Locus 1143

Sequence ID	X_DroMel_CAF1
Location	3,420,123 – 3,420,215
Length	92
Max. P	0.961013

overview

Window 8

Location	3,420,123 – 3,420,215
Length	92
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	85.92
Mean single sequence MFE	-27.93
Consensus MFE	-20.77
Energy contribution	-21.17
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.55
Structure conservation index	0.74
SVM decision value	1.52
SVM RNA-class probability	0.961013
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3420123 92 + 22224390
GACAGCCCAGGCAUAGGCACUUGCUUGCUCCGCACUUUCAGCCUCUC----------------AGGCUGUCAUAAGGCAUUUUCUGCCUUCUCAUCGCCGUGCCAUUA
.........(((((.(((...(((.......)))....(((((....----------------.)))))....((((((.....))))))......)))))))).... ( -28.60)
>DroSec_CAF1 66120 87 + 1
GGCAGCCCAGGCACAGGCACUU----GCUCCGCACUUUCAGCCUCUC----------------AGGCUGUCAUAAGGCAUUUUCUGCCUCCUCAUCGCC-UGCCAUUG
(((.((....))..((((....----............(((((....----------------.))))).....(((((.....))))).......)))-)))).... ( -28.00)
>DroSim_CAF1 68194 95 + 1
GGCAGCCCAGGCACAGGCACUU----GCUCCUCACUUUCAGCCUCUCA--------GGCUCUCAGGCUGUCAUAAGGCAUUUUCUGCCUCCUCAUCGCC-UGCCAUUA
(((.((....))..((((....----............((((((....--------.......)))))).....(((((.....))))).......)))-)))).... ( -27.50)
>DroEre_CAF1 77912 103 + 1
GACAGCCCAGGCACAGGCACUU----GCUCCUCACUUUCAGCCUCUCAUGCUCUCGGGCUCUCAGGCUGUCAUAAGGCAUUUUCUGCCUCCUCAUCGCC-UGCCAUUA
((.((((((((((.((((....----..............))))....))).)).))))).))((((.((.(..(((((.....)))))..).)).)))-)....... ( -29.87)
>DroYak_CAF1 68876 95 + 1
GGCAGCCCAGGCACAGGCACUU----GCUUCCCACUUUCAACCUCUCA--------GGCUCUGAGGCUGUCAUAAGGCAUUUUCUGCCUCCUCAUCGCC-UACCAUUA
((((((((((((..((((....----))))............(.....--------))).))).)))))))...(((((.....)))))..........-........ ( -25.70)
>consensus
GGCAGCCCAGGCACAGGCACUU____GCUCCGCACUUUCAGCCUCUCA________GGCUCU_AGGCUGUCAUAAGGCAUUUUCUGCCUCCUCAUCGCC_UGCCAUUA
.........(((...(((....................((((((...................)))))).....(((((.....))))).......)))..))).... (-20.77 = -21.17 +   0.40)

alignment

secondary structure

dotplot

Window 9

Location	3,420,123 – 3,420,215
Length	92
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	85.92
Mean single sequence MFE	-33.52
Consensus MFE	-25.97
Energy contribution	-25.25
Covariance contribution	-0.72
Combinations/Pair	1.18
Mean z-score	-2.10
Structure conservation index	0.77
SVM decision value	1.06
SVM RNA-class probability	0.909041
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3420123 92 - 22224390
UAAUGGCACGGCGAUGAGAAGGCAGAAAAUGCCUUAUGACAGCCU----------------GAGAGGCUGAAAGUGCGGAGCAAGCAAGUGCCUAUGCCUGGGCUGUC
....(((((.((..((..((((((.....))))))....(((((.----------------....)))))......))..))......)))))...((....)).... ( -29.80)
>DroSec_CAF1 66120 87 - 1
CAAUGGCA-GGCGAUGAGGAGGCAGAAAAUGCCUUAUGACAGCCU----------------GAGAGGCUGAAAGUGCGGAGC----AAGUGCCUGUGCCUGGGCUGCC
....((((-(.(......((((((.....))))))....(((((.----------------....)))))...(..(((.((----....)))))..)...).))))) ( -35.10)
>DroSim_CAF1 68194 95 - 1
UAAUGGCA-GGCGAUGAGGAGGCAGAAAAUGCCUUAUGACAGCCUGAGAGCC--------UGAGAGGCUGAAAGUGAGGAGC----AAGUGCCUGUGCCUGGGCUGCC
....((((-(.(.(.(.(.(((((.......((((((..((((((.......--------....))))))...))))))...----...))))).).).).).))))) ( -34.52)
>DroEre_CAF1 77912 103 - 1
UAAUGGCA-GGCGAUGAGGAGGCAGAAAAUGCCUUAUGACAGCCUGAGAGCCCGAGAGCAUGAGAGGCUGAAAGUGAGGAGC----AAGUGCCUGUGCCUGGGCUGUC
......((-(((......((((((.....))))))......)))))..(((((.((.((((...((((.....((.....))----....)))))))))))))))... ( -38.30)
>DroYak_CAF1 68876 95 - 1
UAAUGGUA-GGCGAUGAGGAGGCAGAAAAUGCCUUAUGACAGCCUCAGAGCC--------UGAGAGGUUGAAAGUGGGAAGC----AAGUGCCUGUGCCUGGGCUGCC
....((((-(.(.(.(.(.(((((.....((((((((..(((((((......--------...)))))))...)))))..))----)..))))).).).).).))))) ( -29.90)
>consensus
UAAUGGCA_GGCGAUGAGGAGGCAGAAAAUGCCUUAUGACAGCCU_AGAGCC________UGAGAGGCUGAAAGUGAGGAGC____AAGUGCCUGUGCCUGGGCUGCC
....((((.((((.....((((((.....))))))....((((((...................))))))...................))))...((....)))))) (-25.97 = -25.25 +  -0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:24 2006