Locus 3641

Sequence ID	2L_DroMel_CAF1
Location	10,605,032 – 10,605,162
Length	130
Max. P	0.983031

overview

Window 4

Location	10,605,032 – 10,605,142
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	95.06
Mean single sequence MFE	-37.24
Consensus MFE	-32.62
Energy contribution	-33.10
Covariance contribution	0.48
Combinations/Pair	1.07
Mean z-score	-1.86
Structure conservation index	0.88
SVM decision value	1.93
SVM RNA-class probability	0.983031
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10605032 110 + 22407834
UCUCUUGAUUACGCGACGUCUUGCGAGAAGAAGUUGAGAAAAGAAAAACGCAGCGCAUCCAAAUUGGCUUUGCCACUGCCGAUUGAGCGGAUGGGUUGCCUCUUCAGUCG
......((((.(((((....))))).(((((.(((...........)))(((((.(((((.(((((((.........)))))))....))))).))))).))))))))). ( -36.40)
>DroSec_CAF1 84690 109 + 1
UCUCUUGAUUACGCGACGUCUCGCGAGAAGAAGUUGA-AAAAGAAGAACGCAGCGCAUCCAAAUUGGCUUUGCCACUGCCGAUUGAGCAGAUGGGUUGCCUCUUCAGUCG
......((((...((((.((((....).))).)))).-....(((((..(((((.((((..(((((((.........))))))).....)))).))))).))))))))). ( -35.60)
>DroSim_CAF1 85261 109 + 1
UCUCUUGAUUACGCGACGUCUCGCGAGAAGAAGUUGA-AAAAGAAGAACGCAGCGCAUCCAAAUUGGCUUUGCCACUGCCGAUUGAGCAGAUGGGUUGCCUCUUCACUCG
((.(((..((.(((((....))))).))..)))..))-....(((((..(((((.((((..(((((((.........))))))).....)))).))))).)))))..... ( -34.10)
>DroEre_CAF1 85645 109 + 1
UCUCUUGAUUACGCGACGUCUCGCGCGAAGAACUUGA-AAAAGAAGAACGCAGCGCAUCCAAAUCGGCUUUGCCACUGCCGAUUGAACGGAUGGGUUGCCCCUUCAGCCG
...........(((((....))))).((((..(((..-..)))......(((((.(((((.(((((((.........)))))))....))))).)))))..))))..... ( -38.70)
>DroYak_CAF1 87836 109 + 1
UCUCUUGAUUACGCGACGUCUCGCGAGAAGAAGUUGC-AAAAGAAGAACGCAGCGCAUCCAAAUUGGCUUUGCCACUGCCGAUUGAACGGAUGGGUUGCCUCUUCAGCCG
............(((((.((((....).))).)))))-....(((((..(((((.(((((.(((((((.........)))))))....))))).))))).)))))..... ( -41.40)
>consensus
UCUCUUGAUUACGCGACGUCUCGCGAGAAGAAGUUGA_AAAAGAAGAACGCAGCGCAUCCAAAUUGGCUUUGCCACUGCCGAUUGAGCGGAUGGGUUGCCUCUUCAGUCG
...........(((((....))))).................(((((..(((((.(((((.(((((((.........)))))))....))))).))))).)))))..... (-32.62 = -33.10 +   0.48)

alignment

secondary structure

dotplot

Window 5

Location	10,605,062 – 10,605,162
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	93.16
Mean single sequence MFE	-30.04
Consensus MFE	-26.22
Energy contribution	-26.86
Covariance contribution	0.64
Combinations/Pair	1.05
Mean z-score	-1.39
Structure conservation index	0.87
SVM decision value	0.65
SVM RNA-class probability	0.811133
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10605062 100 + 22407834
AAGUUGAGAAAAGAAAAACGCAGCGCAUCCAAAUUGGCUUUGCCACUGCCGAUUGAGCGGAUGGGUUGCCUCUUCAGUCGGUCCUCUUGCACUUUAGUAU
..((.(((.(..((.....(((((.(((((.(((((((.........)))))))....))))).)))))........))..).)))..)).......... ( -27.82)
>DroSec_CAF1 84720 99 + 1
AAGUUGA-AAAAGAAGAACGCAGCGCAUCCAAAUUGGCUUUGCCACUGCCGAUUGAGCAGAUGGGUUGCCUCUUCAGUCGGUCGUCUUGCACUUCAGUAU
...((((-(...(((((..(((((.((((..(((((((.........))))))).....)))).))))).))))).((.((....)).))..)))))... ( -29.10)
>DroSim_CAF1 85291 99 + 1
AAGUUGA-AAAAGAAGAACGCAGCGCAUCCAAAUUGGCUUUGCCACUGCCGAUUGAGCAGAUGGGUUGCCUCUUCACUCGGUCGUCUUGCACUUCAGUAU
(((.(((-....(((((..(((((.((((..(((((((.........))))))).....)))).))))).)))))......))).)))............ ( -27.20)
>DroEre_CAF1 85675 99 + 1
AACUUGA-AAAAGAAGAACGCAGCGCAUCCAAAUCGGCUUUGCCACUGCCGAUUGAACGGAUGGGUUGCCCCUUCAGCCGCUCGUCUUGCACUUCAGUUU
((((.((-(...((((...(((((.(((((.(((((((.........)))))))....))))).)))))..))))....((.......))..))))))). ( -34.10)
>DroYak_CAF1 87866 99 + 1
AAGUUGC-AAAAGAAGAACGCAGCGCAUCCAAAUUGGCUUUGCCACUGCCGAUUGAACGGAUGGGUUGCCUCUUCAGCCGCUCGUCUCGCACUUCAGUAU
....(((-....(((((..(((((.(((((.(((((((.........)))))))....))))).))))).)))))....((.......))......))). ( -32.00)
>consensus
AAGUUGA_AAAAGAAGAACGCAGCGCAUCCAAAUUGGCUUUGCCACUGCCGAUUGAGCGGAUGGGUUGCCUCUUCAGUCGGUCGUCUUGCACUUCAGUAU
............(((((..(((((.(((((.(((((((.........)))))))....))))).))))).)))))......................... (-26.22 = -26.86 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:32 2006