Locus 9263

Sequence ID	3R_DroMel_CAF1
Location	24,687,038 – 24,687,165
Length	127
Max. P	0.998906

overview

Window 4

Location	24,687,038 – 24,687,139
Length	101
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	90.17
Mean single sequence MFE	-21.06
Consensus MFE	-15.54
Energy contribution	-16.42
Covariance contribution	0.88
Combinations/Pair	1.08
Mean z-score	-1.85
Structure conservation index	0.74
SVM decision value	0.29
SVM RNA-class probability	0.668879
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24687038 101 + 27905053
UAUCUCUAUAUGGCCAGAGAACCAAACAU-ACCAUUCCCCAGAGACCGAUACCCAUAGAUCUUGUUCUCCGAGGUCUCUACCAUAGCACCAUUGCUUCUCUA
..(((((........))))).........-..........(((((...........((((((((.....)))))))).......((((....))))))))). ( -18.80)
>DroSec_CAF1 8410 101 + 1
UAUCUCUAUAUGGCCAGAGAGCCAAACAU-GCCAUUCCCCAGAGACCGAGACCCAUAGAUCUUGUUCUCCGAGGUCUCUACUAUAGCACCAUUGUUUCUCUA
...............((((((.(((...(-((.((.....(((((((((((..((.......)).))))...)))))))...)).)))...))).)))))). ( -22.60)
>DroSim_CAF1 8369 101 + 1
UAUCUCUAUAUGGCCAGAGAGCCAAACAU-GCCAUUCCUCAGAGACCGAGACCCAUAGAUCUUGCUCUCCGAGGUCUCUACUAUAGCACCAUUGUUUCUCUA
...............((((((.(((...(-((.((.((((.((((.(((((........))))).)))).))))........)).)))...))).)))))). ( -24.30)
>DroEre_CAF1 8482 102 + 1
UAUCUCUAUAUGACCAGAGAGCCAGACAUUACCAUUCCCCAACAAUCGAGACCCAUAGAUCUUGUUCUCUGUGGUCUCUACCAUAGCACCUUUGUUUCUCUA
...............(((((...........................((((((((.(((......))).)).))))))......((((....))))))))). ( -19.00)
>DroYak_CAF1 8596 102 + 1
UAUCUCUAUAUGGCCAGAGAGUCAGAGAUUACCAUUCCCCAGACGACGAGACCCAUAAAUCUUGUUCUCCGAGGUCUCUACCAUAGCACCUUUGUUUCUCUA
...............((((((.(((((..............((.(((((((........))))))).))...(((....))).......))))).)))))). ( -20.60)
>consensus
UAUCUCUAUAUGGCCAGAGAGCCAAACAU_ACCAUUCCCCAGAGACCGAGACCCAUAGAUCUUGUUCUCCGAGGUCUCUACCAUAGCACCAUUGUUUCUCUA
..(((((........)))))....................(((((..(((((((..(((......)))..).))))))......((((....))))))))). (-15.54 = -16.42 +   0.88)

alignment

secondary structure

dotplot

Window 5

Location	24,687,038 – 24,687,139
Length	101
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	90.17
Mean single sequence MFE	-31.32
Consensus MFE	-25.28
Energy contribution	-25.72
Covariance contribution	0.44
Combinations/Pair	1.21
Mean z-score	-2.36
Structure conservation index	0.81
SVM decision value	1.98
SVM RNA-class probability	0.984636
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24687038 101 - 27905053
UAGAGAAGCAAUGGUGCUAUGGUAGAGACCUCGGAGAACAAGAUCUAUGGGUAUCGGUCUCUGGGGAAUGGU-AUGUUUGGUUCUCUGGCCAUAUAGAGAUA
(((((((.(((..(((((((........(((((((((.....(((....))).....))))))))).)))))-))..))).))))))).............. ( -32.00)
>DroSec_CAF1 8410 101 - 1
UAGAGAAACAAUGGUGCUAUAGUAGAGACCUCGGAGAACAAGAUCUAUGGGUCUCGGUCUCUGGGGAAUGGC-AUGUUUGGCUCUCUGGCCAUAUAGAGAUA
((((((..(((..(((((((........(((((((((.(.(((((....))))).).))))))))).)))))-))..)))..)))))).............. ( -35.00)
>DroSim_CAF1 8369 101 - 1
UAGAGAAACAAUGGUGCUAUAGUAGAGACCUCGGAGAGCAAGAUCUAUGGGUCUCGGUCUCUGAGGAAUGGC-AUGUUUGGCUCUCUGGCCAUAUAGAGAUA
((((((..(((..(((((((........(((((((((.(.(((((....))))).).))))))))).)))))-))..)))..)))))).............. ( -38.00)
>DroEre_CAF1 8482 102 - 1
UAGAGAAACAAAGGUGCUAUGGUAGAGACCACAGAGAACAAGAUCUAUGGGUCUCGAUUGUUGGGGAAUGGUAAUGUCUGGCUCUCUGGUCAUAUAGAGAUA
((((((..((....((((((....((((((.((.(((......))).))))))))............)))))).....))..)))))).............. ( -24.09)
>DroYak_CAF1 8596 102 - 1
UAGAGAAACAAAGGUGCUAUGGUAGAGACCUCGGAGAACAAGAUUUAUGGGUCUCGUCGUCUGGGGAAUGGUAAUCUCUGACUCUCUGGCCAUAUAGAGAUA
((((((........(((....)))....(((((((..((.(((((....))))).))..)))))))........))))))..((((((......)))))).. ( -27.50)
>consensus
UAGAGAAACAAUGGUGCUAUGGUAGAGACCUCGGAGAACAAGAUCUAUGGGUCUCGGUCUCUGGGGAAUGGU_AUGUUUGGCUCUCUGGCCAUAUAGAGAUA
((((((..(((....(((((........(((((((((.(.(((((....))))).).))))))))).))))).....)))..)))))).............. (-25.28 = -25.72 +   0.44)

alignment

secondary structure

dotplot

Window 6

Location	24,687,070 – 24,687,165
Length	95
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	92.42
Mean single sequence MFE	-22.68
Consensus MFE	-17.52
Energy contribution	-17.44
Covariance contribution	-0.08
Combinations/Pair	1.24
Mean z-score	-1.76
Structure conservation index	0.77
SVM decision value	0.40
SVM RNA-class probability	0.722667
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24687070 95 + 27905053
AUUCCCCAGAGACCGAUACCCAUAGAUCUUGUUCUCCGAGGUCUCUACCAUAGCACCAUUGCUUCUCUACUGGUUCCGGUUCCAAAAUGGAGAAU
((((.((((..((((..(((...((((((((.....)))))))).......((((....))))........)))..))))..)....))).)))) ( -23.90)
>DroSec_CAF1 8442 95 + 1
AUUCCCCAGAGACCGAGACCCAUAGAUCUUGUUCUCCGAGGUCUCUACUAUAGCACCAUUGUUUCUCUACUGGUUCCGGUUCCAAAAUGGAGAAU
((((.((((..((((..(((...((((((((.....)))))))).......((((....))))........)))..))))..)....))).)))) ( -23.50)
>DroSim_CAF1 8401 95 + 1
AUUCCUCAGAGACCGAGACCCAUAGAUCUUGCUCUCCGAGGUCUCUACUAUAGCACCAUUGUUUCUCUACUGGUUCCGGUUCCAAAAUGGAGAAU
...((((.((((.(((((........))))).)))).))))((((((....((((....)))).....((((....)))).......)))))).. ( -24.20)
>DroEre_CAF1 8515 95 + 1
AUUCCCCAACAAUCGAGACCCAUAGAUCUUGUUCUCUGUGGUCUCUACCAUAGCACCUUUGUUUCUCUACUGGUUCCGGUUCCAAAAUGGAGAUU
..............((((((((.(((......))).)).))))))...........(((..(((....((((....))))....)))..)))... ( -23.10)
>DroYak_CAF1 8629 95 + 1
AUUCCCCAGACGACGAGACCCAUAAAUCUUGUUCUCCGAGGUCUCUACCAUAGCACCUUUGUUUCUCUACUGGUUCCGGUUCCAAAAUGGAGAUU
............((((((........))))))((((((((((((.......)).))))).((((....((((....))))....))))))))).. ( -18.70)
>consensus
AUUCCCCAGAGACCGAGACCCAUAGAUCUUGUUCUCCGAGGUCUCUACCAUAGCACCAUUGUUUCUCUACUGGUUCCGGUUCCAAAAUGGAGAAU
..((.(((..(((((..(((...((((((((.....)))))))).......((((....))))........)))..)))))......))).)).. (-17.52 = -17.44 +  -0.08)

alignment

secondary structure

dotplot

Window 7

Location	24,687,070 – 24,687,165
Length	95
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	92.42
Mean single sequence MFE	-28.96
Consensus MFE	-26.38
Energy contribution	-26.26
Covariance contribution	-0.12
Combinations/Pair	1.23
Mean z-score	-2.16
Structure conservation index	0.91
SVM decision value	3.28
SVM RNA-class probability	0.998906
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24687070 95 - 27905053
AUUCUCCAUUUUGGAACCGGAACCAGUAGAGAAGCAAUGGUGCUAUGGUAGAGACCUCGGAGAACAAGAUCUAUGGGUAUCGGUCUCUGGGGAAU
((((((((....(..(((((.(((.(((((..((((....))))..(((....))).............))))).))).)))))..))))))))) ( -29.70)
>DroSec_CAF1 8442 95 - 1
AUUCUCCAUUUUGGAACCGGAACCAGUAGAGAAACAAUGGUGCUAUAGUAGAGACCUCGGAGAACAAGAUCUAUGGGUCUCGGUCUCUGGGGAAU
..((((.(((.(((.((((....).((......))...))).))).))).))))(((((((((.(.(((((....))))).).)))))))))... ( -29.90)
>DroSim_CAF1 8401 95 - 1
AUUCUCCAUUUUGGAACCGGAACCAGUAGAGAAACAAUGGUGCUAUAGUAGAGACCUCGGAGAGCAAGAUCUAUGGGUCUCGGUCUCUGAGGAAU
..((((.(((.(((.((((....).((......))...))).))).))).))))(((((((((.(.(((((....))))).).)))))))))... ( -32.90)
>DroEre_CAF1 8515 95 - 1
AAUCUCCAUUUUGGAACCGGAACCAGUAGAGAAACAAAGGUGCUAUGGUAGAGACCACAGAGAACAAGAUCUAUGGGUCUCGAUUGUUGGGGAAU
..((((((.((((....))))((((.(((....((....)).))))))).((((((.((.(((......))).))))))))......)))))).. ( -26.90)
>DroYak_CAF1 8629 95 - 1
AAUCUCCAUUUUGGAACCGGAACCAGUAGAGAAACAAAGGUGCUAUGGUAGAGACCUCGGAGAACAAGAUUUAUGGGUCUCGUCGUCUGGGGAAU
..((((.((..(((.((((....).((......))...))).)))..)).))))(((((((..((.(((((....))))).))..)))))))... ( -25.40)
>consensus
AUUCUCCAUUUUGGAACCGGAACCAGUAGAGAAACAAUGGUGCUAUGGUAGAGACCUCGGAGAACAAGAUCUAUGGGUCUCGGUCUCUGGGGAAU
..((((.(((.(((.((((....).((......))...))).))).))).))))(((((((((.(.(((((....))))).).)))))))))... (-26.38 = -26.26 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:30:17 2006