Locus 6851

Sequence ID	3R_DroMel_CAF1
Location	18,131,650 – 18,131,782
Length	132
Max. P	0.980414

overview

Window 7

Location	18,131,650 – 18,131,753
Length	103
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	75.48
Mean single sequence MFE	-33.77
Consensus MFE	-22.50
Energy contribution	-22.45
Covariance contribution	-0.05
Combinations/Pair	1.26
Mean z-score	-2.12
Structure conservation index	0.67
SVM decision value	1.86
SVM RNA-class probability	0.980414
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18131650 103 - 27905053
------GUUG-UCGUCGUCGUCGU-CUCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC-CGCUUCUU-GCGCCCAAUU-CCACCCACUU
------...(-(((.(((((....-..)))))))))(((((((((((((......)))))))))).......((((.(((...-.((.....-))))))))).-..)))..... ( -28.80)
>DroVir_CAF1 176880 101 - 1
------GUCC-UUGUUGUUGUCCUCCAGGGCGCGAUGGUGUGUUUUAUUAUCGCAAAUAAAGCGCAAUCAUUGUUGUUGCACC-CACAGCAACAGC-CAACGUGCAACUC----
------....-..(((((.((((....))))(((.((((((((((((((......))))))))))......((((((((....-..))))))))))-)).))))))))..---- ( -34.90)
>DroPse_CAF1 162523 104 - 1
CCAGUAGUCG-UCGUCGUCGUCGU-CUGGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC-CGCUACUU-GCC-GCACUU-CGGCU----C
.((((.....-((((((.((((..-...))))))))))(((((((((((......)))))))))))...))))..(((((...-.)))))..-(((-(.....-)))).----. ( -35.40)
>DroGri_CAF1 177594 101 - 1
------GUCC-UUGUUGUUGUCCUCCUGGGCGCGAUGGUGUGUUUUAUUAUCGCAAAUAAAGCGCAAUCAUUGUUGUUGCAUCGCGCAGCAA-GGC-GAGCGUGCAUCGC----
------(.((-(((((((.((((....))))((((((.(((((((((((......)))))))))))..((....))...)))))))))))))-)))-..(((.....)))---- ( -38.40)
>DroAna_CAF1 155410 102 - 1
UCA---GUUUUCUGUCGUCGUCGU-CUCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC-CGCUACUU-GCUGCCAAUC-CCACC-----
.((---((...((((((.(((((.-..)))))))))))(((((((((((......)))))))))))...))))...(((((..-.((.....-)))))))...-.....----- ( -31.10)
>DroPer_CAF1 188354 98 - 1
CCAGUAGUCG-UC------GUCGU-CUGGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC-CGCUACUU-GCC-GCACUU-CGGCU----C
.((((..(((-((------(.(((-....)))))))))(((((((((((......)))))))))))...))))..(((((...-.)))))..-(((-(.....-)))).----. ( -34.00)
>consensus
______GUCG_UCGUCGUCGUCGU_CUGGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC_CGCUACUU_GCC_CCACUU_CAACU_____
...........((((((.(((((....)))))))))))(((((((((((......))))))))))).........(((((.....)))))........................ (-22.50 = -22.45 +  -0.05)

alignment

secondary structure

dotplot

Window 8

Location	18,131,681 – 18,131,782
Length	101
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	83.69
Mean single sequence MFE	-31.53
Consensus MFE	-23.40
Energy contribution	-23.48
Covariance contribution	0.09
Combinations/Pair	1.12
Mean z-score	-2.13
Structure conservation index	0.74
SVM decision value	0.36
SVM RNA-class probability	0.704129
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18131681 101 - 27905053
CCCCACCCGCCACCGCCCACUC-UUCCAAC--------GUUG-UCGUCGUCGUCGUCUCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGC
........(((((.((......-.......--------....-((((((.(((((...)))))))))))(((((((((((......)))))))))))......)).))))) ( -30.80)
>DroPse_CAF1 162549 109 - 1
CCACAC-CGCCUUGCCACAUUCUUGCAAGCAUCCAGUAGUCG-UCGUCGUCGUCGUCUGGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGC
(((((.-.((.((((.........))))))...((((.....-((((((.((((.....))))))))))(((((((((((......)))))))))))...)))).))))). ( -34.60)
>DroSec_CAF1 160318 101 - 1
CCCCACCCGCCACAGCCCACUC-UUCCAAC--------GUUG-UCCUCGUCGUCGUCUCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGC
........((((((((......-.......--------....-...((((((.(((....)))))))))(((((((((((......)))))))))))......)))))))) ( -32.40)
>DroSim_CAF1 165188 101 - 1
CAUCACCCGCCACAGCCCACUC-UUCCAAC--------GUUG-UCGUCGUCGUCGUCUCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUAUUGUGGC
........(((((((.......-.......--------....-((((((.(((((...)))))))))))(((((((((((......))))))))))).......))))))) ( -31.60)
>DroYak_CAF1 168913 98 - 1
CACCACCCAA--CAG-CAACUC-UGCCAAC--------GUUG-UCGUCGUCGUCGUCUCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGC
.....(((((--(((-......-(((..((--------(..(-(((.(((((......)))))))))..)))((((((((......)))))))))))....)))))).)). ( -31.90)
>DroAna_CAF1 155436 98 - 1
---CACCCGC------CCUGUU-UUCCGGCCCUCA---GUUUUCUGUCGUCGUCGUCUCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGC
---.......------......-.....((((.((---((...((((((.(((((...)))))))))))(((((((((((......)))))))))))...))))..).))) ( -27.90)
>consensus
CCCCACCCGCCACAGCCCACUC_UUCCAAC________GUUG_UCGUCGUCGUCGUCUCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGC
......((((.................................((((((.((((.....))))))))))(((((((((((......))))))))))).........)))). (-23.40 = -23.48 +   0.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:29 2006