Locus 5351

Sequence ID	X_DroMel_CAF1
Location	13,935,945 – 13,936,192
Length	247
Max. P	0.999732

overview

Window 2

Location	13,935,945 – 13,936,065
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-46.98
Consensus MFE	-43.76
Energy contribution	-43.84
Covariance contribution	0.08
Combinations/Pair	1.05
Mean z-score	-1.74
Structure conservation index	0.93
SVM decision value	1.64
SVM RNA-class probability	0.969562
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13935945 120 - 22224390
CAAAUCGCAGGCGGGCACAUGGGCGUAGCCUUUUGGUCAGCACUGUAGCUGCGUUUUUUUGCAUUUGCUGCAUUCGCGCUGCGAUUGGUUGCGGCCAGCAGCGCCUCAUAUCGAUGAGCC
......((.((((.((...(((.(((((((..(((..((((.(((((((((((......))))...))))))...).)))))))..))))))).)))))..))))((((....)))))). ( -46.10)
>DroSec_CAF1 15690 120 - 1
CAAAUCGCAGGCGGGCACAUGGGCGUAGCCUUUUGGUCAGCACUGUAGCUGCGUUUUUUUGCAUUUGCUGCAUUCGCGCUGCGAUUGGUUGCGGCCAGCAGCGCCUCAUAUCGAUGAGCC
......((.((((.((...(((.(((((((..(((..((((.(((((((((((......))))...))))))...).)))))))..))))))).)))))..))))((((....)))))). ( -46.10)
>DroSim_CAF1 21461 120 - 1
CAAAUCGCAGGCGGGCACAUGGGCGUAGCCUUUUGGUCAGCACUGUAGCUGCGUUUUUUUGCAUUUGCUGCAUUCGCGCUGCGAUUGGUUGCGGCCAGCAGUGCCUCAUAUCGAUGAGCC
.........(((.(((((.(((.(((((((..(((..((((.(((((((((((......))))...))))))...).)))))))..))))))).)))...)))))((((....))))))) ( -49.00)
>DroEre_CAF1 16983 120 - 1
CAAAUCGCAGGCGGGCACAUGGGCGUAGCCUUUUGGUCAGCACUGUAGCUGCGUUUUUUUGCAUUUGCUGCAUUCGCGCUGCCAUUGGUUGCGACCAACAGCGCCUCGUAUCGAUGAGCC
...((((...((((((.(.(((.(((((((...(((.((((.(((((((((((......))))...))))))...).)))))))..))))))).)))...).))).)))..))))..... ( -47.60)
>DroYak_CAF1 18714 120 - 1
CAAAUCGCAGGCGGGCACAUGGGCGUAGCCUUUUGGUCAGCACUGUAGCUGCGUUUUUUUGCAUUUGCUGCAUUCGCGCUGCGAUUGGUUGCGGCCAGCAGCGCCUCAUAUCGAUGAGCC
......((.((((.((...(((.(((((((..(((..((((.(((((((((((......))))...))))))...).)))))))..))))))).)))))..))))((((....)))))). ( -46.10)
>consensus
CAAAUCGCAGGCGGGCACAUGGGCGUAGCCUUUUGGUCAGCACUGUAGCUGCGUUUUUUUGCAUUUGCUGCAUUCGCGCUGCGAUUGGUUGCGGCCAGCAGCGCCUCAUAUCGAUGAGCC
......((.((((.((...(((.(((((((..(((..((((.(((((((((((......))))...))))))...).)))))))..))))))).)))))..))))((((....)))))). (-43.76 = -43.84 +   0.08)

alignment

secondary structure

dotplot

Window 3

Location	13,936,065 – 13,936,166
Length	101
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.27
Mean single sequence MFE	-43.84
Consensus MFE	-38.89
Energy contribution	-38.73
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-2.54
Structure conservation index	0.89
SVM decision value	3.70
SVM RNA-class probability	0.999539
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13936065 101 + 22224390
CAUGCGUCGCC------------------GUCGCAAUCGUCCAGCCACCCCCUUUAACCCUUCGCCGGUGCAGGGGGUGGCUUAUGUGCCGUUGCCU-UGCCGCGUGUGCACGUUAAUUA
(((((((.((.------------------...(((((.(..((((((((((((...(((.......)))..))))))))))...))..).)))))..-.)).)))))))........... ( -41.80)
>DroSec_CAF1 15810 101 + 1
CAUGCGUCGCC------------------GUCGCAAUCGCCCAGCCACCCCCUUUAACCCUUCGCCGGUGCAGGGGGUGGCUUAUGUGCCGUUGCCU-UGCCGCGUGUGCACGUUAAUUA
(((((((.((.------------------...(((((.(((.(((((((((((...(((.......)))..)))))))))))...).)).)))))..-.)).)))))))........... ( -43.10)
>DroSim_CAF1 21581 101 + 1
CAUGCGUCGCC------------------GUCGCAAUCGCCCAGCCACCCCCUUUAACCCUUCGCCGGUGCAGGGGGUGGCUUAUGUGCCGUUGCCU-UGCCGCGUGUGCACCUUAAUUA
(((((((.((.------------------...(((((.(((.(((((((((((...(((.......)))..)))))))))))...).)).)))))..-.)).)))))))........... ( -43.10)
>DroEre_CAF1 17103 119 + 1
CAUGCGUCGCCGUCGCCGUCGCAAUCGCCGUCGCAAUCGCCCAGCCACCCCCUUUAACCCUUCGCCGGUGCAGGGGGUGGCUUAUGUGCCGUUGCCU-UGCCGCGUGUGCACGUUAAUUA
...((((((((((.((....(((((.(((((.((....))..(((((((((((...(((.......)))..))))))))))).))).)).)))))..-.)).))).))).))))...... ( -47.60)
>DroYak_CAF1 18834 102 + 1
CAUGCGUCGCC------------------GUCGCAAUCGCCCAGCCACCCCCUUUAACCCUUCGCCGGUGCAGGGGGUGGCUUAUGUGCCGUUGCCUUUGCCGCGUGUGCACGUUAAUUA
(((((((.((.------------------(..(((((.(((.(((((((((((...(((.......)))..)))))))))))...).)).)))))..).)).)))))))........... ( -43.60)
>consensus
CAUGCGUCGCC__________________GUCGCAAUCGCCCAGCCACCCCCUUUAACCCUUCGCCGGUGCAGGGGGUGGCUUAUGUGCCGUUGCCU_UGCCGCGUGUGCACGUUAAUUA
(((((((.((......................(((((.(((.(((((((((((...(((.......)))..)))))))))))...).)).)))))....)).)))))))........... (-38.89 = -38.73 +  -0.16)

alignment

secondary structure

dotplot

Window 4

Location	13,936,065 – 13,936,166
Length	101
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.27
Mean single sequence MFE	-45.44
Consensus MFE	-41.74
Energy contribution	-41.94
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.42
Structure conservation index	0.92
SVM decision value	3.97
SVM RNA-class probability	0.999732
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13936065 101 - 22224390
UAAUUAACGUGCACACGCGGCA-AGGCAACGGCACAUAAGCCACCCCCUGCACCGGCGAAGGGUUAAAGGGGGUGGCUGGACGAUUGCGAC------------------GGCGACGCAUG
.......(((((...(((.(..-..((((((...(...(((((((((((..(((.......)))...))))))))))).).)).))))..)------------------.)))..))))) ( -42.10)
>DroSec_CAF1 15810 101 - 1
UAAUUAACGUGCACACGCGGCA-AGGCAACGGCACAUAAGCCACCCCCUGCACCGGCGAAGGGUUAAAGGGGGUGGCUGGGCGAUUGCGAC------------------GGCGACGCAUG
.......(((((...(((.(..-..((((((.(.....(((((((((((..(((.......)))...))))))))))).).)).))))..)------------------.)))..))))) ( -44.50)
>DroSim_CAF1 21581 101 - 1
UAAUUAAGGUGCACACGCGGCA-AGGCAACGGCACAUAAGCCACCCCCUGCACCGGCGAAGGGUUAAAGGGGGUGGCUGGGCGAUUGCGAC------------------GGCGACGCAUG
........((((....((....-..))....))))...(((((((((((..(((.......)))...)))))))))))..(((.((((...------------------.)))))))... ( -43.30)
>DroEre_CAF1 17103 119 - 1
UAAUUAACGUGCACACGCGGCA-AGGCAACGGCACAUAAGCCACCCCCUGCACCGGCGAAGGGUUAAAGGGGGUGGCUGGGCGAUUGCGACGGCGAUUGCGACGGCGACGGCGACGCAUG
.......(((((...(((.((.-.(....).((.(...(((((((((((..(((.......)))...))))))))))).)((((((((....))))))))....))).).)))..))))) ( -52.70)
>DroYak_CAF1 18834 102 - 1
UAAUUAACGUGCACACGCGGCAAAGGCAACGGCACAUAAGCCACCCCCUGCACCGGCGAAGGGUUAAAGGGGGUGGCUGGGCGAUUGCGAC------------------GGCGACGCAUG
.......(((((...(((.((...(....).)).(...(((((((((((..(((.......)))...))))))))))).)))).((((...------------------.)))).))))) ( -44.60)
>consensus
UAAUUAACGUGCACACGCGGCA_AGGCAACGGCACAUAAGCCACCCCCUGCACCGGCGAAGGGUUAAAGGGGGUGGCUGGGCGAUUGCGAC__________________GGCGACGCAUG
.......(((((...((((((...(....).)).(...(((((((((((..(((.......)))...))))))))))).).....))))....................(....)))))) (-41.74 = -41.94 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	13,936,087 – 13,936,192
Length	105
Sequences	3
Columns	105
Reading direction	forward
Mean pairwise identity	99.37
Mean single sequence MFE	-35.47
Consensus MFE	-34.60
Energy contribution	-34.60
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.99
Structure conservation index	0.98
SVM decision value	0.86
SVM RNA-class probability	0.868628
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13936087 105 + 22224390
CCAGCCACCCCCUUUAACCCUUCGCCGGUGCAGGGGGUGGCUUAUGUGCCGUUGCCUUGCCGCGUGUGCACGUUAAUUACUCCGCAGUGUUCUCGUUCUCUCUCC
..(((((((((((...(((.......)))..)))))))))))...(..((((.((...)).))).)..)(((.....((((....))))....)))......... ( -35.90)
>DroSec_CAF1 15832 105 + 1
CCAGCCACCCCCUUUAACCCUUCGCCGGUGCAGGGGGUGGCUUAUGUGCCGUUGCCUUGCCGCGUGUGCACGUUAAUUACUCCGCAGUGUUCUCGUUCUCUCUCC
..(((((((((((...(((.......)))..)))))))))))...(..((((.((...)).))).)..)(((.....((((....))))....)))......... ( -35.90)
>DroSim_CAF1 21603 105 + 1
CCAGCCACCCCCUUUAACCCUUCGCCGGUGCAGGGGGUGGCUUAUGUGCCGUUGCCUUGCCGCGUGUGCACCUUAAUUACUCCGCAGUGUUCUCGUUCUCUCUCC
..(((((((((((...(((.......)))..)))))))))))..((..((((.((...)).))).)..)).......((((....))))................ ( -34.60)
>consensus
CCAGCCACCCCCUUUAACCCUUCGCCGGUGCAGGGGGUGGCUUAUGUGCCGUUGCCUUGCCGCGUGUGCACGUUAAUUACUCCGCAGUGUUCUCGUUCUCUCUCC
..(((((((((((...(((.......)))..)))))))))))..((..((((.((...)).))).)..)).......((((....))))................ (-34.60 = -34.60 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:53 2006