Locus 4982

Sequence ID	3R_DroMel_CAF1
Location	13,116,426 – 13,116,555
Length	129
Max. P	0.999162

overview

Window 6

Location	13,116,426 – 13,116,522
Length	96
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	85.83
Mean single sequence MFE	-40.79
Consensus MFE	-34.20
Energy contribution	-35.00
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-3.30
Structure conservation index	0.84
SVM decision value	3.41
SVM RNA-class probability	0.999162
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13116426 96 + 27905053
UGGGCGAGUCUGGUGGAUGGGUG----GCGUGGGGCUGAAGGAACUGGAGGAAGUGGAAAACUGGUACCGGAAGGUGCAACGCCGGCCACCAGACGCCAU
..(((..(((((((((.....((----((((((..(.....)..))......(((.....))).(((((....))))).)))))).)))))))))))).. ( -41.40)
>DroSec_CAF1 146827 96 + 1
UGGGCGAGUCUGGUGGGAGGGUG----GCGUGGAGCUGAAGGAACUGGAGGAAGUGGAAAACCGGUACCGGAAGGUGCAACGCCGGCCACCAGACGCCAU
..(((..(((((((((.....((----((((...(((...((.(((((.............))))).))....)))...)))))).)))))))))))).. ( -41.02)
>DroSim_CAF1 131582 95 + 1
UGGGCGAGUCUGGUGGGAGGGUG----GCGUGGAGCUGAAGGAACUGGAGGAAGUGGA-AACCGGUACCGGAAGGUGCAACGCCGGCCACCAGACGCCAU
..(((..(((((((((.....((----((((.........((.(((......)))...-..)).(((((....))))).)))))).)))))))))))).. ( -41.40)
>DroEre_CAF1 136987 95 + 1
UGGGCGCGCCUGGUGGGAGGGUGAGCGGG-----UGAGAAGGAACUGGAGGAAGUGGAAAACCGGUACCGGAAGGUGCAACGCCGGCCACCAGACGCCAU
..((((...(((((((...((((....((-----(........(((......))).....))).(((((....)))))..))))..))))))).)))).. ( -39.42)
>DroYak_CAF1 144026 100 + 1
UAGGCGGCUGUGGUGGGCUGGAAAGAGGGGUGCAGGGGGAGGUACUGAAGGAAGUGGAAAACCGGUACCGGAAGGUGCAACGCCGGCCACCAGACGCCAU
..((((.(((((((.(((..........(((((........))))).......((((....)).(((((....))))).))))).)))).))).)))).. ( -40.70)
>consensus
UGGGCGAGUCUGGUGGGAGGGUG____GCGUGGAGCUGAAGGAACUGGAGGAAGUGGAAAACCGGUACCGGAAGGUGCAACGCCGGCCACCAGACGCCAU
..((((..((((((((...((((....................(((......))).........(((((....)))))..))))..)))))))))))).. (-34.20 = -35.00 +   0.80)

alignment

secondary structure

dotplot

Window 7

Location	13,116,426 – 13,116,522
Length	96
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	85.83
Mean single sequence MFE	-30.39
Consensus MFE	-23.80
Energy contribution	-24.04
Covariance contribution	0.24
Combinations/Pair	1.05
Mean z-score	-2.69
Structure conservation index	0.78
SVM decision value	2.08
SVM RNA-class probability	0.987544
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13116426 96 - 27905053
AUGGCGUCUGGUGGCCGGCGUUGCACCUUCCGGUACCAGUUUUCCACUUCCUCCAGUUCCUUCAGCCCCACGC----CACCCAUCCACCAGACUCGCCCA
..((((((((((((..(((((.(((((....)))...........(((......))).......))...))))----)......)))))))))..))).. ( -29.40)
>DroSec_CAF1 146827 96 - 1
AUGGCGUCUGGUGGCCGGCGUUGCACCUUCCGGUACCGGUUUUCCACUUCCUCCAGUUCCUUCAGCUCCACGC----CACCCUCCCACCAGACUCGCCCA
..((((((((((((..(((((.(((((....)))...((....))...................))...))))----)......)))))))))..))).. ( -32.40)
>DroSim_CAF1 131582 95 - 1
AUGGCGUCUGGUGGCCGGCGUUGCACCUUCCGGUACCGGUU-UCCACUUCCUCCAGUUCCUUCAGCUCCACGC----CACCCUCCCACCAGACUCGCCCA
..((((((((((((..(((((.((.....(((....)))..-...(((......))).......))...))))----)......)))))))))..))).. ( -32.00)
>DroEre_CAF1 136987 95 - 1
AUGGCGUCUGGUGGCCGGCGUUGCACCUUCCGGUACCGGUUUUCCACUUCCUCCAGUUCCUUCUCA-----CCCGCUCACCCUCCCACCAGGCGCGCCCA
...(((((((((((..((.((.(((((....)))...((....)).....................-----...))..))))..)))))))))))..... ( -31.70)
>DroYak_CAF1 144026 100 - 1
AUGGCGUCUGGUGGCCGGCGUUGCACCUUCCGGUACCGGUUUUCCACUUCCUUCAGUACCUCCCCCUGCACCCCUCUUUCCAGCCCACCACAGCCGCCUA
..((((.(((.(((..(((..((((......(((((.((.............)).)))))......))))............)))..)))))).)))).. ( -26.46)
>consensus
AUGGCGUCUGGUGGCCGGCGUUGCACCUUCCGGUACCGGUUUUCCACUUCCUCCAGUUCCUUCAGCUCCACGC____CACCCUCCCACCAGACUCGCCCA
..((((((((((((((((..(((.......)))..))))......(((......)))...........................))))))))..)))).. (-23.80 = -24.04 +   0.24)

alignment

secondary structure

dotplot

Window 8

Location	13,116,462 – 13,116,555
Length	93
Sequences	6
Columns	93
Reading direction	forward
Mean pairwise identity	79.45
Mean single sequence MFE	-37.59
Consensus MFE	-20.56
Energy contribution	-21.33
Covariance contribution	0.78
Combinations/Pair	1.06
Mean z-score	-1.96
Structure conservation index	0.55
SVM decision value	0.27
SVM RNA-class probability	0.661813
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13116462 93 + 27905053
GGAACUGGAGGAAGUGGAAAACUGGUACCGGAAGGUGCAACGCCGGCCACCAGACGCCAUUGCGAGGCGGCGUCUUCUGGCCCGCUUGUCACA
.............((((.......(((((....)))))...((.(((((..(((((((..........)))))))..))))).))...)))). ( -38.80)
>DroPse_CAF1 137022 77 + 1
-----GUACGGCAACGGC-AACGGCAACCGGAAGGUAUACCGCCGGCCACCAGACGCCGUUG---GGCGUCGUCUUCG-------UUGUCACA
-----....(((((((((-..((((.(((....))).....)))))))....((((((....---))))))......)-------)))))... ( -35.60)
>DroSec_CAF1 146863 93 + 1
GGAACUGGAGGAAGUGGAAAACCGGUACCGGAAGGUGCAACGCCGGCCACCAGACGCCAUUGCGAGGCGGCGUCUUCUGGACCGCUUGUCACA
......(..(.((((((....((((((((....))).....)))))(((..(((((((..........)))))))..))).)))))).)..). ( -37.10)
>DroSim_CAF1 131618 92 + 1
GGAACUGGAGGAAGUGGA-AACCGGUACCGGAAGGUGCAACGCCGGCCACCAGACGCCAUUGCGAGGCGGCGUCUUCUGGCCCGCUUGUCACA
.............((((.-.....(((((....)))))...((.(((((..(((((((..........)))))))..))))).))...)))). ( -38.80)
>DroYak_CAF1 144066 93 + 1
GGUACUGAAGGAAGUGGAAAACCGGUACCGGAAGGUGCAACGCCGGCCACCAGACGCCAUUGCGCGGCGGCGUCUUCUGGCCCGCUUGUCACA
(((((((...............))))))).....((((((.((.(((((..(((((((..........)))))))..))))).))))).))). ( -39.06)
>DroPer_CAF1 203456 77 + 1
-----GUACGGCAACGGC-AACGGCAACCGGAAGGUAUACCGCCGGCCACCAGACGCCGUCG---GGCGUCGUCUUCG-------UUGUCACA
-----....((((((((.-.(((((.(((....)))...(((.((((........)))).))---)..)))))..)))-------)))))... ( -36.20)
>consensus
GGAACUGAAGGAAGUGGA_AACCGGUACCGGAAGGUGCAACGCCGGCCACCAGACGCCAUUGCGAGGCGGCGUCUUCUGGCCCGCUUGUCACA
.........((...(((.......(((((....)))))....))).))...(((((((..........))))))).................. (-20.56 = -21.33 +   0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:33 2006