Locus 9250

Sequence ID	3R_DroMel_CAF1
Location	24,671,780 – 24,671,977
Length	197
Max. P	0.999895

overview

Window 5

Location	24,671,780 – 24,671,900
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.50
Mean single sequence MFE	-45.04
Consensus MFE	-38.60
Energy contribution	-40.20
Covariance contribution	1.60
Combinations/Pair	1.00
Mean z-score	-1.64
Structure conservation index	0.86
SVM decision value	0.85
SVM RNA-class probability	0.865457
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24671780 120 + 27905053
CCCCGCUGGGCGUCACGUGCGCGGCCUUUGUUUUUAUUGCUGCCUUUUGCGGCGAUUCACGCGUUUUUCCGCGAAACGCCGGAUACCAUGCCAACCACCCCCGCACGUUACCGAGCGGGG
(((((((.((....(((((((.(((.(((......((((((((.....))))))))...((((......))))))).)))((........)).........)))))))..)).))))))) ( -50.10)
>DroSec_CAF1 12862 120 + 1
CCCCGCUGGGCGUCACGUGCGCGGCCUUUGUUUUUAUUGCUGCCUUUUGCGGCGAUUCACGCGUUUUUCCGCGAAACGCCGGAUACCAUGCCAACCACCCCCGCUCUUUUCCGAGCGGGG
....(((((..(((.(((.(((((....(((....((((((((.....))))))))....))).....)))))..)))...))).))).)).......((((((((......)))))))) ( -46.40)
>DroSim_CAF1 12863 120 + 1
CCCCGCUGGGCGUCACGUGCGCGGCCUUUGUUUUUAUUGCUGCCUUUUGCGGCGAUUCACGCGUUUUUCCGCGAAACGCCGGAUACCAUGCCAACCACCCCCGCACUUUUCCGAGCGGGG
(((((((.((......(((((.(((.(((......((((((((.....))))))))...((((......))))))).)))((........)).........)))))....)).))))))) ( -45.70)
>DroEre_CAF1 14372 120 + 1
CCCCGCUGGGCGUCACGUGCGCGGCCUUUGUUUUUAUUGCUGCCUUUUGCGGCGAUUCACGCUUUUUUCCGCGAAACGCCGGAUGCUAUGGCAACCACCCCCGCACUUUUCCGUGCAGGG
....((((((((((.(((.(((((.....((....((((((((.....))))))))....))......)))))..)))...)))))).))))......(((.((((......)))).))) ( -43.20)
>DroYak_CAF1 13061 120 + 1
CCCCGCUGGGCGUCACGUGCGCGGCCUUUGUUUUUAUUGCUGCCUUUUGCGGCGAUUCACGCUUUUUUCCGCGAAACGCCGGAUGCCAUGCCAACCACCCCCGCACUUUUCCGAGCAGGG
(((.(((.((((((.(((.(((((.....((....((((((((.....))))))))....))......)))))..)))...)))))).(((...........)))........))).))) ( -39.80)
>consensus
CCCCGCUGGGCGUCACGUGCGCGGCCUUUGUUUUUAUUGCUGCCUUUUGCGGCGAUUCACGCGUUUUUCCGCGAAACGCCGGAUACCAUGCCAACCACCCCCGCACUUUUCCGAGCGGGG
(((((((.(((((......(((((....(((....((((((((.....))))))))....))).....)))))..)))))(((.....(((...........)))....))).))))))) (-38.60 = -40.20 +   1.60)

alignment

secondary structure

dotplot

Window 6

Location	24,671,780 – 24,671,900
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.50
Mean single sequence MFE	-50.97
Consensus MFE	-48.78
Energy contribution	-48.70
Covariance contribution	-0.08
Combinations/Pair	1.06
Mean z-score	-2.58
Structure conservation index	0.96
SVM decision value	4.42
SVM RNA-class probability	0.999895
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24671780 120 - 27905053
CCCCGCUCGGUAACGUGCGGGGGUGGUUGGCAUGGUAUCCGGCGUUUCGCGGAAAAACGCGUGAAUCGCCGCAAAAGGCAGCAAUAAAAACAAAGGCCGCGCACGUGACGCCCAGCGGGG
(((((((.(((.(((((((.((.(.(((.((.........((((.((((((........)))))).))))((.....)).))......)))...).)).)))))))...))).))))))) ( -56.30)
>DroSec_CAF1 12862 120 - 1
CCCCGCUCGGAAAAGAGCGGGGGUGGUUGGCAUGGUAUCCGGCGUUUCGCGGAAAAACGCGUGAAUCGCCGCAAAAGGCAGCAAUAAAAACAAAGGCCGCGCACGUGACGCCCAGCGGGG
((((((((......))))..(((((..((((.((((....((((.((((((........)))))).))))((........)).............)))).)).))...)))))...)))) ( -48.20)
>DroSim_CAF1 12863 120 - 1
CCCCGCUCGGAAAAGUGCGGGGGUGGUUGGCAUGGUAUCCGGCGUUUCGCGGAAAAACGCGUGAAUCGCCGCAAAAGGCAGCAAUAAAAACAAAGGCCGCGCACGUGACGCCCAGCGGGG
(((((((.((....(((((.((.(.(((.((.........((((.((((((........)))))).))))((.....)).))......)))...).)).)))))......)).))))))) ( -50.90)
>DroEre_CAF1 14372 120 - 1
CCCUGCACGGAAAAGUGCGGGGGUGGUUGCCAUAGCAUCCGGCGUUUCGCGGAAAAAAGCGUGAAUCGCCGCAAAAGGCAGCAAUAAAAACAAAGGCCGCGCACGUGACGCCCAGCGGGG
((((((..((....(((((.((.(.((((((........(((((.((((((........)))))).))))).....))))))............).)).)))))......))..)))))) ( -48.74)
>DroYak_CAF1 13061 120 - 1
CCCUGCUCGGAAAAGUGCGGGGGUGGUUGGCAUGGCAUCCGGCGUUUCGCGGAAAAAAGCGUGAAUCGCCGCAAAAGGCAGCAAUAAAAACAAAGGCCGCGCACGUGACGCCCAGCGGGG
(((((((.((....(((((.((.(.(((......((....((((.((((((........)))))).))))((.....)).))......)))...).)).)))))......)).))))))) ( -50.70)
>consensus
CCCCGCUCGGAAAAGUGCGGGGGUGGUUGGCAUGGUAUCCGGCGUUUCGCGGAAAAACGCGUGAAUCGCCGCAAAAGGCAGCAAUAAAAACAAAGGCCGCGCACGUGACGCCCAGCGGGG
(((((((.((....(((((.((.(.(((......((....((((.((((((........)))))).))))((.....)).))......)))...).)).)))))......)).))))))) (-48.78 = -48.70 +  -0.08)

alignment

secondary structure

dotplot

Window 7

Location	24,671,820 – 24,671,940
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.00
Mean single sequence MFE	-43.50
Consensus MFE	-38.74
Energy contribution	-38.10
Covariance contribution	-0.64
Combinations/Pair	1.09
Mean z-score	-2.56
Structure conservation index	0.89
SVM decision value	3.65
SVM RNA-class probability	0.999491
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24671820 120 - 27905053
CAGUUUGUGUACAAAAAUAAGUAGAAAAGUCGCUUUUCCUCCCCGCUCGGUAACGUGCGGGGGUGGUUGGCAUGGUAUCCGGCGUUUCGCGGAAAAACGCGUGAAUCGCCGCAAAAGGCA
...((((....)))).............((((((...(((((((((.((....)).))))))).))..)))........(((((.((((((........)))))).))))).....))). ( -44.70)
>DroSec_CAF1 12902 120 - 1
CAGUUUGUGUACAAAAAUAAGUAGAAAAAUCGCUUUUCCUCCCCGCUCGGAAAAGAGCGGGGGUGGUUGGCAUGGUAUCCGGCGUUUCGCGGAAAAACGCGUGAAUCGCCGCAAAAGGCA
(..(((((((((...........((....))(((...(((((((((((......))))))))).))..)))...))))..((((.((((((........)))))).)))))))))..).. ( -45.20)
>DroSim_CAF1 12903 120 - 1
CAGUUUGUGUACAAAAAUAAGUAGAAAAAUCGCUUUUCCUCCCCGCUCGGAAAAGUGCGGGGGUGGUUGGCAUGGUAUCCGGCGUUUCGCGGAAAAACGCGUGAAUCGCCGCAAAAGGCA
(..(((((((((...........((....))(((...(((((((((.(......).))))))).))..)))...))))..((((.((((((........)))))).)))))))))..).. ( -41.00)
>DroEre_CAF1 14412 120 - 1
CAGUUUUUGUACAAAAAUAAGUAGAAGAAUCGCUUUUCCUCCCUGCACGGAAAAGUGCGGGGGUGGUUGCCAUAGCAUCCGGCGUUUCGCGGAAAAAAGCGUGAAUCGCCGCAAAAGGCA
..((((((.(((........))).)))))).((((((...((((((((......))))))))((((.(((....))).))((((.((((((........)))))).)))))).)))))). ( -46.50)
>DroYak_CAF1 13101 120 - 1
CAGUUUGUGUACGAAAAUAAGUAGAAGAAUCGCUUUUCCUCCCUGCUCGGAAAAGUGCGGGGGUGGUUGGCAUGGCAUCCGGCGUUUCGCGGAAAAAAGCGUGAAUCGCCGCAAAAGGCA
..((((.(.(((........))).).)))).(((...(((((((((.(......).))))))).))..)))...((...(((((.((((((........)))))).)))))......)). ( -40.10)
>consensus
CAGUUUGUGUACAAAAAUAAGUAGAAAAAUCGCUUUUCCUCCCCGCUCGGAAAAGUGCGGGGGUGGUUGGCAUGGUAUCCGGCGUUUCGCGGAAAAACGCGUGAAUCGCCGCAAAAGGCA
..((((.(.(((........))).).)))).(((((((((((((((.(......).))))))).)).............(((((.((((((........)))))).)))))..)))))). (-38.74 = -38.10 +  -0.64)

alignment

secondary structure

dotplot

Window 8

Location	24,671,860 – 24,671,977
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.53
Mean single sequence MFE	-39.24
Consensus MFE	-34.02
Energy contribution	-33.30
Covariance contribution	-0.72
Combinations/Pair	1.17
Mean z-score	-2.21
Structure conservation index	0.87
SVM decision value	2.68
SVM RNA-class probability	0.996271
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24671860 117 - 27905053
--GGCGGUGCGGUGAACUG-GGGGAUGAUGAUGCUACAAACAGUUUGUGUACAAAAAUAAGUAGAAAAGUCGCUUUUCCUCCCCGCUCGGUAACGUGCGGGGGUGGUUGGCAUGGUAUCC
--...(((((.(((.((((-(..((((((....((((......((((....)))).....))))....)))).))..))(((((((.((....)).))))))).)))...))).))))). ( -41.10)
>DroSec_CAF1 12942 115 - 1
----AGGUGCGGUGAGCUG-GGGGAUGAUGAUGCUACAAACAGUUUGUGUACAAAAAUAAGUAGAAAAAUCGCUUUUCCUCCCCGCUCGGAAAAGAGCGGGGGUGGUUGGCAUGGUAUCC
----.(((((.(((.((((-(..((((((....((((......((((....)))).....))))....)))).))..))(((((((((......))))))))).)))...))).))))). ( -42.80)
>DroSim_CAF1 12943 115 - 1
----AGGUGCGGUGAGCUG-GGGGAUGAUGAUGCUACAAACAGUUUGUGUACAAAAAUAAGUAGAAAAAUCGCUUUUCCUCCCCGCUCGGAAAAGUGCGGGGGUGGUUGGCAUGGUAUCC
----.(((((.(((.((((-(..((((((....((((......((((....)))).....))))....)))).))..))(((((((.(......).))))))).)))...))).))))). ( -38.60)
>DroEre_CAF1 14452 119 - 1
AAGAAGGUGCGGUAAGCUG-GGGGAUGAUGAUGUUACAAACAGUUUUUGUACAAAAAUAAGUAGAAGAAUCGCUUUUCCUCCCUGCACGGAAAAGUGCGGGGGUGGUUGCCAUAGCAUCC
.....((((((((((.(.(-(..((((((....((((.....((((((....))))))..))))....)))).))..))(((((((((......))))))))).).)))))...))))). ( -38.40)
>DroYak_CAF1 13141 118 - 1
--AAAGGUGCGGUAAGCUGAGGGGAUGAUGAUGCUACAAACAGUUUGUGUACGAAAAUAAGUAGAAGAAUCGCUUUUCCUCCCUGCUCGGAAAAGUGCGGGGGUGGUUGGCAUGGCAUCC
--...(((((.((..((..(((..(.(.((((.((((......((((....)))).....))))....))))).)..))(((((((.(......).)))))))...)..)))).))))). ( -35.30)
>consensus
____AGGUGCGGUGAGCUG_GGGGAUGAUGAUGCUACAAACAGUUUGUGUACAAAAAUAAGUAGAAAAAUCGCUUUUCCUCCCCGCUCGGAAAAGUGCGGGGGUGGUUGGCAUGGUAUCC
.....(((((.((.((((..((..(.(.((((.((((......((((....)))).....))))....))))).)..))(((((((.(......).))))))).)))).))...))))). (-34.02 = -33.30 +  -0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:29:52 2006