Locus 4104

Sequence ID	X_DroMel_CAF1
Location	10,840,899 – 10,841,162
Length	263
Max. P	0.736525

overview

Window 4

Location	10,840,899 – 10,841,004
Length	105
Sequences	3
Columns	118
Reading direction	forward
Mean pairwise identity	89.83
Mean single sequence MFE	-24.40
Consensus MFE	-20.59
Energy contribution	-21.37
Covariance contribution	0.78
Combinations/Pair	1.05
Mean z-score	-1.96
Structure conservation index	0.84
SVM decision value	0.22
SVM RNA-class probability	0.641587
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10840899 105 + 22224390
CAAACCGAACACC------AGCCCACCGC-------CCACCACCCGCCAACCUCUACUCUAAUGUCCUACCCCCGGGGAGACAUUCUCCCGUGGGUCUUGUGGAGUCAACCCUUUGUU
.....((((....------.((((((.((-------((((...............((......))..........(((((.....)))))))))))...)))).))......)))).. ( -24.00)
>DroSec_CAF1 19697 118 + 1
CAAACCGAACACCACACACAGCCCACCACCCACUUCCCACCACCCUCCAACCUCUACUCUAAUGUCUCACCCCCGGGGAGACAUUUUCCCGUGGGUCUUGUGGAGUCAACCCUUUGUU
...............(((.((......((((((..(((((....................((((((((.((....)))))))))).....)))))....)))).)).....)).))). ( -26.21)
>DroSim_CAF1 569 118 + 1
CAAACCGAACACCACACACAGCCCACCACCCACUUCCCACCACCCGCCAACCUCUACUCUAAUGUCCCACCCCCGGGGAGACAUUUUCCCGUGGGUCUUGUGGAGUCAACCCUUUGUU
......((...(((((....((((((.............................((......)).........((((((....))))))))))))..)))))..))........... ( -23.00)
>consensus
CAAACCGAACACCACACACAGCCCACCACCCACUUCCCACCACCCGCCAACCUCUACUCUAAUGUCCCACCCCCGGGGAGACAUUUUCCCGUGGGUCUUGUGGAGUCAACCCUUUGUU
......((...(((((....((((((.............................((......))..........((((((...))))))))))))..)))))..))........... (-20.59 = -21.37 +   0.78)

alignment

secondary structure

dotplot

Window 5

Location	10,841,004 – 10,841,124
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	98.06
Mean single sequence MFE	-31.57
Consensus MFE	-31.49
Energy contribution	-31.30
Covariance contribution	-0.19
Combinations/Pair	1.03
Mean z-score	-1.58
Structure conservation index	1.00
SVM decision value	0.08
SVM RNA-class probability	0.571723
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10841004 120 - 22224390
AUGCAUAAAUAAAAAUGUGGCAUGUUGGGUCAGAAAUAGCAUGACAUUUUGCCAGCCGGCCGACACAAAAUGGUGGCAGAUACACAGCAAUGGCCAGCGGUAGCAUAAAAUGAAAUGUUC
((((.......(((((((..(((((((.........))))))))))))))(((.((.(((((.(((......)))((.........))..))))).))))).)))).............. ( -30.80)
>DroSec_CAF1 19815 120 - 1
AUGCAUAAAUAAAAAUGUGGCAUGUUGGGUCAGAAAUAGCAUGACAUUUUGCCAGCCGGCCGACACAAAAUGGUGGCAGAUACACAGCAGUGGCCAGCGGUAGCAUAAAAUGAAAUGUUC
((((.......(((((((..(((((((.........))))))))))))))(((.((.(((((.(((......)))((.........))..))))).))))).)))).............. ( -30.70)
>DroSim_CAF1 687 120 - 1
AUGCAUAAAUAAAAAUGUGGCAUGUUGGGUCAGAAAUAGCAUGACAUUUUGCCAGCCGGCCGACACAAAAUGGUGGCAGAUACACAGCAAUGGCCAGCGGUAGCAUAAAAUGAAAUGUUC
((((.......(((((((..(((((((.........))))))))))))))(((.((.(((((.(((......)))((.........))..))))).))))).)))).............. ( -30.80)
>DroYak_CAF1 8798 120 - 1
AUGCAUAAAUAAAAAUGUGGCAUGCUGGGUCAGAAAUAGCAUGACAUUUUGCCAGCCGGCCGACACAAAAUGGUGGCAGACACACAGCAUUGGCCAGCGGUGGCAUAAAAUGAAAUGUUC
((((.......(((((((..(((((((.........))))))))))))))(((.((.(((((((((......)))((.........)).)))))).))))).)))).............. ( -34.00)
>consensus
AUGCAUAAAUAAAAAUGUGGCAUGUUGGGUCAGAAAUAGCAUGACAUUUUGCCAGCCGGCCGACACAAAAUGGUGGCAGAUACACAGCAAUGGCCAGCGGUAGCAUAAAAUGAAAUGUUC
((((.......(((((((..(((((((.........))))))))))))))(((.((.(((((.(((......)))((.........))..))))).))))).)))).............. (-31.49 = -31.30 +  -0.19)

alignment

secondary structure

dotplot

Window 6

Location	10,841,044 – 10,841,162
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.38
Mean single sequence MFE	-25.09
Consensus MFE	-23.00
Energy contribution	-22.81
Covariance contribution	-0.19
Combinations/Pair	1.04
Mean z-score	-1.66
Structure conservation index	0.92
SVM decision value	0.44
SVM RNA-class probability	0.736525
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10841044 118 + 22224390
UCUGCCACCAUUUUGUGUCGGCCGGCUGGCAAAAUGUCAUGCUAUUUCUGACCCAACAUGCCACAUUUUUAUUUAUGCAUGCUUCGGCACCCCGGAACCCCUAAACA--UAAAAAUCCCC
........(((.(((.(((((..(((((((.....)))).)))....))))).))).)))...........((((((..(((....)))....((....))....))--))))....... ( -24.10)
>DroSec_CAF1 19855 118 + 1
UCUGCCACCAUUUUGUGUCGGCCGGCUGGCAAAAUGUCAUGCUAUUUCUGACCCAACAUGCCACAUUUUUAUUUAUGCAUGCUUCGGCACCCAGGAACCCCUAAACA--UAAAAAUCCCC
........(((.(((.(((((..(((((((.....)))).)))....))))).))).)))...........((((((..(((....)))...(((....)))...))--))))....... ( -25.20)
>DroSim_CAF1 727 118 + 1
UCUGCCACCAUUUUGUGUCGGCCGGCUGGCAAAAUGUCAUGCUAUUUCUGACCCAACAUGCCACAUUUUUAUUUAUGCAUGCUUCGGCACCCAGGAACCCCUAAACA--UAAAAAUCUCC
........(((.(((.(((((..(((((((.....)))).)))....))))).))).)))...........((((((..(((....)))...(((....)))...))--))))....... ( -25.20)
>DroYak_CAF1 8838 120 + 1
UCUGCCACCAUUUUGUGUCGGCCGGCUGGCAAAAUGUCAUGCUAUUUCUGACCCAGCAUGCCACAUUUUUAUUUAUGCAUGCCUCGGCACCCAGAAACCCCUAAACCCCCAAAAACCCCU
..((((.......((.(((((..(((((((.....)))).)))....))))).))((((((...............))))))...))))............................... ( -25.86)
>consensus
UCUGCCACCAUUUUGUGUCGGCCGGCUGGCAAAAUGUCAUGCUAUUUCUGACCCAACAUGCCACAUUUUUAUUUAUGCAUGCUUCGGCACCCAGGAACCCCUAAACA__UAAAAAUCCCC
..((((......(((.(((((..(((((((.....)))).)))....))))).)))(((((...............)))))....))))............................... (-23.00 = -22.81 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:27 2006