Locus 5511

Sequence ID	X_DroMel_CAF1
Location	14,275,339 – 14,275,518
Length	179
Max. P	0.987715

overview

Window 2

Location	14,275,339 – 14,275,444
Length	105
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.94
Mean single sequence MFE	-28.26
Consensus MFE	-21.30
Energy contribution	-20.98
Covariance contribution	-0.32
Combinations/Pair	1.15
Mean z-score	-2.20
Structure conservation index	0.75
SVM decision value	0.96
SVM RNA-class probability	0.890938
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14275339 105 + 22224390
AAAUCCGGCUGAAUUCAAAAUGCAAUCAAAUUUAUGCAUAACAAUAUUUGGCGAGCUCAAGGAUUGGCAA-AG--------------UAUGUGAGUGAGUUUUCGCCAAUUACAGUGGAG
...((((.(((........(((((..........))))).....((.((((((((((((....((.(((.-..--------------..))).)))))))..))))))).))))))))). ( -26.50)
>DroSec_CAF1 15976 106 + 1
GAAUCCGGCUGAAAUCAAAAUGCAAUCAAAUUUAUGUAUAACAAUAUUUGGCGAGCUCAAGGAUUGGCAAAAG--------------UAUGUGAGUGAGUUUUCGCCAAUUACAGUGGAG
...((((.(((........(((((..........))))).....((.((((((((((((.......((....)--------------).......)))))..))))))).))))))))). ( -25.14)
>DroSim_CAF1 19480 106 + 1
GAAUCCGGCUGAAAUCAAAAUGCAAUCAAAUUUAUGCAUAACAAUAUUUGGCGAGCUCAAGGAUUGGCAAAAG--------------UAUGUGAGUGAGUUUUCGCCAAUUACAGUGGAG
...((((.(((........(((((..........))))).....((.((((((((((((.......((....)--------------).......)))))..))))))).))))))))). ( -27.14)
>DroEre_CAF1 18390 119 + 1
GAAUCCGACUGAAAUCAAAAUGCAAUCAAAUUUAUGCAUAACAAUAUUUGGCGAGCUCAAGGAUUGCGAA-CGUACAUAUGUACGUGUAUGUGAGUGAGUUUUCGCCAAUUACUGUGGAG
...(((.............(((((..........))))).(((.((.((((((((((((....(..((.(-(((((....))))))...))..).)))))..))))))).)).)))))). ( -35.70)
>DroYak_CAF1 19178 105 + 1
GAAUCCGACUGAAAUCAAAAUGCAAUCAAAUUUAUGCAUAACAAUAUUUGGCGAGCUCGAGGAUUGGGAA-AG--------------UAUGAGAGUGAGUUUUCGCCAAUUAUUGUGGAG
...(((.............(((((..........))))).((((((.((((((((((((....(((....-..--------------..)))...)))))..))))))).))))))))). ( -26.80)
>consensus
GAAUCCGGCUGAAAUCAAAAUGCAAUCAAAUUUAUGCAUAACAAUAUUUGGCGAGCUCAAGGAUUGGCAA_AG______________UAUGUGAGUGAGUUUUCGCCAAUUACAGUGGAG
...(((.((((........(((((..........))))).....((.((((((((((((....................................)))))..))))))).))))))))). (-21.30 = -20.98 +  -0.32)

alignment

secondary structure

dotplot

Window 3

Location	14,275,339 – 14,275,444
Length	105
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.94
Mean single sequence MFE	-22.06
Consensus MFE	-16.60
Energy contribution	-16.64
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.89
Structure conservation index	0.75
SVM decision value	0.52
SVM RNA-class probability	0.767090
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14275339 105 - 22224390
CUCCACUGUAAUUGGCGAAAACUCACUCACAUA--------------CU-UUGCCAAUCCUUGAGCUCGCCAAAUAUUGUUAUGCAUAAAUUUGAUUGCAUUUUGAAUUCAGCCGGAUUU
.(((.(((...(((((((...((((........--------------..-...........)))).)))))))...(((..(((((..........)))))..)))...)))..)))... ( -19.80)
>DroSec_CAF1 15976 106 - 1
CUCCACUGUAAUUGGCGAAAACUCACUCACAUA--------------CUUUUGCCAAUCCUUGAGCUCGCCAAAUAUUGUUAUACAUAAAUUUGAUUGCAUUUUGAUUUCAGCCGGAUUC
.(((.(((..((((((((((.............--------------.))))))))))......((....(((((..((.....))...)))))...))..........)))..)))... ( -17.04)
>DroSim_CAF1 19480 106 - 1
CUCCACUGUAAUUGGCGAAAACUCACUCACAUA--------------CUUUUGCCAAUCCUUGAGCUCGCCAAAUAUUGUUAUGCAUAAAUUUGAUUGCAUUUUGAUUUCAGCCGGAUUC
.(((.(((...(((((((...((((........--------------..............)))).)))))))..((((..(((((..........)))))..))))..)))..)))... ( -20.05)
>DroEre_CAF1 18390 119 - 1
CUCCACAGUAAUUGGCGAAAACUCACUCACAUACACGUACAUAUGUACG-UUCGCAAUCCUUGAGCUCGCCAAAUAUUGUUAUGCAUAAAUUUGAUUGCAUUUUGAUUUCAGUCGGAUUC
.(((((((((.(((((((...((((.........((((((....)))))-)..........)))).))))))).)))))).(((((..........)))))...(((....))))))... ( -31.41)
>DroYak_CAF1 19178 105 - 1
CUCCACAAUAAUUGGCGAAAACUCACUCUCAUA--------------CU-UUCCCAAUCCUCGAGCUCGCCAAAUAUUGUUAUGCAUAAAUUUGAUUGCAUUUUGAUUUCAGUCGGAUUC
.(((((((((.(((((((...(((.........--------------..-............))).))))))).)))))).(((((..........)))))...(((....))))))... ( -22.00)
>consensus
CUCCACUGUAAUUGGCGAAAACUCACUCACAUA______________CU_UUGCCAAUCCUUGAGCUCGCCAAAUAUUGUUAUGCAUAAAUUUGAUUGCAUUUUGAUUUCAGCCGGAUUC
.(((((.(((.(((((((...(((......................................))).))))))).))).)).(((((..........))))).............)))... (-16.60 = -16.64 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	14,275,411 – 14,275,518
Length	107
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	90.00
Mean single sequence MFE	-26.77
Consensus MFE	-20.23
Energy contribution	-20.97
Covariance contribution	0.75
Combinations/Pair	1.11
Mean z-score	-1.90
Structure conservation index	0.76
SVM decision value	0.44
SVM RNA-class probability	0.738654
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14275411 107 + 22224390
UAUGUGAGUGAGUUUUCGCCAAUUACAGUGGAGAACAACUGAAAGGAUAGAGAUUUUGAGAAAAUGUAAGCCUUGAAUGGCUUGUAUUUGGU------GUAAUUCACUUUGAG
.....(((((((((..((((.....((((........))))....................(((((((((((......))))))))))))))------).))))))))).... ( -29.30)
>DroSec_CAF1 16049 107 + 1
UAUGUGAGUGAGUUUUCGCCAAUUACAGUGGAGAACAACUGAAAGGAUAGAGAUUUUGAGAAAAUGUAAGCCUUGAAUGGCUUGUAUUUGAU------GUAUUUCACUUUGAG
...(((((......)))))...(((.(((((((.(((.((.((((........)))).)).(((((((((((......)))))))))))..)------)).))))))).))). ( -25.20)
>DroSim_CAF1 19553 107 + 1
UAUGUGAGUGAGUUUUCGCCAAUUACAGUGGAGAACAACUGAAAGGAUAGAGAUUUUGAGAAAGUGUAAGCCUUGAAUGGCUUGUAUUUGAU------GUAUUUCACUUUGAG
...(((((......)))))...(((.(((((((.(((.((.((((........)))).)).(((((((((((......)))))))))))..)------)).))))))).))). ( -25.20)
>DroYak_CAF1 19250 109 + 1
UAUGAGAGUGAGUUUUCGCCAAUUAUUGUGGAGAACAACUGAAAGGAUAGAGAUUCGGCAAAGUUGUAAGCCUUGAAUGGCUU----UUGGUGUACGAGUAUUUCACUUUGAG
..(.((((((((..((((((((............((((((....((((....)))).....))))))(((((......)))))----))))....))))...)))))))).). ( -27.40)
>consensus
UAUGUGAGUGAGUUUUCGCCAAUUACAGUGGAGAACAACUGAAAGGAUAGAGAUUUUGAGAAAAUGUAAGCCUUGAAUGGCUUGUAUUUGAU______GUAUUUCACUUUGAG
.....(((((((.((((.((.....((((........))))...))...))))........(((((((((((......))))))))))).............))))))).... (-20.23 = -20.97 +   0.75)

alignment

secondary structure

dotplot

Window 5

Location	14,275,411 – 14,275,518
Length	107
Sequences	4
Columns	113
Reading direction	reverse
Mean pairwise identity	90.00
Mean single sequence MFE	-17.12
Consensus MFE	-15.32
Energy contribution	-15.33
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.48
Structure conservation index	0.89
SVM decision value	2.09
SVM RNA-class probability	0.987715
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14275411 107 - 22224390
CUCAAAGUGAAUUAC------ACCAAAUACAAGCCAUUCAAGGCUUACAUUUUCUCAAAAUCUCUAUCCUUUCAGUUGUUCUCCACUGUAAUUGGCGAAAACUCACUCACAUA
.....(((((....(------.((((.((((((((......)))))...........................(((.(....).)))))).)))).).....)))))...... ( -16.60)
>DroSec_CAF1 16049 107 - 1
CUCAAAGUGAAAUAC------AUCAAAUACAAGCCAUUCAAGGCUUACAUUUUCUCAAAAUCUCUAUCCUUUCAGUUGUUCUCCACUGUAAUUGGCGAAAACUCACUCACAUA
......((((.....------.........(((((......)))))...........................((((.(((.(((.......))).)))))))...))))... ( -15.90)
>DroSim_CAF1 19553 107 - 1
CUCAAAGUGAAAUAC------AUCAAAUACAAGCCAUUCAAGGCUUACACUUUCUCAAAAUCUCUAUCCUUUCAGUUGUUCUCCACUGUAAUUGGCGAAAACUCACUCACAUA
......((((.....------.........(((((......)))))...........................((((.(((.(((.......))).)))))))...))))... ( -15.90)
>DroYak_CAF1 19250 109 - 1
CUCAAAGUGAAAUACUCGUACACCAA----AAGCCAUUCAAGGCUUACAACUUUGCCGAAUCUCUAUCCUUUCAGUUGUUCUCCACAAUAAUUGGCGAAAACUCACUCUCAUA
.....(((((................----(((((......))))).....(((((((((..........))).(((((.....)))))....))))))...)))))...... ( -20.10)
>consensus
CUCAAAGUGAAAUAC______ACCAAAUACAAGCCAUUCAAGGCUUACAUUUUCUCAAAAUCUCUAUCCUUUCAGUUGUUCUCCACUGUAAUUGGCGAAAACUCACUCACAUA
.....(((((....................(((((......)))))............................(((.(((.(((.......))).)))))))))))...... (-15.32 = -15.33 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:46 2006