Locus 5064

Sequence ID	2L_DroMel_CAF1
Location	14,497,549 – 14,497,751
Length	202
Max. P	0.999804

overview

Window 2

Location	14,497,549 – 14,497,657
Length	108
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	96.85
Mean single sequence MFE	-29.86
Consensus MFE	-25.78
Energy contribution	-26.02
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.31
Structure conservation index	0.86
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14497549 108 + 22407834
UGUUAUAAAUUACACCCAGAGCCAUUACAAUUUUUCGUAUUCUCGGCUCAAGUUGCCGGUCUCUGAGGGCGGCACACCCAUUUGGGGCGUCAAUCAUGCGUAAAGUGA
.........((((.(((((((((..(((........))).....)))))..((.((((.((.....)).)))))).......))))((((.....))))))))..... ( -30.10)
>DroSec_CAF1 29272 108 + 1
UGUUAUAAAUUACACCCAGAGCCAUUACAAUUUUUCGUAUUCUCGGCUCAAGUUGCCGGUCUCUGAGGGCGGCACACCCAUUUGGGGCGUCAAUCAUGCGUAAAGUGA
.........((((.(((((((((..(((........))).....)))))..((.((((.((.....)).)))))).......))))((((.....))))))))..... ( -30.10)
>DroSim_CAF1 13305 108 + 1
UGUUAUAAAUUACACCCAGAGCCAUUACAAUUUUUCGUAUUCUCGGCUCAAGUUGCCGGUCUCUGAUGGCGGCACACCCAUUUGGGGCGUCAAUCAUGCGUAAAGUGA
.........((((.(((((((((..(((........))).....)))))..(((((((........))))))).........))))((((.....))))))))..... ( -29.70)
>DroEre_CAF1 23283 108 + 1
UGUUAUAAAUUACACCCAAAGCCAUUACAAUUUUUCGUGUUCUCGGCUCAAGUUGCCGCACUCUUAGGGCGGCACACCCAUUUGGGGCGUCAAUCAUGCGUAAAGUGA
.........((((.(((((((((...(((........)))....)))....((.(((((.((....))))))))).....))))))((((.....))))))))..... ( -28.60)
>DroYak_CAF1 18506 107 + 1
UGUUAUAAAUUACACCCAAAGCCAUUACAAUUUUUCGUAUUCUCGGCUCAAGUUGCCGCUC-CUUAGGGCGGCACACCCAUUUGGGGCGUCAAUCAUGCGUAAAGUGA
.........((((.(((((((((..(((........))).....)))....((.(((((((-....))))))))).....))))))((((.....))))))))..... ( -30.80)
>consensus
UGUUAUAAAUUACACCCAGAGCCAUUACAAUUUUUCGUAUUCUCGGCUCAAGUUGCCGGUCUCUGAGGGCGGCACACCCAUUUGGGGCGUCAAUCAUGCGUAAAGUGA
.........((((.(((((((((..(((........))).....)))))..((((((..........)))))).........))))((((.....))))))))..... (-25.78 = -26.02 +   0.24)

alignment

secondary structure

dotplot

Window 3

Location	14,497,549 – 14,497,657
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	96.85
Mean single sequence MFE	-32.22
Consensus MFE	-30.04
Energy contribution	-30.00
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-1.71
Structure conservation index	0.93
SVM decision value	1.98
SVM RNA-class probability	0.984489
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14497549 108 - 22407834
UCACUUUACGCAUGAUUGACGCCCCAAAUGGGUGUGCCGCCCUCAGAGACCGGCAACUUGAGCCGAGAAUACGAAAAAUUGUAAUGGCUCUGGGUGUAAUUUAUAACA
.....((((((.......((((((.....))))))((((..(.....)..))))..((.((((((....(((((....))))).)))))).))))))))......... ( -31.40)
>DroSec_CAF1 29272 108 - 1
UCACUUUACGCAUGAUUGACGCCCCAAAUGGGUGUGCCGCCCUCAGAGACCGGCAACUUGAGCCGAGAAUACGAAAAAUUGUAAUGGCUCUGGGUGUAAUUUAUAACA
.....((((((.......((((((.....))))))((((..(.....)..))))..((.((((((....(((((....))))).)))))).))))))))......... ( -31.40)
>DroSim_CAF1 13305 108 - 1
UCACUUUACGCAUGAUUGACGCCCCAAAUGGGUGUGCCGCCAUCAGAGACCGGCAACUUGAGCCGAGAAUACGAAAAAUUGUAAUGGCUCUGGGUGUAAUUUAUAACA
.....((((((.......((((((.....)))))).......((((((.(((((.......))).....(((((....)))))..))))))))))))))......... ( -30.80)
>DroEre_CAF1 23283 108 - 1
UCACUUUACGCAUGAUUGACGCCCCAAAUGGGUGUGCCGCCCUAAGAGUGCGGCAACUUGAGCCGAGAACACGAAAAAUUGUAAUGGCUUUGGGUGUAAUUUAUAACA
.....((((((.......((((((.....))))))(((((.(.....).)))))..((.((((((...(((........)))..)))))).))))))))......... ( -32.50)
>DroYak_CAF1 18506 107 - 1
UCACUUUACGCAUGAUUGACGCCCCAAAUGGGUGUGCCGCCCUAAG-GAGCGGCAACUUGAGCCGAGAAUACGAAAAAUUGUAAUGGCUUUGGGUGUAAUUUAUAACA
.....((((((.......((((((.....))))))(((((((...)-).)))))..((.((((((....(((((....))))).)))))).))))))))......... ( -35.00)
>consensus
UCACUUUACGCAUGAUUGACGCCCCAAAUGGGUGUGCCGCCCUCAGAGACCGGCAACUUGAGCCGAGAAUACGAAAAAUUGUAAUGGCUCUGGGUGUAAUUUAUAACA
.....((((((.......((((((.....))))))((((...........))))..((.((((((....(((((....))))).)))))).))))))))......... (-30.04 = -30.00 +  -0.04)

alignment

secondary structure

dotplot

Window 4

Location	14,497,629 – 14,497,723
Length	94
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	100.00
Mean single sequence MFE	-26.20
Consensus MFE	-26.20
Energy contribution	-26.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.55
Structure conservation index	1.00
SVM decision value	3.26
SVM RNA-class probability	0.998876
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14497629 94 - 22407834
UAAAGAUACAAAUGUAUCCGCUAGUCACUUACCAACAGUGGGCCCCCGCUGGAUGUCACAUCUGUGUCACUUUACGCAUGAUUGACGCCCCAAA
....(((((....))))).((..............((((((....))))))...((((.((((((((......))))).)))))))))...... ( -26.20)
>DroSec_CAF1 29352 94 - 1
UAAAGAUACAAAUGUAUCCGCUAGUCACUUACCAACAGUGGGCCCCCGCUGGAUGUCACAUCUGUGUCACUUUACGCAUGAUUGACGCCCCAAA
....(((((....))))).((..............((((((....))))))...((((.((((((((......))))).)))))))))...... ( -26.20)
>DroSim_CAF1 13385 94 - 1
UAAAGAUACAAAUGUAUCCGCUAGUCACUUACCAACAGUGGGCCCCCGCUGGAUGUCACAUCUGUGUCACUUUACGCAUGAUUGACGCCCCAAA
....(((((....))))).((..............((((((....))))))...((((.((((((((......))))).)))))))))...... ( -26.20)
>DroEre_CAF1 23363 94 - 1
UAAAGAUACAAAUGUAUCCGCUAGUCACUUACCAACAGUGGGCCCCCGCUGGAUGUCACAUCUGUGUCACUUUACGCAUGAUUGACGCCCCAAA
....(((((....))))).((..............((((((....))))))...((((.((((((((......))))).)))))))))...... ( -26.20)
>DroYak_CAF1 18585 94 - 1
UAAAGAUACAAAUGUAUCCGCUAGUCACUUACCAACAGUGGGCCCCCGCUGGAUGUCACAUCUGUGUCACUUUACGCAUGAUUGACGCCCCAAA
....(((((....))))).((..............((((((....))))))...((((.((((((((......))))).)))))))))...... ( -26.20)
>consensus
UAAAGAUACAAAUGUAUCCGCUAGUCACUUACCAACAGUGGGCCCCCGCUGGAUGUCACAUCUGUGUCACUUUACGCAUGAUUGACGCCCCAAA
....(((((....))))).((..............((((((....))))))...((((.((((((((......))))).)))))))))...... (-26.20 = -26.20 +  -0.00)

alignment

secondary structure

dotplot

Window 5

Location	14,497,657 – 14,497,751
Length	94
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	99.57
Mean single sequence MFE	-31.18
Consensus MFE	-30.62
Energy contribution	-30.62
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.18
Structure conservation index	0.98
SVM decision value	2.72
SVM RNA-class probability	0.996579
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14497657 94 + 22407834
CACAGAUGUGACAUCCAGCGGGGGCCCACUGUUGGUAAGUGACUAGCGGAUACAUUUGUAUCUUUAAGUCUGUGUGCCCAAUGUCAACUGUCAA
.((((...((((((((...))((((.(((.((((((.....))))))((((((....))))))........))).)))).)))))).))))... ( -30.60)
>DroSec_CAF1 29380 94 + 1
CACAGAUGUGACAUCCAGCGGGGGCCCACUGUUGGUAAGUGACUAGCGGAUACAUUUGUAUCUUUAAGUCUGUGUGCCCAAUGUCAACUGUCAA
.((((...((((((((...))((((.(((.((((((.....))))))((((((....))))))........))).)))).)))))).))))... ( -30.60)
>DroSim_CAF1 13413 94 + 1
CACAGAUGUGACAUCCAGCGGGGGCCCACUGUUGGUAAGUGACUAGCGGAUACAUUUGUAUCUUUAAGUCUGUGUGCCCAAUGUCAACUGUCAA
.((((...((((((((...))((((.(((.((((((.....))))))((((((....))))))........))).)))).)))))).))))... ( -30.60)
>DroEre_CAF1 23391 94 + 1
CACAGAUGUGACAUCCAGCGGGGGCCCACUGUUGGUAAGUGACUAGCGGAUACAUUUGUAUCUUUAAGUCUGUGUGCCCAAUGUCAACUGUCAA
.((((...((((((((...))((((.(((.((((((.....))))))((((((....))))))........))).)))).)))))).))))... ( -30.60)
>DroYak_CAF1 18613 94 + 1
CACAGAUGUGACAUCCAGCGGGGGCCCACUGUUGGUAAGUGACUAGCGGAUACAUUUGUAUCUUUAAGUCUGUGUGCCCGAUGUCAACUGUCAA
.((((...((((((((((.((....)).)))..((((...((((.(.((((((....)))))).).))))....)))).))))))).))))... ( -33.50)
>consensus
CACAGAUGUGACAUCCAGCGGGGGCCCACUGUUGGUAAGUGACUAGCGGAUACAUUUGUAUCUUUAAGUCUGUGUGCCCAAUGUCAACUGUCAA
.((((...((((((((...))((((.(((.((((((.....))))))((((((....))))))........))).)))).)))))).))))... (-30.62 = -30.62 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	14,497,657 – 14,497,751
Length	94
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	99.57
Mean single sequence MFE	-32.50
Consensus MFE	-32.66
Energy contribution	-32.50
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-3.38
Structure conservation index	1.00
SVM decision value	4.12
SVM RNA-class probability	0.999804
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14497657 94 - 22407834
UUGACAGUUGACAUUGGGCACACAGACUUAAAGAUACAAAUGUAUCCGCUAGUCACUUACCAACAGUGGGCCCCCGCUGGAUGUCACAUCUGUG
...((((.(((((((((.......((((....(((((....)))))....)))).....))..((((((....)))))))))))))...)))). ( -32.00)
>DroSec_CAF1 29380 94 - 1
UUGACAGUUGACAUUGGGCACACAGACUUAAAGAUACAAAUGUAUCCGCUAGUCACUUACCAACAGUGGGCCCCCGCUGGAUGUCACAUCUGUG
...((((.(((((((((.......((((....(((((....)))))....)))).....))..((((((....)))))))))))))...)))). ( -32.00)
>DroSim_CAF1 13413 94 - 1
UUGACAGUUGACAUUGGGCACACAGACUUAAAGAUACAAAUGUAUCCGCUAGUCACUUACCAACAGUGGGCCCCCGCUGGAUGUCACAUCUGUG
...((((.(((((((((.......((((....(((((....)))))....)))).....))..((((((....)))))))))))))...)))). ( -32.00)
>DroEre_CAF1 23391 94 - 1
UUGACAGUUGACAUUGGGCACACAGACUUAAAGAUACAAAUGUAUCCGCUAGUCACUUACCAACAGUGGGCCCCCGCUGGAUGUCACAUCUGUG
...((((.(((((((((.......((((....(((((....)))))....)))).....))..((((((....)))))))))))))...)))). ( -32.00)
>DroYak_CAF1 18613 94 - 1
UUGACAGUUGACAUCGGGCACACAGACUUAAAGAUACAAAUGUAUCCGCUAGUCACUUACCAACAGUGGGCCCCCGCUGGAUGUCACAUCUGUG
...((((.(((((((((.......((((....(((((....)))))....)))).....))..((((((....)))))))))))))...)))). ( -34.50)
>consensus
UUGACAGUUGACAUUGGGCACACAGACUUAAAGAUACAAAUGUAUCCGCUAGUCACUUACCAACAGUGGGCCCCCGCUGGAUGUCACAUCUGUG
...((((.(((((((((.......((((....(((((....)))))....)))).....))..((((((....)))))))))))))...)))). (-32.66 = -32.50 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:59 2006