Locus 3223

Sequence ID	X_DroMel_CAF1
Location	8,537,716 – 8,537,916
Length	200
Max. P	0.966514

overview

Window 7

Location	8,537,716 – 8,537,836
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.58
Mean single sequence MFE	-48.00
Consensus MFE	-40.12
Energy contribution	-40.84
Covariance contribution	0.72
Combinations/Pair	1.15
Mean z-score	-1.34
Structure conservation index	0.84
SVM decision value	0.20
SVM RNA-class probability	0.628603
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8537716 120 - 22224390
UACGGCUCGACCGCCCAGCCAGACGCCGGAGAACCUCUCUUCCGCGAGCAAGGAUUCGGAACUGGCGGAGGUGGGCAAUGGACCCAAUUCGGGGAGCUUCACCAUGAUGCACCCGGCAUU
...(((((..((((((.(((((...(((((...((((((......)))..))).)))))..))))).).)))))........(((.....)))))))).......(((((.....))))) ( -44.60)
>DroSec_CAF1 1944 120 - 1
UACGGCUCGACCGCCCAGCCAGACGCCGGAGAACCUCUCUUCCGCCAGCAAGGAUUCGGAGCUGGCGUAGGUGAGCAAUGGACCCAGUUCGGGGAACUUCACCAUGAUGCACCCGGUAUU
...((((.(.....).))))....(((((......((.(((.(((((((...........))))))).))).))(((((((.(((.....)))(.....).))))..)))..)))))... ( -40.30)
>DroSim_CAF1 1962 120 - 1
UACGGCUCGACCGCCCAGCCAGACGCCGGAGAACCUCUCUUCCGCCAGCAAGGAUUCGGAGCUGGCGGAGGUGAGCAAUGGACCUAGUUCGGGGAACUUCACAAUGAUGCACCCGGCAUU
...((((.(.....).))))....(((((.....(((.(((((((((((...........))))))))))).)))((.((.....(((((...)))))...)).))......)))))... ( -45.80)
>DroEre_CAF1 2034 120 - 1
UCCGGGUCGACCGCCCAGCCAGACGCCGGAGAACCUCUCCUCCGCCAGCAAGGAUUCCGAUCUGGCGGAGGUAAGCAAUGGACCCAGUGCGGGCAGCUUCACCAUGAUGCACCCGGCAUU
.((((((.....((((........(((((((.....))))((((((((...((...))...)))))))))))..(((.((....)).))))))).((.((.....)).)))))))).... ( -53.10)
>DroYak_CAF1 2022 120 - 1
UCCGGCUCGACCGCCCAGCCAAACGCCGGAGAAUCUCUCCUCCGCCAGCAAGGAUUCCGAGCUGGCGGAGGUGAGUAAUGGACCCAGUGCGGGGAGCUUCACCAUGAUGCACCCGGCAUU
(((((((.(.....).))))...((((((((.....))))(((((((((..((...))..)))))))))))))......)))...(((((.(((.((.((.....)).)).))).))))) ( -56.20)
>consensus
UACGGCUCGACCGCCCAGCCAGACGCCGGAGAACCUCUCUUCCGCCAGCAAGGAUUCGGAGCUGGCGGAGGUGAGCAAUGGACCCAGUUCGGGGAGCUUCACCAUGAUGCACCCGGCAUU
...((((.(.....).))))....(((((......((.(((((((((((...........))))))))))).))(((((((.(((.....)))(.....).))))..)))..)))))... (-40.12 = -40.84 +   0.72)

alignment

secondary structure

dotplot

Window 8

Location	8,537,756 – 8,537,876
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.42
Mean single sequence MFE	-59.90
Consensus MFE	-49.38
Energy contribution	-50.82
Covariance contribution	1.44
Combinations/Pair	1.08
Mean z-score	-2.00
Structure conservation index	0.82
SVM decision value	1.60
SVM RNA-class probability	0.966514
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8537756 120 - 22224390
UGGGCGGUGGAGCGGUGCAGGGCGGAUCCGGCAACGGAGCUACGGCUCGACCGCCCAGCCAGACGCCGGAGAACCUCUCUUCCGCGAGCAAGGAUUCGGAACUGGCGGAGGUGGGCAAUG
((((((((.((((.((....(((...((((....))))))))).)))).))))))))(((...((((((((.....))))(((((.((.............)).)))))))))))).... ( -59.72)
>DroSec_CAF1 1984 120 - 1
UGGGCGGCGGAGCAGUGCAGGGGGGAUCCGGCAACGGGGCUACGGCUCGACCGCCCAGCCAGACGCCGGAGAACCUCUCUUCCGCCAGCAAGGAUUCGGAGCUGGCGUAGGUGAGCAAUG
...((((((((((...))(((((((.((((((..(..((((..(((......))).)))).)..))))))...))))))))))))).))...........(((.((....)).))).... ( -52.80)
>DroSim_CAF1 2002 120 - 1
UGGGCGGCGGAGCAGUGCAGGGGGGAUCCGGCAACGGGGCUACGGCUCGACCGCCCAGCCAGACGCCGGAGAACCUCUCUUCCGCCAGCAAGGAUUCGGAGCUGGCGGAGGUGAGCAAUG
....(((((...(.(.((.(((.((.((((....))((((....)))))))).))).))).).)))))......(((.(((((((((((...........))))))))))).)))..... ( -58.30)
>DroEre_CAF1 2074 120 - 1
UGGGCGGCGGAGCGGUACAGGGGGGAUCCGGCAACGGUGCUCCGGGUCGACCGCCCAGCCAGACGCCGGAGAACCUCUCCUCCGCCAGCAAGGAUUCCGAUCUGGCGGAGGUAAGCAAUG
...(((((((.(((((((..((((.(.(((....)))).))))..))..))))))).)))....(((((((.....))))((((((((...((...))...)))))))))))..)).... ( -59.00)
>DroYak_CAF1 2062 120 - 1
UGGGCGGCGGAGCGGUGCAGGGGGCGUCCGGCAACGGAGCUCCGGCUCGACCGCCCAGCCAAACGCCGGAGAAUCUCUCCUCCGCCAGCAAGGAUUCCGAGCUGGCGGAGGUGAGUAAUG
..((((((((.(((((((..(((((.((((....))))))))).))...))))))).)))....))).......(((.(((((((((((..((...))..))))))))))).)))..... ( -69.70)
>consensus
UGGGCGGCGGAGCGGUGCAGGGGGGAUCCGGCAACGGAGCUACGGCUCGACCGCCCAGCCAGACGCCGGAGAACCUCUCUUCCGCCAGCAAGGAUUCGGAGCUGGCGGAGGUGAGCAAUG
(((((((..((((.((((........((((....)))))).)).))))..)))))))((....((((((((.....))))(((((((((...........))))))))))))).)).... (-49.38 = -50.82 +   1.44)

alignment

secondary structure

dotplot

Window 9

Location	8,537,796 – 8,537,916
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.00
Mean single sequence MFE	-63.14
Consensus MFE	-55.98
Energy contribution	-56.38
Covariance contribution	0.40
Combinations/Pair	1.10
Mean z-score	-1.13
Structure conservation index	0.89
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8537796 120 - 22224390
UGGCGGAUGCGCUGCCUCAGCCUGGGCACGCCCCCCGUCAUGGGCGGUGGAGCGGUGCAGGGCGGAUCCGGCAACGGAGCUACGGCUCGACCGCCCAGCCAGACGCCGGAGAACCUCUCU
.((((..((((((((..((((....)).(((((........))))).))..))))))))((((((.((((....))((((....)))))))))))).......))))((((.....)))) ( -65.80)
>DroSec_CAF1 2024 120 - 1
UGGCGGAUGCGCUGCCUCAGCCUGGGCACGCCUCCCGUCAUGGGCGGCGGAGCAGUGCAGGGGGGAUCCGGCAACGGGGCUACGGCUCGACCGCCCAGCCAGACGCCGGAGAACCUCUCU
.((((..((((((((.((.((....)).((((.(((.....))).))))))))))))))(((.((.((((....))((((....)))))))).))).......))))((((.....)))) ( -63.40)
>DroSim_CAF1 2042 120 - 1
UGGCGGAUGCGCUGCCUCAGCCUGGGAACGCCUCCCGUCAUGGGCGGCGGAGCAGUGCAGGGGGGAUCCGGCAACGGGGCUACGGCUCGACCGCCCAGCCAGACGCCGGAGAACCUCUCU
.((((..(((((((((((.....)))..((((.(((.....))).))))..))))))))(((.((.((((....))((((....)))))))).))).......))))((((.....)))) ( -60.60)
>DroEre_CAF1 2114 120 - 1
UGGCGGAUGCGGUGCCUCAGCCUGGGCACGCCCCCCGUCAUGGGCGGCGGAGCGGUACAGGGGGGAUCCGGCAACGGUGCUCCGGGUCGACCGCCCAGCCAGACGCCGGAGAACCUCUCC
.((((..(((.((((((......))))))(((.(((.....))).)))((.(((((((..((((.(.(((....)))).))))..))..))))))).).))..))))((((.....)))) ( -60.60)
>DroYak_CAF1 2102 120 - 1
UGGCGGAUGCGCUGCCUCAGCCUGGGCACGCCCCCCGUCAUGGGCGGCGGAGCGGUGCAGGGGGCGUCCGGCAACGGAGCUCCGGCUCGACCGCCCAGCCAAACGCCGGAGAAUCUCUCC
.((((..((((((((.((.((....)).((((.(((.....))).)))))))))))))).(((((.((((....)))))))))((((.(.....).))))...))))((((.....)))) ( -65.30)
>consensus
UGGCGGAUGCGCUGCCUCAGCCUGGGCACGCCCCCCGUCAUGGGCGGCGGAGCGGUGCAGGGGGGAUCCGGCAACGGAGCUACGGCUCGACCGCCCAGCCAGACGCCGGAGAACCUCUCU
.((((..((((((((.((.((....)).((((.(((.....))).))))))))))))))(((.((.((((....))((((....)))))))).))).......))))((((.....)))) (-55.98 = -56.38 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:11 2006