Locus 3885

Sequence ID	2L_DroMel_CAF1
Location	11,376,548 – 11,376,739
Length	191
Max. P	0.992824

overview

Window 9

Location	11,376,548 – 11,376,668
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.17
Mean single sequence MFE	-44.16
Consensus MFE	-32.80
Energy contribution	-33.60
Covariance contribution	0.80
Combinations/Pair	1.17
Mean z-score	-2.06
Structure conservation index	0.74
SVM decision value	0.28
SVM RNA-class probability	0.667606
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11376548 120 + 22407834
CGUAACUCACUCCCCUCGCCUAACAAAUGGAGUUCGAGUUGGAGUUCUAGAUAGAGCGGAUGGGGAGGUGGCAUCAUUUGCAUUUGAAGGAAACGAUGCCACACGCACAGAACGGCGUGG
.........(((((((((((((.....((((..((......))..))))..))).))))..))))))((((((((.(((.(.......).))).))))))))((((........)))).. ( -43.20)
>DroSec_CAF1 93624 120 + 1
CGUAACUCACUCUCCUCACCCCGCAAAUGGAGUUCGAGUUGGAGUUCCAGAUAGAGCGGAUGGGGCUGUGGCAUCAUUUGCAUUUGAAGGAAACGAUGCCACACGUACAGAACGGAGUGG
.......(((((.(((((..((((...((((..((......))..))))......)))).))))).(((((((((.(((.(.......).))).)))))))))(((.....)))))))). ( -42.90)
>DroSim_CAF1 98533 120 + 1
CGUAACUCACUUCCCUCGCCCCUCAAAUGGAGUUCGAGUUGGAGUUCCAGAUAGAACGGAUGGGGCUGUGGCAUCAUUUGCAUUUGAAGGAAACGAUGCCACACGCACAGAACGGAGUGG
.......((((((..(((((((((.......((((...((((....))))...)))).)).)))))(((((((((.(((.(.......).))).)))))))))......))..)))))). ( -44.20)
>DroEre_CAF1 97192 120 + 1
CGUAACUCACUCUCCUCGCCCCCCAAAUGGAGUUCGAGGUGGAGUUGCAGAUAGCGCGGAUGGGGCUGUGGCAUCAUUUGCAUUUGAAGGAAACGAUGCCACACGCACAGAACGCAGUGG
.(((((((.(...(((((..(.((....)).)..))))).)))))))).......(((..((..(((((((((((.(((.(.......).))).))))))))).)).))...)))..... ( -47.10)
>DroYak_CAF1 96316 120 + 1
AGUAACUCACUCUCCUCGCCCCUCAAAUGGAGUUCGAGGUGGAGUUGCAGAUAGAGCGGAUGGGGCUGUGGCAUCAUUUGCAUUUGAAGGAAACGAUGCCACACGCACAGAACGGUGUGG
.(((((((.(...(((((...(((.....)))..))))).))))))))...((.(.((..((..(((((((((((.(((.(.......).))).))))))))).)).))...)).).)). ( -43.40)
>consensus
CGUAACUCACUCUCCUCGCCCCUCAAAUGGAGUUCGAGUUGGAGUUCCAGAUAGAGCGGAUGGGGCUGUGGCAUCAUUUGCAUUUGAAGGAAACGAUGCCACACGCACAGAACGGAGUGG
.......(((((((((((((((......)).((((...((((....))))...)))))).)))))..((((((((.(((.(.......).))).))))))))...........)))))). (-32.80 = -33.60 +   0.80)

alignment

secondary structure

dotplot

Window 0

Location	11,376,548 – 11,376,668
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.17
Mean single sequence MFE	-41.38
Consensus MFE	-29.66
Energy contribution	-29.94
Covariance contribution	0.28
Combinations/Pair	1.06
Mean z-score	-2.27
Structure conservation index	0.72
SVM decision value	0.04
SVM RNA-class probability	0.554856
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11376548 120 - 22407834
CCACGCCGUUCUGUGCGUGUGGCAUCGUUUCCUUCAAAUGCAAAUGAUGCCACCUCCCCAUCCGCUCUAUCUAGAACUCCAACUCGAACUCCAUUUGUUAGGCGAGGGGAGUGAGUUACG
..((((........))))((((((((((((.(.......).))))))))))))((((((...(((.(((.(..((..((......))..)).....).)))))).))))))......... ( -35.80)
>DroSec_CAF1 93624 120 - 1
CCACUCCGUUCUGUACGUGUGGCAUCGUUUCCUUCAAAUGCAAAUGAUGCCACAGCCCCAUCCGCUCUAUCUGGAACUCCAACUCGAACUCCAUUUGCGGGGUGAGGAGAGUGAGUUACG
.((((((((.....)))(((((((((((((.(.......).))))))))))))).((.(((((((......((((..((......))..))))...)).))))).)).)))))....... ( -39.60)
>DroSim_CAF1 98533 120 - 1
CCACUCCGUUCUGUGCGUGUGGCAUCGUUUCCUUCAAAUGCAAAUGAUGCCACAGCCCCAUCCGUUCUAUCUGGAACUCCAACUCGAACUCCAUUUGAGGGGCGAGGGAAGUGAGUUACG
.((((((.(((......(((((((((((((.(.......).)))))))))))))(((((....(((((....)))))......(((((.....))))))))))))))).))))....... ( -44.10)
>DroEre_CAF1 97192 120 - 1
CCACUGCGUUCUGUGCGUGUGGCAUCGUUUCCUUCAAAUGCAAAUGAUGCCACAGCCCCAUCCGCGCUAUCUGCAACUCCACCUCGAACUCCAUUUGGGGGGCGAGGAGAGUGAGUUACG
....((((....((((((((((((((((((.(.......).)))))))))))))........)))))....))))((((..(((((..((((....))))..))))).))))........ ( -48.10)
>DroYak_CAF1 96316 120 - 1
CCACACCGUUCUGUGCGUGUGGCAUCGUUUCCUUCAAAUGCAAAUGAUGCCACAGCCCCAUCCGCUCUAUCUGCAACUCCACCUCGAACUCCAUUUGAGGGGCGAGGAGAGUGAGUUACU
...(((..((((.....(((((((((((((.(.......).)))))))))))))(((((....((.......)).........(((((.....)))))))))).))))..)))....... ( -39.30)
>consensus
CCACUCCGUUCUGUGCGUGUGGCAUCGUUUCCUUCAAAUGCAAAUGAUGCCACAGCCCCAUCCGCUCUAUCUGGAACUCCAACUCGAACUCCAUUUGAGGGGCGAGGAGAGUGAGUUACG
......(((.....)))(((((((((((((.(.......).)))))))))))))....................((((((..((((..((((......))))))))....).)))))... (-29.66 = -29.94 +   0.28)

alignment

secondary structure

dotplot

Window 1

Location	11,376,588 – 11,376,699
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.31
Mean single sequence MFE	-34.80
Consensus MFE	-26.96
Energy contribution	-27.04
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-2.07
Structure conservation index	0.77
SVM decision value	1.04
SVM RNA-class probability	0.905211
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11376588 111 + 22407834
GGAGUUCUAGAUAGAGCGGAUGGGGAGGUGGCAUCAUUUGCAUUUGAAGGAAACGAUGCCACACGCACAGAACGGCGUGGUAUCCGCCAUGAGAAGU---------AUCUUCAUAAGAAG
...(((((....)))))..(((((((.((((((((.(((.(.......).))).))))))))((((........))))....))).))))..((((.---------..))))........ ( -34.20)
>DroSec_CAF1 93664 111 + 1
GGAGUUCCAGAUAGAGCGGAUGGGGCUGUGGCAUCAUUUGCAUUUGAAGGAAACGAUGCCACACGUACAGAACGGAGUGGUAUCUUCCAUGAGAAGU---------AUCUUCAUAAGAAG
((((((((...(((((((((((..((....))..))))))).))))..))))..((((((((.(((.....)))..))))))))))))....((((.---------..))))........ ( -35.30)
>DroSim_CAF1 98573 111 + 1
GGAGUUCCAGAUAGAACGGAUGGGGCUGUGGCAUCAUUUGCAUUUGAAGGAAACGAUGCCACACGCACAGAACGGAGUGGUAUCUUCCAUGAGAAGU---------AUCUUCAUAAGAAG
((....))........((..((..(((((((((((.(((.(.......).))).))))))))).)).))...))(((.((((.((((.....)))))---------))))))........ ( -30.70)
>DroEre_CAF1 97232 110 + 1
GGAGUUGCAGAUAGCGCGGAUGGGGCUGUGGCAUCAUUUGCAUUUGAAGGAAACGAUGCCACACGCACAGAACGCAGUGGUAUCUU-CAUAAGAAGU---------AUCUUCAUAAGAAA
((((.(((.......(((((((..((....))..)))))))...(((((....)((((((((..((.......)).))))))))))-))......))---------).))))........ ( -34.50)
>DroYak_CAF1 96356 119 + 1
GGAGUUGCAGAUAGAGCGGAUGGGGCUGUGGCAUCAUUUGCAUUUGAAGGAAACGAUGCCACACGCACAGAACGGUGUGGCAUCUU-CAUAGGAAGUAUGUUCAGUAUCUUCAUAAGAAA
((((.(((.......(((((((..((....))..)))))))...(((((....)((((((((((..........))))))))))..-.............))))))).))))........ ( -39.30)
>consensus
GGAGUUCCAGAUAGAGCGGAUGGGGCUGUGGCAUCAUUUGCAUUUGAAGGAAACGAUGCCACACGCACAGAACGGAGUGGUAUCUUCCAUGAGAAGU_________AUCUUCAUAAGAAG
((((...(((((...(((((((..((....))..))))))))))))..(....)((((((((.((.......))..))))))))........................))))........ (-26.96 = -27.04 +   0.08)

alignment

secondary structure

dotplot

Window 2

Location	11,376,588 – 11,376,699
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.31
Mean single sequence MFE	-32.20
Consensus MFE	-24.44
Energy contribution	-23.92
Covariance contribution	-0.52
Combinations/Pair	1.15
Mean z-score	-3.49
Structure conservation index	0.76
SVM decision value	2.35
SVM RNA-class probability	0.992824
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11376588 111 - 22407834
CUUCUUAUGAAGAU---------ACUUCUCAUGGCGGAUACCACGCCGUUCUGUGCGUGUGGCAUCGUUUCCUUCAAAUGCAAAUGAUGCCACCUCCCCAUCCGCUCUAUCUAGAACUCC
((((....))))..---------.((......(((((((...((((........))))((((((((((((.(.......).))))))))))))......)))))))......))...... ( -34.50)
>DroSec_CAF1 93664 111 - 1
CUUCUUAUGAAGAU---------ACUUCUCAUGGAAGAUACCACUCCGUUCUGUACGUGUGGCAUCGUUUCCUUCAAAUGCAAAUGAUGCCACAGCCCCAUCCGCUCUAUCUGGAACUCC
(((((.((((.((.---------...)))))))))))..........(((((.....(((((((((((((.(.......).)))))))))))))((.......)).......)))))... ( -31.10)
>DroSim_CAF1 98573 111 - 1
CUUCUUAUGAAGAU---------ACUUCUCAUGGAAGAUACCACUCCGUUCUGUGCGUGUGGCAUCGUUUCCUUCAAAUGCAAAUGAUGCCACAGCCCCAUCCGUUCUAUCUGGAACUCC
(((((.((((.((.---------...))))))))))).................((.(((((((((((((.(.......).))))))))))))))).......(((((....)))))... ( -32.40)
>DroEre_CAF1 97232 110 - 1
UUUCUUAUGAAGAU---------ACUUCUUAUG-AAGAUACCACUGCGUUCUGUGCGUGUGGCAUCGUUUCCUUCAAAUGCAAAUGAUGCCACAGCCCCAUCCGCGCUAUCUGCAACUCC
..((((...((((.---------...))))...-))))......((((....((((((((((((((((((.(.......).)))))))))))))........)))))....))))..... ( -33.20)
>DroYak_CAF1 96356 119 - 1
UUUCUUAUGAAGAUACUGAACAUACUUCCUAUG-AAGAUGCCACACCGUUCUGUGCGUGUGGCAUCGUUUCCUUCAAAUGCAAAUGAUGCCACAGCCCCAUCCGCUCUAUCUGCAACUCC
.......(((((..((....((((.....))))-..((((((((((.((.....))))))))))))))...)))))..((((.(((..((.............))..))).))))..... ( -29.82)
>consensus
CUUCUUAUGAAGAU_________ACUUCUCAUGGAAGAUACCACUCCGUUCUGUGCGUGUGGCAUCGUUUCCUUCAAAUGCAAAUGAUGCCACAGCCCCAUCCGCUCUAUCUGGAACUCC
((((....)))).......................(((((......(((.....)))(((((((((((((.(.......).))))))))))))).............)))))........ (-24.44 = -23.92 +  -0.52)

alignment

secondary structure

dotplot

Window 3

Location	11,376,628 – 11,376,739
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.18
Mean single sequence MFE	-33.70
Consensus MFE	-26.42
Energy contribution	-26.74
Covariance contribution	0.32
Combinations/Pair	1.07
Mean z-score	-2.74
Structure conservation index	0.78
SVM decision value	2.09
SVM RNA-class probability	0.987780
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11376628 111 + 22407834
CAUUUGAAGGAAACGAUGCCACACGCACAGAACGGCGUGGUAUCCGCCAUGAGAAGU---------AUCUUCAUAAGAAGCGUUAUGGGCAUCAUAAUGAUGAUGUUCAAUUGCAGCUCA
........((....((((((((.((.......))..))))))))..)).((((..((---------(.((((....)))).....((((((((((....))))))))))..)))..)))) ( -32.90)
>DroSec_CAF1 93704 111 + 1
CAUUUGAAGGAAACGAUGCCACACGUACAGAACGGAGUGGUAUCUUCCAUGAGAAGU---------AUCUUCAUAAGAAGCGUUAUGGGCAUCAUAAUGAUGAUGCUCAAUUGCAGCUCA
........((((..((((((((.(((.....)))..)))))))))))).((((..((---------(.((((....)))).....((((((((((....))))))))))..)))..)))) ( -39.00)
>DroSim_CAF1 98613 111 + 1
CAUUUGAAGGAAACGAUGCCACACGCACAGAACGGAGUGGUAUCUUCCAUGAGAAGU---------AUCUUCAUAAGAAGCGUUAUGGGCAUCAUAAUGAUGAUGUUCAAUUGCAGCUCA
........((((..((((((((.((.......))..)))))))))))).((((..((---------(.((((....)))).....((((((((((....))))))))))..)))..)))) ( -34.60)
>DroEre_CAF1 97272 110 + 1
CAUUUGAAGGAAACGAUGCCACACGCACAGAACGCAGUGGUAUCUU-CAUAAGAAGU---------AUCUUCAUAAGAAACGUUAUGGGCUUCAUAAUGAUGAUGUUCAAUUGCAGCUCA
....((((((....((((((((..((.......)).))))))))((-(....)))..---------.))))))............((((((.((...(((......)))..)).)))))) ( -27.00)
>DroYak_CAF1 96396 119 + 1
CAUUUGAAGGAAACGAUGCCACACGCACAGAACGGUGUGGCAUCUU-CAUAGGAAGUAUGUUCAGUAUCUUCAUAAGAAACGUUAUGGCCACCAUAAUGAUGAUGUUCAAUUGCAGCUCA
((.((((((....)((((((((((..........)))))))))).(-(((..(((((((.....))).))))........((((((((...))))))))))))..))))).))....... ( -35.00)
>consensus
CAUUUGAAGGAAACGAUGCCACACGCACAGAACGGAGUGGUAUCUUCCAUGAGAAGU_________AUCUUCAUAAGAAGCGUUAUGGGCAUCAUAAUGAUGAUGUUCAAUUGCAGCUCA
........(....)((((((((.((.......))..))))))))........((((............)))).........((..((((((((((....))))))))))...))...... (-26.42 = -26.74 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:44 2006