Locus 6589

Sequence ID	2L_DroMel_CAF1
Location	18,514,479 – 18,514,637
Length	158
Max. P	0.989944

overview

Window 9

Location	18,514,479 – 18,514,597
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	74.24
Mean single sequence MFE	-30.77
Consensus MFE	-11.70
Energy contribution	-12.50
Covariance contribution	0.80
Combinations/Pair	1.39
Mean z-score	-1.83
Structure conservation index	0.38
SVM decision value	0.33
SVM RNA-class probability	0.689635
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18514479 118 - 22407834
UUACAAACUAUAAUUUACUUUAAUGGCCAUCUGUAUUUUAUU-UGUGGCUCGUUGUAGUAGGCCGGCCAUUUGGCCAAAGCU-UCAAUGUUCGGAGUUGAUGCAUAAAUAAUGGGUUAAA
...............((((.((((((((((..(((...))).-.))))).))))).))))((((((((....))))...((.-(((((.......))))).))..........))))... ( -31.70)
>DroPse_CAF1 41935 119 - 1
GUACAAGCCAUAAUUUGGCUUAAUGGCCAUCUGCGUUUUGCCGCGUGUGUACACGCAGUAGGCCUCCU-CGGAGCCCCAGCUCUUAGUGCUUCAGGCUAAUGCAUAAAUAAACCCAUAAA
....((((((.....)))))).((((.....((((((..((((((((....))))).(.((((...((-.(((((....))))).)).))))).))).)))))).........))))... ( -38.54)
>DroSec_CAF1 34913 118 - 1
UUACAAACUAUAAUUUGCUUUAAUGGCCAUCCGUAUUUUAUU-UGUGUCUCGUUGUAGUAGGCCGGCCAUUUGGCCAAAGCU-UCACUGGUCGGAGUUGAUGCAUAAAUAAUGUGAUAAA
(((((...........(((.....)))..........(((((-(((((.((.........((((((....))))))..((((-((.......)))))))).))))))))))))))).... ( -26.90)
>DroSim_CAF1 33466 118 - 1
UUACAAACUAUAAUUUGCUUUAAUGGCCAUCUGUAUUUUAUU-UGUGGCUCGUUGUAGUAGGCCGGCCAUUUGGCCAAAGCU-UCACUGGUCGGAGUUGAUGCAUAAAUAAUGUGAUAAA
.....((((....((((((.((((((((((..(((...))).-.))))).))))).))))))(((((((...(((....)))-....)))))))))))...((((.....))))...... ( -31.20)
>DroYak_CAF1 34849 99 - 1
UUACAAACUAUAAUUUGCU-------------------UAUU-UGUGACUCGUUGUAGUAGGCCGGUCAUUCGGCAAAAGCU-UUAAUGGUCGGAGCUAGUGCAUAAAAAAUGGUUUUAA
....(((((((....((((-------------------((.(-(.((((.(((((.(((..(((((....)))))....)))-.))))))))).)).))).)))......)))))))... ( -25.50)
>consensus
UUACAAACUAUAAUUUGCUUUAAUGGCCAUCUGUAUUUUAUU_UGUGGCUCGUUGUAGUAGGCCGGCCAUUUGGCCAAAGCU_UCAAUGGUCGGAGUUGAUGCAUAAAUAAUGGGAUAAA
......................................................(((.(((.(((((((((.(((....)))...)))))))))..))).)))................. (-11.70 = -12.50 +   0.80)

alignment

secondary structure

dotplot

Window 0

Location	18,514,518 – 18,514,637
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	72.53
Mean single sequence MFE	-32.02
Consensus MFE	-16.88
Energy contribution	-18.08
Covariance contribution	1.20
Combinations/Pair	1.30
Mean z-score	-2.24
Structure conservation index	0.53
SVM decision value	2.06
SVM RNA-class probability	0.986849
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18514518 119 + 22407834
CUUUGGCCAAAUGGCCGGCCUACUACAACGAGCCACA-AAUAAAAUACAGAUGGCCAUUAAAGUAAAUUAUAGUUUGUAAGACUAUACAUACAAUUUGACUGUUUUGUCGGGCCAAGAUC
.(((((((.(((((((((((.........).)))...-......((....)))))))))...(((...(((((((.....)))))))..)))....((((......)))))))))))... ( -31.30)
>DroPse_CAF1 41975 107 + 1
CUGGGGCUCCG-AGGAGGCCUACUGCGUGUACACACGCGGCAAAACGCAGAUGGCCAUUAAGCCAAAUUAUGGCUUGUACGG----------AAUUCGGCUCUUAUGCUGGGCCGA--GG
(((((.(((..-..))).))..(((((((....))))))).......)))....((..(((((((.....)))))))...))----------..((((((((.......)))))))--). ( -43.60)
>DroSec_CAF1 34952 119 + 1
CUUUGGCCAAAUGGCCGGCCUACUACAACGAGACACA-AAUAAAAUACGGAUGGCCAUUAAAGCAAAUUAUAGUUUGUAAGACUAUACAUCCCAUUUGACUGUUUUGUCGGGCCAAGAGC
((((((((....))))(((((......((((((((((-(((.......(((((((.......))....(((((((.....)))))))))))).)))))..)))))))).))))).)))). ( -33.80)
>DroSim_CAF1 33505 119 + 1
CUUUGGCCAAAUGGCCGGCCUACUACAACGAGCCACA-AAUAAAAUACAGAUGGCCAUUAAAGCAAAUUAUAGUUUGUAAGACUAUACAUACCAUUUGACUGUUUUGUCGGGCCAAGAGC
.(((((((...((((((...........)).))))..-.((((((((((((((((.......))....(((((((.....))))))).....))))))..))))))))..)))))))... ( -30.90)
>DroYak_CAF1 34888 100 + 1
CUUUUGCCGAAUGACCGGCCUACUACAACGAGUCACA-AAUA-------------------AGCAAAUUAUAGUUUGUAAGACUAUACAUAUAAUUUGACUGUUUUGUCUGCUGAAGAGC
((((.((.((.((((((...........)).))))((-((..-------------------(((((((((((...((((......))))))))))))).))..)))))).)).))))... ( -20.50)
>consensus
CUUUGGCCAAAUGGCCGGCCUACUACAACGAGACACA_AAUAAAAUACAGAUGGCCAUUAAAGCAAAUUAUAGUUUGUAAGACUAUACAUACAAUUUGACUGUUUUGUCGGGCCAAGAGC
....((((........))))...............................(((((............(((((((.....))))))).........((((......)))))))))..... (-16.88 = -18.08 +   1.20)

alignment

secondary structure

dotplot

Window 1

Location	18,514,518 – 18,514,637
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	72.53
Mean single sequence MFE	-33.64
Consensus MFE	-14.42
Energy contribution	-15.42
Covariance contribution	1.00
Combinations/Pair	1.26
Mean z-score	-2.34
Structure conservation index	0.43
SVM decision value	2.19
SVM RNA-class probability	0.989944
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18514518 119 - 22407834
GAUCUUGGCCCGACAAAACAGUCAAAUUGUAUGUAUAGUCUUACAAACUAUAAUUUACUUUAAUGGCCAUCUGUAUUUUAUU-UGUGGCUCGUUGUAGUAGGCCGGCCAUUUGGCCAAAG
......((((.(((......)))((((((((((((......))))...))))))))(((.((((((((((..(((...))).-.))))).))))).))).))))((((....)))).... ( -36.00)
>DroPse_CAF1 41975 107 - 1
CC--UCGGCCCAGCAUAAGAGCCGAAUU----------CCGUACAAGCCAUAAUUUGGCUUAAUGGCCAUCUGCGUUUUGCCGCGUGUGUACACGCAGUAGGCCUCCU-CGGAGCCCCAG
..--(((((.(.......).))))).((----------(((...((((((.....))))))...((((..((((((..((((....).))).))))))..))))....-)))))...... ( -36.80)
>DroSec_CAF1 34952 119 - 1
GCUCUUGGCCCGACAAAACAGUCAAAUGGGAUGUAUAGUCUUACAAACUAUAAUUUGCUUUAAUGGCCAUCCGUAUUUUAUU-UGUGUCUCGUUGUAGUAGGCCGGCCAUUUGGCCAAAG
......((((..((((.((((..((((((((((((((((.......))))))....(((.....)))))))).)))))...)-)))......))))....))))((((....)))).... ( -32.20)
>DroSim_CAF1 33505 119 - 1
GCUCUUGGCCCGACAAAACAGUCAAAUGGUAUGUAUAGUCUUACAAACUAUAAUUUGCUUUAAUGGCCAUCUGUAUUUUAUU-UGUGGCUCGUUGUAGUAGGCCGGCCAUUUGGCCAAAG
......((((.(((......)))..(((((.((((......)))).)))))....((((.((((((((((..(((...))).-.))))).))))).))))))))((((....)))).... ( -38.80)
>DroYak_CAF1 34888 100 - 1
GCUCUUCAGCAGACAAAACAGUCAAAUUAUAUGUAUAGUCUUACAAACUAUAAUUUGCU-------------------UAUU-UGUGACUCGUUGUAGUAGGCCGGUCAUUCGGCAAAAG
.((((.(((((((((((..((.(((((((((((((......))))...)))))))))))-------------------..))-)))..)).)))).)).))(((((....)))))..... ( -24.40)
>consensus
GCUCUUGGCCCGACAAAACAGUCAAAUUGUAUGUAUAGUCUUACAAACUAUAAUUUGCUUUAAUGGCCAUCUGUAUUUUAUU_UGUGGCUCGUUGUAGUAGGCCGGCCAUUUGGCCAAAG
......((((.(((......)))..........((((((.......))))))............))))................................((((((....)))))).... (-14.42 = -15.42 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:03 2006