Locus 2872

Sequence ID	2L_DroMel_CAF1
Location	8,248,193 – 8,248,353
Length	160
Max. P	0.993046

overview

Window 0

Location	8,248,193 – 8,248,313
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.89
Mean single sequence MFE	-42.85
Consensus MFE	-27.41
Energy contribution	-25.95
Covariance contribution	-1.46
Combinations/Pair	1.66
Mean z-score	-2.75
Structure conservation index	0.64
SVM decision value	2.37
SVM RNA-class probability	0.993046
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8248193 120 + 22407834
UGAAGGCAGGAUUAUGAUCCUGUCUGACUUUUUCAGGAGAAUAGGCUCCAGGUGCUGGAGUGUCGCUAGGUUUUUGAAGAUUAUGACGGCCAGCGAAAGAGAAUGCUGGGUUAUGAUCUU
...(((((((((....)))))))))......((((((((..((((((((((...)))))))....)))..))))))))(((((((((..((((((........))))))))))))))).. ( -45.70)
>DroVir_CAF1 29141 120 + 1
UGAAUGCGGGAUUGUGAUCCUGACGGACUUUUUCAGGGGAGUAAGCUCCAGGAGCUGGGGUAUCGCUUGGCUUUUGAAGGUCAUGACGACCAGCAAAUGAAAAGGCGGGAUUAUGGUCUU
.......(((((..((((((((.....((((((((..((((....))))....(((((....((((.((((((....)))))).).))))))))...))))))))))))))))..))))) ( -44.80)
>DroPse_CAF1 33628 120 + 1
AAAAAGCUGGGUUAUGGUCUUGUCGGUUCUUUUCCGGAGAAUAAGCCCCAGGAGCGGGUGUAUCACUUGGCUUAUGGAGGUCGUGGCGACCAGCGAAGGAGAAGGAAGGAUUGUGAUCUU
........((((((..(((((.....(((((((((............(((.(((((((((...))))).)))).))).(((((...)))))......))))))))))))))..)))))). ( -39.00)
>DroWil_CAF1 28948 120 + 1
AAAAGGCAGGAUUGUGAUCUUGUCUAACCUUUUCGGGAGAGUAAGCACCUGGAGCGGGGGUGUCACUAGCUUUGUGAAGGUCGUGACGACCAGCAAACGAAAACGAGGGAGUGUGGUCAA
...(((((((((....)))))))))..((.(((((((.(......).))))))).))....(((((.(.(((....))).).)))))(((((.((..(........)....))))))).. ( -35.50)
>DroMoj_CAF1 31725 120 + 1
AAAAGGCAGGAUUGUGGUCUAGCCGAACUUUCUCUGGGGAAUAGGCUCCAGGAGCAGGAGUAUCGCUUGGUUUGUGAAGAUCAUGGCGGCCAGCGAAAGAAAAGGCGGGAUUAUGGUCUA
........((((..((((((.(((...(((((.((((.......(((((.......))))).(((((((((((....)))))).))))))))).)))))....))).))))))..)))). ( -46.70)
>DroPer_CAF1 35233 120 + 1
UGUAGGAUGGAUUGUAAUCCUGCCGCACCUUCUCAGGAGAGUAUGCUCCAGGAGCGGGAGUAUCACUCGGUUUUUGCAGAUCGUGGCGACCAGCGAAGGAGAAGGAAGGACUAUGAUCCU
........((((..((.((((.((...(((((.(....(((((((((((.......))))))).))))((((.(..(.....)..).)))).).)))))....)).)))).))..)))). ( -45.40)
>consensus
AAAAGGCAGGAUUGUGAUCCUGUCGGACCUUUUCAGGAGAAUAAGCUCCAGGAGCGGGAGUAUCACUUGGUUUUUGAAGAUCAUGACGACCAGCGAAAGAAAAGGAGGGAUUAUGAUCUU
........(((((((((((((......((((((((((((......))))....((.((....(((..((((((....)))))))))...)).))...)))))))).))))))))))))). (-27.41 = -25.95 +  -1.46)

alignment

secondary structure

dotplot

Window 1

Location	8,248,233 – 8,248,353
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.06
Mean single sequence MFE	-43.52
Consensus MFE	-26.38
Energy contribution	-24.53
Covariance contribution	-1.85
Combinations/Pair	1.58
Mean z-score	-1.86
Structure conservation index	0.61
SVM decision value	0.79
SVM RNA-class probability	0.851788
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8248233 120 + 22407834
AUAGGCUCCAGGUGCUGGAGUGUCGCUAGGUUUUUGAAGAUUAUGACGGCCAGCGAAAGAGAAUGCUGGGUUAUGAUCUUGCCUAACUUUCUCGGGAUGAUAAUCACCUGGAGCUGGGGU
...(((((((((((((.(((....(.(((((.....(((((((((((..((((((........)))))))))))))))))))))).)...))).))........)))))))))))..... ( -47.70)
>DroVir_CAF1 29181 120 + 1
GUAAGCUCCAGGAGCUGGGGUAUCGCUUGGCUUUUGAAGGUCAUGACGACCAGCAAAUGAAAAGGCGGGAUUAUGGUCUUGUCUGACCUUCUCAGGGUGAUAAUCACCGGGAGCAGGGGU
....(((((((((((..((......))..))))))((((((((.((((((((.....((......))......)))))..)))))))))))....((((.....)))).)))))...... ( -47.30)
>DroPse_CAF1 33668 120 + 1
AUAAGCCCCAGGAGCGGGUGUAUCACUUGGCUUAUGGAGGUCGUGGCGACCAGCGAAGGAGAAGGAAGGAUUGUGAUCUUGUCUAACAUUCUCUGGAUGGUAGUCUCCCGGGGCGGGAGU
....(((((..(((((((((...))))).))))..(((((.(...((.(((((.(((..(((....(((((....))))).)))....))).)))).).)).)))))).)))))...... ( -40.00)
>DroWil_CAF1 28988 120 + 1
GUAAGCACCUGGAGCGGGGGUGUCACUAGCUUUGUGAAGGUCGUGACGACCAGCAAACGAAAACGAGGGAGUGUGGUCAAGCCUGACUUUUUCUGGAUGGUAGUCUCCAGGAGCAGGUGU
....((((((((((((((...(((((.(.(((....))).).)))))(((((.((..(........)....)))))))...)))).)))((((((((........))))))))))))))) ( -41.90)
>DroMoj_CAF1 31765 120 + 1
AUAGGCUCCAGGAGCAGGAGUAUCGCUUGGUUUGUGAAGAUCAUGGCGGCCAGCGAAAGAAAAGGCGGGAUUAUGGUCUAGUCUGACUUUUUCAGGGUGGUAAUCACCAGGGGCGGGGGU
....((((((((((((((....((((.......))))((((((((((.(((..(....)....))).)..)))))))))..)))).)))))....((((.....)))).)))))...... ( -37.90)
>DroPer_CAF1 35273 120 + 1
GUAUGCUCCAGGAGCGGGAGUAUCACUCGGUUUUUGCAGAUCGUGGCGACCAGCGAAGGAGAAGGAAGGACUAUGAUCCUGCCUAACCUUCUCUGGAUGGUAGUCUCCCGGGGCGGGAGU
....(((((.....((((((((((((.(((((......))))).)....((((.(((((...(((.((((......)))).)))..))))).)))).)))))..)))))).....))))) ( -46.30)
>consensus
AUAAGCUCCAGGAGCGGGAGUAUCACUUGGUUUUUGAAGAUCAUGACGACCAGCGAAAGAAAAGGAGGGAUUAUGAUCUUGCCUAACUUUCUCUGGAUGGUAAUCACCAGGAGCGGGGGU
....(((((.(((((.((....(((..((((((....)))))))))...)).))..............((((((.((((...............)))).))))))))).)))))...... (-26.38 = -24.53 +  -1.85)

alignment

secondary structure

dotplot

Window 2

Location	8,248,233 – 8,248,353
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.06
Mean single sequence MFE	-34.12
Consensus MFE	-19.99
Energy contribution	-18.93
Covariance contribution	-1.05
Combinations/Pair	1.41
Mean z-score	-2.60
Structure conservation index	0.59
SVM decision value	1.71
SVM RNA-class probability	0.973384
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8248233 120 - 22407834
ACCCCAGCUCCAGGUGAUUAUCAUCCCGAGAAAGUUAGGCAAGAUCAUAACCCAGCAUUCUCUUUCGCUGGCCGUCAUAAUCUUCAAAAACCUAGCGACACUCCAGCACCUGGAGCCUAU
......((((((((((...........(((...((((((.(((((.((.(((((((..........)))))..)).)).)))))......))))))....)))...)))))))))).... ( -36.04)
>DroVir_CAF1 29181 120 - 1
ACCCCUGCUCCCGGUGAUUAUCACCCUGAGAAGGUCAGACAAGACCAUAAUCCCGCCUUUUCAUUUGCUGGUCGUCAUGACCUUCAAAAGCCAAGCGAUACCCCAGCUCCUGGAGCUUAC
......(((((.((((.....))))(((.(((((((((((..((((((((..............))).)))))))).))))))))....((...)).......))).....))))).... ( -36.24)
>DroPse_CAF1 33668 120 - 1
ACUCCCGCCCCGGGAGACUACCAUCCAGAGAAUGUUAGACAAGAUCACAAUCCUUCCUUCUCCUUCGCUGGUCGCCACGACCUCCAUAAGCCAAGUGAUACACCCGCUCCUGGGGCUUAU
......((((((((((......(((..(((((.(..((..............))..))))))(((.((((((((...)))))......))).))).))).......)))))))))).... ( -34.76)
>DroWil_CAF1 28988 120 - 1
ACACCUGCUCCUGGAGACUACCAUCCAGAAAAAGUCAGGCUUGACCACACUCCCUCGUUUUCGUUUGCUGGUCGUCACGACCUUCACAAAGCUAGUGACACCCCCGCUCCAGGUGCUUAC
......((.(((((((((((.((..(.(((((.....((..((....))..))....))))))..)).)))))(((((...(((....)))...)))))........)))))).)).... ( -32.80)
>DroMoj_CAF1 31765 120 - 1
ACCCCCGCCCCUGGUGAUUACCACCCUGAAAAAGUCAGACUAGACCAUAAUCCCGCCUUUUCUUUCGCUGGCCGCCAUGAUCUUCACAAACCAAGCGAUACUCCUGCUCCUGGAGCCUAU
.....(((...(((((.........((((.....))))................(((............))))))))((.....))........)))...((((.......))))..... ( -19.40)
>DroPer_CAF1 35273 120 - 1
ACUCCCGCCCCGGGAGACUACCAUCCAGAGAAGGUUAGGCAGGAUCAUAGUCCUUCCUUCUCCUUCGCUGGUCGCCACGAUCUGCAAAAACCGAGUGAUACUCCCGCUCCUGGAGCAUAC
.((((((...)))))).......(((((.(((((..(((.(((((....))))).)))...)))))((.(((((...))))).)).......(((((.......))))))))))...... ( -45.50)
>consensus
ACCCCCGCCCCGGGAGACUACCAUCCAGAGAAAGUCAGACAAGACCAUAAUCCCGCCUUCUCCUUCGCUGGUCGCCACGACCUUCAAAAACCAAGCGAUACUCCCGCUCCUGGAGCUUAC
......((.(((((((...........(((((.(...((...........))...).)))))..((((((((((...)))))...........)))))........))))))).)).... (-19.99 = -18.93 +  -1.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:21 2006