Locus 2673

Sequence ID	2L_DroMel_CAF1
Location	7,489,042 – 7,489,266
Length	224
Max. P	0.999365

overview

Window 4

Location	7,489,042 – 7,489,152
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	90.50
Mean single sequence MFE	-31.90
Consensus MFE	-27.28
Energy contribution	-28.58
Covariance contribution	1.30
Combinations/Pair	1.14
Mean z-score	-2.86
Structure conservation index	0.86
SVM decision value	3.54
SVM RNA-class probability	0.999365
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7489042 110 + 22407834
UCACUUUCGGUUAACUGAAAGCCGUAGAAACAGCAGAUCGUGCUGUCUUUUUGAGGGCAUUAUGUUAGAUACGAUGACCAAUAGAAACUUUCAUUCUGCGGAAAAACAAA
...(((((((....)))))))((((((((((((((.....)))))).((((((..(((((..(((...)))..))).))..))))))......))))))))......... ( -31.70)
>DroSec_CAF1 11792 110 + 1
UCACUUUCGGUUAACAGAAAGCAGCAGAAACAGCAGAUCGUGCUGUCUUUUUGAGGGCAUUAUGUUAGAUACGAUGCCCAAUAGCAACUUUCAUUCUGCGGAAAAACAAA
...(((((........)))))..((((((((((((.....))))))........((((((..(((...)))..))))))..............))))))........... ( -30.60)
>DroSim_CAF1 11916 110 + 1
UCACUUUCGGUGAACAGAAAGCCGUAGAAAUAGCAGAUCGUGCUGUCUUUUUGAGGGCAUUAUGUUAGAUACGAUGCCCAAUAGCAACUUUCAUUCUGCGGAAAAACAAA
...(((((.(....).)))))((((((((((((((.....))))))........((((((..(((...)))..))))))..............))))))))......... ( -32.60)
>DroEre_CAF1 11774 104 + 1
UCACUUUCGGUUAACUGAAGCCCGUAGAAACAGCAGAUCGUGCUGUCUUUUUGAGGGCAU-----UAGAAACGAUGCCCAAAAGCAACUUUCAUUCUGGGGA-AAACAAA
....((((((....))))))(((.(((((((((((.....))))))........((((((-----(......)))))))..............)))))))).-....... ( -30.10)
>DroYak_CAF1 12085 105 + 1
UCACUUUCGGUAAACUGAAGUCCGCAGAAACAGCAGAUCGUGCUGUCUUUUUGAGGGCAU-----UAGAAGCGAUGCCCAAUAGCAACUUUCAUUUUGCGGAAAAACAAA
....((((((....))))))(((((((((((((((.....))))))........((((((-----(......)))))))..............)))))))))........ ( -34.50)
>consensus
UCACUUUCGGUUAACUGAAAGCCGUAGAAACAGCAGAUCGUGCUGUCUUUUUGAGGGCAUUAUGUUAGAUACGAUGCCCAAUAGCAACUUUCAUUCUGCGGAAAAACAAA
...(((((((....)))))))((((((((((((((.....))))))........(((((((...........)))))))..............))))))))......... (-27.28 = -28.58 +   1.30)

alignment

secondary structure

dotplot

Window 5

Location	7,489,077 – 7,489,187
Length	110
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.59
Mean single sequence MFE	-30.77
Consensus MFE	-20.48
Energy contribution	-22.72
Covariance contribution	2.24
Combinations/Pair	1.19
Mean z-score	-2.59
Structure conservation index	0.67
SVM decision value	1.19
SVM RNA-class probability	0.928612
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7489077 110 - 22407834
UUC-----UCUGUUGUUUGCAACUUUUGUAAGCGGCGGCUUUUGUUUUUCCGCAGAAUGAAAGUUUCUAUUGGUCAUCGUAUCUAACAUAAUGCCCUCAAAA----AGACAGCACGA-UC
...-----(((((((((((.((((((..(..((((.(((....)))...))))...)..)))))).)....((.(((..(.......)..))).))......----)))))))).))-.. ( -21.70)
>DroSec_CAF1 11827 110 - 1
UUC-----UCUGUUGUUUGCAACUUUUGUAAGCGGCGGCUUUUGUUUUUCCGCAGAAUGAAAGUUGCUAUUGGGCAUCGUAUCUAACAUAAUGCCCUCAAAA----AGACAGCACGA-UC
...-----((((((((((((((((((..(..((((.(((....)))...))))...)..))))))))....((((((..(.......)..))))))......----)))))))).))-.. ( -35.40)
>DroSim_CAF1 11951 110 - 1
UUC-----UCUGUUGUUUGCAACUUUUGUAAGCGGCGGCUUUUGUUUUUCCGCAGAAUGAAAGUUGCUAUUGGGCAUCGUAUCUAACAUAAUGCCCUCAAAA----AGACAGCACGA-UC
...-----((((((((((((((((((..(..((((.(((....)))...))))...)..))))))))....((((((..(.......)..))))))......----)))))))).))-.. ( -35.40)
>DroEre_CAF1 11809 104 - 1
UUC-----UCUGUUGUUUGCAACUUUUGUAAGCAUAGGCUUUUGUUU-UCCCCAGAAUGAAAGUUGCUUUUGGGCAUCGUUUCUA-----AUGCCCUCAAAA----AGACAGCACGA-UC
...-----((((((((((((((((((..(.(((....)))((((...-....)))))..))))))))....((((((........-----))))))......----)))))))).))-.. ( -30.10)
>DroYak_CAF1 12120 105 - 1
UUC-----UCUGUUGUUUGCAACUUUUGUAAGCGGAGGCUUUUGUUUUUCCGCAAAAUGAAAGUUGCUAUUGGGCAUCGCUUCUA-----AUGCCCUCAAAA----AGACAGCACGA-UC
...-----((((((((((((((((((..(..(((((((........)))))))...)..))))))))....((((((........-----))))))......----)))))))).))-.. ( -37.60)
>DroPer_CAF1 15229 104 - 1
UUCCUAGUUCUGUUCUUUGUG--UUGUGCAAGC-----CUUUUGUUUU--CUUUGAAUGAAAGUUGAAAUUGGGACUC-------CCCUACUGCCCUCAAACUAGGGAAUGGCACAAAGC
..............(((((((--(..(.(((..-----((((..(((.--....)))..))))))).....(((....-------))).....((((......)))).)..)))))))). ( -24.40)
>consensus
UUC_____UCUGUUGUUUGCAACUUUUGUAAGCGGCGGCUUUUGUUUUUCCGCAGAAUGAAAGUUGCUAUUGGGCAUCGUAUCUAACAUAAUGCCCUCAAAA____AGACAGCACGA_UC
..........(((((((((((((((((((..((((.(((....)))...))))...)))))))))))....((((((.............))))))..........))))))))...... (-20.48 = -22.72 +   2.24)

alignment

secondary structure

dotplot

Window 6

Location	7,489,152 – 7,489,266
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	96.75
Mean single sequence MFE	-32.63
Consensus MFE	-30.30
Energy contribution	-30.98
Covariance contribution	0.68
Combinations/Pair	1.05
Mean z-score	-2.21
Structure conservation index	0.93
SVM decision value	3.26
SVM RNA-class probability	0.998874
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7489152 114 - 22407834
GUAAAAAGGCUACUGGCAUAGACAGAGACACUCAUUUGACAUGUCAGUAACCUUUAUUUCAAUCCGCAUGUGUGAUUUGUUCUCUGUUGUUUGCAACUUUUGUAAGCGGCGGCU
....(((((.(((((((((.(.((((........)))).)))))))))).)))))....(((..(((....)))..)))....((((((((((((.....)))))))))))).. ( -34.30)
>DroSec_CAF1 11902 114 - 1
GUAAAAAGGCUACUGGCAUAGACAGAGACACUCAUUUGACAUGUCAGUAACCUUUAUUUCAAUCCGCAUGUGUGAUUUGUUCUCUGUUGUUUGCAACUUUUGUAAGCGGCGGCU
....(((((.(((((((((.(.((((........)))).)))))))))).)))))....(((..(((....)))..)))....((((((((((((.....)))))))))))).. ( -34.30)
>DroSim_CAF1 12026 114 - 1
GUAAAAAGGCUACUGGCAUAGACAGAGACACUCAUUUGACAUGUCAGUAACCUUUAUUUGAAUUCGCAUGUGUGAUUUGUUCUCUGUUGUUUGCAACUUUUGUAAGCGGCGGCU
....(((((.(((((((((.(.((((........)))).)))))))))).)))))....((((((((....))))...)))).((((((((((((.....)))))))))))).. ( -35.40)
>DroEre_CAF1 11878 114 - 1
GUAAAAAGGCUACUGGCAUAGACAGAGAGACUCAUUUGACAUGUCAGUAACCUUUAUUUCAAUCCGCAUGUGUGAUUUGUUCUCUGUUGUUUGCAACUUUUGUAAGCAUAGGCU
....(((((.(((((((((.(.((((........)))).)))))))))).)))))....(((..(((....)))..)))...(((((.(((((((.....)))))))))))).. ( -30.30)
>DroYak_CAF1 12190 114 - 1
GUAAAAGGGCUACUGGCAUAGACAGAGAUACUCAUUUGACAUGUCAGUAACCUUUAUUUCAAUCCGCAUGUGUCAUUUGUUCUCUGUUGUUUGCAACUUUUGUAAGCGGAGGCU
.......((((.((((((..((((((((....((..(((((((((....................).))))))))..)).))))))))...))).((....))...))).)))) ( -28.85)
>consensus
GUAAAAAGGCUACUGGCAUAGACAGAGACACUCAUUUGACAUGUCAGUAACCUUUAUUUCAAUCCGCAUGUGUGAUUUGUUCUCUGUUGUUUGCAACUUUUGUAAGCGGCGGCU
....(((((.(((((((((.(.((((........)))).)))))))))).)))))....(((..(((....)))..)))....((((((((((((.....)))))))))))).. (-30.30 = -30.98 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:24 2006