Locus 9963

Sequence ID	3R_DroMel_CAF1
Location	26,684,718 – 26,684,918
Length	200
Max. P	0.998895

overview

Window 7

Location	26,684,718 – 26,684,838
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.67
Mean single sequence MFE	-34.26
Consensus MFE	-28.02
Energy contribution	-28.74
Covariance contribution	0.72
Combinations/Pair	1.12
Mean z-score	-1.42
Structure conservation index	0.82
SVM decision value	0.06
SVM RNA-class probability	0.564586
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26684718 120 + 27905053
AUUAGGGCUUGCUGCGCUCCCAGGAUACAAGGAUAUGUGUGCAGGAUGUGCAGAGCGCCUAAAACAAAAGGGGUAGUUAGCGAGUUGAACUUGCCAGCGAAACGCAACAAAAAAGCAAGU
......((((((((((((((..(.(((((......))))).).))).))))...((((((........)))....(((.(((((.....))))).)))....)))........))))))) ( -36.60)
>DroSec_CAF1 275461 120 + 1
AUUAGGGCUUGCUGCGCUCCCAGGAUACAAGGAUAUGUGUGCAGGAUGUGCGGAGCGCCUAAAACAAAAGGGGUAGUUAGCGAGUUGGACUUGCCAGCGAAACGCUACAAAAAAGCAAGU
......((((((((((((((....(((((......)))))(((.....)))))))))).................((.((((.(((((.....)))))....)))))).....))))))) ( -38.70)
>DroSim_CAF1 272202 120 + 1
AUUAGGGUUUGCUGCGCUCCCAGGAUACAAGGAUAUGUGUGCAGGAUGUGCGGAGCGCCUAAAACAAAAGGGGUAGUUAGCGAGUUGGACUUGCCAGCGAAACGCUACAAAAAAGCAAGU
.......(((((((((((((....(((((......)))))(((.....)))))))))).................((.((((.(((((.....)))))....)))))).....)))))). ( -35.10)
>DroEre_CAF1 291413 120 + 1
AUUAGAGUUUUCUGCGCUCCCAGGAUACAAGGAUAUGUGCGCAGGAUGUGCGGAGCGCCUAAAACAAAAGGGGUAGUUAGCGAUUUGAAUUUGCCAGCGAAACGCUACAAAAAUGCAAGU
......(((((..(((((((......(((......)))((((.....)))))))))))..)))))....((.((.(((.((((.......)))).)))...)).)).............. ( -30.80)
>DroYak_CAF1 280387 120 + 1
AUUAGAGUUUGCAGCGCUCCCAGGAUAUAAGGAUAUGUGCGCAGGAUGUGCGGAGCGCCUAAAACAAAAGGGGUAGUUAGCGAUUUGAAUUUGCCAGCGAAACGUUACAAAAAAGCAAGU
.......(((((.(((((((....(((((....)))))((((.....))))))))))).........((.(..(.(((.((((.......)))).))).)..).))........))))). ( -30.10)
>consensus
AUUAGGGUUUGCUGCGCUCCCAGGAUACAAGGAUAUGUGUGCAGGAUGUGCGGAGCGCCUAAAACAAAAGGGGUAGUUAGCGAGUUGAACUUGCCAGCGAAACGCUACAAAAAAGCAAGU
......((((.(((((((((..(.(((((......))))).).))).))))))(((((((........)))....(((.(((((.....))))).)))....))))......)))).... (-28.02 = -28.74 +   0.72)

alignment

secondary structure

dotplot

Window 8

Location	26,684,718 – 26,684,838
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.67
Mean single sequence MFE	-28.46
Consensus MFE	-23.28
Energy contribution	-23.68
Covariance contribution	0.40
Combinations/Pair	1.08
Mean z-score	-1.42
Structure conservation index	0.82
SVM decision value	0.06
SVM RNA-class probability	0.563121
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26684718 120 - 27905053
ACUUGCUUUUUUGUUGCGUUUCGCUGGCAAGUUCAACUCGCUAACUACCCCUUUUGUUUUAGGCGCUCUGCACAUCCUGCACACAUAUCCUUGUAUCCUGGGAGCGCAGCAAGCCCUAAU
.((((((.....((((((....(((....)))......))).))).................((((((((((.....)))..(((......)))......)))))))))))))....... ( -27.90)
>DroSec_CAF1 275461 120 - 1
ACUUGCUUUUUUGUAGCGUUUCGCUGGCAAGUCCAACUCGCUAACUACCCCUUUUGUUUUAGGCGCUCCGCACAUCCUGCACACAUAUCCUUGUAUCCUGGGAGCGCAGCAAGCCCUAAU
.((((((......(((((....(((....)))......)))))...................((((((((((.....)))..(((......)))......)))))))))))))....... ( -31.80)
>DroSim_CAF1 272202 120 - 1
ACUUGCUUUUUUGUAGCGUUUCGCUGGCAAGUCCAACUCGCUAACUACCCCUUUUGUUUUAGGCGCUCCGCACAUCCUGCACACAUAUCCUUGUAUCCUGGGAGCGCAGCAAACCCUAAU
(((((((.......((((...))))))))))).......(((........((........))((((((((((.....)))..(((......)))......)))))))))).......... ( -29.71)
>DroEre_CAF1 291413 120 - 1
ACUUGCAUUUUUGUAGCGUUUCGCUGGCAAAUUCAAAUCGCUAACUACCCCUUUUGUUUUAGGCGCUCCGCACAUCCUGCGCACAUAUCCUUGUAUCCUGGGAGCGCAGAAAACUCUAAU
..(((....(((((((((...)))).)))))..)))...................(((((..((((((((((.....)))..(((......)))......)))))))..)))))...... ( -29.00)
>DroYak_CAF1 280387 120 - 1
ACUUGCUUUUUUGUAACGUUUCGCUGGCAAAUUCAAAUCGCUAACUACCCCUUUUGUUUUAGGCGCUCCGCACAUCCUGCGCACAUAUCCUUAUAUCCUGGGAGCGCUGCAAACUCUAAU
..((((......)))).((((.((((((...........))))..................(((((((((((.....)))....(((....)))......))))))))))))))...... ( -23.90)
>consensus
ACUUGCUUUUUUGUAGCGUUUCGCUGGCAAGUUCAACUCGCUAACUACCCCUUUUGUUUUAGGCGCUCCGCACAUCCUGCACACAUAUCCUUGUAUCCUGGGAGCGCAGCAAACCCUAAU
..((((...(((((((((...)))).)))))...............................((((((((((.....)))..(((......)))......))))))).))))........ (-23.28 = -23.68 +   0.40)

alignment

secondary structure

dotplot

Window 9

Location	26,684,758 – 26,684,878
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.50
Mean single sequence MFE	-30.92
Consensus MFE	-29.38
Energy contribution	-29.54
Covariance contribution	0.16
Combinations/Pair	1.08
Mean z-score	-1.49
Structure conservation index	0.95
SVM decision value	1.52
SVM RNA-class probability	0.961274
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26684758 120 + 27905053
GCAGGAUGUGCAGAGCGCCUAAAACAAAAGGGGUAGUUAGCGAGUUGAACUUGCCAGCGAAACGCAACAAAAAAGCAAGUUCAGCAGUUCGAAACUGAAAUCGGGAUAUUGGCAAACCAA
...((...(((.((((((((..........)))).........(((((((((((..(((...))).........))))))))))).))))....(((....))).......)))..)).. ( -30.50)
>DroSec_CAF1 275501 120 + 1
GCAGGAUGUGCGGAGCGCCUAAAACAAAAGGGGUAGUUAGCGAGUUGGACUUGCCAGCGAAACGCUACAAAAAAGCAAGUUCAGCAGUUCGAAACUGAAAUCGGGAUAUUGGCAAACCAA
((..(((((.(.((((.(((........))).))((((..((((((((((((((.((((...))))........)))))))))))...))).))))....)).).))))).))....... ( -33.20)
>DroSim_CAF1 272242 120 + 1
GCAGGAUGUGCGGAGCGCCUAAAACAAAAGGGGUAGUUAGCGAGUUGGACUUGCCAGCGAAACGCUACAAAAAAGCAAGUUCAGCAGUUCGAAACUGAAAUCGGGAUAUUGGCAAACCAA
((..(((((.(.((((.(((........))).))((((..((((((((((((((.((((...))))........)))))))))))...))).))))....)).).))))).))....... ( -33.20)
>DroEre_CAF1 291453 120 + 1
GCAGGAUGUGCGGAGCGCCUAAAACAAAAGGGGUAGUUAGCGAUUUGAAUUUGCCAGCGAAACGCUACAAAAAUGCAAGUUCAGUAGUUCGAAACUGAAAUCGGGAUAUUGGCAAACCAA
((..(((((.(.((((.(((........))).))((((..(((.((((((((((.((((...))))........))))))))))....))).))))....)).).))))).))....... ( -29.30)
>DroYak_CAF1 280427 120 + 1
GCAGGAUGUGCGGAGCGCCUAAAACAAAAGGGGUAGUUAGCGAUUUGAAUUUGCCAGCGAAACGUUACAAAAAAGCAAGUUCUGCAGUUCGAAACUGAAAUCGGGAUAUUGGCAAACCAA
(((((((.(((...((.(((........))).)).(((.((((.......)))).)))................))).)))))))..(((((........)))))...((((....)))) ( -28.40)
>consensus
GCAGGAUGUGCGGAGCGCCUAAAACAAAAGGGGUAGUUAGCGAGUUGAACUUGCCAGCGAAACGCUACAAAAAAGCAAGUUCAGCAGUUCGAAACUGAAAUCGGGAUAUUGGCAAACCAA
((..(((((.(.((((.(((........))).))((((..((((((((((((((.((((...))))........)))))))))))...))).))))....)).).))))).))....... (-29.38 = -29.54 +   0.16)

alignment

secondary structure

dotplot

Window 0

Location	26,684,798 – 26,684,918
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.00
Mean single sequence MFE	-35.52
Consensus MFE	-34.50
Energy contribution	-33.54
Covariance contribution	-0.96
Combinations/Pair	1.13
Mean z-score	-1.94
Structure conservation index	0.97
SVM decision value	3.27
SVM RNA-class probability	0.998895
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26684798 120 + 27905053
CGAGUUGAACUUGCCAGCGAAACGCAACAAAAAAGCAAGUUCAGCAGUUCGAAACUGAAAUCGGGAUAUUGGCAAACCAAUUUUUGAGGGCUUUUGUUUCGCUGAACGACGCGAGUAAGC
...(((..(((((((((((((((((.........))((((((..((((.....))))...((((((.(((((....)))))))))))))))))..)))))))))......)))))).))) ( -34.60)
>DroSec_CAF1 275541 120 + 1
CGAGUUGGACUUGCCAGCGAAACGCUACAAAAAAGCAAGUUCAGCAGUUCGAAACUGAAAUCGGGAUAUUGGCAAACCAAUUUUCGAGGGCUUUUGUUUCGCUGAACGACGCGAGUAAGC
...(((..((((((((((((((((((.......)))((((((..((((.....))))...(((..(.(((((....))))))..)))))))))..)))))))))......)))))).))) ( -39.00)
>DroSim_CAF1 272282 120 + 1
CGAGUUGGACUUGCCAGCGAAACGCUACAAAAAAGCAAGUUCAGCAGUUCGAAACUGAAAUCGGGAUAUUGGCAAACCAAUUUUCGAGGGCUUUUGUUUCGCUGAACGACGCGAGUAAGC
...(((..((((((((((((((((((.......)))((((((..((((.....))))...(((..(.(((((....))))))..)))))))))..)))))))))......)))))).))) ( -39.00)
>DroEre_CAF1 291493 120 + 1
CGAUUUGAAUUUGCCAGCGAAACGCUACAAAAAUGCAAGUUCAGUAGUUCGAAACUGAAAUCGGGAUAUUGGCAAACCAAUUUUUGAGGGCUUUUGUUUUGCUGAACGACGCGAGUAAGC
.........(((((..(((....((.........))..(((((((((..(((((((....((((((.(((((....))))))))))).)).)))))..)))))))))..)))..))))). ( -32.10)
>DroYak_CAF1 280467 120 + 1
CGAUUUGAAUUUGCCAGCGAAACGUUACAAAAAAGCAAGUUCUGCAGUUCGAAACUGAAAUCGGGAUAUUGGCAAACCAAUUUUCGAGGGCUUUUGUUUCGCUGAACGACGCGAGUAAGC
........((((((((((((((((((.......)))((((((..((((.....))))...(((..(.(((((....))))))..)))))))))..)))))))))......)))))).... ( -32.90)
>consensus
CGAGUUGAACUUGCCAGCGAAACGCUACAAAAAAGCAAGUUCAGCAGUUCGAAACUGAAAUCGGGAUAUUGGCAAACCAAUUUUCGAGGGCUUUUGUUUCGCUGAACGACGCGAGUAAGC
........(((((((((((((((((.........))((((((..((((.....))))...((((((.(((((....)))))))))))))))))..)))))))))......)))))).... (-34.50 = -33.54 +  -0.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:45:51 2006