Locus 1362

Sequence ID	3R_DroMel_CAF1
Location	4,001,298 – 4,001,519
Length	221
Max. P	0.627389

overview

Window 1

Location	4,001,298 – 4,001,406
Length	108
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.67
Mean single sequence MFE	-30.90
Consensus MFE	-22.24
Energy contribution	-22.80
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.88
Structure conservation index	0.72
SVM decision value	-0.05
SVM RNA-class probability	0.509099
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4001298 108 + 27905053
UUUGCCGCCGAGAUUCUGUCCAGGCACGCUAU--------AUCGCCAUAUCGC---UAUAUGCCU-AGCUAUAUUCGCUAUAUAACCCAUAAGCCGUGUGCUUGCAGUCGGUAAAUUACA
......(((((....(((..((((((((((((--------((.((.((((.((---((......)-))).))))..)).)))))...........)))))))))))))))))........ ( -27.80)
>DroSec_CAF1 6904 108 + 1
UUUGCCGCCGAGAUUCUGUCCAGGCACGCUAU--------AUCGCCAUAUCGC---UAUAUGCCU-AGCUAUAUUCGCUAUAUAACCCAUAAGCCGUGUGCUUGCAGUCGGUAAAUUACA
......(((((....(((..((((((((((((--------((.((.((((.((---((......)-))).))))..)).)))))...........)))))))))))))))))........ ( -27.80)
>DroSim_CAF1 6967 108 + 1
UUUGCCGCCGAGAUUCUGUCCAGGCACGCUAU--------AUCGCCAUAUCGC---UAUAUGCCU-AGCUAUAUUCGCUAUAUAACCCAUAAGCCGUGUGCUUGCAGUCGGUAAAUUACA
......(((((....(((..((((((((((((--------((.((.((((.((---((......)-))).))))..)).)))))...........)))))))))))))))))........ ( -27.80)
>DroYak_CAF1 6822 120 + 1
UUUGCCGCCGAGAUUCUGUCCAGGCACGCUAUGUCGCUAUAUCGCCAUAUCGCUGGUAUAUGCCUUGGCUAUAUUCGCUAUAUGGCCCAUAAGCCUGCUGCCUGCAGUCGGUAAAUUACA
......(((((....(((..((((((.((......(((.....(((((((.((..(((((.((....)))))))..)).))))))).....)))..))))))))))))))))........ ( -40.20)
>consensus
UUUGCCGCCGAGAUUCUGUCCAGGCACGCUAU________AUCGCCAUAUCGC___UAUAUGCCU_AGCUAUAUUCGCUAUAUAACCCAUAAGCCGUGUGCUUGCAGUCGGUAAAUUACA
......(((((....(((..(((((((((...........................((((.((....))))))...(((.(((.....)))))).)))))))))))))))))........ (-22.24 = -22.80 +   0.56)

alignment

secondary structure

dotplot

Window 2

Location	4,001,406 – 4,001,519
Length	113
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.87
Mean single sequence MFE	-32.61
Consensus MFE	-28.19
Energy contribution	-28.69
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.65
Structure conservation index	0.86
SVM decision value	0.19
SVM RNA-class probability	0.627389
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4001406 113 + 27905053
ACAACUAUUACGGCCCAGCCCCACCAAAA------GCCCAGGCCAAAGCCAUGGCAAUUUCUUGGAAAACUUU-UUUUGUUCGCUUUCGGGCCUGGCCACAUGAAAAUUUAUGAGUGGAC
....(((((..((((..((((........------(((..(((....)))..)))........((..(((...-....)))..))...))))..)))).(((((....)))))))))).. ( -31.40)
>DroSec_CAF1 7012 114 + 1
ACAACUAUUACGGCCCAGCCCCACCAAAA------GCCCAUGCCAAAGCCAUGGCAAUUUCUUGGAAAACUCUGUUUUGUGCGCUUUCGGGCCUGGCCACAUGAAAAUUUAUGAGUGGAC
....(((((..((((..((((.....(((------((.(((((((......))))........(((....))).....))).))))).))))..)))).(((((....)))))))))).. ( -31.90)
>DroSim_CAF1 7075 114 + 1
ACAACUAUUACGGCCCAGCCCCACCAAAA------GCCCAGGCCAAAGCCAUGGCAAUUUCUUGGAAAACUCUGUUGUGUGCGCUUUCGGGCCUGGCCACAUGAAAAUUUAUGAGUGGAC
...........(((...)))((((.....------(.(((((((.((((((((.((((...((....))....)))))))).))))...))))))).).(((((....))))).)))).. ( -33.00)
>DroYak_CAF1 6942 120 + 1
ACAACUAUUACGGCCCAGCCCCACCAAAAGCCAAAGCCCAGGCCAAAACCAUGGCAAUUUCUUGGAAAACUCUGUUUUGUGCGCUUUCGGGCCUGGCCACAUGAAAAUUUAUGAGUGGAC
....(((((..((((..((((........((((((((..((((((......))))..((((...)))).))..)))))).))......))))..)))).(((((....)))))))))).. ( -34.14)
>consensus
ACAACUAUUACGGCCCAGCCCCACCAAAA______GCCCAGGCCAAAGCCAUGGCAAUUUCUUGGAAAACUCUGUUUUGUGCGCUUUCGGGCCUGGCCACAUGAAAAUUUAUGAGUGGAC
....(((((..((((..((((..((((........(((..(((....)))..)))......))))...((........))........))))..)))).(((((....)))))))))).. (-28.19 = -28.69 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:06 2006