Locus 7238

Sequence ID	2L_DroMel_CAF1
Location	20,273,623 – 20,273,772
Length	149
Max. P	0.939315

overview

Window 5

Location	20,273,623 – 20,273,732
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.84
Mean single sequence MFE	-19.80
Consensus MFE	-17.86
Energy contribution	-18.06
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.51
Structure conservation index	0.90
SVM decision value	1.30
SVM RNA-class probability	0.939315
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20273623 109 - 22407834
ACACCGCACUGCAAAUAUCUUUUGUUUUAUUUUGUGGCAAGCGUUGCCAUUUCCGCCAUAAAACCGAAUCCCUUUGCAGCCCCACACCUCCUCCGAAACCCAUCGCCGA-----------
...(.((.(((((((....(((.(((((((...((((((.....)))))).......))))))).)))....)))))))...............((......)))).).----------- ( -20.20)
>DroSec_CAF1 24476 109 - 1
ACACCGCACUGCAAAUAUCUUUUGUUUUAUUUUGUGGCAAGCGUUGCCAUUUCCGCCAUAAAACCGAAUCCCUUUGCAGCCCCACUCCUCCUCCGAAACCCAUCGCCGA-----------
...(.((.(((((((....(((.(((((((...((((((.....)))))).......))))))).)))....)))))))...............((......)))).).----------- ( -20.20)
>DroSim_CAF1 23354 109 - 1
ACACCGCACUGCAAAUAUCUUUUGUUUUAUUUUGUGGCAAGCGUUGCCAUUUCCGCCAUAAAACCGAAUCCCUUUGCAGCCCCACUCCUCCUCCGAAACCCAUCGCCGA-----------
...(.((.(((((((....(((.(((((((...((((((.....)))))).......))))))).)))....)))))))...............((......)))).).----------- ( -20.20)
>DroEre_CAF1 4608 117 - 1
ACACCGCACUGCAAAUAUCUUUUGUUUUAUUUUGUGGCAAGCGUUGCCAUUUCCGCCAUAAAACCGAAUCCCUUUGCAGCCCCACU---CCUCCGAAACCCAUCCCCGAGCCCCGAGUCC
........(((((((....(((.(((((((...((((((.....)))))).......))))))).)))....)))))))....(((---((((.(..........).)))....)))).. ( -21.00)
>DroYak_CAF1 5067 106 - 1
ACACCGCACAGCAAAUAUCUUUUGUUUUAUUUUGUGGCAAGCGUUGCCAUUUCCGCCAUAAAACCGAAUCCCUUUGCAGCCCCACU---CCUCCGAAACCCAUCUUCGA-----------
..........(((((....(((.(((((((...((((((.....)))))).......))))))).)))....))))).........---....((((.......)))).----------- ( -17.40)
>consensus
ACACCGCACUGCAAAUAUCUUUUGUUUUAUUUUGUGGCAAGCGUUGCCAUUUCCGCCAUAAAACCGAAUCCCUUUGCAGCCCCACUCCUCCUCCGAAACCCAUCGCCGA___________
........(((((((....(((.(((((((...((((((.....)))))).......))))))).)))....)))))))......................................... (-17.86 = -18.06 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	20,273,652 – 20,273,772
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.67
Mean single sequence MFE	-26.96
Consensus MFE	-26.16
Energy contribution	-26.36
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.33
Structure conservation index	0.97
SVM decision value	0.25
SVM RNA-class probability	0.652793
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20273652 120 + 22407834
GCUGCAAAGGGAUUCGGUUUUAUGGCGGAAAUGGCAACGCUUGCCACAAAAUAAAACAAAAGAUAUUUGCAGUGCGGUGUGUGCGACGAUAAAGUAGACUAGGUCGAAAUAAAGAUAAAA
((((((((....((..((((((((((((...((....)).)))))).....))))))..))....))))))))(((.....)))..((((..((....))..)))).............. ( -27.20)
>DroSec_CAF1 24505 120 + 1
GCUGCAAAGGGAUUCGGUUUUAUGGCGGAAAUGGCAACGCUUGCCACAAAAUAAAACAAAAGAUAUUUGCAGUGCGGUGUGUGCGACGAUAAAGUAGACUAGGUCGAAAUAAAGAUAAAA
((((((((....((..((((((((((((...((....)).)))))).....))))))..))....))))))))(((.....)))..((((..((....))..)))).............. ( -27.20)
>DroSim_CAF1 23383 120 + 1
GCUGCAAAGGGAUUCGGUUUUAUGGCGGAAAUGGCAACGCUUGCCACAAAAUAAAACAAAAGAUAUUUGCAGUGCGGUGUGUGCGACGAUAAAGUAGACUAGGUCGAAAUAAAGAUAAAA
((((((((....((..((((((((((((...((....)).)))))).....))))))..))....))))))))(((.....)))..((((..((....))..)))).............. ( -27.20)
>DroEre_CAF1 4645 120 + 1
GCUGCAAAGGGAUUCGGUUUUAUGGCGGAAAUGGCAACGCUUGCCACAAAAUAAAACAAAAGAUAUUUGCAGUGCGGUGUGUGCGACGAUAAAGUAGACUAGGUCGAAAUAAAGAUAAAA
((((((((....((..((((((((((((...((....)).)))))).....))))))..))....))))))))(((.....)))..((((..((....))..)))).............. ( -27.20)
>DroYak_CAF1 5093 120 + 1
GCUGCAAAGGGAUUCGGUUUUAUGGCGGAAAUGGCAACGCUUGCCACAAAAUAAAACAAAAGAUAUUUGCUGUGCGGUGUGUGCGACGAUAAAGUAGACUAGGUCGAAAUAAAGAUAAAA
((((((.((.((.((.((((((((((((...((....)).)))))).....))))))....))...)).)).))))))........((((..((....))..)))).............. ( -26.00)
>consensus
GCUGCAAAGGGAUUCGGUUUUAUGGCGGAAAUGGCAACGCUUGCCACAAAAUAAAACAAAAGAUAUUUGCAGUGCGGUGUGUGCGACGAUAAAGUAGACUAGGUCGAAAUAAAGAUAAAA
((((((((....((..((((((((((((...((....)).)))))).....))))))..))....))))))))(((.....)))..((((..((....))..)))).............. (-26.16 = -26.36 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	20,273,652 – 20,273,772
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	99.67
Mean single sequence MFE	-20.76
Consensus MFE	-20.36
Energy contribution	-20.56
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.23
Structure conservation index	0.98
SVM decision value	-0.05
SVM RNA-class probability	0.506127
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20273652 120 - 22407834
UUUUAUCUUUAUUUCGACCUAGUCUACUUUAUCGUCGCACACACCGCACUGCAAAUAUCUUUUGUUUUAUUUUGUGGCAAGCGUUGCCAUUUCCGCCAUAAAACCGAAUCCCUUUGCAGC
...............(((.(((......)))..)))((.......)).(((((((....(((.(((((((...((((((.....)))))).......))))))).)))....))))))). ( -21.40)
>DroSec_CAF1 24505 120 - 1
UUUUAUCUUUAUUUCGACCUAGUCUACUUUAUCGUCGCACACACCGCACUGCAAAUAUCUUUUGUUUUAUUUUGUGGCAAGCGUUGCCAUUUCCGCCAUAAAACCGAAUCCCUUUGCAGC
...............(((.(((......)))..)))((.......)).(((((((....(((.(((((((...((((((.....)))))).......))))))).)))....))))))). ( -21.40)
>DroSim_CAF1 23383 120 - 1
UUUUAUCUUUAUUUCGACCUAGUCUACUUUAUCGUCGCACACACCGCACUGCAAAUAUCUUUUGUUUUAUUUUGUGGCAAGCGUUGCCAUUUCCGCCAUAAAACCGAAUCCCUUUGCAGC
...............(((.(((......)))..)))((.......)).(((((((....(((.(((((((...((((((.....)))))).......))))))).)))....))))))). ( -21.40)
>DroEre_CAF1 4645 120 - 1
UUUUAUCUUUAUUUCGACCUAGUCUACUUUAUCGUCGCACACACCGCACUGCAAAUAUCUUUUGUUUUAUUUUGUGGCAAGCGUUGCCAUUUCCGCCAUAAAACCGAAUCCCUUUGCAGC
...............(((.(((......)))..)))((.......)).(((((((....(((.(((((((...((((((.....)))))).......))))))).)))....))))))). ( -21.40)
>DroYak_CAF1 5093 120 - 1
UUUUAUCUUUAUUUCGACCUAGUCUACUUUAUCGUCGCACACACCGCACAGCAAAUAUCUUUUGUUUUAUUUUGUGGCAAGCGUUGCCAUUUCCGCCAUAAAACCGAAUCCCUUUGCAGC
...............(((.(((......)))..)))((.......))...(((((....(((.(((((((...((((((.....)))))).......))))))).)))....)))))... ( -18.20)
>consensus
UUUUAUCUUUAUUUCGACCUAGUCUACUUUAUCGUCGCACACACCGCACUGCAAAUAUCUUUUGUUUUAUUUUGUGGCAAGCGUUGCCAUUUCCGCCAUAAAACCGAAUCCCUUUGCAGC
...............(((.(((......)))..)))((.......)).(((((((....(((.(((((((...((((((.....)))))).......))))))).)))....))))))). (-20.36 = -20.56 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:15 2006