Locus 7223

Sequence ID 2L_DroMel_CAF1
Location 20,256,232 – 20,256,432
Length 200
Max. P 0.854859
window11556 window11557 window11558

overview

Window 6

Location 20,256,232 – 20,256,352
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -28.11
Consensus MFE -27.11
Energy contribution -26.34
Covariance contribution -0.77
Combinations/Pair 1.15
Mean z-score -1.93
Structure conservation index 0.96
SVM decision value 0.80
SVM RNA-class probability 0.854859
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20256232 120 + 22407834
UGCAUUUUGCCCAUUAACACCUGUACAACACAUGCGAAACAUUAUUACCACCCGCGGCGAUAGGUAACUAUUUUAUUUAUUUUCCCCUCAUAUGCUUUGUUUCGCAAGGGCGUUAUUUUA
........((((.........(((.....)))(((((((((............(.((.(((((((((.....)))))))))..)))...........))))))))).))))......... ( -24.10)
>DroSec_CAF1 17856 120 + 1
UGCAUUUCGCCCAUUAACACCUGCACAGCACAUGCGAAACAUUAUUACCACCCGCGGCGAUAGGGAACUAUUUUAUUUAUUUUCUCCUCAGAUGCUUUGUUUCGCAAGGGCGUUAUUUUA
.......(((((.........(((...)))..(((((((((.((((.((......)).(((((....)))))..................))))...))))))))).)))))........ ( -27.50)
>DroSim_CAF1 16288 120 + 1
UGCAUUUCGCCCAUUAACACCUGCACAGCACAUGCGAAACAUUAUUACCACCCGCGGCGAUGGGGAACUAUUUUAUUUAUUUUCCCCUCAGAUGCUUUGUUUCGCAAGGGCGUUAUUUUA
.......(((((.........(((...)))..(((((((((.((((.((......)).((.((((((..............)))))))).))))...))))))))).)))))........ ( -32.74)
>consensus
UGCAUUUCGCCCAUUAACACCUGCACAGCACAUGCGAAACAUUAUUACCACCCGCGGCGAUAGGGAACUAUUUUAUUUAUUUUCCCCUCAGAUGCUUUGUUUCGCAAGGGCGUUAUUUUA
.......(((((.........(((...)))..(((((((((.(((..((......))..)))(((((..............)))))...........))))))))).)))))........ (-27.11 = -26.34 +  -0.77)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 20,256,232 – 20,256,352
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -32.85
Consensus MFE -29.84
Energy contribution -30.17
Covariance contribution 0.34
Combinations/Pair 1.07
Mean z-score -1.97
Structure conservation index 0.91
SVM decision value 0.41
SVM RNA-class probability 0.723263
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20256232 120 - 22407834
UAAAAUAACGCCCUUGCGAAACAAAGCAUAUGAGGGGAAAAUAAAUAAAAUAGUUACCUAUCGCCGCGGGUGGUAAUAAUGUUUCGCAUGUGUUGUACAGGUGUUAAUGGGCAAAAUGCA
.....(((((((..(((((((((..........((.....................))(((((((...)))))))....)))))))))((((...)))))))))))....((.....)). ( -28.20)
>DroSec_CAF1 17856 120 - 1
UAAAAUAACGCCCUUGCGAAACAAAGCAUCUGAGGAGAAAAUAAAUAAAAUAGUUCCCUAUCGCCGCGGGUGGUAAUAAUGUUUCGCAUGUGCUGUGCAGGUGUUAAUGGGCGAAAUGCA
........(((((..((((((((.(.((((((.((.((.....(((......))).....)).)).)))))).).....))))))))((.(((...))).))......)))))....... ( -32.20)
>DroSim_CAF1 16288 120 - 1
UAAAAUAACGCCCUUGCGAAACAAAGCAUCUGAGGGGAAAAUAAAUAAAAUAGUUCCCCAUCGCCGCGGGUGGUAAUAAUGUUUCGCAUGUGCUGUGCAGGUGUUAAUGGGCGAAAUGCA
........(((((..((((((((..........((((((..............))))))((((((...)))))).....))))))))((.(((...))).))......)))))....... ( -38.14)
>consensus
UAAAAUAACGCCCUUGCGAAACAAAGCAUCUGAGGGGAAAAUAAAUAAAAUAGUUCCCUAUCGCCGCGGGUGGUAAUAAUGUUUCGCAUGUGCUGUGCAGGUGUUAAUGGGCGAAAUGCA
........(((((..((((((((..........((((((..............))))))((((((...)))))).....))))))))((.(((...))).))......)))))....... (-29.84 = -30.17 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 20,256,312 – 20,256,432
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.89
Mean single sequence MFE -30.34
Consensus MFE -30.11
Energy contribution -30.44
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 0.99
SVM decision value 0.26
SVM RNA-class probability 0.657309
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20256312 120 + 22407834
UUUCCCCUCAUAUGCUUUGUUUCGCAAGGGCGUUAUUUUAAUCAACGCUUUGGCGAAACUCUCUCGUUCGGCAGACACACCUGCUCCUGCUGCGACCUUUGCCCUUCCUGCUGCAAUUGC
............(((...(((((((.((((((((.........)))))))).)))))))..........((((((.......((....)).......)))))).........)))..... ( -29.74)
>DroSec_CAF1 17936 120 + 1
UUUCUCCUCAGAUGCUUUGUUUCGCAAGGGCGUUAUUUUAAUCAACGCUUUGGCGAAACUCUCUCGUUCGGCAGACACACCUGCUCCUGCUGCGACCUUUGCCCUUCCUGCUGCAAUUGC
........(((.(((...(((((((.((((((((.........)))))))).)))))))..........((((((.......((....)).......)))))).........))).))). ( -30.64)
>DroSim_CAF1 16368 120 + 1
UUUCCCCUCAGAUGCUUUGUUUCGCAAGGGCGUUAUUUUAAUCAACGCUUUGGCGAAACUCUCUCGUUCGGCAGACACACCUGCUCCUGCUGCGACCUUUGCCCUUCCUGCUGCAAUUGC
........(((.(((...(((((((.((((((((.........)))))))).)))))))..........((((((.......((....)).......)))))).........))).))). ( -30.64)
>consensus
UUUCCCCUCAGAUGCUUUGUUUCGCAAGGGCGUUAUUUUAAUCAACGCUUUGGCGAAACUCUCUCGUUCGGCAGACACACCUGCUCCUGCUGCGACCUUUGCCCUUCCUGCUGCAAUUGC
........(((.(((...(((((((.((((((((.........)))))))).)))))))..........((((((.......((....)).......)))))).........))).))). (-30.11 = -30.44 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:30:48 2006