Locus 401

Sequence ID	2R_DroMel_CAF1
Location	2,396,689 – 2,396,821
Length	132
Max. P	0.915718

overview

Window 6

Location	2,396,689 – 2,396,789
Length	100
Sequences	3
Columns	105
Reading direction	forward
Mean pairwise identity	84.62
Mean single sequence MFE	-28.83
Consensus MFE	-21.07
Energy contribution	-19.97
Covariance contribution	-1.10
Combinations/Pair	1.15
Mean z-score	-2.09
Structure conservation index	0.73
SVM decision value	0.41
SVM RNA-class probability	0.724472
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2396689 100 + 20766785
-----UUAAAAUUCCAAGCGGAGUGAUUACAUUUUAAGUUAAGGAUCAAUGUGGACAGCAGUCCACGUUGUGACGGAAGGGUAACGCAGCGAAGGUAGGUUGUCC
-----......((((.(((.(((((....)))))...)))..(...((((((((((....))))))))))...)))))((..(((.(.((....)).))))..)) ( -30.60)
>DroSec_CAF1 52428 102 + 1
UGGUUCUAAAAUUCCAAACGGAAUGAUUAAAUUUUAAGUUACGGAUCACUGUGGACGGUAGUCCACGUAGUGACG-AAGGGUAACGCUGCGAAGGCAACUAAU--
(((((.....(((((....))))).............(((((...(((((((((((....))))))..)))))(.-...))))))...((....)))))))..-- ( -29.60)
>DroSim_CAF1 9808 102 + 1
UGGUUCUAAAAUUCCAAACGAAAUGAUUAAAUUUUAAGUUACGGAUCACUGUGGACGGCAGUCCACGUAGUGACG-AAGGGUAACGCUGCGAAGGCAACUAAU--
(((..........)))...(((((......)))))..(((((...(((((((((((....))))))..)))))(.-...))))))..(((....)))......-- ( -26.30)
>consensus
UGGUUCUAAAAUUCCAAACGGAAUGAUUAAAUUUUAAGUUACGGAUCACUGUGGACGGCAGUCCACGUAGUGACG_AAGGGUAACGCUGCGAAGGCAACUAAU__
............(((.(((.((((......))))...)))..)))((...((((((....))))))((((((((......))..))))))))............. (-21.07 = -19.97 +  -1.10)

alignment

secondary structure

dotplot

Window 7

Location	2,396,689 – 2,396,789
Length	100
Sequences	3
Columns	105
Reading direction	reverse
Mean pairwise identity	84.62
Mean single sequence MFE	-24.17
Consensus MFE	-17.44
Energy contribution	-19.33
Covariance contribution	1.89
Combinations/Pair	1.07
Mean z-score	-2.26
Structure conservation index	0.72
SVM decision value	0.59
SVM RNA-class probability	0.792019
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2396689 100 - 20766785
GGACAACCUACCUUCGCUGCGUUACCCUUCCGUCACAACGUGGACUGCUGUCCACAUUGAUCCUUAACUUAAAAUGUAAUCACUCCGCUUGGAAUUUUAA-----
((((((..............((.((......)).))...((((((....)))))).))).)))....................(((....))).......----- ( -16.40)
>DroSec_CAF1 52428 102 - 1
--AUUAGUUGCCUUCGCAGCGUUACCCUU-CGUCACUACGUGGACUACCGUCCACAGUGAUCCGUAACUUAAAAUUUAAUCAUUCCGUUUGGAAUUUUAGAACCA
--....(((((....)))))(((((....-.((((((..((((((....))))))))))))..)))))......(((((..(((((....))))).))))).... ( -29.10)
>DroSim_CAF1 9808 102 - 1
--AUUAGUUGCCUUCGCAGCGUUACCCUU-CGUCACUACGUGGACUGCCGUCCACAGUGAUCCGUAACUUAAAAUUUAAUCAUUUCGUUUGGAAUUUUAGAACCA
--....(((((....)))))(((((....-.((((((..((((((....))))))))))))..)))))(((((((((...(.....)....)))))))))..... ( -27.00)
>consensus
__AUUAGUUGCCUUCGCAGCGUUACCCUU_CGUCACUACGUGGACUGCCGUCCACAGUGAUCCGUAACUUAAAAUUUAAUCAUUCCGUUUGGAAUUUUAGAACCA
......(((((....)))))(((((......((((((..((((((....))))))))))))..))))).............(((((....))))).......... (-17.44 = -19.33 +   1.89)

alignment

secondary structure

dotplot

Window 8

Location	2,396,722 – 2,396,821
Length	99
Sequences	3
Columns	106
Reading direction	forward
Mean pairwise identity	82.86
Mean single sequence MFE	-28.30
Consensus MFE	-19.21
Energy contribution	-19.10
Covariance contribution	-0.11
Combinations/Pair	1.05
Mean z-score	-1.75
Structure conservation index	0.68
SVM decision value	0.02
SVM RNA-class probability	0.543734
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2396722 99 + 20766785
UUAAGGAUCAAUGUGGACAGCAGUCCACGUUGUGACGGAAGGGUAACGCAGCGAAGGUAGGUUGUCCAGUAGGUUGGUAAUAGGGAGUAGAAG-----UGGUAU--
......((((((.((((((((...((.(((((((.(....).....)))))))..))...))))))))....))))))...............-----......-- ( -27.40)
>DroSec_CAF1 52466 103 + 1
UUACGGAUCACUGUGGACGGUAGUCCACGUAGUGACG-AAGGGUAACGCUGCGAAGGCAACUAAU--AAUAGGUAGGUAAUAGGUAGUAGUAGGUGACUGGUAGGC
((((..(((...((((((....))))))((((((.(.-...)....))))))..((....))...--....)))..)))).......((.(((....))).))... ( -28.90)
>DroSim_CAF1 9846 103 + 1
UUACGGAUCACUGUGGACGGCAGUCCACGUAGUGACG-AAGGGUAACGCUGCGAAGGCAACUAAU--AAUAGGUAGGUAAUAGGUAGUAGUAGGUGACUGGUGGGC
((((..(((...((((((....))))))((((((.(.-...)....))))))..((....))...--....)))..)))).......((.(((....))).))... ( -28.60)
>consensus
UUACGGAUCACUGUGGACGGCAGUCCACGUAGUGACG_AAGGGUAACGCUGCGAAGGCAACUAAU__AAUAGGUAGGUAAUAGGUAGUAGUAGGUGACUGGUAGGC
((((..(((...((((((....))))))((((((((......))..))))))...................)))..)))).......................... (-19.21 = -19.10 +  -0.11)

alignment

secondary structure

dotplot

Window 9

Location	2,396,722 – 2,396,821
Length	99
Sequences	3
Columns	106
Reading direction	reverse
Mean pairwise identity	82.86
Mean single sequence MFE	-19.53
Consensus MFE	-14.25
Energy contribution	-15.70
Covariance contribution	1.45
Combinations/Pair	1.06
Mean z-score	-2.39
Structure conservation index	0.73
SVM decision value	1.10
SVM RNA-class probability	0.915718
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2396722 99 - 20766785
--AUACCA-----CUUCUACUCCCUAUUACCAACCUACUGGACAACCUACCUUCGCUGCGUUACCCUUCCGUCACAACGUGGACUGCUGUCCACAUUGAUCCUUAA
--......-----..........................((((((..............((.((......)).))...((((((....)))))).))).))).... ( -14.80)
>DroSec_CAF1 52466 103 - 1
GCCUACCAGUCACCUACUACUACCUAUUACCUACCUAUU--AUUAGUUGCCUUCGCAGCGUUACCCUU-CGUCACUACGUGGACUACCGUCCACAGUGAUCCGUAA
...(((..(((((..........................--....(((((....))))).........-.........((((((....)))))).)))))..))). ( -22.40)
>DroSim_CAF1 9846 103 - 1
GCCCACCAGUCACCUACUACUACCUAUUACCUACCUAUU--AUUAGUUGCCUUCGCAGCGUUACCCUU-CGUCACUACGUGGACUGCCGUCCACAGUGAUCCGUAA
.................(((...................--....(((((....))))).........-.((((((..((((((....))))))))))))..))). ( -21.40)
>consensus
GCCUACCAGUCACCUACUACUACCUAUUACCUACCUAUU__AUUAGUUGCCUUCGCAGCGUUACCCUU_CGUCACUACGUGGACUGCCGUCCACAGUGAUCCGUAA
.............................................(((((....)))))...........((((((..((((((....))))))))))))...... (-14.25 = -15.70 +   1.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:41 2006