Locus 5045

Sequence ID	3R_DroMel_CAF1
Location	13,287,427 – 13,287,532
Length	105
Max. P	0.740004

overview

Window 3

Location	13,287,427 – 13,287,532
Length	105
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	81.65
Mean single sequence MFE	-29.85
Consensus MFE	-20.80
Energy contribution	-21.47
Covariance contribution	0.67
Combinations/Pair	1.19
Mean z-score	-1.82
Structure conservation index	0.70
SVM decision value	0.44
SVM RNA-class probability	0.739165
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13287427 105 + 27905053
AGUUG-CU------------UGGCAACAUUACGCCAAUUCAAUUGAUUUGCUCUUCGAGCGCAGUGCGUUUUUAAGCGCAGUGCAAAUAAAACUAAUGCAAUGUGCUCUCUGA-AAAGU
(((((-.(------------((((........)))))..))))).....(((.((((((((((.((((((....)))))).((((...........)))).)))))))...))-).))) ( -28.40)
>DroPse_CAF1 59300 109 + 1
AGUUG-GCU-------GG-CUGGCAACAUUGCGCCAAUUCAAUUGAUUUGCUUCUGAAGUGCAAUGCGUUUUUGAGCGCUGUGCAAAUAAAACUAAUGCAAUGUGUGCCCCAA-AAACU
((((.-..(-------((-..(((((((((((((.((.((....)).))))........((((..(((((....)))))..))))............))))))).))))))).-.)))) ( -31.10)
>DroGri_CAF1 41460 118 + 1
AGUUG-CCUUGGAUGGGGCUUGGCAACAUUGCGCAAAUUCAAUUGAUUUGCCUCUGAAGUGCAGUGCGUUUUUAAGCGCUCCACAAAUACAACUAAUGCAAUGCAUACCCCAAAAAACU
.....-.......(((((..((....(((((((((((((.....))))))).......(((.(((((........))))).))).............))))))))..)))))....... ( -33.30)
>DroWil_CAF1 43744 106 + 1
AGUUAUCC------------UGGCAACAUUGCGUCAAUUCAAUUGAUUUGCUUUUGAAGUGCAAUGCGUUUUUAAGCGCUGCACAAAUAAAACUAAUGCAAUGUAUGCCCCCA-GAAGU
........------------.(((((((((((((...(((((..(.....)..)))))(((((..(((((....))))))))))...........))))))))).))))....-..... ( -31.10)
>DroAna_CAF1 62522 105 + 1
AGUUG-CC------------UGGUAACAUUGCGCCAAUUCAAUUGAUUUGACUUUCGAGUGCAAUGCGUUUUUAAGCGCUGCGCAAACAAAACUAAUGCACUGUGUGCCCUGA-AAGGA
.....-((------------((((((((.((((.(((.((....)).)))........(((((..(((((....))))))))))............)))).))).))))....-.))). ( -24.70)
>DroPer_CAF1 53286 109 + 1
AGUUG-GCU-------GG-CUGGCAACAUUGCGCCAAUUCAAUUGAUUUGCUUCUGAAGUGCAAUGCGUUUUUGAGCGCUGUGCAAAUAAAACUAAUGCAAUGUGUGCCCCGA-AAACU
((((.-.(.-------((-..(((((((((((((.((.((....)).))))........((((..(((((....)))))..))))............))))))).))))))).-.)))) ( -30.50)
>consensus
AGUUG_CC____________UGGCAACAUUGCGCCAAUUCAAUUGAUUUGCUUCUGAAGUGCAAUGCGUUUUUAAGCGCUGCGCAAAUAAAACUAAUGCAAUGUGUGCCCCGA_AAACU
.....................((((((((((((.(((.((....)).)))........(((((..(((((....))))))))))............)))))))).)))).......... (-20.80 = -21.47 +   0.67)

alignment

secondary structure

dotplot

Window 4

Location	13,287,427 – 13,287,532
Length	105
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	81.65
Mean single sequence MFE	-29.18
Consensus MFE	-19.94
Energy contribution	-19.28
Covariance contribution	-0.66
Combinations/Pair	1.39
Mean z-score	-1.88
Structure conservation index	0.68
SVM decision value	0.45
SVM RNA-class probability	0.740004
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13287427 105 - 27905053
ACUUU-UCAGAGAGCACAUUGCAUUAGUUUUAUUUGCACUGCGCUUAAAAACGCACUGCGCUCGAAGAGCAAAUCAAUUGAAUUGGCGUAAUGUUGCCA------------AG-CAACU
.....-.....(.(((((((((.(((((((.(((.(((.((((........)))).)))((((...)))).....))).))))))).)))))).)))).------------..-..... ( -26.20)
>DroPse_CAF1 59300 109 - 1
AGUUU-UUGGGGCACACAUUGCAUUAGUUUUAUUUGCACAGCGCUCAAAAACGCAUUGCACUUCAGAAGCAAAUCAAUUGAAUUGGCGCAAUGUUGCCAG-CC-------AGC-CAACU
((((.-((((((((.(((((((.(((((((.((((((...(((........))).(((.....)))..)))))).....))))))).)))))))))))..-))-------)).-.)))) ( -28.90)
>DroGri_CAF1 41460 118 - 1
AGUUUUUUGGGGUAUGCAUUGCAUUAGUUGUAUUUGUGGAGCGCUUAAAAACGCACUGCACUUCAGAGGCAAAUCAAUUGAAUUUGCGCAAUGUUGCCAAGCCCCAUCCAAGG-CAACU
.(((((.((((((..(((((((.............(((.((.((........)).)).))).......(((((((....).)))))))))))))......))))))...))))-).... ( -35.10)
>DroWil_CAF1 43744 106 - 1
ACUUC-UGGGGGCAUACAUUGCAUUAGUUUUAUUUGUGCAGCGCUUAAAAACGCAUUGCACUUCAAAAGCAAAUCAAUUGAAUUGACGCAAUGUUGCCA------------GGAUAACU
...((-(...((((.(((((((....(((((....((((((.((........)).))))))....)))))...(((((...))))).))))))))))).------------)))..... ( -32.30)
>DroAna_CAF1 62522 105 - 1
UCCUU-UCAGGGCACACAGUGCAUUAGUUUUGUUUGCGCAGCGCUUAAAAACGCAUUGCACUCGAAAGUCAAAUCAAUUGAAUUGGCGCAAUGUUACCA------------GG-CAACU
.....-...((..(((...(((.....(((((..((((..(((........)))..))))..)))))(((((.((....)).)))))))).)))..))(------------(.-...)) ( -25.40)
>DroPer_CAF1 53286 109 - 1
AGUUU-UCGGGGCACACAUUGCAUUAGUUUUAUUUGCACAGCGCUCAAAAACGCAUUGCACUUCAGAAGCAAAUCAAUUGAAUUGGCGCAAUGUUGCCAG-CC-------AGC-CAACU
.....-..((((((.(((((((.(((((((.((((((...(((........))).(((.....)))..)))))).....))))))).)))))))))))..-))-------...-..... ( -27.20)
>consensus
ACUUU_UCGGGGCACACAUUGCAUUAGUUUUAUUUGCACAGCGCUUAAAAACGCAUUGCACUUCAAAAGCAAAUCAAUUGAAUUGGCGCAAUGUUGCCA____________GG_CAACU
..........((((.(((((((....(((((...((((..(((........)))..)))).....)))))...(((((...))))).)))))))))))..................... (-19.94 = -19.28 +  -0.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:56 2006