Locus 2049

Sequence ID	2R_DroMel_CAF1
Location	7,718,949 – 7,719,078
Length	129
Max. P	0.938540

overview

Window 3

Location	7,718,949 – 7,719,041
Length	92
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	79.50
Mean single sequence MFE	-27.53
Consensus MFE	-17.86
Energy contribution	-18.42
Covariance contribution	0.56
Combinations/Pair	1.17
Mean z-score	-2.18
Structure conservation index	0.65
SVM decision value	1.27
SVM RNA-class probability	0.938540
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7718949 92 + 20766785
GGAUCGAAAA-A-------GAGGAGAAAUGGGGUUGGGGCGUCGCGAGACGG-AACCAUUGACCCCAUGAAUGGGAAAAGCUUCGGGGAAACUGAACUCUG
..........-(-------(((.....(((((((..(((((((....)))).-..)).)..))))))).............(((((.....))))))))). ( -31.20)
>DroSec_CAF1 4957 92 + 1
GGAUCGAAAA-A-------GUGGAAAAAUGGGGUUGGGGCGUCGCGAGACGG-AACCAUUGACCCCAUGAAUGGGAAAAGCUUCGGGGAAACUGAACUCUG
(((.((((..-.-------........(((((((..(((((((....)))).-..)).)..))))))).............))))((....))....))). ( -27.85)
>DroEre_CAF1 2886 92 + 1
GGAUCGAAAA-A-------GCGGAAAAAUGGGGUGUGGGCGUCGCAAGACGG-AACCAUUGACCCCAUGAAUGGGAAAAGCUUCGGGGAAACUGAACUCUG
(((.(((...-(-------((......(((((((((((.((((....)))).-..))))..)))))))...........))))))((....))....))). ( -29.53)
>DroYak_CAF1 2700 91 + 1
GGAUCGAA-A-A-------GCGGAAAAAUGGGGUGGGGGCGUCGCGAGACGG-AACCAUUGACCCCAUGAAUGGGAAAUGCUUUGGGGAAACUGAACUCUG
(((((..(-(-(-------(((.....(((((((.((((((((....)))).-..)).)).)))))))..........)))))).((....))))..))). ( -28.16)
>DroAna_CAF1 2715 93 + 1
GGGUGGGAAAAAGUCCCCAACAGAAAAUUAGGGUAGCAGAUUCACGAGACGAAAACCAUUGACCCCAUGAAUGGAA-------UGGAGGUCUCCAGCUCU-
((((.(((....((((((............)))..............)))..........((((((((.......)-------))).))))))).)))).- ( -20.93)
>consensus
GGAUCGAAAA_A_______GCGGAAAAAUGGGGUGGGGGCGUCGCGAGACGG_AACCAUUGACCCCAUGAAUGGGAAAAGCUUCGGGGAAACUGAACUCUG
.....................(((...(((((((..((.((((....))))....))....))))))).................((....))....))). (-17.86 = -18.42 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	7,718,949 – 7,719,041
Length	92
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	79.50
Mean single sequence MFE	-21.79
Consensus MFE	-11.98
Energy contribution	-12.26
Covariance contribution	0.28
Combinations/Pair	1.15
Mean z-score	-1.96
Structure conservation index	0.55
SVM decision value	0.35
SVM RNA-class probability	0.701358
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7718949 92 - 20766785
CAGAGUUCAGUUUCCCCGAAGCUUUUCCCAUUCAUGGGGUCAAUGGUU-CCGUCUCGCGACGCCCCAACCCCAUUUCUCCUC-------U-UUUUCGAUCC
.((((...((((((...))))))..........(((((((...(((..-.((((....))))..)))))))))).....)))-------)-.......... ( -22.40)
>DroSec_CAF1 4957 92 - 1
CAGAGUUCAGUUUCCCCGAAGCUUUUCCCAUUCAUGGGGUCAAUGGUU-CCGUCUCGCGACGCCCCAACCCCAUUUUUCCAC-------U-UUUUCGAUCC
.(((((..((((((...))))))..........(((((((...(((..-.((((....))))..))))))))))......))-------)-))........ ( -21.00)
>DroEre_CAF1 2886 92 - 1
CAGAGUUCAGUUUCCCCGAAGCUUUUCCCAUUCAUGGGGUCAAUGGUU-CCGUCUUGCGACGCCCACACCCCAUUUUUCCGC-------U-UUUUCGAUCC
.(((((..((((((...))))))..........(((((((...(((..-.((((....)))).))).)))))))......))-------)-))........ ( -21.00)
>DroYak_CAF1 2700 91 - 1
CAGAGUUCAGUUUCCCCAAAGCAUUUCCCAUUCAUGGGGUCAAUGGUU-CCGUCUCGCGACGCCCCCACCCCAUUUUUCCGC-------U-U-UUCGAUCC
.(((((...((((.....))))...........(((((((....((..-.((((....))))...)))))))))......))-------)-)-)....... ( -17.40)
>DroAna_CAF1 2715 93 - 1
-AGAGCUGGAGACCUCCA-------UUCCAUUCAUGGGGUCAAUGGUUUUCGUCUCGUGAAUCUGCUACCCUAAUUUUCUGUUGGGGACUUUUUCCCACCC
-.(((.((((((((...(-------(((((....))))))....)))))))).)))(((.........(((((((.....))))))).........))).. ( -27.17)
>consensus
CAGAGUUCAGUUUCCCCGAAGCUUUUCCCAUUCAUGGGGUCAAUGGUU_CCGUCUCGCGACGCCCCAACCCCAUUUUUCCGC_______U_UUUUCGAUCC
.................................(((((((....((....((((....))))))...)))))))........................... (-11.98 = -12.26 +   0.28)

alignment

secondary structure

dotplot

Window 5

Location	7,718,968 – 7,719,078
Length	110
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	82.17
Mean single sequence MFE	-36.47
Consensus MFE	-22.39
Energy contribution	-23.80
Covariance contribution	1.41
Combinations/Pair	1.19
Mean z-score	-1.82
Structure conservation index	0.61
SVM decision value	0.08
SVM RNA-class probability	0.572946
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7718968 110 + 20766785
AUGGGGUUGGGGCGUCGCGAGACGG-AACCAUUGACCCCAUGAAUGGGAAAAGCUUCGGGGAAACUGAACUCUGAACUAGCGACGGAAAACAAAGCGGAUCCCUGGUG---GUA
(((((((..(((((((....)))).-..)).)..)))))))....((((...((((.(((....))....((((.........))))...).))))...)))).....---... ( -37.50)
>DroSec_CAF1 4976 110 + 1
AUGGGGUUGGGGCGUCGCGAGACGG-AACCAUUGACCCCAUGAAUGGGAAAAGCUUCGGGGAAACUGAACUCUGAACUAGCGACAGAAAACAAAGCGGAUCCCUGGUG---GUA
(((((((..(((((((....)))).-..)).)..)))))))....((((...((((.(((....))....((((.........))))...).))))...)))).....---... ( -38.20)
>DroEre_CAF1 2905 110 + 1
AUGGGGUGUGGGCGUCGCAAGACGG-AACCAUUGACCCCAUGAAUGGGAAAAGCUUCGGGGAAACUGAACUCUGAACUAGCGACAGAGAACAACGCGGAUCUCUGGUG---GUA
(((((((((((.((((....)))).-..))))..)))))))...........(((((((((........))))))...)))..((((((.(......).))))))...---... ( -39.50)
>DroYak_CAF1 2718 110 + 1
AUGGGGUGGGGGCGUCGCGAGACGG-AACCAUUGACCCCAUGAAUGGGAAAUGCUUUGGGGAAACUGAACUCUGAACUAGCGACAGAGAACAACGCGGAUCUCUGGUG---GCA
(((((((.((((((((....)))).-..)).)).)))))))....((((..(((.(((((....))...(((((.........)))))..))).)))..)))).....---... ( -38.00)
>DroAna_CAF1 2742 103 + 1
UUAGGGUAGCAGAUUCACGAGACGAAAACCAUUGACCCCAUGAAUGGAA-------UGGAGGUCUCCAGCUCU---CGAGCGG-AGGGAACAAAGCGGAUCUGUGGUGAGAGUG
........((((((((.(((((.(.........((((((((.......)-------))).)))).....))))---)).((..-.(....)...)))))))))).......... ( -29.14)
>consensus
AUGGGGUGGGGGCGUCGCGAGACGG_AACCAUUGACCCCAUGAAUGGGAAAAGCUUCGGGGAAACUGAACUCUGAACUAGCGACAGAGAACAAAGCGGAUCUCUGGUG___GUA
(((((((..((.((((....))))....))....)))))))....((((...((....((....))...(((((.........)))))......))...))))........... (-22.39 = -23.80 +   1.41)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:55 2006