Locus 3318

Sequence ID	2R_DroMel_CAF1
Location	11,305,437 – 11,305,558
Length	121
Max. P	0.923000

overview

Window 9

Location	11,305,437 – 11,305,540
Length	103
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	87.18
Mean single sequence MFE	-35.94
Consensus MFE	-27.44
Energy contribution	-27.56
Covariance contribution	0.12
Combinations/Pair	1.07
Mean z-score	-2.21
Structure conservation index	0.76
SVM decision value	1.15
SVM RNA-class probability	0.923000
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11305437 103 + 20766785
UGCGGGAAAUAACCAAGACGUGUGGGCCACACGAUGGUAGUGCUAAGCU-AACAGUGGAUUGGGAAAUUUUCGGGAACGGGAUACUUUCCCAACCUGCUG---CUUC
.(((((......(((...((((((...)))))).((.((((.....)))-).)).))).((((((((.(..((....))..)...)))))))))))))..---.... ( -35.80)
>DroSec_CAF1 92668 106 + 1
UGCGGGAAAUAACCAAGACGUGUGGGCCACACGAUGGUAGAGCCAAGCU-AACAGUGGAUUGGGAAAUUUUCGGGAACGAGAUACUUUCCCAACCUGCUGCUGCUGC
.((.((.....((((...((((((...)))))).))))....)).(((.-..(((..(.((((((((.(((((....)))))...)))))))).)..)))..))))) ( -39.80)
>DroSim_CAF1 96349 106 + 1
UGCGGGAAAUAACCAAGACGUGUGGGCCACACGAUGGUAGUGCCAAGCU-AACAGUGGAUUGGGAAAUUUUCGGGAACGAGAUACUUUCCCAACCUGCUGCUGCUGC
.((((.(....((((...((((((...)))))).))))..).)).(((.-..(((..(.((((((((.(((((....)))))...)))))))).)..)))..))))) ( -40.30)
>DroEre_CAF1 93890 95 + 1
UGCGGGAAAUAACCAAGACGUGUGGGCCACACUCUGUCAGAG-----CU-ACCAGUGGAUUGGGAAAAUUUCCGGAACGGGAUACUUUCCCAACCUGCUG------U
.((((.......))..((((.(((.....)))..))))...)-----).-..(((..(.((((((((..(((((...)))))...)))))))).)..)))------. ( -32.20)
>DroYak_CAF1 95012 100 + 1
UGCGGGAAAUAACCAAGACGUGUGGGCCACACUCUUGCAGAG-----CUCACCAGUGGAUUGGGAAAUUUUCGGUAACAGGAUACUUUCCCAACCUGCUGCU--UGC
.(((((.......(((((.(((((...)))))))))).....-----.....(((..(.((((((((..(((.......)))...)))))))).)..)))))--))) ( -31.60)
>consensus
UGCGGGAAAUAACCAAGACGUGUGGGCCACACGAUGGUAGAGC_AAGCU_AACAGUGGAUUGGGAAAUUUUCGGGAACGGGAUACUUUCCCAACCUGCUGCU_CUGC
(((((.......)).....(((((...)))))....))).............(((..(.((((((((.(((((....)))))...)))))))).)..)))....... (-27.44 = -27.56 +   0.12)

alignment

secondary structure

dotplot

Window 0

Location	11,305,437 – 11,305,540
Length	103
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	87.18
Mean single sequence MFE	-34.50
Consensus MFE	-23.19
Energy contribution	-24.15
Covariance contribution	0.96
Combinations/Pair	1.04
Mean z-score	-2.57
Structure conservation index	0.67
SVM decision value	0.69
SVM RNA-class probability	0.823985
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11305437 103 - 20766785
GAAG---CAGCAGGUUGGGAAAGUAUCCCGUUCCCGAAAAUUUCCCAAUCCACUGUU-AGCUUAGCACUACCAUCGUGUGGCCCACACGUCUUGGUUAUUUCCCGCA
..((---(((..((((((((((...((........))...))))))))))..)))))-.((........((((.((((((...))))))...))))........)). ( -32.09)
>DroSec_CAF1 92668 106 - 1
GCAGCAGCAGCAGGUUGGGAAAGUAUCUCGUUCCCGAAAAUUUCCCAAUCCACUGUU-AGCUUGGCUCUACCAUCGUGUGGCCCACACGUCUUGGUUAUUUCCCGCA
((((((((((..((((((((((.....(((....)))...))))))))))..)))))-.))).((....((((.((((((...))))))...))))......)))). ( -38.20)
>DroSim_CAF1 96349 106 - 1
GCAGCAGCAGCAGGUUGGGAAAGUAUCUCGUUCCCGAAAAUUUCCCAAUCCACUGUU-AGCUUGGCACUACCAUCGUGUGGCCCACACGUCUUGGUUAUUUCCCGCA
((((((((((..((((((((((.....(((....)))...))))))))))..)))))-.))).((....((((.((((((...))))))...))))......)))). ( -38.20)
>DroEre_CAF1 93890 95 - 1
A------CAGCAGGUUGGGAAAGUAUCCCGUUCCGGAAAUUUUCCCAAUCCACUGGU-AG-----CUCUGACAGAGUGUGGCCCACACGUCUUGGUUAUUUCCCGCA
.------(((..((((((((((((.(((......))).))))))))))))..)))((-((-----((..(((...(((((...))))))))..))))))........ ( -34.50)
>DroYak_CAF1 95012 100 - 1
GCA--AGCAGCAGGUUGGGAAAGUAUCCUGUUACCGAAAAUUUCCCAAUCCACUGGUGAG-----CUCUGCAAGAGUGUGGCCCACACGUCUUGGUUAUUUCCCGCA
((.--..(((..((((((((((...((........))...))))))))))..))).....-----.....((((((((((...))))).)))))..........)). ( -29.50)
>consensus
GCAG_AGCAGCAGGUUGGGAAAGUAUCCCGUUCCCGAAAAUUUCCCAAUCCACUGUU_AGCUU_GCUCUACCAUCGUGUGGCCCACACGUCUUGGUUAUUUCCCGCA
.......(((..((((((((((...((........))...))))))))))..)))....((........((((.((((((...))))))...))))........)). (-23.19 = -24.15 +   0.96)

alignment

secondary structure

dotplot

Window 1

Location	11,305,464 – 11,305,558
Length	94
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	84.70
Mean single sequence MFE	-33.84
Consensus MFE	-22.57
Energy contribution	-22.89
Covariance contribution	0.32
Combinations/Pair	1.08
Mean z-score	-2.20
Structure conservation index	0.67
SVM decision value	0.60
SVM RNA-class probability	0.797080
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11305464 94 + 20766785
CACACGAUGGUAGUGCUAAGCU-AACAGUGGAUUGGGAAAUUUUCGGGAACGGGAUACUUUCCCAACCUGCUG---CUUCUACCUGCUGGGCGGCGCA
............(((((..((.-..(((..(.((((((((.(..((....))..)...)))))))).)..)))---......((....))))))))). ( -32.50)
>DroSec_CAF1 92695 97 + 1
CACACGAUGGUAGAGCCAAGCU-AACAGUGGAUUGGGAAAUUUUCGGGAACGAGAUACUUUCCCAACCUGCUGCUGCUGCUACCUGCUGGGCGGCGCA
.......(((.....))).((.-..(((..(.((((((((.(((((....)))))...)))))))).)..)))..((((((........)))))))). ( -37.70)
>DroSim_CAF1 96376 97 + 1
CACACGAUGGUAGUGCCAAGCU-AACAGUGGAUUGGGAAAUUUUCGGGAACGAGAUACUUUCCCAACCUGCUGCUGCUGCUACCUGCUGGGCGGCGCA
............(((((.(((.-..(((..(.((((((((.(((((....)))))...)))))))).)..)))..)))(((........)))))))). ( -39.40)
>DroEre_CAF1 93917 84 + 1
CACACUCUGUCAGAG-----CU-ACCAGUGGAUUGGGAAAAUUUCCGGAACGGGAUACUUUCCCAACCUGCUG------UUACCUGCUGGGCGG--CA
......(((((..((-----(.-..(((..(.((((((((..(((((...)))))...)))))))).)..)))------......))).)))))--.. ( -29.80)
>DroYak_CAF1 95039 89 + 1
CACACUCUUGCAGAG-----CUCACCAGUGGAUUGGGAAAUUUUCGGUAACAGGAUACUUUCCCAACCUGCUGCU--UGCUACCUGCUGGGCGG--CA
..(.(((..((((((-----(....(((..(.((((((((..(((.......)))...)))))))).)..)))..--.)))..)))).))).).--.. ( -29.80)
>consensus
CACACGAUGGUAGAGC_AAGCU_AACAGUGGAUUGGGAAAUUUUCGGGAACGGGAUACUUUCCCAACCUGCUGCU_CUGCUACCUGCUGGGCGGCGCA
.......((((((.(..........(((..(.((((((((.(((((....)))))...)))))))).)..))).........)))))))......... (-22.57 = -22.89 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:36 2006