Locus 8296

Sequence ID	3R_DroMel_CAF1
Location	22,151,656 – 22,151,854
Length	198
Max. P	0.919488

overview

Window 9

Location	22,151,656 – 22,151,774
Length	118
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	96.11
Mean single sequence MFE	-29.23
Consensus MFE	-26.04
Energy contribution	-26.27
Covariance contribution	0.23
Combinations/Pair	1.06
Mean z-score	-2.51
Structure conservation index	0.89
SVM decision value	0.93
SVM RNA-class probability	0.884721
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22151656 118 - 27905053
AAAUUGAGAGGGAAAUUAAUAGCUAUUGUGGAGUAUUUUCAGCCAAUCAGGUUGAACUAAUAUUAAAUAAUUGUUGUUUCUCCUAAUUGGCGGCCACCUUUUACGUGAACUUU--CAAAA
...((((((((((....((((((.(((((..(((((((((((((.....)))))))..))))))..))))).))))))..)))...((.(((...........))).))))))--))).. ( -30.90)
>DroSec_CAF1 82105 120 - 1
AAAUUGAGAGGGAAAUUAAUAGCUAUUGUGGAGUAUUUUCAGCCAAUCAGGUUGAGCUAAUAUUAAAUAAUUGUUAUUUCUCCUAAUUGCCGACCACCUUUUACGUGAACUUUCUCAUAA
....(((((((((....((((((.(((((..(((((((((((((.....)))))))..))))))..))))).))))))..))))..........(((.......))).....)))))... ( -28.40)
>DroSim_CAF1 76588 120 - 1
AAAUUGAGAGGGAAAUUAAUAGCUAUUGUGGAGUAUUUUCAGCCAAUCAGGUUGAGCUAAUAUUAAAUAAUUGUUAUUUCUCCUAAUUGCCGACCACCUUUUACGUGAACUUUCUCAUAA
....(((((((((....((((((.(((((..(((((((((((((.....)))))))..))))))..))))).))))))..))))..........(((.......))).....)))))... ( -28.40)
>consensus
AAAUUGAGAGGGAAAUUAAUAGCUAUUGUGGAGUAUUUUCAGCCAAUCAGGUUGAGCUAAUAUUAAAUAAUUGUUAUUUCUCCUAAUUGCCGACCACCUUUUACGUGAACUUUCUCAUAA
....(((((((((....((((((.(((((..(((((((((((((.....)))))))..))))))..))))).))))))..))))..........(((.......))).....)))))... (-26.04 = -26.27 +   0.23)

alignment

secondary structure

dotplot

Window 0

Location	22,151,694 – 22,151,814
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.78
Mean single sequence MFE	-27.60
Consensus MFE	-27.94
Energy contribution	-27.50
Covariance contribution	-0.44
Combinations/Pair	1.05
Mean z-score	-1.95
Structure conservation index	1.01
SVM decision value	1.13
SVM RNA-class probability	0.919488
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22151694 120 - 27905053
UACAAAUAGUUCUAAGCUGAUUGCUCUCUAAUUACAGUGCAAAUUGAGAGGGAAAUUAAUAGCUAUUGUGGAGUAUUUUCAGCCAAUCAGGUUGAACUAAUAUUAAAUAAUUGUUGUUUC
..(((.((((.....)))).)))((((((.....((((....)))))))))).....((((((.(((((..(((((((((((((.....)))))))..))))))..))))).)))))).. ( -27.70)
>DroSec_CAF1 82145 120 - 1
UACAAAUAGUUCUAAGCUGAUUGCUCUCUAAAUUCAGUGCAAAUUGAGAGGGAAAUUAAUAGCUAUUGUGGAGUAUUUUCAGCCAAUCAGGUUGAGCUAAUAUUAAAUAAUUGUUAUUUC
..(((.((((.....)))).)))(((((.....(((((....)))))))))).....((((((.(((((..(((((((((((((.....)))))))..))))))..))))).)))))).. ( -27.70)
>DroSim_CAF1 76628 120 - 1
UACAAAUAGUUCUAAGCUGAUUGCUCUCUAAUUACAGUGCAAAUUGAGAGGGAAAUUAAUAGCUAUUGUGGAGUAUUUUCAGCCAAUCAGGUUGAGCUAAUAUUAAAUAAUUGUUAUUUC
..(((.((((.....)))).)))((((((.....((((....)))))))))).....((((((.(((((..(((((((((((((.....)))))))..))))))..))))).)))))).. ( -27.40)
>consensus
UACAAAUAGUUCUAAGCUGAUUGCUCUCUAAUUACAGUGCAAAUUGAGAGGGAAAUUAAUAGCUAUUGUGGAGUAUUUUCAGCCAAUCAGGUUGAGCUAAUAUUAAAUAAUUGUUAUUUC
..(((.((((.....)))).)))((((((.....((((....)))))))))).....((((((.(((((..(((((((((((((.....)))))))..))))))..))))).)))))).. (-27.94 = -27.50 +  -0.44)

alignment

secondary structure

dotplot

Window 1

Location	22,151,734 – 22,151,854
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-24.11
Consensus MFE	-23.43
Energy contribution	-23.77
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.50
Structure conservation index	0.97
SVM decision value	0.08
SVM RNA-class probability	0.574637
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22151734 120 - 27905053
UCAACCUCAACAGCUUCAUAUGUAUUUCCAUUAACAAGUCUACAAAUAGUUCUAAGCUGAUUGCUCUCUAAUUACAGUGCAAAUUGAGAGGGAAAUUAAUAGCUAUUGUGGAGUAUUUUC
....((.(((.((((........((((((.............(((.((((.....)))).)))(((((.((((........)))))))))))))))....)))).))).))......... ( -24.50)
>DroSec_CAF1 82185 120 - 1
UCAACCUCAACAGCUUCAUAUGUAUUUCCAUUAACAACUCUACAAAUAGUUCUAAGCUGAUUGCUCUCUAAAUUCAGUGCAAAUUGAGAGGGAAAUUAAUAGCUAUUGUGGAGUAUUUUC
....((.(((.((((........((((((.............(((.((((.....)))).)))(((((.................)))))))))))....)))).))).))......... ( -23.33)
>DroSim_CAF1 76668 120 - 1
UCAACCUCAACAGCUUCAUAUGUAUUUCCAUUAACAACUCUACAAAUAGUUCUAAGCUGAUUGCUCUCUAAUUACAGUGCAAAUUGAGAGGGAAAUUAAUAGCUAUUGUGGAGUAUUUUC
....((.(((.((((........((((((.............(((.((((.....)))).)))(((((.((((........)))))))))))))))....)))).))).))......... ( -24.50)
>consensus
UCAACCUCAACAGCUUCAUAUGUAUUUCCAUUAACAACUCUACAAAUAGUUCUAAGCUGAUUGCUCUCUAAUUACAGUGCAAAUUGAGAGGGAAAUUAAUAGCUAUUGUGGAGUAUUUUC
....((.(((.((((........((((((.............(((.((((.....)))).)))(((((.((((........)))))))))))))))....)))).))).))......... (-23.43 = -23.77 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:08:13 2006