Locus 5700

Sequence ID	2L_DroMel_CAF1
Location	16,217,386 – 16,217,522
Length	136
Max. P	0.947967

overview

Window 0

Location	16,217,386 – 16,217,491
Length	105
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	91.46
Mean single sequence MFE	-23.57
Consensus MFE	-19.14
Energy contribution	-19.45
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-1.64
Structure conservation index	0.81
SVM decision value	0.27
SVM RNA-class probability	0.659915
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16217386 105 + 22407834
AAAUCUCGGAGAUUUGAAAUCUCAUUGACAAUUGGAAAUGUGACCAAAAUCAUGCAUUUCCGUCGCCAUCUCUGGCCAAACCAGACCAAUGCAGCCAGCCGCCCA
...((...(((((.....)))))...)).....((((((((............))))))))((.((....(((((.....))))).....)).)).......... ( -21.80)
>DroSec_CAF1 134728 98 + 1
AAAUCUCGGAGAUUUGAAAUCUCAUUGACAAUUGGAAAUGUGACCAAAAUCAUGCAUUUCCGUCGCCAUCUCUGGUCAAACCAGACCAGUGCAG-------CCCA
........(((((.....)))))...(((....((((((((............)))))))))))((...(.((((((......)))))).)..)-------)... ( -25.00)
>DroSim_CAF1 136142 98 + 1
AAAUCUCGGAGAUUUGAAAUCUCAUUGACAAUUGGAAAUGUGACCAAAAUCAUGCAUUUCCGUCGCCAUCUCUGGUCAAACCAGACCAGUGCAG-------CCCA
........(((((.....)))))...(((....((((((((............)))))))))))((...(.((((((......)))))).)..)-------)... ( -25.00)
>DroEre_CAF1 138282 98 + 1
AAAUCUCGGAGAUUUGAAAUCUCAUUGACAAUUGGAAAUGUGACCAAAAUCAUGCAUUUCCGUCGCCAUCUCUGACCAGAGUAGACCAGACCAG-------GGCA
........(((((.....)))))...(((....((((((((............)))))))))))(((...((((..(......)..))))....-------))). ( -22.50)
>consensus
AAAUCUCGGAGAUUUGAAAUCUCAUUGACAAUUGGAAAUGUGACCAAAAUCAUGCAUUUCCGUCGCCAUCUCUGGCCAAACCAGACCAGUGCAG_______CCCA
........(((((.....)))))...(((....((((((((............)))))))))))((....(((((.....))))).....))............. (-19.14 = -19.45 +   0.31)

alignment

secondary structure

dotplot

Window 1

Location	16,217,386 – 16,217,491
Length	105
Sequences	4
Columns	105
Reading direction	reverse
Mean pairwise identity	91.46
Mean single sequence MFE	-29.02
Consensus MFE	-26.60
Energy contribution	-25.98
Covariance contribution	-0.63
Combinations/Pair	1.11
Mean z-score	-1.41
Structure conservation index	0.92
SVM decision value	0.26
SVM RNA-class probability	0.657406
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16217386 105 - 22407834
UGGGCGGCUGGCUGCAUUGGUCUGGUUUGGCCAGAGAUGGCGACGGAAAUGCAUGAUUUUGGUCACAUUUCCAAUUGUCAAUGAGAUUUCAAAUCUCCGAGAUUU
...((((....)))).((((...((((((((((....))))((((((((((..((((....)))))))))))....)))..........)))))).))))..... ( -31.60)
>DroSec_CAF1 134728 98 - 1
UGGG-------CUGCACUGGUCUGGUUUGACCAGAGAUGGCGACGGAAAUGCAUGAUUUUGGUCACAUUUCCAAUUGUCAAUGAGAUUUCAAAUCUCCGAGAUUU
...(-------((((.((((((......)))))).).))))((((((((((..((((....)))))))))))....)))...(((((.....)))))........ ( -28.70)
>DroSim_CAF1 136142 98 - 1
UGGG-------CUGCACUGGUCUGGUUUGACCAGAGAUGGCGACGGAAAUGCAUGAUUUUGGUCACAUUUCCAAUUGUCAAUGAGAUUUCAAAUCUCCGAGAUUU
...(-------((((.((((((......)))))).).))))((((((((((..((((....)))))))))))....)))...(((((.....)))))........ ( -28.70)
>DroEre_CAF1 138282 98 - 1
UGCC-------CUGGUCUGGUCUACUCUGGUCAGAGAUGGCGACGGAAAUGCAUGAUUUUGGUCACAUUUCCAAUUGUCAAUGAGAUUUCAAAUCUCCGAGAUUU
.(((-------....((((..(......)..))))...)))((((((((((..((((....)))))))))))....)))...(((((.....)))))........ ( -27.10)
>consensus
UGGG_______CUGCACUGGUCUGGUUUGACCAGAGAUGGCGACGGAAAUGCAUGAUUUUGGUCACAUUUCCAAUUGUCAAUGAGAUUUCAAAUCUCCGAGAUUU
................((((((......))))))...((((((.(((((((..((((....)))))))))))..))))))..(((((.....)))))........ (-26.60 = -25.98 +  -0.63)

alignment

secondary structure

dotplot

Window 2

Location	16,217,423 – 16,217,522
Length	99
Sequences	4
Columns	108
Reading direction	forward
Mean pairwise identity	78.73
Mean single sequence MFE	-20.61
Consensus MFE	-10.75
Energy contribution	-12.31
Covariance contribution	1.56
Combinations/Pair	1.05
Mean z-score	-2.75
Structure conservation index	0.52
SVM decision value	1.38
SVM RNA-class probability	0.947967
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16217423 99 + 22407834
AUGUGACCAAAAUCAUGCAUUUCCGUCGCCAUCUCUGGCCAAACCAGACCAAUGCAGCCAGCCGCCCAUCGCUGCCCACCCCCA---AAGCC------CAAAUCCACC
..(((((..((((.....))))..)))))....(((((.....))))).....(((((.(........).))))).........---.....------.......... ( -16.60)
>DroSec_CAF1 134765 91 + 1
AUGUGACCAAAAUCAUGCAUUUCCGUCGCCAUCUCUGGUCAAACCAGACCAGUGCAG-------CCCAUCGCUGCACAAAACCA---AA-CC------CAAACCCACC
..(((((..((((.....))))..)))))......(((((......)))))((((((-------(.....))))))).......---..-..------.......... ( -23.90)
>DroSim_CAF1 136179 91 + 1
AUGUGACCAAAAUCAUGCAUUUCCGUCGCCAUCUCUGGUCAAACCAGACCAGUGCAG-------CCCAUCGCUGCACAAAACCA---AA-CC------CAAGCCCACC
..(((((..((((.....))))..)))))......(((((......)))))((((((-------(.....))))))).......---..-..------.......... ( -23.90)
>DroEre_CAF1 138319 99 + 1
AUGUGACCAAAAUCAUGCAUUUCCGUCGCCAUCUCUGACCAGAGUAGACCAGACCAG-------GGCAAUGCAACCCAGCCC-AGGCAA-CCAACCAACCAGCCGACC
............((.((((((((((((.....((((....)))).......)))..)-------)).)))))).........-.(((..-...........))))).. ( -18.02)
>consensus
AUGUGACCAAAAUCAUGCAUUUCCGUCGCCAUCUCUGGCCAAACCAGACCAGUGCAG_______CCCAUCGCUGCACAAAACCA___AA_CC______CAAACCCACC
..(((((..((((.....))))..)))))....(((((.....)))))...((((((..............))))))............................... (-10.75 = -12.31 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:32 2006