Locus 1239

Sequence ID	X_DroMel_CAF1
Location	3,692,570 – 3,692,661
Length	91
Max. P	0.983669

overview

Window 3

Location	3,692,570 – 3,692,661
Length	91
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	86.98
Mean single sequence MFE	-38.00
Consensus MFE	-28.06
Energy contribution	-27.90
Covariance contribution	-0.16
Combinations/Pair	1.15
Mean z-score	-3.00
Structure conservation index	0.74
SVM decision value	1.95
SVM RNA-class probability	0.983669
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3692570 91 + 22224390
CAUUGAUCUGCCAGUCAUCGCUGUUU-------UCGCUGCUGGAUUCUCGGCUUAAGACAUCUGCAGCAUGGAGUGCAAGCUGCUGGUGGCAGGUUGC
....((((((((.(((...((.....-------..)).(((((....)))))....)))(((.(((((.((.....)).))))).))))))))))).. ( -32.10)
>DroSec_CAF1 26149 90 + 1
CAUAGAUCUGCCAGUCAUCGCU-UUU-------UCGCUGCUGGAUUCUCGGUCUGAGACAUCUGUAGCAUGGAGUGCAAGCUGCUGGCGGCAGGUUGC
....((((((((.((((..(((-((.-------..(((((.((((((((.....)))).)))))))))..)))))((.....)))))))))))))).. ( -33.00)
>DroSim_CAF1 29205 90 + 1
CAUAGAUCUGCCAGUCAUCGCU-UUU-------UCGCUGCUGGAUUCUCGGCCUGAGACAUCUGUAGCAUGAAGUGCAAGCUGCUGGCGGCAGGUUGC
....((((((((.((((..(((-((.-------..(((((.((((((((.....)))).)))))))))..)))))((.....)))))))))))))).. ( -33.40)
>DroEre_CAF1 31099 91 + 1
CAUUGAUCUGCCUGCCACCGCUGAUU-------UCGCUGCUGGAUUCUCGGCUUGCGGCAUCUGCAGCAUGGGUUGCAUGCUGCUGGUGGCAGGUUGC
.........((((((((((...(((.-------((((.(((((....)))))..)))).))).((((((((.....)))))))).))))))))))... ( -46.90)
>DroYak_CAF1 26663 98 + 1
CAUUGAUCUGCCAGCCAUCGCUGUUUUAGAUUCUCGCUGCUGGAUUCUCGGCUUGAGACAUCUGCAGCAUGGGUUGCAUGCUGCUGCUGGCAGGUUUC
....(((((((((((............(((((((((..(((((....))))).))))).))))((((((((.....)))))))).))))))))))).. ( -44.60)
>consensus
CAUUGAUCUGCCAGUCAUCGCUGUUU_______UCGCUGCUGGAUUCUCGGCUUGAGACAUCUGCAGCAUGGAGUGCAAGCUGCUGGUGGCAGGUUGC
....((((((((.((((..................(((((.((((((((.....)))).))))))))).......((.....)))))))))))))).. (-28.06 = -27.90 +  -0.16)

alignment

secondary structure

dotplot

Window 4

Location	3,692,570 – 3,692,661
Length	91
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	86.98
Mean single sequence MFE	-30.02
Consensus MFE	-20.38
Energy contribution	-21.02
Covariance contribution	0.64
Combinations/Pair	1.05
Mean z-score	-2.08
Structure conservation index	0.68
SVM decision value	0.27
SVM RNA-class probability	0.663974
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3692570 91 - 22224390
GCAACCUGCCACCAGCAGCUUGCACUCCAUGCUGCAGAUGUCUUAAGCCGAGAAUCCAGCAGCGA-------AAACAGCGAUGACUGGCAGAUCAAUG
((((.((((.....)))).)))).(((((((((((.(((.((((.....)))))))..)))))).-------...((....))..))).))....... ( -24.50)
>DroSec_CAF1 26149 90 - 1
GCAACCUGCCGCCAGCAGCUUGCACUCCAUGCUACAGAUGUCUCAGACCGAGAAUCCAGCAGCGA-------AAA-AGCGAUGACUGGCAGAUCUAUG
((((.((((.....)))).)))).(((((((((...(((.((((.....))))))).))))((..-------...-.))......))).))....... ( -23.60)
>DroSim_CAF1 29205 90 - 1
GCAACCUGCCGCCAGCAGCUUGCACUUCAUGCUACAGAUGUCUCAGGCCGAGAAUCCAGCAGCGA-------AAA-AGCGAUGACUGGCAGAUCUAUG
.....((((((.((...((((....(((.((((...(((.((((.....))))))).))))..))-------).)-)))..))..))))))....... ( -24.30)
>DroEre_CAF1 31099 91 - 1
GCAACCUGCCACCAGCAGCAUGCAACCCAUGCUGCAGAUGCCGCAAGCCGAGAAUCCAGCAGCGA-------AAUCAGCGGUGGCAGGCAGAUCAAUG
....(((((((((.((((((((.....)))))))).(((..(((..((.(......).)).))).-------.)))...))))))))).......... ( -40.50)
>DroYak_CAF1 26663 98 - 1
GAAACCUGCCAGCAGCAGCAUGCAACCCAUGCUGCAGAUGUCUCAAGCCGAGAAUCCAGCAGCGAGAAUCUAAAACAGCGAUGGCUGGCAGAUCAAUG
.....((((((((.((((((((.....))))))))((((.((((..((.(......).))...))))))))............))))))))....... ( -37.20)
>consensus
GCAACCUGCCACCAGCAGCUUGCACUCCAUGCUGCAGAUGUCUCAAGCCGAGAAUCCAGCAGCGA_______AAACAGCGAUGACUGGCAGAUCAAUG
.....(((((....((.....))......((((((.(((.((((.....)))))))..))))))......................)))))....... (-20.38 = -21.02 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:44 2006