Locus 1369

Sequence ID 3R_DroMel_CAF1
Location 4,006,565 – 4,006,666
Length 101
Max. P 0.736825
window2257 window2258

overview

Window 7

Location 4,006,565 – 4,006,666
Length 101
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 91.40
Mean single sequence MFE -14.78
Consensus MFE -12.27
Energy contribution -12.53
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.83
SVM decision value 0.44
SVM RNA-class probability 0.736825
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4006565 101 + 27905053
AUCAAUUUAUCUAUCUAUCGGCAGCAGAAGCAGCGAUAA-UGAAGUGAAAAAAUAUGACAAAAA----AAAAAAUGAAAAAAAAUGAGAAGCAGACACUUUUCAUU
.(((.(((((.....(((((.(.((....)).)))))))-)))).)))................----..............(((((((((......))))))))) ( -14.60)
>DroSec_CAF1 12120 95 + 1
AUCAAUUUAUCUAUCUAUCGGCAGCAGAAGCAGCGAUAA-UGAAGUGAAAAAAUACGACAAAA--------AAAUGAAA-AAAAUGAGAAGCAGA-ACUUUUCAUU
.(((.(((((.....(((((.(.((....)).)))))))-)))).)))...............--------........-..(((((((((....-.))))))))) ( -14.40)
>DroSim_CAF1 12701 96 + 1
AUCAAUUUAUCUAUCUAUCGGCAGCAGAAGCAGCGAUAA-UGAAGUGAAAAAAUACGACAAAA--------AAAUGAAA-AAAAUGAGAAGCAGACACUUUUCAUU
.(((.(((((.....(((((.(.((....)).)))))))-)))).)))...............--------........-..(((((((((......))))))))) ( -14.60)
>DroYak_CAF1 12114 106 + 1
AUCAAUUUAUCUAUCUAUCGGCAGCAGAAGCAGCGAUAAGUGAAGUGAAAAAAUACGAAAAAAAUUGAAAAAAUUAAAAAAAAACGAGAAGCAGACACUUUUCAUU
.(((((((...((..(((((.(.((....)).))))))..))..(((......))).....))))))).................((((((......))))))... ( -15.50)
>consensus
AUCAAUUUAUCUAUCUAUCGGCAGCAGAAGCAGCGAUAA_UGAAGUGAAAAAAUACGACAAAA________AAAUGAAA_AAAAUGAGAAGCAGACACUUUUCAUU
.(((.((((......(((((.(.((....)).))))))..)))).)))..................................(((((((((......))))))))) (-12.27 = -12.53 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 4,006,565 – 4,006,666
Length 101
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 91.40
Mean single sequence MFE -15.62
Consensus MFE -12.97
Energy contribution -13.04
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -1.41
Structure conservation index 0.83
SVM decision value -0.03
SVM RNA-class probability 0.519748
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4006565 101 - 27905053
AAUGAAAAGUGUCUGCUUCUCAUUUUUUUUCAUUUUUU----UUUUUGUCAUAUUUUUUCACUUCA-UUAUCGCUGCUUCUGCUGCCGAUAGAUAGAUAAAUUGAU
(((((.((((....)))).)))))............((----..((((((.((((...........-.((((((.((....)).).)))))))))))))))..)). ( -14.50)
>DroSec_CAF1 12120 95 - 1
AAUGAAAAGU-UCUGCUUCUCAUUUU-UUUCAUUU--------UUUUGUCGUAUUUUUUCACUUCA-UUAUCGCUGCUUCUGCUGCCGAUAGAUAGAUAAAUUGAU
(((((.(((.-....))).)))))..-..(((.((--------(((((((((........))....-.((((((.((....)).).))))))))))).))).))). ( -15.60)
>DroSim_CAF1 12701 96 - 1
AAUGAAAAGUGUCUGCUUCUCAUUUU-UUUCAUUU--------UUUUGUCGUAUUUUUUCACUUCA-UUAUCGCUGCUUCUGCUGCCGAUAGAUAGAUAAAUUGAU
(((((.((((....)))).)))))..-..(((.((--------(((((((((........))....-.((((((.((....)).).))))))))))).))).))). ( -16.60)
>DroYak_CAF1 12114 106 - 1
AAUGAAAAGUGUCUGCUUCUCGUUUUUUUUUAAUUUUUUCAAUUUUUUUCGUAUUUUUUCACUUCACUUAUCGCUGCUUCUGCUGCCGAUAGAUAGAUAAAUUGAU
(((((.((((....)))).)))))..............(((((((...((((........)).....(((((((.((....)).).))))))...)).))))))). ( -15.80)
>consensus
AAUGAAAAGUGUCUGCUUCUCAUUUU_UUUCAUUU________UUUUGUCGUAUUUUUUCACUUCA_UUAUCGCUGCUUCUGCUGCCGAUAGAUAGAUAAAUUGAU
(((((.((((....)))).)))))....................((((((.((((.............((((((.((....)).).)))))))))))))))..... (-12.97 = -13.04 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:21 2006