Locus 171

Sequence ID	3L_DroMel_CAF1
Location	527,520 – 527,736
Length	216
Max. P	0.999568

overview

Window 0

Location	527,520 – 527,636
Length	116
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	81.63
Mean single sequence MFE	-25.89
Consensus MFE	-19.56
Energy contribution	-19.48
Covariance contribution	-0.08
Combinations/Pair	1.22
Mean z-score	-1.45
Structure conservation index	0.76
SVM decision value	-0.05
SVM RNA-class probability	0.507609
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 527520 116 + 23771897
AUGUAGUCCGUAAAGUGGGUAAGUCUGGAAUGCCCUGGAACUAAAUAAGUCUCAGUAGGUUGAAUAAUUUGUCCACUUUUGGGACUUUUAUCCCCUUCCCUCGGGCAAUUUUUAUU
.....(((((.(((((((..((((.((....((((((..(((.....)))..)))..)))....))))))..))))))).((((......)))).......))))).......... ( -32.30)
>DroSec_CAF1 1771 99 + 1
AUAUU-----------------GUCUGGAAUGCCCUGGAACAAAAUAAGUCUCAGUAGGUUGAAAAAUUUGUCCACUUUUGGGACUUUUAUCCCCUUCCCUCGGGCAAUUUUUAUU
.....-----------------........(((((.((((......(((((((((.((((.((........)).)))))))))))))........))))...)))))......... ( -24.34)
>DroSim_CAF1 1764 99 + 1
AUAUU-----------------GUCUGGAAAGCCCUGGAACAGAAUAAGUCUCAGUAGGUUGAAUAAUUUGUCCACUUUUGGGACUUUUAUCCCCUUCCCUCGGGCAAUUUUUAUU
.....-----------------.........((((.((((..((..(((((((((.((((.((........)).)))))))))))))...))...))))...)))).......... ( -24.50)
>DroEre_CAF1 1753 116 + 1
UCCUUCUCCAUGAAGUGUGUUACUCUAGAAGCUUCUACAACAAAAUAAGUCUCAGUAGGUUGAAUAAUUUGUCCACUUCUGGGACUUUUAUCCCCUUCCCUCGGGCAAUUUGUAUU
...........(((((...((......)).)))))....(((((..(((((((((.((((.((........)).))))))))))))).....(((.......)))...)))))... ( -23.70)
>DroYak_CAF1 1845 116 + 1
UCGUUUUCCAUGAAGUGUGUUGGUCUAGAAUGCUCUGCAACAGAAUGAGUCCCAGUAGGUUGAAUAAUUUGUCCACUUUUGGGACUUUUAUCCCCUUCCCUCGGGCAAUUUUUAUU
..(((.(((..((((..(((((...((((....)))))))))((..(((((((((.((((.((........)).)))))))))))))...))..))))....))).)))....... ( -24.60)
>consensus
AUAUU_UCC_U_AAGUG_GU__GUCUGGAAUGCCCUGGAACAAAAUAAGUCUCAGUAGGUUGAAUAAUUUGUCCACUUUUGGGACUUUUAUCCCCUUCCCUCGGGCAAUUUUUAUU
...............................((((.((((......(((((((((.((((.((........)).)))))))))))))........))))...)))).......... (-19.56 = -19.48 +  -0.08)

alignment

secondary structure

dotplot

Window 1

Location	527,520 – 527,636
Length	116
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	81.63
Mean single sequence MFE	-25.39
Consensus MFE	-18.14
Energy contribution	-19.18
Covariance contribution	1.04
Combinations/Pair	1.12
Mean z-score	-1.69
Structure conservation index	0.71
SVM decision value	0.30
SVM RNA-class probability	0.679237
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 527520 116 - 23771897
AAUAAAAAUUGCCCGAGGGAAGGGGAUAAAAGUCCCAAAAGUGGACAAAUUAUUCAACCUACUGAGACUUAUUUAGUUCCAGGGCAUUCCAGACUUACCCACUUUACGGACUACAU
...........(((.......)))......(((((..(((((((.................(((..(((.....)))..)))((....))........)))))))..))))).... ( -26.80)
>DroSec_CAF1 1771 99 - 1
AAUAAAAAUUGCCCGAGGGAAGGGGAUAAAAGUCCCAAAAGUGGACAAAUUUUUCAACCUACUGAGACUUAUUUUGUUCCAGGGCAUUCCAGAC-----------------AAUAU
.........(((((...((((.(((((((..(((((....).)))).....(((((......))))).))))))).)))).)))))........-----------------..... ( -27.20)
>DroSim_CAF1 1764 99 - 1
AAUAAAAAUUGCCCGAGGGAAGGGGAUAAAAGUCCCAAAAGUGGACAAAUUAUUCAACCUACUGAGACUUAUUCUGUUCCAGGGCUUUCCAGAC-----------------AAUAU
..........((((...((((.(((((((..(((((....).))))......((((......))))..))))))).)))).)))).........-----------------..... ( -27.70)
>DroEre_CAF1 1753 116 - 1
AAUACAAAUUGCCCGAGGGAAGGGGAUAAAAGUCCCAGAAGUGGACAAAUUAUUCAACCUACUGAGACUUAUUUUGUUGUAGAAGCUUCUAGAGUAACACACUUCAUGGAGAAGGA
............(((.......(((((....))))).((((((((((((.((((((......))))...)).)))))).((((....))))........)))))).)))....... ( -23.00)
>DroYak_CAF1 1845 116 - 1
AAUAAAAAUUGCCCGAGGGAAGGGGAUAAAAGUCCCAAAAGUGGACAAAUUAUUCAACCUACUGGGACUCAUUCUGUUGCAGAGCAUUCUAGACCAACACACUUCAUGGAAAACGA
............(((...(((((((((...(((((((...((((..............))))))))))).)))))((((.((......))....))))...)))).)))....... ( -22.24)
>consensus
AAUAAAAAUUGCCCGAGGGAAGGGGAUAAAAGUCCCAAAAGUGGACAAAUUAUUCAACCUACUGAGACUUAUUUUGUUCCAGGGCAUUCCAGAC__AC_CACUU_A_GGA_AACAU
..........((((...((((.(((((((..(((((....).))))......((((......))))..))))))).)))).))))............................... (-18.14 = -19.18 +   1.04)

alignment

secondary structure

dotplot

Window 2

Location	527,560 – 527,663
Length	103
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	97.09
Mean single sequence MFE	-23.99
Consensus MFE	-23.04
Energy contribution	-22.92
Covariance contribution	-0.12
Combinations/Pair	1.08
Mean z-score	-2.05
Structure conservation index	0.96
SVM decision value	3.20
SVM RNA-class probability	0.998723
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 527560 103 + 23771897
CUAAAUAAGUCUCAGUAGGUUGAAUAAUUUGUCCACUUUUGGGACUUUUAUCCCCUUCCCUCGGGCAAUUUUUAUUGUUUGGGAUUUAUUGCCAACUCUUUUG
...((((((((((((.....((((....((((((......((((......))))........))))))..))))....))))))))))))............. ( -22.84)
>DroSec_CAF1 1794 103 + 1
CAAAAUAAGUCUCAGUAGGUUGAAAAAUUUGUCCACUUUUGGGACUUUUAUCCCCUUCCCUCGGGCAAUUUUUAUUGUUUGGGAUUUAUUGCCAACUCUUUUG
...((((((((((((.....((((((..((((((......((((......))))........))))))))))))....))))))))))))............. ( -23.84)
>DroSim_CAF1 1787 103 + 1
CAGAAUAAGUCUCAGUAGGUUGAAUAAUUUGUCCACUUUUGGGACUUUUAUCCCCUUCCCUCGGGCAAUUUUUAUUGUUUGGGAUUUAUUGCCAACUCUUUUG
...((((((((((((.....((((....((((((......((((......))))........))))))..))))....))))))))))))............. ( -22.94)
>DroEre_CAF1 1793 103 + 1
CAAAAUAAGUCUCAGUAGGUUGAAUAAUUUGUCCACUUCUGGGACUUUUAUCCCCUUCCCUCGGGCAAUUUGUAUUGUUUGGGAUUUAUUGCCAACUCUUUUG
(((((.(((((((((.((((.((........)).)))))))))))))............((((((((((....))))))))))...............))))) ( -24.30)
>DroYak_CAF1 1885 103 + 1
CAGAAUGAGUCCCAGUAGGUUGAAUAAUUUGUCCACUUUUGGGACUUUUAUCCCCUUCCCUCGGGCAAUUUUUAUUGUUUGGGAUUUAUUGCCAACUCUUUUG
...((((((((((((.....((((....((((((......((((......))))........))))))..))))....))))))))))))............. ( -26.04)
>consensus
CAAAAUAAGUCUCAGUAGGUUGAAUAAUUUGUCCACUUUUGGGACUUUUAUCCCCUUCCCUCGGGCAAUUUUUAUUGUUUGGGAUUUAUUGCCAACUCUUUUG
...((((((((((((.....((((....((((((......((((......))))........))))))..))))....))))))))))))............. (-23.04 = -22.92 +  -0.12)

alignment

secondary structure

dotplot

Window 3

Location	527,560 – 527,663
Length	103
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	97.09
Mean single sequence MFE	-20.58
Consensus MFE	-19.24
Energy contribution	-19.24
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.53
Structure conservation index	0.94
SVM decision value	1.39
SVM RNA-class probability	0.949274
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 527560 103 - 23771897
CAAAAGAGUUGGCAAUAAAUCCCAAACAAUAAAAAUUGCCCGAGGGAAGGGGAUAAAAGUCCCAAAAGUGGACAAAUUAUUCAACCUACUGAGACUUAUUUAG
.(((.(((((((((((..................))))))..(((.....((((((..(((((....).))))...))))))..))).....))))).))).. ( -19.27)
>DroSec_CAF1 1794 103 - 1
CAAAAGAGUUGGCAAUAAAUCCCAAACAAUAAAAAUUGCCCGAGGGAAGGGGAUAAAAGUCCCAAAAGUGGACAAAUUUUUCAACCUACUGAGACUUAUUUUG
(((((..(((.((......((((...((((....)))).....))))..(((((....)))))....)).))).....(((((......)))))....))))) ( -20.40)
>DroSim_CAF1 1787 103 - 1
CAAAAGAGUUGGCAAUAAAUCCCAAACAAUAAAAAUUGCCCGAGGGAAGGGGAUAAAAGUCCCAAAAGUGGACAAAUUAUUCAACCUACUGAGACUUAUUCUG
....((((((.((......((((...((((....)))).....))))..(((((....)))))....)).)))......((((......))))......))). ( -19.60)
>DroEre_CAF1 1793 103 - 1
CAAAAGAGUUGGCAAUAAAUCCCAAACAAUACAAAUUGCCCGAGGGAAGGGGAUAAAAGUCCCAGAAGUGGACAAAUUAUUCAACCUACUGAGACUUAUUUUG
((((((((((((((((..................))))))..(((.....((((((..(((((....).))))...))))))..))).....))))).))))) ( -20.27)
>DroYak_CAF1 1885 103 - 1
CAAAAGAGUUGGCAAUAAAUCCCAAACAAUAAAAAUUGCCCGAGGGAAGGGGAUAAAAGUCCCAAAAGUGGACAAAUUAUUCAACCUACUGGGACUCAUUCUG
....(((((.........(((((...((((....))))((....))...)))))...(((((((...((((..............))))))))))).))))). ( -23.34)
>consensus
CAAAAGAGUUGGCAAUAAAUCCCAAACAAUAAAAAUUGCCCGAGGGAAGGGGAUAAAAGUCCCAAAAGUGGACAAAUUAUUCAACCUACUGAGACUUAUUUUG
((..((.(((((......(((((...((((....))))((....))...)))))....(((((....).)))).......)))))))..))............ (-19.24 = -19.24 +   0.00)

alignment

secondary structure

dotplot

Window 4

Location	527,600 – 527,696
Length	96
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	97.08
Mean single sequence MFE	-25.02
Consensus MFE	-25.02
Energy contribution	-24.82
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-2.12
Structure conservation index	1.00
SVM decision value	3.73
SVM RNA-class probability	0.999568
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 527600 96 + 23771897
GGGACUUUUAUCCCCUUCCCUCGGGCAAUUUUUAUUGUUUGGGAUUUAUUGCCAACUCUUUUGGCAUUUAUCAAAACAAAAGAGGAACAAUAGCUG
((((......)))).....((((((((((....))))))))))..((((((....((((((((.............))))))))...))))))... ( -25.32)
>DroSec_CAF1 1834 95 + 1
GGGACUUUUAUCCCCUUCCCUCGGGCAAUUUUUAUUGUUUGGGAUUUAUUGCCAACUCUUUUGGCAUUUAUCAAAACAAAAGAGGAACGAU-GCUG
((((......)))).....((((((((((....))))))))))...(((((....((((((((.............))))))))...))))-)... ( -24.12)
>DroSim_CAF1 1827 96 + 1
GGGACUUUUAUCCCCUUCCCUCGGGCAAUUUUUAUUGUUUGGGAUUUAUUGCCAACUCUUUUGGCAUUUAUCAAAACAAAAGAGGAACGAUAGCUG
((((......)))).....((((((((((....))))))))))..((((((....((((((((.............))))))))...))))))... ( -25.02)
>DroEre_CAF1 1833 96 + 1
GGGACUUUUAUCCCCUUCCCUCGGGCAAUUUGUAUUGUUUGGGAUUUAUUGCCAACUCUUUUGGCGUUUAUCAAAACAAAAGAGGCACGAUAACUG
((((......)))).....((((((((((....))))))))))..((((((....((((((((.............))))))))...))))))... ( -25.32)
>DroYak_CAF1 1925 96 + 1
GGGACUUUUAUCCCCUUCCCUCGGGCAAUUUUUAUUGUUUGGGAUUUAUUGCCAACUCUUUUGGCAUUUAUCAAAACAAAAGAGGCACGAUAACUG
((((......)))).....((((((((((....))))))))))..((((((....((((((((.............))))))))...))))))... ( -25.32)
>consensus
GGGACUUUUAUCCCCUUCCCUCGGGCAAUUUUUAUUGUUUGGGAUUUAUUGCCAACUCUUUUGGCAUUUAUCAAAACAAAAGAGGAACGAUAGCUG
((((......)))).....((((((((((....))))))))))..((((((....((((((((.............))))))))...))))))... (-25.02 = -24.82 +  -0.20)

alignment

secondary structure

dotplot

Window 5

Location	527,636 – 527,736
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-27.03
Consensus MFE	-24.88
Energy contribution	-26.42
Covariance contribution	1.54
Combinations/Pair	1.04
Mean z-score	-2.02
Structure conservation index	0.92
SVM decision value	3.03
SVM RNA-class probability	0.998182
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 527636 100 + 23771897
GUUUGGGAUUUAUUGCCAACUCUUUUGGCAUUUAUCAAAACAAAAGAGGAACAAUAGCUGGCAGGCGGAAAUGGAAAUAACUGCCUUAUCCCUUCUCUCC
....(((((....(((((.((((((((.............))))))))..........)))))(((((..((....))..)))))..)))))........ ( -27.62)
>DroSec_CAF1 1870 99 + 1
GUUUGGGAUUUAUUGCCAACUCUUUUGGCAUUUAUCAAAACAAAAGAGGAACGAU-GCUGGCAGGCGGAAAUGGAAAUAACUGCCUUAUCCCUUCUCUCC
....(((((....(((((.((((((((.............)))))))).......-..)))))(((((..((....))..)))))..)))))........ ( -27.72)
>DroSim_CAF1 1863 100 + 1
GUUUGGGAUUUAUUGCCAACUCUUUUGGCAUUUAUCAAAACAAAAGAGGAACGAUAGCUGGCAGGCGGAAAUGGAAAUAACUGCUUUAUCCCUUCUCUCC
((((..(((....((((((.....))))))...))).))))...((((((..(((((..(((((................))))))))))..)))))).. ( -25.59)
>DroEre_CAF1 1869 100 + 1
GUUUGGGAUUUAUUGCCAACUCUUUUGGCGUUUAUCAAAACAAAAGAGGCACGAUAACUGGCUGGCGGAAAUGGAAAUAACUGCCUUAUCCCUCCUCCUA
....(((((.....((((.((((((((.............))))))))..........)))).(((((..((....))..)))))..)))))........ ( -26.02)
>DroYak_CAF1 1961 100 + 1
GUUUGGGAUUUAUUGCCAACUCUUUUGGCAUUUAUCAAAACAAAAGAGGCACGAUAACUGGCAGGCGGAAAUGGAAAUAACUGCCUUAUCCCUCCUCUCC
((((..(((....((((((.....))))))...))).))))...(((((...(((((..(((((................))))))))))...))))).. ( -28.19)
>consensus
GUUUGGGAUUUAUUGCCAACUCUUUUGGCAUUUAUCAAAACAAAAGAGGAACGAUAGCUGGCAGGCGGAAAUGGAAAUAACUGCCUUAUCCCUUCUCUCC
....(((((....(((((.((((((((.............))))))))..........)))))(((((..((....))..)))))..)))))........ (-24.88 = -26.42 +   1.54)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:23 2006