Locus 415

Sequence ID	2L_DroMel_CAF1
Location	1,235,720 – 1,235,960
Length	240
Max. P	0.937335

overview

Window 0

Location	1,235,720 – 1,235,840
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.58
Mean single sequence MFE	-41.80
Consensus MFE	-35.74
Energy contribution	-36.80
Covariance contribution	1.06
Combinations/Pair	1.03
Mean z-score	-1.62
Structure conservation index	0.85
SVM decision value	0.12
SVM RNA-class probability	0.593144
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1235720 120 + 22407834
AUGCGUGCGGCAAAAGUUUUGCGGGCAGGAAGGCCAAAACUCGAGUGCAGCUCGCAGGACACGACCAGUGGAAUAAUCCUUUGUCCUGCCACGGAUGCUCUCCCCAAAAACUUUUGCGGU
......((.(((((((((((..(((..((....)).......(((.(((.((.(((((((((.....))(((....)))...)))))))...)).))).)))))).))))))))))).)) ( -43.50)
>DroSec_CAF1 13050 120 + 1
AUGCGUGCGGCAAAAGUUUUACGGGCAGGAAGGCCAAAACUCGAGUGCAGCUCGCAGGACACGACCAGAGGAAUAAUCCUUUGUCCUGCCACGGAUGCUCUCCCCAAAAACUUUUGCGGU
......((.(((((((((((..(((..((....)).......(((.(((.((.((((((((......(((((....)))))))))))))...)).))).)))))).))))))))))).)) ( -44.40)
>DroSim_CAF1 8833 120 + 1
AUGCGUGCGGCAAAAGUUUUGCGGGCAGGAAGGCCAAAACUCGAGUGCAGCUCGCAGGACACGACCAGUGGAAUAAUCCUUUGUCCUGCCACGGAUGCUCUCCCCAAAAACUUUUGCGGU
......((.(((((((((((..(((..((....)).......(((.(((.((.(((((((((.....))(((....)))...)))))))...)).))).)))))).))))))))))).)) ( -43.50)
>DroYak_CAF1 9137 119 + 1
AUGCGUGCGGCAAAAGUUUUGUGGGCAGAAAGGCUAAGACUCGAGUGCAGCUCACAGGACACGACCAGUGGAAUAAUCCUUUGUCCUGCCACGGAUGUGCCUCCCAA-AAGUUUUGCGGU
......((.((((((.(((((.(((((.(..(((........(((.....)))..(((((((.....))(((....)))...)))))))).....).)))))..)))-)).)))))).)) ( -35.80)
>consensus
AUGCGUGCGGCAAAAGUUUUGCGGGCAGGAAGGCCAAAACUCGAGUGCAGCUCGCAGGACACGACCAGUGGAAUAAUCCUUUGUCCUGCCACGGAUGCUCUCCCCAAAAACUUUUGCGGU
......((.(((((((((((..(((.(((....((.......(((.....)))(((((((((.....).(((....)))..))))))))...))....))).))).))))))))))).)) (-35.74 = -36.80 +   1.06)

alignment

secondary structure

dotplot

Window 1

Location	1,235,760 – 1,235,880
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.25
Mean single sequence MFE	-34.67
Consensus MFE	-29.92
Energy contribution	-30.04
Covariance contribution	0.12
Combinations/Pair	1.06
Mean z-score	-1.90
Structure conservation index	0.86
SVM decision value	0.31
SVM RNA-class probability	0.683550
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1235760 120 + 22407834
UCGAGUGCAGCUCGCAGGACACGACCAGUGGAAUAAUCCUUUGUCCUGCCACGGAUGCUCUCCCCAAAAACUUUUGCGGUUCAAUUUGAAAAGGAAACUGCAAAGGAAAUUCCAAGGACA
..(((.(((.((.(((((((((.....))(((....)))...)))))))...)).))).)))........(((((((((((...(((....))).))))))))))).............. ( -35.00)
>DroSec_CAF1 13090 120 + 1
UCGAGUGCAGCUCGCAGGACACGACCAGAGGAAUAAUCCUUUGUCCUGCCACGGAUGCUCUCCCCAAAAACUUUUGCGGUUCAAUUUGAAAAGGAAACUGCAAAGGAAAUUCCAAGGACA
..(((.(((.((.((((((((......(((((....)))))))))))))...)).))).)))........(((((((((((...(((....))).))))))))))).............. ( -37.50)
>DroSim_CAF1 8873 120 + 1
UCGAGUGCAGCUCGCAGGACACGACCAGUGGAAUAAUCCUUUGUCCUGCCACGGAUGCUCUCCCCAAAAACUUUUGCGGUUCAAUUUGAAAAGGAAACUGCAAAGGAAAUUCCAAGGACA
..(((.(((.((.(((((((((.....))(((....)))...)))))))...)).))).)))........(((((((((((...(((....))).))))))))))).............. ( -35.00)
>DroYak_CAF1 9177 119 + 1
UCGAGUGCAGCUCACAGGACACGACCAGUGGAAUAAUCCUUUGUCCUGCCACGGAUGUGCCUCCCAA-AAGUUUUGCGGUUCAAUUUGAAAAGAAAACUGCAAAGGAAAUUCCAAGGACA
..(((.....)))..(((.((((.((.((((.((((....))))....)))))).))))))).((..-....(((((((((...(((....))).)))))))))((.....))..))... ( -31.20)
>consensus
UCGAGUGCAGCUCGCAGGACACGACCAGUGGAAUAAUCCUUUGUCCUGCCACGGAUGCUCUCCCCAAAAACUUUUGCGGUUCAAUUUGAAAAGGAAACUGCAAAGGAAAUUCCAAGGACA
..(((.(((.((.(((((((((.....).(((....)))..))))))))...)).))).))).((.......(((((((((..............)))))))))((.....))..))... (-29.92 = -30.04 +   0.12)

alignment

secondary structure

dotplot

Window 2

Location	1,235,840 – 1,235,960
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.25
Mean single sequence MFE	-28.12
Consensus MFE	-25.13
Energy contribution	-25.32
Covariance contribution	0.19
Combinations/Pair	1.09
Mean z-score	-2.49
Structure conservation index	0.89
SVM decision value	1.26
SVM RNA-class probability	0.937335
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1235840 120 - 22407834
UUCCUCUGAUAUCCCAGGGCCAUGUACAUUUUCAUUAGUUUAAUUAAAAUUUUAUUCAUCCUCGUGUGUGCGUGGCUGUGUGUCCUUGGAAUUUCCUUUGCAGUUUCCUUUUCAAAUUGA
((((...((((...((.((((((((((((........(..(((........)))..)........)))))))))))).))))))...)))).........((((((.......)))))). ( -27.99)
>DroSec_CAF1 13170 120 - 1
UUCCUCUGAUAUCCCAGGGCCAUGUACAUUUUCAUUAGUUUAAUUAAAAUUUUAUUCAUCCUCGUGUGUGCGUGGCUGUGUGUCCUUGGAAUUUCCUUUGCAGUUUCCUUUUCAAAUUGA
((((...((((...((.((((((((((((........(..(((........)))..)........)))))))))))).))))))...)))).........((((((.......)))))). ( -27.99)
>DroSim_CAF1 8953 120 - 1
UUCCUCUGAUAUCCCAGGGCCAUGUACAUUUUCAUUAGUUUAAUUAAAAUUUUAUUCAUCCUCGUGUGUGCGUGGCUGUGUGUCCUUGGAAUUUCCUUUGCAGUUUCCUUUUCAAAUUGA
((((...((((...((.((((((((((((........(..(((........)))..)........)))))))))))).))))))...)))).........((((((.......)))))). ( -27.99)
>DroYak_CAF1 9256 120 - 1
UUCCUCUGGCAUCCAGGGGCCAUGUACAUAUUCAUUAGUUUAAUUAAAAUUGUAUUCAUCCUUGUGUGUGCGUGCCUGUGUGUCCUUGGAAUUUCCUUUGCAGUUUUCUUUUCAAAUUGA
((((...((((..((((.((((..((((.......((((((.....))))))..........))))..)).)).))))..))))...)))).........((((((.......)))))). ( -28.53)
>consensus
UUCCUCUGAUAUCCCAGGGCCAUGUACAUUUUCAUUAGUUUAAUUAAAAUUUUAUUCAUCCUCGUGUGUGCGUGGCUGUGUGUCCUUGGAAUUUCCUUUGCAGUUUCCUUUUCAAAUUGA
((((...((((...((.((((((((((((........(..(((........)))..)........)))))))))))).))))))...)))).........((((((.......)))))). (-25.13 = -25.32 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:37 2006