Locus 2412

Sequence ID	3L_DroMel_CAF1
Location	6,784,034 – 6,784,162
Length	128
Max. P	0.992896

overview

Window 7

Location	6,784,034 – 6,784,136
Length	102
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	69.09
Mean single sequence MFE	-29.02
Consensus MFE	-12.46
Energy contribution	-13.46
Covariance contribution	1.00
Combinations/Pair	1.25
Mean z-score	-1.98
Structure conservation index	0.43
SVM decision value	1.09
SVM RNA-class probability	0.913731
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6784034 102 + 23771897
AAA---CCCAAGCCGAGAUGCCAACUGAAACUGGGAUCCAGACUCAGA--CUCAGACUCAGACCGAAACUGAGAUU--CAGACUCAGACUCCGGCUGGAGCUGAGACUC
...---........(((.......((((..((((...))))..)))).--(((((..((((.(((...(((((...--....)))))....)))))))..))))).))) ( -31.70)
>DroSec_CAF1 44808 102 + 1
AAA---CCCAAGCCGAGAUGCCAACUGAAACUGGGAUCCAGACUCAGA--CUCAGUCUCAGACCGAAACUGAGACU--CAGACUCAGACUCCGGCUGGAGCUGAGUCUC
...---........(((.......((((..((((...))))..)))).--((((((.((.....)).)))))).))--)((((((((.((((....)))))))))))). ( -38.80)
>DroSim_CAF1 48377 102 + 1
AAA---CCCAAGCCGAGAUGCCAACUGAAACUGGGAUCCAGACUCAGA--CUCAGACCGAAACUGAGACUUAGACU--CAGACUCAGACUCCGGCUGGAGCUGAGACUC
...---........(((.......((((..((((...))))..)))).--(((((.......))))).......))--)...(((((.((((....))))))))).... ( -30.20)
>DroYak_CAF1 48463 82 + 1
AAA---CC--------------AACUGAAGCUGGCAUCCAGACUCAGA--CUGAGACUGA------GACUGAGACU--GAGACGGAGACUCCGAUUCGAGCGCAGAUUC
...---..--------------....(((.(((((.(((((.(((((.--......))))------).))).)).(--(((.(((.....))).)))).)).))).))) ( -22.00)
>DroAna_CAF1 55273 97 + 1
CAGGCUCACAGGCCGAAA--CAAACUGAAAC------CCAUACAGAGAUGCCCAGACUUGGCC-AA-A--GAGGCUCUGCGACUCGGAUUCGAGCUCAAACUGAAUCUC
..((((....))))....--...........------.......(((((...(((.(..((((-..-.--..))))..).((((((....)))).))...))).))))) ( -22.40)
>consensus
AAA___CCCAAGCCGAGAUGCCAACUGAAACUGGGAUCCAGACUCAGA__CUCAGACUCAGAC_GAAACUGAGACU__CAGACUCAGACUCCGGCUGGAGCUGAGACUC
........................((((..(((.....)))..))))...................................(((((.((((....))))))))).... (-12.46 = -13.46 +   1.00)

alignment

secondary structure

dotplot

Window 8

Location	6,784,034 – 6,784,136
Length	102
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	69.09
Mean single sequence MFE	-36.70
Consensus MFE	-14.70
Energy contribution	-17.70
Covariance contribution	3.00
Combinations/Pair	1.38
Mean z-score	-2.43
Structure conservation index	0.40
SVM decision value	2.36
SVM RNA-class probability	0.992896
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6784034 102 - 23771897
GAGUCUCAGCUCCAGCCGGAGUCUGAGUCUG--AAUCUCAGUUUCGGUCUGAGUCUGAG--UCUGAGUCUGGAUCCCAGUUUCAGUUGGCAUCUCGGCUUGGG---UUU
....((((((((..(((((((.(((((....--...))))))))))))..))).)))))--((..((((.((((.((((......)))).)))).))))..))---... ( -42.30)
>DroSec_CAF1 44808 102 - 1
GAGACUCAGCUCCAGCCGGAGUCUGAGUCUG--AGUCUCAGUUUCGGUCUGAGACUGAG--UCUGAGUCUGGAUCCCAGUUUCAGUUGGCAUCUCGGCUUGGG---UUU
.((((((((((((....)))).)))))))).--((((((((.......))))))))((.--.(..((((.((((.((((......)))).)))).))))..).---.)) ( -48.00)
>DroSim_CAF1 48377 102 - 1
GAGUCUCAGCUCCAGCCGGAGUCUGAGUCUG--AGUCUAAGUCUCAGUUUCGGUCUGAG--UCUGAGUCUGGAUCCCAGUUUCAGUUGGCAUCUCGGCUUGGG---UUU
.((.((((((((..(((((((.(((((.((.--......)).))))))))))))..)))--.))))).))....((((.....((((((....))))))))))---... ( -38.90)
>DroYak_CAF1 48463 82 - 1
GAAUCUGCGCUCGAAUCGGAGUCUCCGUCUC--AGUCUCAGUC------UCAGUCUCAG--UCUGAGUCUGGAUGCCAGCUUCAGUU--------------GG---UUU
(((.(((.((..((..(((.....)))..))--.(((.(((.(------((((......--.))))).))))))))))).)))....--------------..---... ( -26.20)
>DroAna_CAF1 55273 97 - 1
GAGAUUCAGUUUGAGCUCGAAUCCGAGUCGCAGAGCCUC--U-UU-GGCCAAGUCUGGGCAUCUCUGUAUGG------GUUUCAGUUUG--UUUCGGCCUGUGAGCCUG
((((((((....((.((((....))))))((((((....--.-.(-(.(((....))).)).)))))).)))------)))))......--....(((......))).. ( -28.10)
>consensus
GAGUCUCAGCUCCAGCCGGAGUCUGAGUCUG__AGUCUCAGUCUC_GUCUCAGUCUGAG__UCUGAGUCUGGAUCCCAGUUUCAGUUGGCAUCUCGGCUUGGG___UUU
.((.(((((((((....)))).))))).))..................(((((.(((((...(((((.(((.....))).))))).......))))))))))....... (-14.70 = -17.70 +   3.00)

alignment

secondary structure

dotplot

Window 9

Location	6,784,070 – 6,784,162
Length	92
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	74.97
Mean single sequence MFE	-30.72
Consensus MFE	-14.10
Energy contribution	-15.54
Covariance contribution	1.44
Combinations/Pair	1.39
Mean z-score	-1.77
Structure conservation index	0.46
SVM decision value	0.08
SVM RNA-class probability	0.575581
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6784070 92 - 23771897
CAGGAAAAUUAGUUGCUAGGUCCGC---CGAGUCUCAGCUCCAGCCGGAGUCUGAGUCUG--AAUCUCAGUUUCGGUCUGAGUCUGAG--UCUGAGUCU
..(((...((((...)))).)))((---..((.((((((((..(((((((.(((((....--...))))))))))))..))).)))))--.))..)).. ( -33.70)
>DroSec_CAF1 44844 92 - 1
CAGGAAAAUUAGUUGCUAGGUCCGC---CGAGACUCAGCUCCAGCCGGAGUCUGAGUCUG--AGUCUCAGUUUCGGUCUGAGACUGAG--UCUGAGUCU
..(((...((((...)))).)))..---..((((((((((((....)))).)))))))).--((.(((((.(((((((...)))))))--.))))).)) ( -39.00)
>DroSim_CAF1 48413 92 - 1
CAGGAAAAUUAGUUGCUAGGUCCGC---UGAGUCUCAGCUCCAGCCGGAGUCUGAGUCUG--AGUCUAAGUCUCAGUUUCGGUCUGAG--UCUGAGUCU
..(((...((((...)))).)))..---..((.((((((((..(((((((.(((((.((.--......)).))))))))))))..)))--.))))).)) ( -35.20)
>DroYak_CAF1 48485 86 - 1
CAGGAAAAUUAGUUGCUAGGUCCGC---UGAAUCUGCGCUCGAAUCGGAGUCUCCGUCUC--AGUCUCAGUC------UCAGUCUCAG--UCUGAGUCU
..(((...((((...)))).)))((---(((..(((.(((.((..(((.....)))..))--)).).)))..------)))))(((..--...)))... ( -21.20)
>DroAna_CAF1 55304 95 - 1
CAAGAAAAUUAGUUACCAAGUCUGCAGCUGAGAUUCAGUUUGAGCUCGAAUCCGAGUCGCAGAGCCUC--U-UU-GGCCAAGUCUGGGCAUCUCUGUAU
...............(((..(((((.(((..((((((((....))).)))))..))).)))))(((..--.-..-)))......)))............ ( -24.50)
>consensus
CAGGAAAAUUAGUUGCUAGGUCCGC___UGAGUCUCAGCUCCAGCCGGAGUCUGAGUCUG__AGUCUCAGUCUC_GUCUCAGUCUGAG__UCUGAGUCU
..(((...((((...)))).))).......((.(((((((((....)))).))))).))......(((((.(((((.......)))))...)))))... (-14.10 = -15.54 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:48 2006