Locus 5100

Sequence ID	2R_DroMel_CAF1
Location	16,591,082 – 16,591,174
Length	92
Max. P	0.939262

overview

Window 3

Location	16,591,082 – 16,591,174
Length	92
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	89.24
Mean single sequence MFE	-22.70
Consensus MFE	-17.30
Energy contribution	-18.18
Covariance contribution	0.88
Combinations/Pair	1.09
Mean z-score	-2.34
Structure conservation index	0.76
SVM decision value	1.30
SVM RNA-class probability	0.939262
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16591082 92 + 20766785
AAUGUCACCAUUCUUCGGUGACCUCAAAUCGGGUACAGCGCGAUUAAACCGCACUGCAAUGCAAAUCGCUCAGAUAUCGGGCUAUACUCAUU
...((((((.......))))))........(((((.(((.((((......(((......)))..(((.....))))))).))).)))))... ( -27.10)
>DroSec_CAF1 12668 84 + 1
AAUGUCACCAUUCUUCGGUGACCUCAAAUCAGGUACAACGCGAUUAAACCGCACUGCAAUGCAAAUCGGCCAGAU--------AUACUCAUU
...((((((.......)))))).....(((.(((.....(((.......)))..(((...))).....))).)))--------......... ( -16.90)
>DroSim_CAF1 12713 92 + 1
AAUGUCACCAUUCUUCGGUGACCUCAAAUCAGGUACAGCCCGAUUAAACCGCACUGCAAUGCAAAUCGCCCAGAUAUCGGGCUAUACUCAUU
...((((((.......)))))).........((((.((((((((......(((......)))..(((.....))))))))))).)))).... ( -28.40)
>DroEre_CAF1 12662 92 + 1
AAUGUCACUAUUCUUCAGUGACCUCAAAUCAGGUUCAGCACGAUUAAACCGCACUGCAAUGCAAAUCGCAGAGAUAUCGGGCUCUACUCAUU
...((((((.......)))))).........(((..(((.((((.......(.((((.((....)).)))).)..)))).)))..))).... ( -18.70)
>DroYak_CAF1 13056 92 + 1
AAUGUCACUUUUCUUCAGUGACCUCAAAUCAGGUUCAGCGCGAUUAAUCCGCACUGCAAUGCAAAUCGCAGAGAUAUCGGGCUAAACUCAUU
...((((((.......)))))).........((((.(((.((((...((.((..(((...)))....)).))...)))).))).)))).... ( -22.40)
>consensus
AAUGUCACCAUUCUUCGGUGACCUCAAAUCAGGUACAGCGCGAUUAAACCGCACUGCAAUGCAAAUCGCACAGAUAUCGGGCUAUACUCAUU
...((((((.......)))))).........((((.(((.((((......(((......)))..(((.....))))))).))).)))).... (-17.30 = -18.18 +   0.88)

alignment

secondary structure

dotplot

Window 4

Location	16,591,082 – 16,591,174
Length	92
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	89.24
Mean single sequence MFE	-27.68
Consensus MFE	-20.58
Energy contribution	-21.66
Covariance contribution	1.08
Combinations/Pair	1.08
Mean z-score	-1.91
Structure conservation index	0.74
SVM decision value	0.48
SVM RNA-class probability	0.752967
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16591082 92 - 20766785
AAUGAGUAUAGCCCGAUAUCUGAGCGAUUUGCAUUGCAGUGCGGUUUAAUCGCGCUGUACCCGAUUUGAGGUCACCGAAGAAUGGUGACAUU
..((.(((((((.((((...(((((....(((((....)))))))))))))).))))))).)).......(((((((.....)))))))... ( -28.40)
>DroSec_CAF1 12668 84 - 1
AAUGAGUAU--------AUCUGGCCGAUUUGCAUUGCAGUGCGGUUUAAUCGCGUUGUACCUGAUUUGAGGUCACCGAAGAAUGGUGACAUU
.....(((.--------(((.....))).)))..(((((((((((...)))))))))))...........(((((((.....)))))))... ( -21.70)
>DroSim_CAF1 12713 92 - 1
AAUGAGUAUAGCCCGAUAUCUGGGCGAUUUGCAUUGCAGUGCGGUUUAAUCGGGCUGUACCUGAUUUGAGGUCACCGAAGAAUGGUGACAUU
.....((((((((((((..(((.(((((....)))))....)))....))))))))))))..........(((((((.....)))))))... ( -34.40)
>DroEre_CAF1 12662 92 - 1
AAUGAGUAGAGCCCGAUAUCUCUGCGAUUUGCAUUGCAGUGCGGUUUAAUCGUGCUGAACCUGAUUUGAGGUCACUGAAGAAUAGUGACAUU
.....((((((........))))))...........(((..((((...))))..))).............(((((((.....)))))))... ( -24.30)
>DroYak_CAF1 13056 92 - 1
AAUGAGUUUAGCCCGAUAUCUCUGCGAUUUGCAUUGCAGUGCGGAUUAAUCGCGCUGAACCUGAUUUGAGGUCACUGAAGAAAAGUGACAUU
.....(((((((.((((...((((((...(((...))).))))))...)))).)))))))..........((((((.......))))))... ( -29.60)
>consensus
AAUGAGUAUAGCCCGAUAUCUGGGCGAUUUGCAUUGCAGUGCGGUUUAAUCGCGCUGUACCUGAUUUGAGGUCACCGAAGAAUGGUGACAUU
.....(((((((.(((((((.....)))((((((....))))))....)))).)))))))..........((((((.......))))))... (-20.58 = -21.66 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:31 2006