Locus 891

Sequence ID	2R_DroMel_CAF1
Location	4,041,000 – 4,041,236
Length	236
Max. P	0.665915

overview

Window 4

Location	4,041,000 – 4,041,120
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.29
Mean single sequence MFE	-28.24
Consensus MFE	-22.76
Energy contribution	-22.20
Covariance contribution	-0.56
Combinations/Pair	1.17
Mean z-score	-1.63
Structure conservation index	0.81
SVM decision value	0.28
SVM RNA-class probability	0.665915
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4041000 120 - 20766785
UCCUCUGACACUUUUAGGACUUACAUAAGCAGAGGAAACUUCUUCAGCGAGUGCUUUAAUCUCCAUUAAAUAUUUAUGCUUGAGUCCUUUGAUUUAUGAAGCUCCUGCUGGAAGUUCGUU
......((.(((((((((((((.(((((((((((((.....(((.((((((((.((((((....)))))))))))..))).)))))))))).))))))))).)))))...)))))))... ( -29.70)
>DroSec_CAF1 23616 119 - 1
UCCUCAGCCAGUUUUAGGACUUACAUAAGCAAAG-AAACUUCUUCGGCGAGUGCUUUAAUCUCCAUUAAAUAUUUAUGCUUGAGUCCUUUGAUUUAUGAAGCUCCUGCUGGAAGUUCGCC
.......(((((...(((((((.(((((((((((-......(((.((((((((.((((((....)))))))))))..))).)))..))))).))))))))).)))))))))......... ( -27.40)
>DroSim_CAF1 25766 120 - 1
UCCUCAUUCACUUUUAGGACUUACAUAAGCAAAGGAAACUUCUUUAGCGAGUGCUUUAAUCUCCAUUAAAUAUUUAUGCUUGAGUCCUUUGAUUUAUGAAGCUCCUGCUGGAAGUUCGCC
.........(((((((((((((.(((((((((((((.....(((.((((((((.((((((....)))))))))))..))).)))))))))).))))))))).)))))...)))))..... ( -28.30)
>DroEre_CAF1 23000 105 - 1
---GCAACCAUCUUGAGUACUUGCAUAAGCAAAGGAAACUUCCGCAGCGAGUGCUUUAAGCUCUAUUAAAUAUUUAUGCUUCGGUCCUUUGAUUUAUGAAGCUGCCGC------------
---(((.....(((((((((((((....((.(((....)))..)).)))))))).))))).................(((((((((....)))...)))))))))...------------ ( -26.70)
>DroYak_CAF1 26652 117 - 1
---GCAGGCAUUUUGAGGACUUAGAUAAGCGAAGGAAACAUCUUCAGCGAGUGCUUUAAUCUUCCUUAAAUAUUUAUGCUUCAGUCCUUUGAUUUAUGAAGCUCCUGCUGGAUGUUCGUA
---(((((...((((((((...(((((((((..(....).((......)).)))))..)))))))))))).......(((((((((....)))...)))))).)))))............ ( -29.10)
>consensus
UCCUCAGCCACUUUUAGGACUUACAUAAGCAAAGGAAACUUCUUCAGCGAGUGCUUUAAUCUCCAUUAAAUAUUUAUGCUUGAGUCCUUUGAUUUAUGAAGCUCCUGCUGGAAGUUCGCC
...............(((((((.(((((((((((((.....(((.((((((((.(((((......))))))))))..))).)))))))))).))))))))).)))).............. (-22.76 = -22.20 +  -0.56)

alignment

secondary structure

dotplot

Window 5

Location	4,041,080 – 4,041,196
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.25
Mean single sequence MFE	-29.65
Consensus MFE	-20.30
Energy contribution	-19.55
Covariance contribution	-0.75
Combinations/Pair	1.16
Mean z-score	-1.70
Structure conservation index	0.68
SVM decision value	0.15
SVM RNA-class probability	0.607272
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4041080 116 - 20766785
CACCCAAAUUGAAAUACAAUUGGCUCCGGGAUGCGCUUUUGUGCAAU---UGGAGCCAUACAUUUUGUAUAGCCC-CCACUCCUCUGACACUUUUAGGACUUACAUAAGCAGAGGAAACU
.............((((((.(((((((((..(((((....))))).)---))))))))......)))))).....-....(((((((...(((...(......)..)))))))))).... ( -34.50)
>DroSec_CAF1 23696 119 - 1
CACCCAAAUUGAAAUACAAUUGGCUCUGGGAUGCGCUUUUGUGCAAUUGUUGGAGCCAUACAUUUUGUAUCGCCCCCCACUCCUCAGCCAGUUUUAGGACUUACAUAAGCAAAG-AAACU
......(((((.....)))))((((..(((((((((....)))))...((.((.((.((((.....)))).))..)).)))))).))))((((((..(.(((....))))...)-))))) ( -27.40)
>DroSim_CAF1 25846 119 - 1
CACCCAAAUUGAAAUACAAUUGGCUCUGGGAUGCGCUUUUGUGCAAUUGUUGGAGCCAUACAUUUUGUAUCGCCC-CCUCUCCUCAUUCACUUUUAGGACUUACAUAAGCAAAGGAAACU
...((.....(..((((((.((((((..(.((((((....)))))..).)..))))))......))))))..)..-....((((.(.......).))))..............))..... ( -26.00)
>DroYak_CAF1 26732 111 - 1
CACCCAAAUUGAAAUACAAUAGGCUUUGAGAUGCGCUUUUGUGCAAU---UGGAGCCUUACAUUUUGUAUCGGCC-CC-----GCAGGCAUUUUGAGGACUUAGAUAAGCGAAGGAAACA
..((((((.....((((((.((((((..(..(((((....))))).)---..))))))......))))))..(((-..-----...)))..)))).))...............(....). ( -30.70)
>consensus
CACCCAAAUUGAAAUACAAUUGGCUCUGGGAUGCGCUUUUGUGCAAU___UGGAGCCAUACAUUUUGUAUCGCCC_CCACUCCUCAGACACUUUUAGGACUUACAUAAGCAAAGGAAACU
.............((((((.((((((((...(((((....))))).....))))))))......)))))).................................................. (-20.30 = -19.55 +  -0.75)

alignment

secondary structure

dotplot

Window 6

Location	4,041,120 – 4,041,236
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.34
Mean single sequence MFE	-37.52
Consensus MFE	-27.90
Energy contribution	-27.84
Covariance contribution	-0.06
Combinations/Pair	1.21
Mean z-score	-1.52
Structure conservation index	0.74
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4041120 116 + 20766785
GUGG-GGGCUAUACAAAAUGUAUGGCUCCA---AUUGCACAAAAGCGCAUCCCGGAGCCAAUUGUAUUUCAAUUUGGGUGCCGGGCAGCUCAUUAGUGCAGGAUGUUCCUCCUUCGAUUG
...(-(((((((((.....)))))))))).---..(((((.((.(.((..(((((.(((.((((.....))))...))).)))))..)).).)).)))))(((......)))........ ( -43.20)
>DroSec_CAF1 23735 120 + 1
GUGGGGGGCGAUACAAAAUGUAUGGCUCCAACAAUUGCACAAAAGCGCAUCCCAGAGCCAAUUGUAUUUCAAUUUGGGUGCCGGGCAGCUCAUUAGUGCAGGAUGUUCGUCUUCCGAUUG
.((((((((.((((.....)))).)))))((((.((((((.((.(.((..(((.(.(((.((((.....))))...))).).)))..)).).)).))))))..))))......))).... ( -37.70)
>DroSim_CAF1 25886 119 + 1
GAGG-GGGCGAUACAAAAUGUAUGGCUCCAACAAUUGCACAAAAGCGCAUCCCAGAGCCAAUUGUAUUUCAAUUUGGGUGCCGGGCAGCUCAUUAGUGCAGGAUGUUCGUCUUCCGAUUG
...(-((((.((((.....)))).)))))..(((((((((.((.(.((..(((.(.(((.((((.....))))...))).).)))..)).).)).)))).(((.(.....).)))))))) ( -36.30)
>DroYak_CAF1 26769 114 + 1
--GG-GGCCGAUACAAAAUGUAAGGCUCCA---AUUGCACAAAAGCGCAUCUCAAAGCCUAUUGUAUUUCAAUUUGGGUGCCGGGCAGCUCAUUAGUGCGGGAUGUUCCAUUUCCUAAUG
--((-((((..(((.....))).)))))).---...((......))(((((((...((((...((((((......)))))).)))).((........))))))))).............. ( -32.90)
>consensus
GUGG_GGGCGAUACAAAAUGUAUGGCUCCA___AUUGCACAAAAGCGCAUCCCAGAGCCAAUUGUAUUUCAAUUUGGGUGCCGGGCAGCUCAUUAGUGCAGGAUGUUCCUCUUCCGAUUG
..((.((((((.(((...(((((((((((.......((......))(((.((((((................)))))))))..)).)))).....)))))...))))))))).))..... (-27.90 = -27.84 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:15 2006