Locus 2130

Sequence ID 3L_DroMel_CAF1
Location 5,819,720 – 5,819,828
Length 108
Max. P 0.940094
window3317 window3318

overview

Window 7

Location 5,819,720 – 5,819,828
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.47
Mean single sequence MFE -29.36
Consensus MFE -25.30
Energy contribution -25.06
Covariance contribution -0.24
Combinations/Pair 1.04
Mean z-score -1.57
Structure conservation index 0.86
SVM decision value 1.01
SVM RNA-class probability 0.900632
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5819720 108 + 23771897
GUCGGAAUUUGUUCGACUGCGUUCGGCCGUGUUCGAAUAUCUUCGGCACGCUCAUUUCGCUCAAACGUUGAGUGUUUUCU------------CCAACGUUUUCUUCUCACAGCAACGCCA
((((((.....)))))).(((((.(..(((((.((((....)))))))))..).....(((.((((((((((......))------------.)))))))).........)))))))).. ( -29.50)
>DroSec_CAF1 27488 108 + 1
GUCGGAAUUUGUUCGACUGCGUUCGGCCGUGUUCGAAUAUCUUCGGCACGCUCUUUUCGCUCAAACGUUGAGUGUUUUCU------------CCAACGUUUUCUUCUCACAGCAACGCCA
((((((.....)))))).(((((.(..(((((.((((....)))))))))..).....(((.((((((((((......))------------.)))))))).........)))))))).. ( -29.00)
>DroSim_CAF1 9869 108 + 1
GUCGGAAUUUGUUCGACUGCGUUCGGCCGUGUUCGAAUAUCUUCGGCACGCUCUUUUCGCUCAAACGUUGAGUGUUUUCU------------CCAACGUUUUCUUCUCGCAGCAACGCCA
((((((.....)))))).((((((.(((((((.((((....)))))))))............((((((((((......))------------.)))))))).......)).).))))).. ( -29.80)
>DroEre_CAF1 27910 105 + 1
GUCGGAAUUUGUUCGACUGCGUUCGGCCGUGUUCGAAUAUCUUCGGCACACUCUUUUCGCUCAAACGUUGAGUGUUUUCU------------UCAACGUUUU---CUCACAGCAACGCCA
((((((.....)))))).......(((.(((((((((....))))).)))).......(((.((((((((((.......)------------))))))))).---.....)))...))). ( -28.70)
>DroYak_CAF1 30004 117 + 1
GUCGGAAUUUGUUCGACUGCGUUCGGCCGUGUUCGAAUAUCUUCGGCACACUCAUUUCGCUCAAACGUUGAGUGUUUUUUUUUUUUUUUGGUUUAACGUUUU---CUCACAGCAACGCCA
...((...(((((.((..(((((..((((((((((((....))))).))))......((((((.....))))))...............)))..)))))..)---)....)))))..)). ( -29.80)
>consensus
GUCGGAAUUUGUUCGACUGCGUUCGGCCGUGUUCGAAUAUCUUCGGCACGCUCUUUUCGCUCAAACGUUGAGUGUUUUCU____________CCAACGUUUUCUUCUCACAGCAACGCCA
((((((.....)))))).((((...((.(((((((((....))))).))))......((((((.....)))))).....................................)).)))).. (-25.30 = -25.06 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,819,720 – 5,819,828
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.47
Mean single sequence MFE -29.64
Consensus MFE -25.76
Energy contribution -25.68
Covariance contribution -0.08
Combinations/Pair 1.07
Mean z-score -1.64
Structure conservation index 0.87
SVM decision value 1.28
SVM RNA-class probability 0.940094
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5819720 108 - 23771897
UGGCGUUGCUGUGAGAAGAAAACGUUGG------------AGAAAACACUCAACGUUUGAGCGAAAUGAGCGUGCCGAAGAUAUUCGAACACGGCCGAACGCAGUCGAACAAAUUCCGAC
..(((((((((((......((((((((.------------((......))))))))))..((.......))....((((....))))..))))))..))))).((((.........)))) ( -30.10)
>DroSec_CAF1 27488 108 - 1
UGGCGUUGCUGUGAGAAGAAAACGUUGG------------AGAAAACACUCAACGUUUGAGCGAAAAGAGCGUGCCGAAGAUAUUCGAACACGGCCGAACGCAGUCGAACAAAUUCCGAC
..(((((((((((......((((((((.------------((......))))))))))..((.......))....((((....))))..))))))..))))).((((.........)))) ( -30.10)
>DroSim_CAF1 9869 108 - 1
UGGCGUUGCUGCGAGAAGAAAACGUUGG------------AGAAAACACUCAACGUUUGAGCGAAAAGAGCGUGCCGAAGAUAUUCGAACACGGCCGAACGCAGUCGAACAAAUUCCGAC
..(((((.(.((.....(.((((((((.------------((......))))))))))...)........((((.((((....))))..)))))).)))))).((((.........)))) ( -27.40)
>DroEre_CAF1 27910 105 - 1
UGGCGUUGCUGUGAG---AAAACGUUGA------------AGAAAACACUCAACGUUUGAGCGAAAAGAGUGUGCCGAAGAUAUUCGAACACGGCCGAACGCAGUCGAACAAAUUCCGAC
..(((((((((((.(---.(((((((((------------.........)))))))))...).....((((((.......))))))...))))))..))))).((((.........)))) ( -30.10)
>DroYak_CAF1 30004 117 - 1
UGGCGUUGCUGUGAG---AAAACGUUAAACCAAAAAAAAAAAAAAACACUCAACGUUUGAGCGAAAUGAGUGUGCCGAAGAUAUUCGAACACGGCCGAACGCAGUCGAACAAAUUCCGAC
..(((((((((((..---...........................(((((((.(((....)))...)))))))..((((....))))..))))))..))))).((((.........)))) ( -30.50)
>consensus
UGGCGUUGCUGUGAGAAGAAAACGUUGG____________AGAAAACACUCAACGUUUGAGCGAAAAGAGCGUGCCGAAGAUAUUCGAACACGGCCGAACGCAGUCGAACAAAUUCCGAC
..(((((((((((......(((((((((.....................)))))))))..((.......))....((((....))))..))))))..))))).((((.........)))) (-25.76 = -25.68 +  -0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:08 2006