGCAGCGGUAAGUGAUCAGUGAUCAAUGAUUGAAA________________
..((((((((.((((....))))..(((...((((........))))...)))....))))))))......................................... (-19.06 = -19.25 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:31 2006