Locus 5333

Sequence ID 3R_DroMel_CAF1
Location 13,979,544 – 13,979,710
Length 166
Max. P 0.715705
window8693 window8694

overview

Window 3

Location 13,979,544 – 13,979,638
Length 94
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 81.97
Mean single sequence MFE -39.53
Consensus MFE -26.16
Energy contribution -26.80
Covariance contribution 0.64
Combinations/Pair 1.08
Mean z-score -1.67
Structure conservation index 0.66
SVM decision value 0.13
SVM RNA-class probability 0.598337
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13979544 94 - 27905053
UGGCGGCACCAAAGGG--GCGUC-CGGGUGCCACA-UGCGUGGCGCAU-GCGUGGUGGAGUCGG------UGACUAUGACAAAUCGCCACAUGGCAGGCGGCCAA
((((.((.(((.....--((((.-...(((((((.-...)))))))))-))(((((((.((((.------...)...)))...))))))).)))...)).)))). ( -41.10)
>DroSim_CAF1 259426 94 - 1
UGGCGGCCCCAAAGGA--GCGUC-CGGGUGCCACA-UGCGUGGCGCAU-GCGUGGUGGAGUCGG------UGACUAUGACAAAUCGCCACAUGGCAGGCGGCCAA
((((.((((((.....--((((.-...(((((((.-...)))))))))-))(((((((.((((.------...)...)))...))))))).)))..))).)))). ( -43.40)
>DroEre_CAF1 241125 93 - 1
UGGCGGGCGUAAGGAG--GCGU--CGGGUGCCACA-UGCGUGGCGCAU-GCGUGGUGGAGUCGG------UGACUAUGACAAAUCGCCACAUGGCAGGCGGCCAA
..((((((((......--))))--)..(((((((.-...))))))).)-))(((((((.((((.------...)...)))...))))))).((((.....)))). ( -38.80)
>DroYak_CAF1 262514 93 - 1
UGGCGGGCCUAAAGGG--GCGU--CGGGUGCCAUA-UGCGUGGCGCAU-GCGUGGUGGAGUCGG------UGACUAUGACAAAUCGCCACAUGGCAGGCGGCCAA
((((.(((((....))--))((--((.(((((((.-...)))))))..-..(((((((.((((.------...)...)))...))))))).))))...).)))). ( -39.60)
>DroMoj_CAF1 341553 98 - 1
UGUCGGAGUCAGA--G--ACGUAGAUGGAGCCACAUUGCGUGGCGCAUUGCGU---GGAGUCGUGUGGCCGCUUAUAGACAAAUCGCCACAUGGCGGGCGGCCAA
.....((.((...--.--((((((.((..(((((.....))))).))))))))---.)).))...(((((((((...((....))(((....)))))))))))). ( -39.10)
>DroAna_CAF1 241667 92 - 1
UGGAGGGA----AGAGUCAAGUG-AGGCUGCCACA-UGCGUGGCGCAU-GCGUGGUGGAGUCGG------UGACUAUGACAAAUCGCCACAUGGCAGGCGGCCAA
........----...........-.(((((((.((-((((...)))))-).(((((((.((((.------...)...)))...)))))))......))))))).. ( -35.20)
>consensus
UGGCGGGCCCAAAGGG__GCGU__CGGGUGCCACA_UGCGUGGCGCAU_GCGUGGUGGAGUCGG______UGACUAUGACAAAUCGCCACAUGGCAGGCGGCCAA
((((((............((((.....(((((((.....)))))))...))))......((((.............))))...))))))..((((.....)))). (-26.16 = -26.80 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 13,979,603 – 13,979,710
Length 107
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 84.19
Mean single sequence MFE -36.13
Consensus MFE -23.36
Energy contribution -24.84
Covariance contribution 1.48
Combinations/Pair 1.10
Mean z-score -2.07
Structure conservation index 0.65
SVM decision value 0.39
SVM RNA-class probability 0.715705
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13979603 107 + 27905053
GCAUGUGGCACCCGGACGCCCCUUUGGUGCCGCCACGCCUCUCGCCCCCCCCCCCUCUUUCCACACGAUGCGGUGGGGCGUAAAAGCCACACGCAACAGCUACACGA
((.((((((...(((.((((.....)))))))..(((((((((((........................)))).)))))))....)))))).))............. ( -37.16)
>DroSec_CAF1 254817 94 + 1
GCAUGUGGCACCCGUACGCCCCUUUGGGGCCGCCACGCC------------CCCCUC-UUCCGCCCGAUGCGGUGGGGCGUAAAAGCCACACGCAACAGCUACACGA
((.((((((.....((((((((...(((((......)))------------))....-..((((.....)))).))))))))...)))))).))............. ( -44.60)
>DroSim_CAF1 259485 94 + 1
GCAUGUGGCACCCGGACGCUCCUUUGGGGCCGCCACGCC------------CCCCUC-AUCCGCCCGAUGCGGUGGGGCGUAAAAGCCACACGCAACAGCUACACGA
((.((((((....((..(((((...)))))..))(((((------------((((.(-(((.....)))).)).)))))))....)))))).))............. ( -45.70)
>DroEre_CAF1 241184 89 + 1
GCAUGUGGCACCCG-ACGCCUCCUUACGCCCGCCACGCC------------CCCCU----CCGCCUGA-GCAGUGGGGCGAAAAAGCCACACGCAACAGCUACACGA
((.((((((.....-..((........))......((((------------((.((----.(......-).)).)))))).....)))))).))............. ( -28.80)
>DroYak_CAF1 262573 89 + 1
GCAUAUGGCACCCG-ACGCCCCUUUAGGCCCGCCACGCC------------CCCCU----CCGUCUGA-CCAGUGGGGCGAAAAAGCCACACGCAACAGCUACACGA
((...((((.....-..(((......)))......((((------------((.((----........-..)).)))))).....))))...))............. ( -24.40)
>consensus
GCAUGUGGCACCCG_ACGCCCCUUUGGGGCCGCCACGCC____________CCCCUC__UCCGCCCGAUGCGGUGGGGCGUAAAAGCCACACGCAACAGCUACACGA
((.((((((......(((((((....((....))..........................((((.....)))).)))))))....)))))).))............. (-23.36 = -24.84 +   1.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:12 2006