Locus 1617

Sequence ID	2R_DroMel_CAF1
Location	6,058,845 – 6,058,942
Length	97
Max. P	0.997591

overview

Window 9

Location	6,058,845 – 6,058,942
Length	97
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	91.65
Mean single sequence MFE	-27.84
Consensus MFE	-26.42
Energy contribution	-26.82
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.88
Structure conservation index	0.95
SVM decision value	2.89
SVM RNA-class probability	0.997591
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6058845 97 + 20766785
AAAUCGAGCGGCAGCCAAGCAUGAUCCCCUCCGACCACA-GUUGCAACCCUAUAGACCUCCAUCCCUUCGAGCGGAUGUUGCUGCCGCUCCCUCUCCA--------
.....((((((((((...(((((.((......)).))..-..)))...............((((((.....).)))))..))))))))))........-------- ( -29.00)
>DroSec_CAF1 77305 97 + 1
AAAUCGAGCGGCAGCCAAGCAUGAUCCCCUCCGACAUAA-GUUGCAACCCUAUAGACCUCCAUCCCUUCGAGCGGAUGUUGCUGCCGCUCCCUCUCCA--------
.....((((((((((..((((...(((.(((((((....-))))..........((......)).....))).)))))))))))))))))........-------- ( -29.20)
>DroSim_CAF1 81049 97 + 1
AAAUCGAGCGGCAGCCAAGCAUGAUCCCCUCCGACCCAA-GUUGCAACCCUAUAGACCUCCAUCCCUUCGAGCGGAUGUUGCUGCCGCUCCCUCUCCA--------
.....((((((((((..((((...(((.(((((((....-))))..........((......)).....))).)))))))))))))))))........-------- ( -28.70)
>DroEre_CAF1 78877 96 + 1
AAAUCGAGCGGCAGCCAAGCAUGAUCCCCUCCGACCACAAGUUGCAACCCUAUAGACCUCCAUCCCUUCGAGCGGAUGUUGCCGCCGCUCCCUCCC----------
.....(((((((.((..((((...(((.(((((((.....))))..........((......)).....))).))))))))).)))))))......---------- ( -24.10)
>DroYak_CAF1 77831 105 + 1
AAAUCGAGCGGCAGCCAAGCAUGAUCCCCUCCGAGCACA-GUUGCAACCCUAUAGACCGCCAUCCCUUCGAGCGGAUGUUGCCGCCGCUCCCUCCCCGUCUGCGUC
.....(((((((.((..(((((............(((..-..)))...........(((((........).))))))))))).)))))))................ ( -28.20)
>consensus
AAAUCGAGCGGCAGCCAAGCAUGAUCCCCUCCGACCACA_GUUGCAACCCUAUAGACCUCCAUCCCUUCGAGCGGAUGUUGCUGCCGCUCCCUCUCCA________
.....((((((((((...(((.....................)))...............((((((.....).)))))..))))))))))................ (-26.42 = -26.82 +   0.40)

alignment

secondary structure

dotplot

Window 0

Location	6,058,845 – 6,058,942
Length	97
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	91.65
Mean single sequence MFE	-37.70
Consensus MFE	-33.30
Energy contribution	-33.86
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-1.45
Structure conservation index	0.88
SVM decision value	0.87
SVM RNA-class probability	0.871355
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6058845 97 - 20766785
--------UGGAGAGGGAGCGGCAGCAACAUCCGCUCGAAGGGAUGGAGGUCUAUAGGGUUGCAAC-UGUGGUCGGAGGGGAUCAUGCUUGGCUGCCGCUCGAUUU
--------........((((((((((....((((..(....)..))))(((((....((..((...-.))..)).....))))).......))))))))))..... ( -38.70)
>DroSec_CAF1 77305 97 - 1
--------UGGAGAGGGAGCGGCAGCAACAUCCGCUCGAAGGGAUGGAGGUCUAUAGGGUUGCAAC-UUAUGUCGGAGGGGAUCAUGCUUGGCUGCCGCUCGAUUU
--------........((((((((((...((((.(((((.(((.((.((.((....)).)).)).)-))...)).))).))))((....))))))))))))..... ( -36.50)
>DroSim_CAF1 81049 97 - 1
--------UGGAGAGGGAGCGGCAGCAACAUCCGCUCGAAGGGAUGGAGGUCUAUAGGGUUGCAAC-UUGGGUCGGAGGGGAUCAUGCUUGGCUGCCGCUCGAUUU
--------........((((((((((...((((.(((((.(((.((.((.((....)).)).)).)-))...)).))).))))((....))))))))))))..... ( -37.60)
>DroEre_CAF1 78877 96 - 1
----------GGGAGGGAGCGGCGGCAACAUCCGCUCGAAGGGAUGGAGGUCUAUAGGGUUGCAACUUGUGGUCGGAGGGGAUCAUGCUUGGCUGCCGCUCGAUUU
----------......((((((((((....((((..(....)..))))(((((....((..((.....))..)).....))))).......))))))))))..... ( -38.00)
>DroYak_CAF1 77831 105 - 1
GACGCAGACGGGGAGGGAGCGGCGGCAACAUCCGCUCGAAGGGAUGGCGGUCUAUAGGGUUGCAAC-UGUGCUCGGAGGGGAUCAUGCUUGGCUGCCGCUCGAUUU
................((((((((((..(((((........)))))..(((((...((((.((...-.)))))).....))))).......))))))))))..... ( -37.70)
>consensus
________UGGAGAGGGAGCGGCAGCAACAUCCGCUCGAAGGGAUGGAGGUCUAUAGGGUUGCAAC_UGUGGUCGGAGGGGAUCAUGCUUGGCUGCCGCUCGAUUU
................((((((((((..(((((........)))))..(((((....((..((.....))..)).....))))).......))))))))))..... (-33.30 = -33.86 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:59 2006