Locus 2776

Sequence ID	3L_DroMel_CAF1
Location	7,858,857 – 7,858,951
Length	94
Max. P	0.703422

overview

Window 4

Location	7,858,857 – 7,858,951
Length	94
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	79.52
Mean single sequence MFE	-29.79
Consensus MFE	-19.71
Energy contribution	-21.22
Covariance contribution	1.50
Combinations/Pair	1.24
Mean z-score	-1.32
Structure conservation index	0.66
SVM decision value	0.11
SVM RNA-class probability	0.586390
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7858857 94 + 23771897
AUGGAGACGAACCAAGUUUCAUGGCAAAUGUAUGGCCUGGGAAUUGGCCAU---CAACGCUCCGUCUCUUUCGGGCCAACAAUUGCCGUCUCUUUCG---------
..(((((((((......)))..(((((.(((.(((((((..(...(((...---.........)))..)..)))))))))).)))))))))))....--------- ( -34.60)
>DroSec_CAF1 14579 97 + 1
AUGGAGACGAGCCAAGUUUCAUGGCAUAUGUAUGGCCUGGGAAUUGGCCAUCAUCAACGCUCCGUCUCGUUCGGGCCAACAAUCGCCGUCUCUUUCG---------
..(((((((.((((.......))))..(((.((((((........)))))))))....((.(((.......)))))..........)))))))....--------- ( -31.40)
>DroSim_CAF1 14709 97 + 1
AUGGAGACGAGCCAAGUUUCAUGGCAUAUGUAUGGCCUGGGAAUUGGCCAUCAUCAACGCUCCGUCUCUUUCGGGCCAACAAUCGCCGUCUCUUUCG---------
..(((((((.((((.......))))...(((.(((((((..(...(((...............)))..)..)))))))))).....)))))))....--------- ( -32.06)
>DroEre_CAF1 17802 94 + 1
AUGGAGACGAGCCAAGUUUCAUGGCAAAUGUAUGGCCUGGGAAUUGGCCAUCAU---CGCGCCAUCUCUUUCGGGCCAGCAAUACCCAUCUCUUUCG---------
..(((((.(.((((.......))))...(((.(((((((..(..(((((.....---.).))))....)..)))))))))).....).)))))....--------- ( -31.40)
>DroYak_CAF1 7204 94 + 1
AUGGAGACGAGCCAAGUGCCAUGGCAAAUGUAUGGCCUGGGAAUUGGCCAUCAU---CGCUGCAUCUCUUUCGUGCCAGCACUACCCAUCUCUUUCG---------
..(((((.((((((.......))))...((.((((((........)))))))))---)(((((((.......))).))))........)))))....--------- ( -27.60)
>DroAna_CAF1 17566 92 + 1
AUGGAAGCGAGCCAAGUCUCAU------UGUGGGGCCUGGGAAUUGGCCAUC--------CCCGUCUCUUUUUUUCCGCAUCUUGCUGUCUCUGUCGCUGCAUACA
(((..(((((.(..((.(.((.------(((((((...((((..(((.....--------.)))..))))...)))))))...))..).))..)))))).)))... ( -21.70)
>consensus
AUGGAGACGAGCCAAGUUUCAUGGCAAAUGUAUGGCCUGGGAAUUGGCCAUCAU___CGCUCCGUCUCUUUCGGGCCAACAAUAGCCGUCUCUUUCG_________
..(((((((.(((((.(((((.(((.........)))))))).)))))..........((.(((.......)))))..........)))))))............. (-19.71 = -21.22 +   1.50)

alignment

secondary structure

dotplot

Window 5

Location	7,858,857 – 7,858,951
Length	94
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	79.52
Mean single sequence MFE	-31.75
Consensus MFE	-19.29
Energy contribution	-19.98
Covariance contribution	0.70
Combinations/Pair	1.17
Mean z-score	-1.74
Structure conservation index	0.61
SVM decision value	0.36
SVM RNA-class probability	0.703422
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7858857 94 - 23771897
---------CGAAAGAGACGGCAAUUGUUGGCCCGAAAGAGACGGAGCGUUG---AUGGCCAAUUCCCAGGCCAUACAUUUGCCAUGAAACUUGGUUCGUCUCCAU
---------.....((((((((((.(((((((((....)....((.(.((((---.....)))).))).))))).))).)))))..(((......))))))))... ( -32.80)
>DroSec_CAF1 14579 97 - 1
---------CGAAAGAGACGGCGAUUGUUGGCCCGAACGAGACGGAGCGUUGAUGAUGGCCAAUUCCCAGGCCAUACAUAUGCCAUGAAACUUGGCUCGUCUCCAU
---------(....)....(((.(....).))).....(((((((.......(((((((((........)))))).)))..((((.......)))))))))))... ( -31.60)
>DroSim_CAF1 14709 97 - 1
---------CGAAAGAGACGGCGAUUGUUGGCCCGAAAGAGACGGAGCGUUGAUGAUGGCCAAUUCCCAGGCCAUACAUAUGCCAUGAAACUUGGCUCGUCUCCAU
---------(....)....(((.(....).))).....(((((((.......(((((((((........)))))).)))..((((.......)))))))))))... ( -31.50)
>DroEre_CAF1 17802 94 - 1
---------CGAAAGAGAUGGGUAUUGCUGGCCCGAAAGAGAUGGCGCG---AUGAUGGCCAAUUCCCAGGCCAUACAUUUGCCAUGAAACUUGGCUCGUCUCCAU
---------.....(((((((((..........(....)..((((((.(---(((((((((........)))))).))))))))))........)))))))))... ( -34.60)
>DroYak_CAF1 7204 94 - 1
---------CGAAAGAGAUGGGUAGUGCUGGCACGAAAGAGAUGCAGCG---AUGAUGGCCAAUUCCCAGGCCAUACAUUUGCCAUGGCACUUGGCUCGUCUCCAU
---------.....((((((((((((((((((((....).........(---(((((((((........)))))).))))))))..))))))..)))))))))... ( -39.30)
>DroAna_CAF1 17566 92 - 1
UGUAUGCAGCGACAGAGACAGCAAGAUGCGGAAAAAAAGAGACGGG--------GAUGGCCAAUUCCCAGGCCCCACA------AUGAGACUUGGCUCGCUUCCAU
...(((.(((((..(((...((.....))..............(((--------(.(((.......)))..))))...------......)))...)))))..))) ( -20.70)
>consensus
_________CGAAAGAGACGGCAAUUGUUGGCCCGAAAGAGACGGAGCG___AUGAUGGCCAAUUCCCAGGCCAUACAUUUGCCAUGAAACUUGGCUCGUCUCCAU
.........(....).......................(((((((..........((((((........))))))......((((.......)))))))))))... (-19.29 = -19.98 +   0.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:24 2006