Locus 7558

Sequence ID	2L_DroMel_CAF1
Location	20,935,760 – 20,936,042
Length	282
Max. P	0.971001

overview

Window 0

Location	20,935,760 – 20,935,868
Length	108
Sequences	3
Columns	108
Reading direction	reverse
Mean pairwise identity	98.77
Mean single sequence MFE	-23.97
Consensus MFE	-22.73
Energy contribution	-23.07
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.91
Structure conservation index	0.95
SVM decision value	1.67
SVM RNA-class probability	0.971001
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20935760 108 - 22407834
CUGCUCCAAAUUCGAAUGUGAAACAUGGAAAAAGUUAUACCAAACAUGGAAAUGUAUGUCAUUGACUAAAUGACAAAUCACUUGACAGUUUUUCUAUUCUCACACAAU
................(((((...(((((((((((((......((((....)))).(((((((.....))))))).......))))..)))))))))..))))).... ( -22.90)
>DroSec_CAF1 22105 108 - 1
CUGCUCCAAAUUCGAAUGUGCAACAUGGAAAAAGUUAUACCAAACAUGGAAAUGUAUGUCAUUGACUAAAUGACAAAUCACUUGACAGUUUUUCUAUUCUCGCACAAU
................(((((...(((((((((((((......((((....)))).(((((((.....))))))).......))))..)))))))))....))))).. ( -24.50)
>DroSim_CAF1 20422 108 - 1
CUGCUCCAAAUUCGAAUGUGCAACAUGGAAAAAGUUAUACCAAACAUGGAAAUGUAUGUCAUUGACUAAAUGACAAAUCACUUGACAGUUUUUCUAUUCUCGCACAAU
................(((((...(((((((((((((......((((....)))).(((((((.....))))))).......))))..)))))))))....))))).. ( -24.50)
>consensus
CUGCUCCAAAUUCGAAUGUGCAACAUGGAAAAAGUUAUACCAAACAUGGAAAUGUAUGUCAUUGACUAAAUGACAAAUCACUUGACAGUUUUUCUAUUCUCGCACAAU
................(((((...(((((((((((((......((((....)))).(((((((.....))))))).......))))..)))))))))....))))).. (-22.73 = -23.07 +   0.33)

alignment

secondary structure

dotplot

Window 1

Location	20,935,868 – 20,935,980
Length	112
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	93.89
Mean single sequence MFE	-41.11
Consensus MFE	-39.04
Energy contribution	-38.60
Covariance contribution	-0.44
Combinations/Pair	1.06
Mean z-score	-1.69
Structure conservation index	0.95
SVM decision value	0.39
SVM RNA-class probability	0.717807
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20935868 112 + 22407834
UUCCCGGCGCUGCUGUUGUAAUUGAAGCAUGUAAUGCAGCAAACCCAACUGCAGA--------CCGGUGACCUCCGCCCCCGGCAGUUGGGGGAAUUGUCAUACAAAAGCUUUUGGGAGC
(((((((....(((.(((((.(((..((((...))))..))).(((((((((...--------..((((.....))))....)))))))))..........))))).)))..))))))). ( -40.90)
>DroSec_CAF1 22213 120 + 1
UUCCCGCCGCUGCUGUUGUAAUUGAAGCAUGUAAUGCAGCAAACCCAACUGCAGACCUCCCAACCGGUGACCUCCGCCCCCGGCAGUCGGGGGAAUUGUCAUACAAAAGCUUUUGGGAGC
.........((((.((((...(((..((((...))))..)))...)))).))))..(((((((...(((((.....((((((.....))))))....)))))..........))))))). ( -40.22)
>DroSim_CAF1 20530 120 + 1
UUCCCGCCGCUGCUGUUGUAAUUGAAGCAUGUAAUGCAGCAAACCCAACUGCAGACCUCCCAACCGGUGACCUCCGCCCCCGGCAGCCGGGGGAAUUGUCAUACAAAAGCUUUUGGGAGC
.........((((.((((...(((..((((...))))..)))...)))).))))..(((((((...(((((.....(((((((...)))))))....)))))..........))))))). ( -42.22)
>consensus
UUCCCGCCGCUGCUGUUGUAAUUGAAGCAUGUAAUGCAGCAAACCCAACUGCAGACCUCCCAACCGGUGACCUCCGCCCCCGGCAGUCGGGGGAAUUGUCAUACAAAAGCUUUUGGGAGC
((((((...((((.((((...(((..((((...))))..)))...)))).))))............(((((.....(((((((...)))))))....)))))...........)))))). (-39.04 = -38.60 +  -0.44)

alignment

secondary structure

dotplot

Window 2

Location	20,935,940 – 20,936,042
Length	102
Sequences	3
Columns	102
Reading direction	reverse
Mean pairwise identity	98.69
Mean single sequence MFE	-30.97
Consensus MFE	-30.89
Energy contribution	-30.67
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-1.33
Structure conservation index	1.00
SVM decision value	-0.04
SVM RNA-class probability	0.515133
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20935940 102 - 22407834
GGCUUGUGGGGCGGAUUUGUUGCCUUGAGGUCAUUAUAUCGAAAACAGCAGUUGCCCAAAAUGCUCCCAAAAGCUUUUGUAUGACAAUUCCCCCAACUGCCG
(((...(((((.((((((((((..((((..........))))...)))))((((..(((((.(((......))))))))..))))))))))))))...))). ( -31.50)
>DroSec_CAF1 22293 102 - 1
GGCUUGUGGGGCGGAUUUGUUGCCUUGAGGUCAUUAUAUCGAAAACAGCAGUUGCCCAAAAUGCUCCCAAAAGCUUUUGUAUGACAAUUCCCCCGACUGCCG
(((...(((((.((((((((((..((((..........))))...)))))((((..(((((.(((......))))))))..))))))))))))))...))). ( -30.80)
>DroSim_CAF1 20610 102 - 1
GGCUUGUGGGGCGGAUUUGUUGCCUUGAGGUCAUUAUAUCGAAAACAGCAGUUGCCCAAAAUGCUCCCAAAAGCUUUUGUAUGACAAUUCCCCCGGCUGCCG
(((..((.(((.(((..(((((..((((..........))))...)))))((((..(((((.(((......))))))))..))))...)))))).)).))). ( -30.60)
>consensus
GGCUUGUGGGGCGGAUUUGUUGCCUUGAGGUCAUUAUAUCGAAAACAGCAGUUGCCCAAAAUGCUCCCAAAAGCUUUUGUAUGACAAUUCCCCCGACUGCCG
(((...(((((.((((((((((..((((..........))))...)))))((((..(((((.(((......))))))))..))))))))))))))...))). (-30.89 = -30.67 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:39:50 2006