Locus 1268

Sequence ID	3R_DroMel_CAF1
Location	3,781,888 – 3,782,045
Length	157
Max. P	0.999950

overview

Window 8

Location	3,781,888 – 3,782,005
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.28
Mean single sequence MFE	-41.24
Consensus MFE	-33.44
Energy contribution	-33.80
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-1.81
Structure conservation index	0.81
SVM decision value	0.97
SVM RNA-class probability	0.893140
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3781888 117 + 27905053
AGCAAAGUUUUUCGUUGUCUGCCAGG-GGUUUUUCAGUCGAAUUGGCGGCACUAAAUGUUCUAGACAGACAACUGGGA--GAUCUGUUGGCCAGGCACCAGGUCUUUUGGGCCUGGCCAG
((((..((((..(((((((((.(.((-..(.(((..((((......))))...))).)..)).).)))))))).)..)--))).))))((((((((.((((.....)))))))))))).. ( -46.60)
>DroSec_CAF1 11375 120 + 1
AGCAAAGUUUUUCGUUCUCUACCAGGGGGUUUUUCAGUCGAAUUGGCGGCACUAAAUGUUCUAGACAGACAACUGGGAGAGAUCUGUUGGCCAGGCACCAGGUCUUUUGGGCCUGGCCAG
.............(.(((((.((((...((((.((.((((......))))((.....))....)).))))..)))).))))).)...(((((((((.((((.....))))))))))))). ( -44.00)
>DroSim_CAF1 15044 120 + 1
AGCAAAGUUUUUCGUUCUCUACCAGGGGGUUUUUCAGUCGAAUUGGCGGCACUAAAUGUUCUAGACAGACAACUGGGAGAGAUCUGUUGGCCAGGCACCAGGUCUUUUGGGCCUGGCCAG
.............(.(((((.((((...((((.((.((((......))))((.....))....)).))))..)))).))))).)...(((((((((.((((.....))))))))))))). ( -44.00)
>DroEre_CAF1 1705 115 + 1
AGCAAAGUUUUUG-UUUC-UGCCAGG-GGUUUUUCAGUCGAAUUGGCGGCACUAAAUGUUCUAGACAGACAACUGGGA--GAUCUUUUGGUCUGGCACCAGGUCUUUUGGGCCUGGCCAG
(((((.....)))-))((-(.((((.-.((((.((.((((......))))((.....))....)).))))..)))).)--)).....(((((.(((.((((.....))))))).))))). ( -36.20)
>DroYak_CAF1 14984 116 + 1
AGCAAAGUUUUUG-UUUCCAGCCAGG-GGUUUUUCAGUCGAAUUGGCGGCACUAAAUGUUCUAGACAGACAACUGGGA--GAUCUUUUGGUCUUGCACCAGGUCUUUUGGGCCUGGCCAG
.((..........-.......((((.-.((((.((.((((......))))((.....))....)).))))..))))((--((((....)))))))).(((((((.....))))))).... ( -35.40)
>consensus
AGCAAAGUUUUUCGUUCUCUGCCAGG_GGUUUUUCAGUCGAAUUGGCGGCACUAAAUGUUCUAGACAGACAACUGGGA__GAUCUGUUGGCCAGGCACCAGGUCUUUUGGGCCUGGCCAG
.....................((((...((((.((.((((......))))((.....))....)).))))..))))...........(((((((((.((((.....))))))))))))). (-33.44 = -33.80 +   0.36)

alignment

secondary structure

dotplot

Window 9

Location	3,781,888 – 3,782,005
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.28
Mean single sequence MFE	-33.07
Consensus MFE	-24.85
Energy contribution	-25.77
Covariance contribution	0.92
Combinations/Pair	1.08
Mean z-score	-1.73
Structure conservation index	0.75
SVM decision value	-0.04
SVM RNA-class probability	0.512962
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3781888 117 - 27905053
CUGGCCAGGCCCAAAAGACCUGGUGCCUGGCCAACAGAUC--UCCCAGUUGUCUGUCUAGAACAUUUAGUGCCGCCAAUUCGACUGAAAAACC-CCUGGCAGACAACGAAAAACUUUGCU
.((((((((((((.......))).))))))))).((((..--.....((((((((.((((....((((((..((......)))))))).....-.)))))))))))).......)))).. ( -41.64)
>DroSec_CAF1 11375 120 - 1
CUGGCCAGGCCCAAAAGACCUGGUGCCUGGCCAACAGAUCUCUCCCAGUUGUCUGUCUAGAACAUUUAGUGCCGCCAAUUCGACUGAAAAACCCCCUGGUAGAGAACGAAAAACUUUGCU
.((((((((((((.......))).)))))))))...(.(((((.((((.(((((....)).)))((((((..((......)))))))).......)))).))))).)............. ( -37.60)
>DroSim_CAF1 15044 120 - 1
CUGGCCAGGCCCAAAAGACCUGGUGCCUGGCCAACAGAUCUCUCCCAGUUGUCUGUCUAGAACAUUUAGUGCCGCCAAUUCGACUGAAAAACCCCCUGGUAGAGAACGAAAAACUUUGCU
.((((((((((((.......))).)))))))))...(.(((((.((((.(((((....)).)))((((((..((......)))))))).......)))).))))).)............. ( -37.60)
>DroEre_CAF1 1705 115 - 1
CUGGCCAGGCCCAAAAGACCUGGUGCCAGACCAAAAGAUC--UCCCAGUUGUCUGUCUAGAACAUUUAGUGCCGCCAAUUCGACUGAAAAACC-CCUGGCA-GAAA-CAAAAACUUUGCU
...(((((((......).))))))(((((.......(.((--(..(((....)))...))).).((((((..((......)))))))).....-.))))).-....-............. ( -23.20)
>DroYak_CAF1 14984 116 - 1
CUGGCCAGGCCCAAAAGACCUGGUGCAAGACCAAAAGAUC--UCCCAGUUGUCUGUCUAGAACAUUUAGUGCCGCCAAUUCGACUGAAAAACC-CCUGGCUGGAAA-CAAAAACUUUGCU
(..((((((......((((((((.(..(((.(....).))--))))))..))))..........((((((..((......)))))))).....-))))))..)...-............. ( -25.30)
>consensus
CUGGCCAGGCCCAAAAGACCUGGUGCCUGGCCAACAGAUC__UCCCAGUUGUCUGUCUAGAACAUUUAGUGCCGCCAAUUCGACUGAAAAACC_CCUGGCAGAAAACGAAAAACUUUGCU
.((((((((((((.......))).)))))))))............((((((..........((.....))..........))))))...........((((((...........)))))) (-24.85 = -25.77 +   0.92)

alignment

secondary structure

dotplot

Window 0

Location	3,781,927 – 3,782,045
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.48
Mean single sequence MFE	-42.72
Consensus MFE	-39.48
Energy contribution	-39.84
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-1.75
Structure conservation index	0.92
SVM decision value	2.08
SVM RNA-class probability	0.987330
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3781927 118 + 27905053
AAUUGGCGGCACUAAAUGUUCUAGACAGACAACUGGGA--GAUCUGUUGGCCAGGCACCAGGUCUUUUGGGCCUGGCCAGGAGGCGCUGCCUGUCUUAAGAGCCCGAAAUUAGCACAACC
....((((((.....((.((((((........))))))--.))((.((((((((((.((((.....)))))))))))))).))..))))))(((.((((..........)))).)))... ( -44.90)
>DroSec_CAF1 11415 120 + 1
AAUUGGCGGCACUAAAUGUUCUAGACAGACAACUGGGAGAGAUCUGUUGGCCAGGCACCAGGUCUUUUGGGCCUGGCCAGGAGGCGCUGCCUGUCUUAAGAGCCCGAAAUUAGCACAACC
....((((((......(.((((((........)))))).)(.(((.((((((((((.((((.....)))))))))))))).))))))))))(((.((((..........)))).)))... ( -45.20)
>DroSim_CAF1 15084 120 + 1
AAUUGGCGGCACUAAAUGUUCUAGACAGACAACUGGGAGAGAUCUGUUGGCCAGGCACCAGGUCUUUUGGGCCUGGCCAGGAGGCGCUGCCUGUCUUAAGAGCCCGAAAUUAGCACAACC
....((((((......(.((((((........)))))).)(.(((.((((((((((.((((.....)))))))))))))).))))))))))(((.((((..........)))).)))... ( -45.20)
>DroEre_CAF1 1742 118 + 1
AAUUGGCGGCACUAAAUGUUCUAGACAGACAACUGGGA--GAUCUUUUGGUCUGGCACCAGGUCUUUUGGGCCUGGCCAGGAGGCGCUGCCUGUCUUAAGGGCCCAAAAUUAGCACAACC
....((((((.....((.((((((........))))))--.))(((((((((.(((.((((.....))))))).)))))))))..)))))).(((.....)))................. ( -39.60)
>DroYak_CAF1 15022 118 + 1
AAUUGGCGGCACUAAAUGUUCUAGACAGACAACUGGGA--GAUCUUUUGGUCUUGCACCAGGUCUUUUGGGCCUGGCCAGGAGGCGCUGCCUGUCUUAAGAGCCCGAAAUUAGCACAACC
..(((((..........(((((((((......((((((--((((....))))))...(((((((.....))))))))))).((((...))))))))..))))).........)).))).. ( -38.71)
>consensus
AAUUGGCGGCACUAAAUGUUCUAGACAGACAACUGGGA__GAUCUGUUGGCCAGGCACCAGGUCUUUUGGGCCUGGCCAGGAGGCGCUGCCUGUCUUAAGAGCCCGAAAUUAGCACAACC
....((((((........((((((........))))))..(.(((.((((((((((.((((.....)))))))))))))).))))))))))(((.((((..........)))).)))... (-39.48 = -39.84 +   0.36)

alignment

secondary structure

dotplot

Window 1

Location	3,781,927 – 3,782,045
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.48
Mean single sequence MFE	-46.64
Consensus MFE	-43.58
Energy contribution	-44.78
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-3.37
Structure conservation index	0.93
SVM decision value	4.78
SVM RNA-class probability	0.999950
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3781927 118 - 27905053
GGUUGUGCUAAUUUCGGGCUCUUAAGACAGGCAGCGCCUCCUGGCCAGGCCCAAAAGACCUGGUGCCUGGCCAACAGAUC--UCCCAGUUGUCUGUCUAGAACAUUUAGUGCCGCCAAUU
(((.(..((((.....(..(((..(((((((((((......((((((((((((.......))).)))))))))...(...--...).)))))))))))))).)..))))..).))).... ( -50.60)
>DroSec_CAF1 11415 120 - 1
GGUUGUGCUAAUUUCGGGCUCUUAAGACAGGCAGCGCCUCCUGGCCAGGCCCAAAAGACCUGGUGCCUGGCCAACAGAUCUCUCCCAGUUGUCUGUCUAGAACAUUUAGUGCCGCCAAUU
(((.(..((((.....(..(((..(((((((((((......((((((((((((.......))).)))))))))..((....))....)))))))))))))).)..))))..).))).... ( -51.10)
>DroSim_CAF1 15084 120 - 1
GGUUGUGCUAAUUUCGGGCUCUUAAGACAGGCAGCGCCUCCUGGCCAGGCCCAAAAGACCUGGUGCCUGGCCAACAGAUCUCUCCCAGUUGUCUGUCUAGAACAUUUAGUGCCGCCAAUU
(((.(..((((.....(..(((..(((((((((((......((((((((((((.......))).)))))))))..((....))....)))))))))))))).)..))))..).))).... ( -51.10)
>DroEre_CAF1 1742 118 - 1
GGUUGUGCUAAUUUUGGGCCCUUAAGACAGGCAGCGCCUCCUGGCCAGGCCCAAAAGACCUGGUGCCAGACCAAAAGAUC--UCCCAGUUGUCUGUCUAGAACAUUUAGUGCCGCCAAUU
(((.(..((((...((..(.....((((((((((((((....)))..((((((.......))).))).............--.....))))))))))).)..)).))))..).))).... ( -41.90)
>DroYak_CAF1 15022 118 - 1
GGUUGUGCUAAUUUCGGGCUCUUAAGACAGGCAGCGCCUCCUGGCCAGGCCCAAAAGACCUGGUGCAAGACCAAAAGAUC--UCCCAGUUGUCUGUCUAGAACAUUUAGUGCCGCCAAUU
(((.(..((((.....(..(((..((((((((((((((....)))...(((((.......))).))..............--.....)))))))))))))).)..))))..).))).... ( -38.50)
>consensus
GGUUGUGCUAAUUUCGGGCUCUUAAGACAGGCAGCGCCUCCUGGCCAGGCCCAAAAGACCUGGUGCCUGGCCAACAGAUC__UCCCAGUUGUCUGUCUAGAACAUUUAGUGCCGCCAAUU
(((.(..((((....(..((....(((((((((((......((((((((((((.......))).)))))))))...((....))...)))))))))))))..)..))))..).))).... (-43.58 = -44.78 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:11 2006