Locus 2708

Sequence ID	X_DroMel_CAF1
Location	7,264,001 – 7,264,207
Length	206
Max. P	0.768932

overview

Window 2

Location	7,264,001 – 7,264,106
Length	105
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	79.30
Mean single sequence MFE	-37.52
Consensus MFE	-25.49
Energy contribution	-24.13
Covariance contribution	-1.35
Combinations/Pair	1.43
Mean z-score	-1.54
Structure conservation index	0.68
SVM decision value	0.52
SVM RNA-class probability	0.768932
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7264001 105 + 22224390
AUGGCCGGAUUAUUUGGUCUUUUGCCUGAUGUUGGCCAUUUGCGCCGUUAUCGGUAUAUAUUUUUGCCUGCAACUGCGCUUAGAGUCCAGGAAACAAAAGGCCAA
.((((((((((....((((..((((..((((.(((((....).)))).))))((((........)))).))))..).)))...))))).(....)....))))). ( -35.20)
>DroVir_CAF1 22327 105 + 1
UUGGCCAGACUAUGUGGUCUUUUGUCUCAUGCUGGCCAUCUGCGCCGUCAUCGGCAUCUAUUUCUGCCUGCAGCUGCGUCGCGAGUCGAAGGAGGUGAAGGCCUC
..(((((((((....)))))((..((((.(((.(((.......((((....))))..........))).))).((.((.(....).)).))))))..)))))).. ( -36.63)
>DroGri_CAF1 18935 105 + 1
CUGGCCGGACUAUCUGGUCUUUAGCCUCAUGCUGGCCAUUUGCGCCUUUAUCGGCAUCUACUUUUGCCUGCAGAUGCGCCGGGAGUCCAGACAGCUCAAGGCCAG
((((((.((((.(((((.(((((((.....)))(((((((((((........((((........)))))))))))).))).)))).))))).)).))..)))))) ( -44.30)
>DroEre_CAF1 23690 105 + 1
AUGGCUGGACUACUUGGUCUUCUGCCUGAUGCUGGCCAUUUGCGCCGUGAUCGGGAUUUAUUUCUGCCUGCAACUGCGUGGCGAGUCCAGGAGGAAGAAGGCGCA
(((((..(.(.....(((.....)))....))..))))).((((((....((.((((((......((((((....))).)))))))))..)).......)))))) ( -35.40)
>DroYak_CAF1 38806 105 + 1
AUGGCCGGAUUAUGUGGUCUUUUGCCUGAUGUUGGCCAUUUGUGCUGUAAUUGGCAUUUACUUUUGCCUGCAACUGCGUGGCGAGUCCAGGAAAAAGAAGUCCUU
((((((((((((.(..(....)..).)))).))))))))..(((((......))))).....(((((((((....))).))))))...((((........)))). ( -30.00)
>DroMoj_CAF1 22047 105 + 1
CUGGCCGGACUACGUGGUCUUCUGCCUCAUGCUGGCCAUCUGCGCCGUCAUCGGCAUCCACUUCUGCCUGCAGCUGCGCCGCGAGUCCCGCCAGCUGAAGGCCAC
(((((.(((((.(((((((..((((...(((.(((((....).)))).))).((((........)))).))))..).))))))))))).)))))........... ( -43.60)
>consensus
AUGGCCGGACUAUGUGGUCUUUUGCCUCAUGCUGGCCAUUUGCGCCGUCAUCGGCAUCUACUUCUGCCUGCAACUGCGCCGCGAGUCCAGGAAGCAGAAGGCCAA
..(((((((((.(((((((....((.....)).))))....((((.((....((((........))))....)).)))).))))))))...........)))).. (-25.49 = -24.13 +  -1.35)

alignment

secondary structure

dotplot

Window 3

Location	7,264,041 – 7,264,146
Length	105
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	77.30
Mean single sequence MFE	-43.87
Consensus MFE	-26.41
Energy contribution	-26.13
Covariance contribution	-0.27
Combinations/Pair	1.33
Mean z-score	-1.43
Structure conservation index	0.60
SVM decision value	0.08
SVM RNA-class probability	0.572658
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7264041 105 + 22224390
UGCGCCGUUAUCGGUAUAUAUUUUUGCCUGCAACUGCGCUUAGAGUCCAGGAAACAAAAGGCCAA---UGGCUCAGAGGAGGCGGCGAGUAGUGCUGCCUCGUAUUUG
.((((.(((...((((........))))...))).))))...(((((..((...(....).))..---.)))))....(((((((((.....)))))))))....... ( -35.40)
>DroVir_CAF1 22367 105 + 1
UGCGCCGUCAUCGGCAUCUAUUUCUGCCUGCAGCUGCGUCGCGAGUCGAAGGAGGUGAAGGCCUC---CGGUGGCGAGGAGGCGGCCAAUAGCGCCGCCUCCUAUUUG
.....(((((((((((........))))........((.(....).))..((((((....)))))---))))))))(((((((((((....).))))))))))..... ( -50.20)
>DroEre_CAF1 23730 105 + 1
UGCGCCGUGAUCGGGAUUUAUUUCUGCCUGCAACUGCGUGGCGAGUCCAGGAGGAAGAAGGCGCA---UGGCGAAGAGGAGGCGGCGACUAGUGCUGCCUCAUAUUUG
((((((....((.((((((......((((((....))).)))))))))..)).......))))))---...((((...(((((((((.....)))))))))...)))) ( -41.30)
>DroYak_CAF1 38846 105 + 1
UGUGCUGUAAUUGGCAUUUACUUUUGCCUGCAACUGCGUGGCGAGUCCAGGAAAAAGAAGUCCUU---CGGCGAAGAGGAGGCGGCCACUAGUGCUGCCUCGUAUUUG
.(((((......)))))...(((((((((((....))).)))..(((.((((........)))).---.))).)))))(((((((((....).))))))))....... ( -35.40)
>DroMoj_CAF1 22087 105 + 1
UGCGCCGUCAUCGGCAUCCACUUCUGCCUGCAGCUGCGCCGCGAGUCCCGCCAGCUGAAGGCCAC---CGGCGCCGAGGAGGCGGCCAGCAGCGCCGCCUCCUACCUG
.((((((.....((...))......((((.((((((((.(....)...)).)))))).))))...---))))))..(((((((((((....).))))))))))..... ( -52.00)
>DroPer_CAF1 67355 108 + 1
UGCGCCGUGAUUGGGGUCUACUUCUGCCUGCAGCUGCGUCGAGAGUCCCGCAAGCAGCGGGCCCACGGUGGCGCCGAGGAGGCGGCCAACAGUGCAGCCUCCUAUCUG
..(((((((...((((....)))).((((((.((((((.(....)...))).))).)))))).)))))))......(((((((.(((....).)).)))))))..... ( -48.90)
>consensus
UGCGCCGUCAUCGGCAUCUACUUCUGCCUGCAACUGCGUCGCGAGUCCAGGAAGCAGAAGGCCAA___CGGCGCAGAGGAGGCGGCCAAUAGUGCUGCCUCCUAUUUG
.((((.((....((((........))))....)).)))).....................(((......)))......((((((((.......))))))))....... (-26.41 = -26.13 +  -0.27)

alignment

secondary structure

dotplot

Window 4

Location	7,264,106 – 7,264,207
Length	101
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	80.59
Mean single sequence MFE	-36.62
Consensus MFE	-27.03
Energy contribution	-27.40
Covariance contribution	0.37
Combinations/Pair	1.26
Mean z-score	-1.46
Structure conservation index	0.74
SVM decision value	0.40
SVM RNA-class probability	0.722649
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7264106 101 + 22224390
UGGCUCAGAGGAGGCGGCGAGUAGUGCUGCCUCGUAUUUGGUUGGUGGCAGGCAGAUGAAGAUCUUUCCCAUAACCAUGUCACUGAUAUCCAGGUGAGGAA----
...(((....(((((((((.....)))))))))..(((((((..((((((((...(((..((....)).)))..)).))))))..)...)))))))))...---- ( -36.00)
>DroVir_CAF1 22432 105 + 1
CGGUGGCGAGGAGGCGGCCAAUAGCGCCGCCUCCUAUUUGGUCGGCGGCAGAAAAAUGAAAAUCUUUCCCAUUACCAUGUCGCUAAUCUCUAGGUGAGUACGAAA
.((((((((((((((((((....).))))))))))...((((.(..((..((((.((....)).)))))).).)))))))))))...(((.....)))....... ( -37.40)
>DroPse_CAF1 40897 105 + 1
UGGCGCCGAGGAGGCGGCCAACAGUGCAGCCUCCUAUCUAGUGGGCGGCAGGCAGAUGAAGAUAUUUCCCAUCACCAUGUCUCUGAUAUCGAGGUGGGUAUGAAU
(((((((.....))).)))).((.(((.(((.(((((...))))).)))..)))..)).........((((((.(.(((((...))))).).))))))....... ( -35.60)
>DroWil_CAF1 21575 101 + 1
CAGUGCAGAGGAGGCAGCUGAUAGUGCUGCAUCCUAUCUGGUGGGUGGCAGGCAAAUGAAAAUCUUUCCCAUUACCAUGUCGCUGAUAGCAAGGUGAGUUA----
(..(((..((((.(((((.......))))).)))).....((.(((((((((..((((...........)))).)).))))))).)).)))..).......---- ( -30.20)
>DroMoj_CAF1 22152 105 + 1
CGGCGCCGAGGAGGCGGCCAGCAGCGCCGCCUCCUACCUGGUGGGCGGCAGGAAAAUGAAAAUCUUUCCCAUCACCAUGUCGCUUAUCUCGAGGUGAGUACAAAA
...((((.(((((((((((....).))))))))))....((((((((((((((((((....)).)))))........)))))))))))....))))......... ( -44.90)
>DroPer_CAF1 67423 105 + 1
UGGCGCCGAGGAGGCGGCCAACAGUGCAGCCUCCUAUCUGGUGGGCGGCAGGCAGAUGAAGAUAUUUCCCAUCACCAUGUCUCUGAUAUCGAGGUGGGUAUGAAU
(((((((.....))).)))).((.(((.(((.(((((...))))).)))..)))..)).........((((((.(.(((((...))))).).))))))....... ( -35.60)
>consensus
CGGCGCCGAGGAGGCGGCCAACAGUGCAGCCUCCUAUCUGGUGGGCGGCAGGCAAAUGAAAAUCUUUCCCAUCACCAUGUCGCUGAUAUCGAGGUGAGUAAGAA_
........((((((((((.......))))))))))((((.((.(((((((....((((...........))))....))))))).))....)))).......... (-27.03 = -27.40 +   0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:27 2006