Locus 4227

Sequence ID	3R_DroMel_CAF1
Location	11,367,840 – 11,368,040
Length	200
Max. P	0.999780

overview

Window 7

Location	11,367,840 – 11,367,960
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.61
Mean single sequence MFE	-47.92
Consensus MFE	-38.12
Energy contribution	-39.44
Covariance contribution	1.32
Combinations/Pair	1.03
Mean z-score	-1.49
Structure conservation index	0.80
SVM decision value	0.20
SVM RNA-class probability	0.630757
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11367840 120 + 27905053
UUAUUGCUCGCUGUAUUCAGGUGUGGAGAAAGCCACUCCCCGAAAAGUGACUUCUUACCGAGUUGGCUGCCCUGGACUGAACCUCCUGGGUGACCGGGUGGCGCCUGCGGAUGACGCAGA
...(((((((((...(((.((.((((......)))).))..))).))))).......(((....(((.(((..((......)).(((((....))))).))))))..))).....)))). ( -42.90)
>DroSec_CAF1 115478 112 + 1
UUAUUGCUCGCUG--------UGGGGAGAAAGCCACUCCCCGAAAAGCGACUUCUUACCGAGUUGGCUGCACGGGACUGAACCUCCUGGGUGACCGGGUGGCGGCUGCGGAUGACGCAGA
...(((((((((.--------(((((((.......)))))))...))))).......(((....((((((..((.......)).(((((....)))))..)))))).))).....)))). ( -48.90)
>DroSim_CAF1 106509 112 + 1
UUAUUGCUCGCUG--------UGGGGAGGAAGCCACUCCUCGAAAAGCGACUUCUUACCGAGUUGGCUGCCCGGGACUGAACCUCCUGGGUGACCGGGUGGCGCCUGCGGAUGACGCAGA
.....(((((((.--------(((((((.......)))))))...)))))...............((..(((((((.......))))((....)))))..))))(((((.....))))). ( -48.00)
>DroEre_CAF1 103280 120 + 1
AAAUUGCUCGCCGUAUUCAGGUGUGGAGAAAGCCACUCCCCGAAAAGCGACUUCUUACCGAGUUGGCUGCCCGGGACUGAACCUCCUGGGUGACCGGGUGGCGCCUGCGGAUGACGCAGA
...(((((((((((((((((..((((......))))..((((...((((((((......))))).)))...)))).)))))((.(((((....))))).))....))))).))).)))). ( -49.90)
>DroYak_CAF1 105579 120 + 1
AAAUUGCUCGCCGUAUUCAGGUGUGGAGAAAGCCACUCCCCGAAAAGCGACUUCUUACCGAGUUAGCUGCCCGGGACUGAACCUCCUGGGUGACCGGGUGGCGCCUGCGGAUGACGCAGA
...(((((((((((((((((..((((......))))..((((...((((((((......))))).)))...)))).)))))((.(((((....))))).))....))))).))).)))). ( -49.90)
>consensus
UUAUUGCUCGCUGUAUUCAGGUGUGGAGAAAGCCACUCCCCGAAAAGCGACUUCUUACCGAGUUGGCUGCCCGGGACUGAACCUCCUGGGUGACCGGGUGGCGCCUGCGGAUGACGCAGA
...((.(.((((.......)))).).))...(((((((..........(((((......)))))((..((((((((.......))))))))..)))))))))..(((((.....))))). (-38.12 = -39.44 +   1.32)

alignment

secondary structure

dotplot

Window 8

Location	11,367,880 – 11,368,000
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.50
Mean single sequence MFE	-51.76
Consensus MFE	-48.48
Energy contribution	-49.24
Covariance contribution	0.76
Combinations/Pair	1.03
Mean z-score	-1.30
Structure conservation index	0.94
SVM decision value	0.51
SVM RNA-class probability	0.765382
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11367880 120 + 27905053
CGAAAAGUGACUUCUUACCGAGUUGGCUGCCCUGGACUGAACCUCCUGGGUGACCGGGUGGCGCCUGCGGAUGACGCAGACGCACGAGCCACAGCCGCCCUCCAGGCACAUGUACUUGGU
................(((((((.(((((...(((..((...(.(((((....))))).)(((.(((((.....))))).))).))..))))))))(((.....)))......))))))) ( -49.30)
>DroSec_CAF1 115510 120 + 1
CGAAAAGCGACUUCUUACCGAGUUGGCUGCACGGGACUGAACCUCCUGGGUGACCGGGUGGCGGCUGCGGAUGACGCAGACGCAGGAGCCACAGCCGCCCUCCAGGCACAUGUACUUGGU
................(((((((.(((((....((.(((..((.(((((....))))).))((.(((((.....))))).)))))...)).)))))(((.....)))......))))))) ( -49.40)
>DroSim_CAF1 106541 120 + 1
CGAAAAGCGACUUCUUACCGAGUUGGCUGCCCGGGACUGAACCUCCUGGGUGACCGGGUGGCGCCUGCGGAUGACGCAGACGCAGGAGCCACAGCCGCCCUCCAGGCACAUGUACUUGGU
................(((((((.((((((((((((.......))))))))......(((((.((((((..((...))..)))))).)))))))))(((.....)))......))))))) ( -54.50)
>DroEre_CAF1 103320 120 + 1
CGAAAAGCGACUUCUUACCGAGUUGGCUGCCCGGGACUGAACCUCCUGGGUGACCGGGUGGCGCCUGCGGAUGACGCAGACGCAGGAGCCGCAGCCGCCCUCCAGGCACAUGUACUUGGU
................(((((((.((((((..((.......)).(((((....))))).(((.((((((..((...))..)))))).)))))))))(((.....)))......))))))) ( -54.80)
>DroYak_CAF1 105619 120 + 1
CGAAAAGCGACUUCUUACCGAGUUAGCUGCCCGGGACUGAACCUCCUGGGUGACCGGGUGGCGCCUGCGGAUGACGCAGACGCAGGAGCCGCAGCCGCCCUCCAGGCACAUGUACUUGGU
................(((((((..(((((..((.......)).(((((....))))).(((.((((((..((...))..)))))).)))))))).(((.....)))......))))))) ( -50.80)
>consensus
CGAAAAGCGACUUCUUACCGAGUUGGCUGCCCGGGACUGAACCUCCUGGGUGACCGGGUGGCGCCUGCGGAUGACGCAGACGCAGGAGCCACAGCCGCCCUCCAGGCACAUGUACUUGGU
................(((((((.((((((((((((.......))))))))......(((((.((((((..((...))..)))))).)))))))))(((.....)))......))))))) (-48.48 = -49.24 +   0.76)

alignment

secondary structure

dotplot

Window 9

Location	11,367,920 – 11,368,040
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.83
Mean single sequence MFE	-65.80
Consensus MFE	-60.96
Energy contribution	-64.36
Covariance contribution	3.40
Combinations/Pair	1.05
Mean z-score	-3.10
Structure conservation index	0.93
SVM decision value	4.06
SVM RNA-class probability	0.999780
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11367920 120 + 27905053
ACCUCCUGGGUGACCGGGUGGCGCCUGCGGAUGACGCAGACGCACGAGCCACAGCCGCCCUCCAGGCACAUGUACUUGGUGGCCGUCAGGUGCAGGUGCUCCCGCAGGAAGGUGUUGAGG
(((((((((....)((((.((((((((((..((((((....))..(.(((((.(((........))).((......))))))))))))..)))))))))))))))))).))))....... ( -59.50)
>DroSec_CAF1 115550 120 + 1
ACCUCCUGGGUGACCGGGUGGCGGCUGCGGAUGACGCAGACGCAGGAGCCACAGCCGCCCUCCAGGCACAUGUACUUGGUGGCCGUCAGGUGCAGGUGCUCCCGGAGGAAGGCGUUGAGG
.((((((((....))))(((((..(((((..((...))..)))))..))))).(((..(((((.(((((.(((((((((......))))))))).)))))...)))))..)))...)))) ( -65.90)
>DroSim_CAF1 106581 120 + 1
ACCUCCUGGGUGACCGGGUGGCGCCUGCGGAUGACGCAGACGCAGGAGCCACAGCCGCCCUCCAGGCACAUGUACUUGGUGGCCGUCAGGUGCAGGUGCUCCCGGAGGAAGGCGUUGAGG
.((((((((....))))(((((.((((((..((...))..)))))).))))).(((..(((((.(((((.(((((((((......))))))))).)))))...)))))..)))...)))) ( -69.30)
>DroEre_CAF1 103360 120 + 1
ACCUCCUGGGUGACCGGGUGGCGCCUGCGGAUGACGCAGACGCAGGAGCCGCAGCCGCCCUCCAGGCACAUGUACUUGGUGGCCGUCAGGUGCAGGUGCUCCCGGAGAAAGGCGUUGAGG
.((((((((....))))(((((.((((((..((...))..)))))).))))).(((...((((.(((((.(((((((((......))))))))).)))))...))))...)))...)))) ( -65.40)
>DroYak_CAF1 105659 120 + 1
ACCUCCUGGGUGACCGGGUGGCGCCUGCGGAUGACGCAGACGCAGGAGCCGCAGCCGCCCUCCAGGCACAUGUACUUGGUGGCCGUCAGGUGCAGGUGCUCCCGGAGGAAGGCGUUGAGG
.((((((((....))))(((((.((((((..((...))..)))))).))))).(((..(((((.(((((.(((((((((......))))))))).)))))...)))))..)))...)))) ( -68.90)
>consensus
ACCUCCUGGGUGACCGGGUGGCGCCUGCGGAUGACGCAGACGCAGGAGCCACAGCCGCCCUCCAGGCACAUGUACUUGGUGGCCGUCAGGUGCAGGUGCUCCCGGAGGAAGGCGUUGAGG
.((((((((....))))(((((.((((((..((...))..)))))).))))).(((..(((((.(((((.(((((((((......))))))))).)))))...)))))..)))...)))) (-60.96 = -64.36 +   3.40)

alignment

secondary structure

dotplot

Window 0

Location	11,367,920 – 11,368,040
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.83
Mean single sequence MFE	-54.16
Consensus MFE	-51.08
Energy contribution	-51.32
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.66
Structure conservation index	0.94
SVM decision value	1.70
SVM RNA-class probability	0.972634
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11367920 120 - 27905053
CCUCAACACCUUCCUGCGGGAGCACCUGCACCUGACGGCCACCAAGUACAUGUGCCUGGAGGGCGGCUGUGGCUCGUGCGUCUGCGUCAUCCGCAGGCGCCACCCGGUCACCCAGGAGGU
.........(((((((((((.((....)).))))..((((.(((.(((....))).))).(((.(((....((....))(((((((.....)))))))))).)))))))...))))))). ( -54.30)
>DroSec_CAF1 115550 120 - 1
CCUCAACGCCUUCCUCCGGGAGCACCUGCACCUGACGGCCACCAAGUACAUGUGCCUGGAGGGCGGCUGUGGCUCCUGCGUCUGCGUCAUCCGCAGCCGCCACCCGGUCACCCAGGAGGU
............((((((((.((((.((.((.((........)).)).)).))))((((..(((((((((((.....(((....)))...)))))))))))..))))...))).))))). ( -55.10)
>DroSim_CAF1 106581 120 - 1
CCUCAACGCCUUCCUCCGGGAGCACCUGCACCUGACGGCCACCAAGUACAUGUGCCUGGAGGGCGGCUGUGGCUCCUGCGUCUGCGUCAUCCGCAGGCGCCACCCGGUCACCCAGGAGGU
((((...(((((((..((((.((....)).))))..(((((.........)).))).)))))))(((((((((.((((((..((...))..)))))).)))))..))))......)))). ( -55.00)
>DroEre_CAF1 103360 120 - 1
CCUCAACGCCUUUCUCCGGGAGCACCUGCACCUGACGGCCACCAAGUACAUGUGCCUGGAGGGCGGCUGCGGCUCCUGCGUCUGCGUCAUCCGCAGGCGCCACCCGGUCACCCAGGAGGU
............((((((((.((....)).......((((.(((.(((....))).))).(((.(((.((((...))))(((((((.....)))))))))).))))))).))).))))). ( -52.10)
>DroYak_CAF1 105659 120 - 1
CCUCAACGCCUUCCUCCGGGAGCACCUGCACCUGACGGCCACCAAGUACAUGUGCCUGGAGGGCGGCUGCGGCUCCUGCGUCUGCGUCAUCCGCAGGCGCCACCCGGUCACCCAGGAGGU
............((((((((.((....)).......((((.(((.(((....))).))).(((.(((.((((...))))(((((((.....)))))))))).))))))).))).))))). ( -54.30)
>consensus
CCUCAACGCCUUCCUCCGGGAGCACCUGCACCUGACGGCCACCAAGUACAUGUGCCUGGAGGGCGGCUGUGGCUCCUGCGUCUGCGUCAUCCGCAGGCGCCACCCGGUCACCCAGGAGGU
((((...(((((((..((((.((....)).))))..(((((.........)).))).)))))))(((((.((.....(((((((((.....)))))))))..)))))))......)))). (-51.08 = -51.32 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:33 2006