Locus 3270

Sequence ID	2R_DroMel_CAF1
Location	11,177,486 – 11,177,590
Length	104
Max. P	0.918696

overview

Window 4

Location	11,177,486 – 11,177,590
Length	104
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	79.85
Mean single sequence MFE	-47.80
Consensus MFE	-26.76
Energy contribution	-28.93
Covariance contribution	2.17
Combinations/Pair	1.14
Mean z-score	-2.61
Structure conservation index	0.56
SVM decision value	1.12
SVM RNA-class probability	0.918696
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11177486 104 + 20766785
AGGCCACCGCGGCAUUUUGCAACGAAGCAGCGGAAUGAGCAGCUGCAGCUGCCGACUGCUGACCAGCUGACAUGA-AGGAGGCCAAACCGGAUGCGGAAGCGGCA
.((((.((((..((((((((.........)))))))).))(((((((((........))))..))))).......-.)).))))........(((....)))... ( -39.30)
>DroPse_CAF1 92356 92 + 1
GGGCCACGGCUGCGUUCUGCAGCGAA------GAAUGGGCGGC---GGCGGCCGAUGGCUGAGAGGC---CAUGA-AGGAGGCCAGUCCGCCAGCGGACGCAGCA
........(((((((.((((.((...------......))(((---(((((((.((((((....)))---)))..-....)))).).))))).))))))))))). ( -48.60)
>DroSec_CAF1 92053 104 + 1
AGGCCACUGCGGCAUUUUGCAACGAGGCAGCGGAAUGAGCAGCUGCGGCUGCCGACUGCUGGCCGGCCGACAUGA-AGGAGGCCAGGCCGGAUGCGGAAGCGGCA
..(((.((((..((((((((.........)))))))).)))).....(((.(((....((((((((((..(....-.)..)))).))))))...))).)))))). ( -50.70)
>DroEre_CAF1 94604 104 + 1
AGGCCACUGCGGCAUUUUGCAGCGAGGCAGCGGAAUGGGCAGCUGCGGCUGCCGACUGCUGACCGGCCGACAUGA-AGGAGGCCAGACUGGAUGCAGAAGCGGCA
..(((.((...(((((...((((..((((((((..(.((((((....)))))).))))))).))((((..(....-.)..)))).).))))))))...)).))). ( -49.40)
>DroYak_CAF1 92104 104 + 1
AGGCCACGGCGGCAUUUUGCAGAGAGGCAGCGGAAUGAGCAGCUGCGGCUGCCGACUGCUGACCGGCCGACAUGA-AGGAGGCCAGGCCGGAUGCGGAAGCGGCA
..(((.((((.((.....)).....((((((((..((.(((((....))))))).)))))).))((((..(....-.)..))))..))))...((....))))). ( -49.80)
>DroPer_CAF1 92149 93 + 1
GGGCCACGGCUGCGUUCUGCAGCGAA------GAGUGGGCGGC---GGCGGCCGAUGGCUGAGAGGC---CAUGAAAGGAGGCCAGUCCGCCAGCGGACGCAGCA
........(((((((.((((.((...------..)).((((((---(((..((.((((((....)))---)))....))..))).).))))).))))))))))). ( -49.00)
>consensus
AGGCCACGGCGGCAUUUUGCAGCGAAGCAGCGGAAUGAGCAGCUGCGGCUGCCGACUGCUGACCGGCCGACAUGA_AGGAGGCCAGACCGGAUGCGGAAGCGGCA
........((.((.((((((.......((((((..((.(((((....))))))).))))))...((((..(......)..)))).........)))))))).)). (-26.76 = -28.93 +   2.17)

alignment

secondary structure

dotplot

Window 5

Location	11,177,486 – 11,177,590
Length	104
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	79.85
Mean single sequence MFE	-41.58
Consensus MFE	-25.61
Energy contribution	-25.92
Covariance contribution	0.31
Combinations/Pair	1.33
Mean z-score	-2.02
Structure conservation index	0.62
SVM decision value	0.71
SVM RNA-class probability	0.829591
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11177486 104 - 20766785
UGCCGCUUCCGCAUCCGGUUUGGCCUCCU-UCAUGUCAGCUGGUCAGCAGUCGGCAGCUGCAGCUGCUCAUUCCGCUGCUUCGUUGCAAAAUGCCGCGGUGGCCU
....(((.((((..((((((.(((.....-....)))))))))...(((....(((((.(((((..........)))))...)))))....))).)))).))).. ( -37.50)
>DroPse_CAF1 92356 92 - 1
UGCUGCGUCCGCUGGCGGACUGGCCUCCU-UCAUG---GCCUCUCAGCCAUCGGCCGCC---GCCGCCCAUUC------UUCGCUGCAGAACGCAGCCGUGGCCC
....(((.(((.((((.((..((((....-....)---)))..)).)))).))).))).---(((((......------...(((((.....))))).))))).. ( -40.20)
>DroSec_CAF1 92053 104 - 1
UGCCGCUUCCGCAUCCGGCCUGGCCUCCU-UCAUGUCGGCCGGCCAGCAGUCGGCAGCCGCAGCUGCUCAUUCCGCUGCCUCGUUGCAAAAUGCCGCAGUGGCCU
.((((((...((....((((.((((..(.-....)..)))))))).(((....(((((.(((((..........)))))...)))))....))).)))))))).. ( -44.90)
>DroEre_CAF1 94604 104 - 1
UGCCGCUUCUGCAUCCAGUCUGGCCUCCU-UCAUGUCGGCCGGUCAGCAGUCGGCAGCCGCAGCUGCCCAUUCCGCUGCCUCGCUGCAAAAUGCCGCAGUGGCCU
.((((((.(.((((...(.((((((..(.-....)..)))))).).(((((.((((((.((....)).......))))))..)))))...)))).).)))))).. ( -44.10)
>DroYak_CAF1 92104 104 - 1
UGCCGCUUCCGCAUCCGGCCUGGCCUCCU-UCAUGUCGGCCGGUCAGCAGUCGGCAGCCGCAGCUGCUCAUUCCGCUGCCUCUCUGCAAAAUGCCGCCGUGGCCU
.(((((..(.((((..((((.((((..(.-....)..)))))))).((((..((((((.((....)).......))))))...))))...)))).)..))))).. ( -42.30)
>DroPer_CAF1 92149 93 - 1
UGCUGCGUCCGCUGGCGGACUGGCCUCCUUUCAUG---GCCUCUCAGCCAUCGGCCGCC---GCCGCCCACUC------UUCGCUGCAGAACGCAGCCGUGGCCC
.((.(((.(((.((((.((..((((.........)---)))..)).)))).))).))).---))...((((..------...(((((.....))))).))))... ( -40.50)
>consensus
UGCCGCUUCCGCAUCCGGACUGGCCUCCU_UCAUGUCGGCCGGUCAGCAGUCGGCAGCCGCAGCUGCCCAUUCCGCUGCCUCGCUGCAAAAUGCCGCCGUGGCCU
.((((((...((..((((.(((((..........)))))))))...))....((((((....))))))..............((.((.....)).)))))))).. (-25.61 = -25.92 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:33 2006