Locus 9887

Sequence ID	3R_DroMel_CAF1
Location	26,394,853 – 26,394,951
Length	98
Max. P	0.993342

overview

Window 2

Location	26,394,853 – 26,394,951
Length	98
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	66.16
Mean single sequence MFE	-30.23
Consensus MFE	-14.66
Energy contribution	-17.58
Covariance contribution	2.92
Combinations/Pair	1.12
Mean z-score	-1.80
Structure conservation index	0.49
SVM decision value	1.11
SVM RNA-class probability	0.916945
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26394853 98 + 27905053
UGAGACGACAGAGGGCUUCAGGCAAU-------GGGCGUAGAACCUGGAGAGGAGCUCUUCACGUAAGUUGGUUUAUUUGAAACUAACGUUCCACAGGCCCGUUG
(((..(........)..)))..((((-------((((((.((((.(((((((...))))))).....((((((((.....)))))))))))).))..)))))))) ( -29.70)
>DroPse_CAF1 115421 83 + 1
--AGCUGAAGGAGGGCCAAAAGCCAA-------AAGCCAAAAGCCA---AAGC-------CGA---AAACGGUAGUCGUACAUCUACCGUUGCAAGACCCCGUUC
--.(((...((..(((.....)))..-------...))...)))..---..((-------...---.((((((((........))))))))))............ ( -20.30)
>DroSec_CAF1 124120 98 + 1
UGAGCAGACAGAGGGCUUGAGGCGAU-------GGGCGGAGAACCUGGAGAGCAGUUCUCCAAGUAAGUUGGUUUAUUUGGAACUAAAGUUCCACAGGCCCGUUG
........(((.(((((((((.((((-------..(((((((((.((.....)))))))))..))..)))).))....((((((....))))))))))))).))) ( -35.30)
>DroSim_CAF1 121755 89 + 1
UGAGAUGACAGAGGGCUUGAGGCAAU-------GGGCGGAGAACCUGGAGAGCAGCUCUCCAAGUAAGUU---------GGAACUAACGUUCCACAGGCCCGUUG
........(((.(((((((..((...-------..)).....((.(((((((...))))))).))....(---------(((((....))))))))))))).))) ( -33.60)
>DroEre_CAF1 128618 105 + 1
UGGGAUGACAGAGGGCUGGAGGCGGUGGGCGGUGGGCGGAGAACCUGGAGAGGAGCUCUCCAAGUGAGUUGGUUUAUUUGGAACUAACGUUCCACAGGCCCGUUG
......(((.....((((....))))((((.((((((.....((.(((((((...))))))).))..((((((((.....))))))))).)))))..))))))). ( -37.60)
>DroYak_CAF1 123293 76 + 1
UGAGAUGACAGAGGGCUG-----------------------------GAGAAGAGCUCUCCAAGUAAGUUGGUUUAUUUGGAACUAACGUUCCCCAGGCCCGUUG
........(((.((((((-----------------------------((((.....)))))(((((((....)))))))(((((....)))))...))))).))) ( -24.90)
>consensus
UGAGAUGACAGAGGGCUUGAGGCAAU_______GGGCGGAGAACCUGGAGAGCAGCUCUCCAAGUAAGUUGGUUUAUUUGGAACUAACGUUCCACAGGCCCGUUG
............(((((............................((((((.....)))))).................(((((....)))))...))))).... (-14.66 = -17.58 +   2.92)

alignment

secondary structure

dotplot

Window 3

Location	26,394,853 – 26,394,951
Length	98
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	66.16
Mean single sequence MFE	-27.23
Consensus MFE	-16.34
Energy contribution	-18.40
Covariance contribution	2.06
Combinations/Pair	1.17
Mean z-score	-2.61
Structure conservation index	0.60
SVM decision value	2.39
SVM RNA-class probability	0.993342
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26394853 98 - 27905053
CAACGGGCCUGUGGAACGUUAGUUUCAAAUAAACCAACUUACGUGAAGAGCUCCUCUCCAGGUUCUACGCCC-------AUUGCCUGAAGCCCUCUGUCGUCUCA
...(((((..((((...(((.((((.....)))).)))....(((.((((((........)))))).)))))-------)).))))).................. ( -23.40)
>DroPse_CAF1 115421 83 - 1
GAACGGGGUCUUGCAACGGUAGAUGUACGACUACCGUUU---UCG-------GCUU---UGGCUUUUGGCUU-------UUGGCUUUUGGCCCUCCUUCAGCU--
(((.((((((....((((((((........)))))))).---..(-------(((.---.(((.....))).-------..))))...))))).).)))....-- ( -27.30)
>DroSec_CAF1 124120 98 - 1
CAACGGGCCUGUGGAACUUUAGUUCCAAAUAAACCAACUUACUUGGAGAACUGCUCUCCAGGUUCUCCGCCC-------AUCGCCUCAAGCCCUCUGUCUGCUCA
....((((.((((((((....)))))).................((((((((........))))))))....-------.......)).))))............ ( -28.40)
>DroSim_CAF1 121755 89 - 1
CAACGGGCCUGUGGAACGUUAGUUCC---------AACUUACUUGGAGAGCUGCUCUCCAGGUUCUCCGCCC-------AUUGCCUCAAGCCCUCUGUCAUCUCA
(((.((((...((((((....)))))---------)....((((((((((...)))))))))).....))))-------.)))...................... ( -30.20)
>DroEre_CAF1 128618 105 - 1
CAACGGGCCUGUGGAACGUUAGUUCCAAAUAAACCAACUCACUUGGAGAGCUCCUCUCCAGGUUCUCCGCCCACCGCCCACCGCCUCCAGCCCUCUGUCAUCCCA
....((((...((((((....)))))).............((((((((((...)))))))))).....))))................................. ( -30.00)
>DroYak_CAF1 123293 76 - 1
CAACGGGCCUGGGGAACGUUAGUUCCAAAUAAACCAACUUACUUGGAGAGCUCUUCUC-----------------------------CAGCCCUCUGUCAUCUCA
....((((.(((((((.(....((((((.(((......))).))))))....))))))-----------------------------))))))............ ( -24.10)
>consensus
CAACGGGCCUGUGGAACGUUAGUUCCAAAUAAACCAACUUACUUGGAGAGCUCCUCUCCAGGUUCUCCGCCC_______AUCGCCUCAAGCCCUCUGUCAUCUCA
....((((....(((((....)))))..............(((((((((.....)))))))))..........................))))............ (-16.34 = -18.40 +   2.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:44:16 2006