Locus 2542

Sequence ID	2L_DroMel_CAF1
Location	7,026,842 – 7,026,962
Length	120
Max. P	0.824282

overview

Window 3

Location	7,026,842 – 7,026,933
Length	91
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	80.18
Mean single sequence MFE	-25.33
Consensus MFE	-16.12
Energy contribution	-16.90
Covariance contribution	0.78
Combinations/Pair	1.05
Mean z-score	-1.57
Structure conservation index	0.64
SVM decision value	0.21
SVM RNA-class probability	0.636245
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7026842 91 - 22407834
ACGCAUAACUUAUGUCUGAUAAAAGUGCGAAGGAAUCAUGUAUCAGUAAGAGUGCGAGCUGCAGCAGCAGGCGCAAGAGAAGAAAGUGAG---------------------C--
.(((...((((.((.((((((...((((....)...))).)))))))).))))(((..((((....)))).)))...........)))..---------------------.-- ( -23.00)
>DroPse_CAF1 14797 103 - 1
AUGUAUAACUUAUGUCUGAUAAAAGUGCAAAGGAAUCCUGUAUCAGUCGUAGUGCGAGCUGCAGCAGCAGGCGCAAAAGAAGAAAGUGAAUUCGC-GC---------AGCAGG-
.(((......((((.((((((.........(((...))).)))))).))))(((((((((((....)))).(((...........)))..)))))-))---------.)))..- ( -25.80)
>DroGri_CAF1 122694 110 - 1
AUGUAGAACUUAUGUCUGAUACAAGUGCGCUGGAAUUAUGUAUAUGUCGUAGUGCGAGCUGCAGUAGCAGGCGCAA-AGAAGAAAGUGAAGCUGCUGCAUCAAAACC---AACA
.((((..((....))....)))).....(((.(.((((((.......)))))).).)))(((((((((...(((..-........)))..)))))))))........---.... ( -26.70)
>DroYak_CAF1 13313 91 - 1
ACGCAUAACUUAUGUCUGAUAAAAGUGCAAAGGAAUCAUGUAUCAGUAAGAGUGCGAGCUGCAGCAGCAGGCGCAAGAGAAGAAAGUGAG---------------------C--
.(((...((((.((.((((((...(((.........))).)))))))).))))(((..((((....)))).)))...........)))..---------------------.-- ( -21.80)
>DroAna_CAF1 14649 99 - 1
AUGCAUAACUUAUGUCUGAUAAAAGUGCGAAGGAAUCAUGUAUCAGUCGUAGUGCGAUCUGCAGCAGCAGGCGCAAAAGAAGAAAGUGAG---GC-GU---------GGAGU--
((((...(((((((.((((((...((((....)...))).)))))).)))..((((.(((((....)))))))))........))))...---))-))---------.....-- ( -28.90)
>DroPer_CAF1 15762 103 - 1
AUGUAUAACUUAUGUCUGAUAAAAGUGCAAAGGAAUCCUGUAUCAGUCGUAGUGCGAGCUGCAGCAGCAGGCGCAAAAGAAGAAAGUGAAUUCGC-GC---------AGCAGG-
.(((......((((.((((((.........(((...))).)))))).))))(((((((((((....)))).(((...........)))..)))))-))---------.)))..- ( -25.80)
>consensus
AUGCAUAACUUAUGUCUGAUAAAAGUGCAAAGGAAUCAUGUAUCAGUCGUAGUGCGAGCUGCAGCAGCAGGCGCAAAAGAAGAAAGUGAA___GC_GC____________AC__
.......(((((((.((((((......(....).......)))))).)))..((((..((((....)))).))))........))))........................... (-16.12 = -16.90 +   0.78)

alignment

secondary structure

dotplot

Window 4

Location	7,026,856 – 7,026,962
Length	106
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	78.72
Mean single sequence MFE	-20.25
Consensus MFE	-14.98
Energy contribution	-14.98
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.22
Structure conservation index	0.74
SVM decision value	0.40
SVM RNA-class probability	0.722634
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7026856 106 + 22407834
CUUGCGCCUGCUGCUGCAGCUCGCACUCUUACUGAUACAUGAUUCCUUCGCACUUUUAUCAGACAUAAGUUAUGCGUAUGUUGGCAAGCACACUUUUUUCACGAAA-
..((.((.((((...(((...((((..((((((((((..(((.....)))......))))))...))))...))))..))).)))).)).))..............- ( -21.40)
>DroVir_CAF1 100088 94 + 1
UUUGCGCCUGCUACUGCAGCUCGCACUACAACUGAUACAUAAUUCCAGCGCACCUGUAUCAGACAUAAGUUCUACAUAUGUUU-------------UUGCACAACUC
..((((.((((....))))..))))......((((((((...............))))))))(((((.(.....).)))))..-------------........... ( -20.06)
>DroPse_CAF1 14823 94 + 1
UUUGCGCCUGCUGCUGCAGCUCGCACUACGACUGAUACAGGAUUCCUUUGCACUUUUAUCAGACAUAAGUUAUACAUAUGA------------UUUGUUCACUCAG-
..((((.((((....))))..))))......((((((.(((...........))).))))))..(((((((((....))))------------)))))........- ( -19.50)
>DroMoj_CAF1 130221 94 + 1
UUUGCGCCUGCUACUGCAGCUCGCACUACAACUGAUACAUAAUUCCAGAGCACUUGUAUCAGACAUAAGUUCUACAUAUGUUU-------------UUGCACAAUUU
..((((.((((....))))..))))......((((((((...............))))))))(((((.(.....).)))))..-------------........... ( -20.86)
>DroAna_CAF1 14671 104 + 1
UUUGCGCCUGCUGCUGCAGAUCGCACUACGACUGAUACAUGAUUCCUUCGCACUUUUAUCAGACAUAAGUUAUGCAUAUGCUGGACACCACAAUU--UGCACGAAA-
..((((.((((....))))..))))...((.((((((..(((.....)))......))))))..........((((..((.(((...)))))...--))))))...- ( -20.20)
>DroPer_CAF1 15788 94 + 1
UUUGCGCCUGCUGCUGCAGCUCGCACUACGACUGAUACAGGAUUCCUUUGCACUUUUAUCAGACAUAAGUUAUACAUAUGA------------UUUGUUCACUCAG-
..((((.((((....))))..))))......((((((.(((...........))).))))))..(((((((((....))))------------)))))........- ( -19.50)
>consensus
UUUGCGCCUGCUGCUGCAGCUCGCACUACGACUGAUACAUGAUUCCUUCGCACUUUUAUCAGACAUAAGUUAUACAUAUGUU___________UU_UUGCACAAAA_
..((((.((((....))))..))))......((((((...................)))))).((((.(.....).))))........................... (-14.98 = -14.98 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	7,026,856 – 7,026,962
Length	106
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	78.72
Mean single sequence MFE	-25.97
Consensus MFE	-17.64
Energy contribution	-17.67
Covariance contribution	0.03
Combinations/Pair	1.10
Mean z-score	-1.60
Structure conservation index	0.68
SVM decision value	0.69
SVM RNA-class probability	0.824282
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7026856 106 - 22407834
-UUUCGUGAAAAAAGUGUGCUUGCCAACAUACGCAUAACUUAUGUCUGAUAAAAGUGCGAAGGAAUCAUGUAUCAGUAAGAGUGCGAGCUGCAGCAGCAGGCGCAAG
-..............(((((((((.......(((((..((((...((((((...((((....)...))).)))))))))).))))).((....)).))))))))).. ( -30.10)
>DroVir_CAF1 100088 94 - 1
GAGUUGUGCAA-------------AAACAUAUGUAGAACUUAUGUCUGAUACAGGUGCGCUGGAAUUAUGUAUCAGUUGUAGUGCGAGCUGCAGUAGCAGGCGCAAA
(((((.((((.-------------.......)))).)))))....((((((((....(....).....))))))))......((((..((((....)))).)))).. ( -27.10)
>DroPse_CAF1 14823 94 - 1
-CUGAGUGAACAAA------------UCAUAUGUAUAACUUAUGUCUGAUAAAAGUGCAAAGGAAUCCUGUAUCAGUCGUAGUGCGAGCUGCAGCAGCAGGCGCAAA
-....((((.....------------)))).........(((((.((((((.........(((...))).)))))).)))))((((..((((....)))).)))).. ( -21.80)
>DroMoj_CAF1 130221 94 - 1
AAAUUGUGCAA-------------AAACAUAUGUAGAACUUAUGUCUGAUACAAGUGCUCUGGAAUUAUGUAUCAGUUGUAGUGCGAGCUGCAGUAGCAGGCGCAAA
......(((((-------------..(((((.(.....).)))))(((((((((((........))).))))))))))))).((((..((((....)))).)))).. ( -24.70)
>DroAna_CAF1 14671 104 - 1
-UUUCGUGCA--AAUUGUGGUGUCCAGCAUAUGCAUAACUUAUGUCUGAUAAAAGUGCGAAGGAAUCAUGUAUCAGUCGUAGUGCGAUCUGCAGCAGCAGGCGCAAA
-....(((((--...(((((...))).))..)))))...(((((.((((((...((((....)...))).)))))).)))))((((.(((((....))))))))).. ( -30.30)
>DroPer_CAF1 15788 94 - 1
-CUGAGUGAACAAA------------UCAUAUGUAUAACUUAUGUCUGAUAAAAGUGCAAAGGAAUCCUGUAUCAGUCGUAGUGCGAGCUGCAGCAGCAGGCGCAAA
-....((((.....------------)))).........(((((.((((((.........(((...))).)))))).)))))((((..((((....)))).)))).. ( -21.80)
>consensus
_AUUAGUGAAA_AA___________AACAUAUGUAUAACUUAUGUCUGAUAAAAGUGCGAAGGAAUCAUGUAUCAGUCGUAGUGCGAGCUGCAGCAGCAGGCGCAAA
.......................................(((((.((((((......(....).......)))))).)))))((((..((((....)))).)))).. (-17.64 = -17.67 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:22 2006