Locus 1629

Sequence ID	3L_DroMel_CAF1
Location	4,754,198 – 4,754,296
Length	98
Max. P	0.998705

overview

Window 1

Location	4,754,198 – 4,754,296
Length	98
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	90.22
Mean single sequence MFE	-25.68
Consensus MFE	-22.22
Energy contribution	-22.92
Covariance contribution	0.70
Combinations/Pair	1.03
Mean z-score	-2.34
Structure conservation index	0.87
SVM decision value	1.50
SVM RNA-class probability	0.959368
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4754198 98 + 23771897
UUUGCCGGCACAUGCUGUUGCUGCAG----AACUGCAGCUGCGACAAAUAUUUAUUCAUAUUCAUGGGUAACAAACACAAUUUUUGUUUAUUUAUCGCGCCU------------------
......(((..........((((((.----...)))))).((((.(((((..(((((((....)))))))(((((.......))))).))))).))))))).------------------ ( -27.00)
>DroSec_CAF1 17623 97 + 1
UUUGCCGGCACAUGCUGUUGCUGCA-----AACUGCAGCUGCGACAAAUAUUUAUUCAUAUUCAUGGGUAACAAACACAAUUUUUGUUUAUUUAUCGCGCCU------------------
......(((..........(((((.-----....))))).((((.(((((..(((((((....)))))))(((((.......))))).))))).))))))).------------------ ( -25.50)
>DroSim_CAF1 15004 97 + 1
UUUGCCGGCACAUGCUGUUGCUGCA-----AACUGCAACUGCGACAAAUAUUUAUUCAUAUUCAUGGGUAACAAACACAAUUUUUGUUUAUUUAUCGCGCCU------------------
......(((.......(((((....-----....))))).((((.(((((..(((((((....)))))))(((((.......))))).))))).))))))).------------------ ( -23.30)
>DroEre_CAF1 6895 97 + 1
UUUGCCGGCACAUGCUGUUGCUGCA-----AACUGCAGCUGCUACAAAUAUUUAUUCAUAUUCAUGGGUAACAAACACAAUUUUUGUUUAUUUAUCGCGCCU------------------
......(((.(.((..((.(((((.-----....))))).))..)).....((((((((....)))))))).(((((.......))))).......).))).------------------ ( -21.20)
>DroYak_CAF1 13306 97 + 1
UUUGCCGGCACAUGCUGUUGCUGCA-----AACUGCAGCUGCGACAAAUAUUUAUUCAUAUUCAUGGGUAACAAACACAAUUUUUGUUUAUUUAUCGCGCCU------------------
......(((..........(((((.-----....))))).((((.(((((..(((((((....)))))))(((((.......))))).))))).))))))).------------------ ( -25.50)
>DroAna_CAF1 7208 119 + 1
UUUGCCGCCACAUGCUGUUGCUGCAACGCAAACUGCAGCUGCGACAAAUAUUUAUUCAUAUUCAUGG-AAGCAAAUACAAUUUUUGUUUAUUUAUCGCGCCUCACUGGGAUGGGGCUGUG
...((.(((.(((.((...((((((........)))))).((((.(((((....(((((....))))-)((((((.......))))))))))).))))........)).))).))).)). ( -31.60)
>consensus
UUUGCCGGCACAUGCUGUUGCUGCA_____AACUGCAGCUGCGACAAAUAUUUAUUCAUAUUCAUGGGUAACAAACACAAUUUUUGUUUAUUUAUCGCGCCU__________________
......(((..........((((((........)))))).((((.(((((..(((((((....)))))))(((((.......))))).))))).)))))))................... (-22.22 = -22.92 +   0.70)

alignment

secondary structure

dotplot

Window 2

Location	4,754,198 – 4,754,296
Length	98
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	90.22
Mean single sequence MFE	-29.22
Consensus MFE	-26.30
Energy contribution	-26.52
Covariance contribution	0.22
Combinations/Pair	1.07
Mean z-score	-3.13
Structure conservation index	0.90
SVM decision value	3.19
SVM RNA-class probability	0.998705
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4754198 98 - 23771897
------------------AGGCGCGAUAAAUAAACAAAAAUUGUGUUUGUUACCCAUGAAUAUGAAUAAAUAUUUGUCGCAGCUGCAGUU----CUGCAGCAACAGCAUGUGCCGGCAAA
------------------.(((((((((((((........(..((((..(.....)..))))..).....)))))))))).((((((...----.))))))..........)))...... ( -30.22)
>DroSec_CAF1 17623 97 - 1
------------------AGGCGCGAUAAAUAAACAAAAAUUGUGUUUGUUACCCAUGAAUAUGAAUAAAUAUUUGUCGCAGCUGCAGUU-----UGCAGCAACAGCAUGUGCCGGCAAA
------------------.(((((((((((((........(..((((..(.....)..))))..).....)))))))))).(((((....-----.)))))..........)))...... ( -28.72)
>DroSim_CAF1 15004 97 - 1
------------------AGGCGCGAUAAAUAAACAAAAAUUGUGUUUGUUACCCAUGAAUAUGAAUAAAUAUUUGUCGCAGUUGCAGUU-----UGCAGCAACAGCAUGUGCCGGCAAA
------------------.(((((((((((((........(..((((..(.....)..))))..).....))))))))((.(((((....-----....))))).))..)))))...... ( -26.52)
>DroEre_CAF1 6895 97 - 1
------------------AGGCGCGAUAAAUAAACAAAAAUUGUGUUUGUUACCCAUGAAUAUGAAUAAAUAUUUGUAGCAGCUGCAGUU-----UGCAGCAACAGCAUGUGCCGGCAAA
------------------.((((((...((((((((.......))))))))....(..(((((......)))))..).((.(((((....-----.)))))....)).))))))...... ( -26.40)
>DroYak_CAF1 13306 97 - 1
------------------AGGCGCGAUAAAUAAACAAAAAUUGUGUUUGUUACCCAUGAAUAUGAAUAAAUAUUUGUCGCAGCUGCAGUU-----UGCAGCAACAGCAUGUGCCGGCAAA
------------------.(((((((((((((........(..((((..(.....)..))))..).....)))))))))).(((((....-----.)))))..........)))...... ( -28.72)
>DroAna_CAF1 7208 119 - 1
CACAGCCCCAUCCCAGUGAGGCGCGAUAAAUAAACAAAAAUUGUAUUUGCUU-CCAUGAAUAUGAAUAAAUAUUUGUCGCAGCUGCAGUUUGCGUUGCAGCAACAGCAUGUGGCGGCAAA
....(((((((....(((..(.((((((((((........(..(((((....-....)))))..).....)))))))))).(((((((......)))))))..)..))))))).)))... ( -34.72)
>consensus
__________________AGGCGCGAUAAAUAAACAAAAAUUGUGUUUGUUACCCAUGAAUAUGAAUAAAUAUUUGUCGCAGCUGCAGUU_____UGCAGCAACAGCAUGUGCCGGCAAA
...................(((((((((((((........(..(((((((.....)))))))..).....)))))))))).((((((........))))))..........)))...... (-26.30 = -26.52 +   0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:21 2006