Locus 6737

Sequence ID	2L_DroMel_CAF1
Location	18,835,647 – 18,835,767
Length	120
Max. P	0.985535

overview

Window 2

Location	18,835,647 – 18,835,767
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	83.73
Mean single sequence MFE	-41.16
Consensus MFE	-29.92
Energy contribution	-30.80
Covariance contribution	0.88
Combinations/Pair	1.07
Mean z-score	-2.78
Structure conservation index	0.73
SVM decision value	2.01
SVM RNA-class probability	0.985535
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18835647 120 + 22407834
AGGCGCCAUCUAGCGGCAACCCGCGCAGAUAGACUUGUGAAUGAAAGAAUAGAUGGAUAUAUCGUAACAUCGAUUGUAACGUGUAAGUGCGCCAUCUAUAGGCGAGUCAUAUUUGGCGCG
..(((((((((.((((....))))..)))).(((((((...(....).((((((((.((((.(((.(((.....))).)))))))......))))))))..)))))))......))))). ( -42.20)
>DroSim_CAF1 2998 120 + 1
AGGCGCCAUCUAGCGGCAACCCGCGCAGCGACACUUGUGAAUGAAAGAAUAGAUGGAUAUAUCGUAACAUCGAUUGUAACGUGUAAUUGCGCCAUCUUUAGGCGAGUUCUAUUUGGCGCG
..((((((..((((((....))))((((..(((((((..(.(((.......((((....))))......))).)..))).))))..))))(((.......)))......))..)))))). ( -36.82)
>DroEre_CAF1 3070 118 + 1
UUGCGCCACCUAGCGGCAACCCGCGUAGCGAGG-UUGUUAAUGAAA-AAUCGAUGGAAAUAUCGAAACAUCGAUUUCAGCAUUGAAGUGCGCCAUCUAUGGGCGAUACUUAUCCGGCGCG
..(((((.....((((((((((((...))).))-)))))..((((.-.(((((((............)))))))))))))....(((((((((.......)))).)))))....))))). ( -45.30)
>DroYak_CAF1 3100 119 + 1
AGGCGCCACCUAGCGGCAACCCGCGUACCAAGACCUGUGAAUAAAA-AAUCGAUGGAAAUAUCGAAACAUCGAUUUCAGCACUUAAGUGCGCCAUCUAUAGGCGAUACUUAUUCGGCGCG
..(((((.....((((....))))..............((((((.(-((((((((............)))))))))..((((....))))(((.......))).....))))))))))). ( -40.30)
>consensus
AGGCGCCACCUAGCGGCAACCCGCGCAGCGAGACUUGUGAAUGAAA_AAUAGAUGGAAAUAUCGAAACAUCGAUUGCAACAUGUAAGUGCGCCAUCUAUAGGCGAGACUUAUUCGGCGCG
..(((((.....((((....)))).............((((((....((((((((............))))))))....))))))....((((.......))))..........))))). (-29.92 = -30.80 +   0.88)

alignment

secondary structure

dotplot

Window 3

Location	18,835,647 – 18,835,767
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	83.73
Mean single sequence MFE	-37.00
Consensus MFE	-27.58
Energy contribution	-27.07
Covariance contribution	-0.50
Combinations/Pair	1.12
Mean z-score	-1.92
Structure conservation index	0.75
SVM decision value	0.74
SVM RNA-class probability	0.838750
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18835647 120 - 22407834
CGCGCCAAAUAUGACUCGCCUAUAGAUGGCGCACUUACACGUUACAAUCGAUGUUACGAUAUAUCCAUCUAUUCUUUCAUUCACAAGUCUAUCUGCGCGGGUUGCCGCUAGAUGGCGCCU
.(((((......((((((((.......))))........(((.(((.....))).)))...........................)))).(((((.((((....)))))))))))))).. ( -33.20)
>DroSim_CAF1 2998 120 - 1
CGCGCCAAAUAGAACUCGCCUAAAGAUGGCGCAAUUACACGUUACAAUCGAUGUUACGAUAUAUCCAUCUAUUCUUUCAUUCACAAGUGUCGCUGCGCGGGUUGCCGCUAGAUGGCGCCU
.((((((..((((((((((....((.((((((........((.(((.....))).))(((......))).................))))))))..)))))))....)))..)))))).. ( -32.10)
>DroEre_CAF1 3070 118 - 1
CGCGCCGGAUAAGUAUCGCCCAUAGAUGGCGCACUUCAAUGCUGAAAUCGAUGUUUCGAUAUUUCCAUCGAUU-UUUCAUUAACAA-CCUCGCUACGCGGGUUGCCGCUAGGUGGCGCAA
.(((((.(((....)))(((..(((.((((.......((((..((((((((((............))))))))-)).))))...((-((.(((...)))))))))))))))))))))).. ( -39.90)
>DroYak_CAF1 3100 119 - 1
CGCGCCGAAUAAGUAUCGCCUAUAGAUGGCGCACUUAAGUGCUGAAAUCGAUGUUUCGAUAUUUCCAUCGAUU-UUUUAUUCACAGGUCUUGGUACGCGGGUUGCCGCUAGGUGGCGCCU
.((((((..((.(((((((((...(((((.((((....))))....(((((....)))))....)))))((..-......))..))))...)))))((((....))))))..)))))).. ( -42.80)
>consensus
CGCGCCAAAUAAGAAUCGCCUAUAGAUGGCGCACUUAAACGCUAAAAUCGAUGUUACGAUAUAUCCAUCGAUU_UUUCAUUCACAAGUCUCGCUACGCGGGUUGCCGCUAGAUGGCGCCU
.((((((.................(((((.((........))....((((......))))....))))).......................(((.((((....))))))).)))))).. (-27.58 = -27.07 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:18:51 2006