Locus 2390

Sequence ID 3R_DroMel_CAF1
Location 6,743,300 – 6,743,416
Length 116
Max. P 0.790388
window3861 window3862

overview

Window 1

Location 6,743,300 – 6,743,416
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 76.98
Mean single sequence MFE -24.00
Consensus MFE -14.41
Energy contribution -17.35
Covariance contribution 2.94
Combinations/Pair 1.10
Mean z-score -1.92
Structure conservation index 0.60
SVM decision value 0.58
SVM RNA-class probability 0.790388
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6743300 116 + 27905053
GUUUGGAAAUUGGCUAGAGUUACUUUUUAAUAGAAGUGCCAUUAUGCCAAAGAGUACAAAAUGAAAUGGGAAAUGGGUUCCGUAAAUCGUUUUGUUUUUCGAAUAUUUAUUAUGUU----
(((((((((((((((((.(.(((((((....))))))).).))).))))).....(((((((((.((((((......))))))...))))))))))))))))))............---- ( -28.80)
>DroSec_CAF1 8078 90 + 1
GUUUGGAAAUUGGCAAGAGUUACUUUUUAAUAAAAGUGCAAUUAUGCCAAAGAGUACAAAAUGAAAUGGGAAAUAGGAUCCGUAAAUCGU------------------------------
.((((....((((((.((..(((((((....)))))))...)).))))))......))))((((.(((((........)))))...))))------------------------------ ( -16.00)
>DroSim_CAF1 12417 116 + 1
GUUUGGAAAUUGGCAAGAGUUACUUUUUAAUAAAAGUGCAAUUAUGCCAAAGAGUACAAAAUGAAAUGGGAAAUAGGAUCCUUAAAUCGUUUUGUAUAUUGAAUAAUUAUUAUGUU----
(((..(...((((((.((..(((((((....)))))))...)).))))))...(((((((((((...((((.......))))....))))))))))).)..)))............---- ( -28.20)
>DroYak_CAF1 3405 120 + 1
GUUUGGAAAUUGGCAAGAGUUGCUUUUUAAUAAAAGUAAAAUUAUGCCAAAGAGUACAAAAUAUGACGGGAAAUGGGCUGCAGAAAUCGUUUUACAUAUGGCAUCUAUAUUAUUUCGCAC
...((((((((((((....((((((((....)))))))).....))))))(((((.....(((((....(((((((.(....)...))))))).))))).)).)))......)))).)). ( -23.00)
>consensus
GUUUGGAAAUUGGCAAGAGUUACUUUUUAAUAAAAGUGCAAUUAUGCCAAAGAGUACAAAAUGAAAUGGGAAAUAGGAUCCGUAAAUCGUUUUGUAUAU_GAAUAUUUAUUAUGUU____
.........((((((.((..(((((((....)))))))...)).))))))...(((((((((((....(((.......))).....)))))))))))....................... (-14.41 = -17.35 +   2.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 6,743,300 – 6,743,416
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 76.98
Mean single sequence MFE -16.45
Consensus MFE -8.22
Energy contribution -8.97
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.24
Structure conservation index 0.50
SVM decision value 0.33
SVM RNA-class probability 0.693488
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6743300 116 - 27905053
----AACAUAAUAAAUAUUCGAAAAACAAAACGAUUUACGGAACCCAUUUCCCAUUUCAUUUUGUACUCUUUGGCAUAAUGGCACUUCUAUUAAAAAGUAACUCUAGCCAAUUUCCAAAC
----................((((.((((((.((.....((((.....))))....)).)))))).....(((((.((..(..((((........))))..)..)))))))))))..... ( -16.70)
>DroSec_CAF1 8078 90 - 1
------------------------------ACGAUUUACGGAUCCUAUUUCCCAUUUCAUUUUGUACUCUUUGGCAUAAUUGCACUUUUAUUAAAAAGUAACUCUUGCCAAUUUCCAAAC
------------------------------..((.....(((.......)))....))..((((......((((((.......((((((....))))))......))))))....)))). ( -12.72)
>DroSim_CAF1 12417 116 - 1
----AACAUAAUAAUUAUUCAAUAUACAAAACGAUUUAAGGAUCCUAUUUCCCAUUUCAUUUUGUACUCUUUGGCAUAAUUGCACUUUUAUUAAAAAGUAACUCUUGCCAAUUUCCAAAC
----....................(((((((.((.....(((.......)))....)).)))))))....((((((.......((((((....))))))......))))))......... ( -17.92)
>DroYak_CAF1 3405 120 - 1
GUGCGAAAUAAUAUAGAUGCCAUAUGUAAAACGAUUUCUGCAGCCCAUUUCCCGUCAUAUUUUGUACUCUUUGGCAUAAUUUUACUUUUAUUAAAAAGCAACUCUUGCCAAUUUCCAAAC
((((((((((....(((((.....((((..........))))...))))).......))))))))))...((((((........(((((....))))).......))))))......... ( -18.46)
>consensus
____AACAUAAUAAAUAUUC_AUAUACAAAACGAUUUACGGAUCCCAUUUCCCAUUUCAUUUUGUACUCUUUGGCAUAAUUGCACUUUUAUUAAAAAGUAACUCUUGCCAAUUUCCAAAC
............................................................((((......((((((.......((((((....))))))......))))))....)))). ( -8.22 =  -8.97 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:15 2006