Locus 3228

Sequence ID	X_DroMel_CAF1
Location	8,543,881 – 8,544,072
Length	191
Max. P	0.765739

overview

Window 6

Location	8,543,881 – 8,543,992
Length	111
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.22
Mean single sequence MFE	-26.52
Consensus MFE	-24.71
Energy contribution	-24.53
Covariance contribution	-0.19
Combinations/Pair	1.06
Mean z-score	-1.36
Structure conservation index	0.93
SVM decision value	0.12
SVM RNA-class probability	0.592616
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8543881 111 - 22224390
UUUCCAGUUGCAGCGGCAUGUGGAAAAUUAGCGCUCAAUGUUAACAUUUGCCCACAUUGUUGCGUUGUGUUAAUGUAUUUUAAUUUUCCUCAGCCUCGAGUCCUCUGACAU---------
....(((..((.(.(((.((.((((((((((......((((((((((.(((..........)))..))))))))))...)))))))))).))))).)..))...)))....--------- ( -26.90)
>DroSec_CAF1 8074 111 - 1
UUUCCAGUUGCAGCGGCAUGUGGAAAAUUAGCGCUCAAUGUUAACAUUUGCCCACAUUGUUGCGUUGUGUUAAUGUAUUUUAAUUUUCCUCAGCCUCGAGUUCUCUGACAU---------
....(((..((.(.(((.((.((((((((((......((((((((((.(((..........)))..))))))))))...)))))))))).))))).)..))...)))....--------- ( -27.60)
>DroEre_CAF1 8100 111 - 1
UUUCCAGUUGCAGCGGCAUGUGGAAAAUUAGCGCUCAAUGUUAACAUUUGCCCACAUUGUUGCGUUGUGUUAAUGCAUUUUAAUUUUCCUCAGCCUCAAAUCCUCUGACAU---------
....(((.....(.(((.((.(((((((((((((.((((((...(....)...))))))..)))).((((....))))..))))))))).))))).).......)))....--------- ( -27.50)
>DroYak_CAF1 9856 120 - 1
UUUCCAGUUGCAGCGGCAUGUGGAAAAUUAGCGCUCAAUGUUAACAUUUGCCCACAUUGUUGCGUUGUGUUAAUGCAUUUUAAUUAUUCUCAGCCUCAAGUCCUCUGACAUUAUCUGAAA
....(((.(((((.(((.((.((......(((((.((((((...(....)...))))))..)))))((((....))))...............)).)).).)).))).))....)))... ( -24.10)
>consensus
UUUCCAGUUGCAGCGGCAUGUGGAAAAUUAGCGCUCAAUGUUAACAUUUGCCCACAUUGUUGCGUUGUGUUAAUGCAUUUUAAUUUUCCUCAGCCUCAAGUCCUCUGACAU_________
....(((.....(.(((.((.(((((((((((((.((((((...(....)...))))))..)))).(((......)))..))))))))).))))).).......)))............. (-24.71 = -24.53 +  -0.19)

alignment

secondary structure

dotplot

Window 7

Location	8,543,912 – 8,544,032
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.97
Mean single sequence MFE	-35.05
Consensus MFE	-31.64
Energy contribution	-31.83
Covariance contribution	0.19
Combinations/Pair	1.09
Mean z-score	-1.80
Structure conservation index	0.90
SVM decision value	0.51
SVM RNA-class probability	0.765739
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8543912 120 + 22224390
AAAUACAUUAACACAACGCAACAAUGUGGGCAAAUGUUAACAUUGAGCGCUAAUUUUCCACAUGCCGCUGCAACUGGAAAAUGUGGAGGCUGCUCCGGUGCAGUGAAAACGGCUGGGGAA
...........(((..(((..((((((..((....))..)))))).)))...((((((((..(((....)))..))))))))))).......(((((((...((....)).))))))).. ( -34.90)
>DroSec_CAF1 8105 120 + 1
AAAUACAUUAACACAACGCAACAAUGUGGGCAAAUGUUAACAUUGAGCGCUAAUUUUCCACAUGCCGCUGCAACUGGAAAAUGCGGAGGCUGUUCCGGUGCAGUGAAAACGGCUGGGGAA
................(((..((((((..((....))..)))))).))).....(((((.((.(((((((((.((((((...((....))..)))))))))))......))))))))))) ( -38.30)
>DroEre_CAF1 8131 120 + 1
AAAUGCAUUAACACAACGCAACAAUGUGGGCAAAUGUUAACAUUGAGCGCUAAUUUUCCACAUGCCGCUGCAACUGGAAAAUGUGGAGGUUGUUUCGGAGCAGUGAAAACGGCUGGGGAA
............(((((((..((((((..((....))..)))))).)).......((((((((.(((.......)))...)))))))))))))(((..(((.((....)).)))..))). ( -32.60)
>DroYak_CAF1 9896 120 + 1
AAAUGCAUUAACACAACGCAACAAUGUGGGCAAAUGUUAACAUUGAGCGCUAAUUUUCCACAUGCCGCUGCAACUGGAAAAUGUGCAGGCUUUUCCGGAGCAGGGAAAACGGCUGGGGAA
................(((..((((((..((....))..)))))).))).....(((((.((.((((((((..((((((((.((....)))))))))).))))......))))))))))) ( -34.40)
>consensus
AAAUACAUUAACACAACGCAACAAUGUGGGCAAAUGUUAACAUUGAGCGCUAAUUUUCCACAUGCCGCUGCAACUGGAAAAUGUGGAGGCUGUUCCGGAGCAGUGAAAACGGCUGGGGAA
................(((..((((((..((....))..)))))).))).....(((((.((.(((((((((.((((((...((....))..)))))))))))......))))))))))) (-31.64 = -31.83 +   0.19)

alignment

secondary structure

dotplot

Window 8

Location	8,543,952 – 8,544,072
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.03
Mean single sequence MFE	-34.55
Consensus MFE	-29.71
Energy contribution	-30.15
Covariance contribution	0.44
Combinations/Pair	1.09
Mean z-score	-1.50
Structure conservation index	0.86
SVM decision value	0.01
SVM RNA-class probability	0.538907
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8543952 120 + 22224390
CAUUGAGCGCUAAUUUUCCACAUGCCGCUGCAACUGGAAAAUGUGGAGGCUGCUCCGGUGCAGUGAAAACGGCUGGGGAAAAUACGCGUGGCAAGUGAGAGACAGAUGACAAAGGAAAUU
((((..((((..(((((((.((.(((((((((.(((((....(..(...)..)))))))))))......)))))).)))))))..))))....))))....................... ( -34.70)
>DroSec_CAF1 8145 120 + 1
CAUUGAGCGCUAAUUUUCCACAUGCCGCUGCAACUGGAAAAUGCGGAGGCUGUUCCGGUGCAGUGAAAACGGCUGGGGAAAAUAAGAGUGGCAAGUGAGAGGCAGAUGACAAAGGAAAUU
((((...((((.(((((((.((.(((((((((.((((((...((....))..)))))))))))......)))))).)))))))...))))...))))....................... ( -37.20)
>DroEre_CAF1 8171 120 + 1
CAUUGAGCGCUAAUUUUCCACAUGCCGCUGCAACUGGAAAAUGUGGAGGUUGUUUCGGAGCAGUGAAAACGGCUGGGGAAAAUACGAGUGGCAAGUGAGAGACAGAUGACAAAAGAAAUU
..(((....((...(((((((.(((((((((((((............))))))(((..(((.((....)).)))..))).......))))))).))).)))).))....)))........ ( -28.70)
>DroYak_CAF1 9936 120 + 1
CAUUGAGCGCUAAUUUUCCACAUGCCGCUGCAACUGGAAAAUGUGCAGGCUUUUCCGGAGCAGGGAAAACGGCUGGGGAAAAUGCGAGUGGCAAGUGAGAGACAGAUGACAAUGGAAAUU
(((((....((...(((((((.((((((((((.((((((((.((....))))))))))(((.(......).)))........))).))))))).))).)))).))....)))))...... ( -37.60)
>consensus
CAUUGAGCGCUAAUUUUCCACAUGCCGCUGCAACUGGAAAAUGUGGAGGCUGUUCCGGAGCAGUGAAAACGGCUGGGGAAAAUACGAGUGGCAAGUGAGAGACAGAUGACAAAGGAAAUU
((((...((((.(((((((.((.(((((((((.((((((...((....))..)))))))))))......)))))).)))))))...))))...))))....................... (-29.71 = -30.15 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:19 2006