Locus 1690

Sequence ID	2L_DroMel_CAF1
Location	4,611,195 – 4,611,322
Length	127
Max. P	0.756651

overview

Window 8

Location	4,611,195 – 4,611,290
Length	95
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	88.22
Mean single sequence MFE	-22.65
Consensus MFE	-19.25
Energy contribution	-19.45
Covariance contribution	0.20
Combinations/Pair	1.16
Mean z-score	-1.87
Structure conservation index	0.85
SVM decision value	0.49
SVM RNA-class probability	0.756651
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4611195 95 - 22407834
UUCAAAGAGCUA--GCGAAAUUCUGCGUCGCAGAAAAUUGCAAACAAAUGUUUGCCGUGACGCCUGAAUGGCCACAGCCUUGAAUAUAAAUCACAAA
(((((.(.(((.--((...((((.(((((((........((((((....)))))).)))))))..)))).))...)))))))))............. ( -25.10)
>DroSec_CAF1 48585 95 - 1
UUCAAAGAGCUA--GCGAAAUUCUGCGUCGCAGAAAAUUGCAAACAAAUGUUUGCCGUGACGCCUGAAUGGCCACAGCCUUGAAUAUAAAUCACAAA
(((((.(.(((.--((...((((.(((((((........((((((....)))))).)))))))..)))).))...)))))))))............. ( -25.10)
>DroSim_CAF1 46230 95 - 1
UUCAAAGAGCUA--GCGAAAUUCUGCGUCGCAGAAAAUUGCAAACAAAUGUUUGCCGUGACGCCUGAAUGGCCACAGCCUUGAAUAUAAAUCACAAA
(((((.(.(((.--((...((((.(((((((........((((((....)))))).)))))))..)))).))...)))))))))............. ( -25.10)
>DroEre_CAF1 51210 95 - 1
UUCAAAGAGCUA--ACGAAAUUCUGCGUCGCAAAAAAUUGCAAACAAAUGUUUGCCGUGACGCCUGAAUGGCCACAGCCUUGAAUUUAAAUCACAAA
(((((.(.(((.--..(..((((.(((((((........((((((....)))))).)))))))..))))..)...)))))))))............. ( -25.00)
>DroAna_CAF1 49180 95 - 1
UUCAAAGGUUUA--UCGAAAUUUUGCAACGCAGGGAGUUGCAAACAAAUGUUUGCCGUGAUGCCUGAAUGACUACAGCCUUGAAUAUAAAUCAGAUG
(((((.((((..--.....((((.(((.(((........((((((....)))))).))).)))..))))......)))))))))............. ( -17.32)
>DroPer_CAF1 54018 97 - 1
UUCAAAAGAGUAAUUCGCAAAACAGCGUCGCAGAGAAUUGCAAGCAAAUGUUUGCCGUAAUGCCUGAAUGGCCACAGCCUUGAAUUUAAAUCAGUAA
(((((.......((((((......))...(((....((.((((((....)))))).))..)))..))))(((....))))))))............. ( -18.30)
>consensus
UUCAAAGAGCUA__GCGAAAUUCUGCGUCGCAGAAAAUUGCAAACAAAUGUUUGCCGUGACGCCUGAAUGGCCACAGCCUUGAAUAUAAAUCACAAA
(((((..............((((.(((((((........((((((....)))))).)))))))..))))(((....))))))))............. (-19.25 = -19.45 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	4,611,213 – 4,611,322
Length	109
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	88.98
Mean single sequence MFE	-30.95
Consensus MFE	-25.72
Energy contribution	-26.70
Covariance contribution	0.98
Combinations/Pair	1.22
Mean z-score	-1.96
Structure conservation index	0.83
SVM decision value	0.34
SVM RNA-class probability	0.697316
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4611213 109 + 22407834
GGCUGUGGCCAUUCAGGCGUCACGGCAAACAUUUGUUUGCAAUUUUCUGCGACGCAGAAUUUCGCUAGCUCUUUGAAAAGAUUUGCCGAAAAUUAAACAAAUGCGG-----ACA
.(((((((((.....)))..)))))).......((((((((...((((((...))))))(((((.(((.((((....)))).))).)))))..........)))))-----))) ( -33.00)
>DroSec_CAF1 48603 109 + 1
GGCUGUGGCCAUUCAGGCGUCACGGCAAACAUUUGUUUGCAAUUUUCUGCGACGCAGAAUUUCGCUAGCUCUUUGAAAAGAUUUACCGAAAAUUAAACGAAUGCGG-----ACA
.(((((((((.....)))..)))))).......((((((((...((((((...))))))(((((.(((.((((....)))).))).)))))..........)))))-----))) ( -33.30)
>DroSim_CAF1 46248 109 + 1
GGCUGUGGCCAUUCAGGCGUCACGGCAAACAUUUGUUUGCAAUUUUCUGCGACGCAGAAUUUCGCUAGCUCUUUGAAAAGAUUUACCGAAAAUUAAACGAAUGCGG-----ACA
.(((((((((.....)))..)))))).......((((((((...((((((...))))))(((((.(((.((((....)))).))).)))))..........)))))-----))) ( -33.30)
>DroEre_CAF1 51228 109 + 1
GGCUGUGGCCAUUCAGGCGUCACGGCAAACAUUUGUUUGCAAUUUUUUGCGACGCAGAAUUUCGUUAGCUCUUUGAAAAGAUUUACCGAAAAUUAAACGAAUGCGG-----ACA
.(((((((((.....)))..)))))).......((((((((...((((((...))))))(((((.(((.((((....)))).))).)))))..........)))))-----))) ( -30.70)
>DroYak_CAF1 51833 109 + 1
GGCUGUGGCCAUUCAGGCGUCACGGCAAACAUUUGUUUGCCAUUUUCUGAGACGCAGAAUUUUGCUAGCUCUUUGAAAAGAUUUACCGAAAAUUAAACGAAUGCGG-----ACA
.(((((((((.....)))..))))))...((((((((((..((((((.(((..((((....))))...)))(((....)))......))))))))))))))))...-----... ( -29.40)
>DroAna_CAF1 49198 114 + 1
GGCUGUAGUCAUUCAGGCAUCACGGCAAACAUUUGUUUGCAACUCCCUGCGUUGCAAAAUUUCGAUAAACCUUUGAAAAAAUCUCCCAAAAACCAAAUGGAAACGUGUUCCGCA
(((....))).....((...((((.....((((((((((((((.......)))))))).((((((.......))))))...............))))))....))))..))... ( -26.00)
>consensus
GGCUGUGGCCAUUCAGGCGUCACGGCAAACAUUUGUUUGCAAUUUUCUGCGACGCAGAAUUUCGCUAGCUCUUUGAAAAGAUUUACCGAAAAUUAAACGAAUGCGG_____ACA
.(((((((((.....)))..))))))...((((((((((.....((((((...))))))(((((.(((.((((....)))).))).)))))..))))))))))........... (-25.72 = -26.70 +   0.98)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:28 2006