Locus 142

Sequence ID 4_DroMel_CAF1
Location 957,450 – 957,559
Length 109
Max. P 0.992336
window226 window227

overview

Window 6

Location 957,450 – 957,559
Length 109
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 89.71
Mean single sequence MFE -28.23
Consensus MFE -23.86
Energy contribution -24.43
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -3.40
Structure conservation index 0.85
SVM decision value 2.32
SVM RNA-class probability 0.992336
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 957450 109 + 1281640
UU-UU-AGGGCUUUCGCUAACACAUUGCUUUUGCAGCUUCAGAGCAACGCCAUCAUCAGUACCAUUCUUUUUGGUAC---UUGGCUUGUCCUUACAUUCCAAAGCUUUUGCUGU
..-..-(((((....(((......((((....))))......)))...((((.....(((((((.......))))))---)))))..)))))..........(((....))).. ( -28.90)
>DroSim_CAF1 17793 112 + 1
UU-UU-AGGGCUUUCGCUAACACAUUGCUUUUGCAGCUUCAGAGCAACGCCAUCACCAGUACCAUUCUUUUUGGUACUUCUUGGCGUGUCCUUACAUUCCAAAGCUUUUUCUGU
..-..-(((((....(((......((((....))))......))).((((((.....(((((((.......)))))))...)))))))))))...................... ( -31.10)
>DroEre_CAF1 23177 107 + 1
UUUUUAAGGGCUUUUGCUAACACAUUGCUUUUGCAGCUUCAGAGCAACGCCAUCAUCAGUACCAUUCUUUUUGGUACUUCUUUGCUUGUCCUUACAUUUCGAAGCUU-------
....(((((((..(((((......((((....))))......))))).((.......(((((((.......))))))).....))..))))))).............------- ( -25.50)
>DroYak_CAF1 22900 113 + 1
UUUUU-AGGGCUUUUGCUAACACAUUGCUUUUGCAGCUUCAGAGCAACGCCAUCAUCAGUACCAUCCUAUUUGGUACUUCUUGUCUUGCCCUUACAUUCCAAAGCUUUUGCUGU
.....-(((((..(((((......((((....))))......)))))..........(((((((.......))))))).........)))))..........(((....))).. ( -27.40)
>consensus
UU_UU_AGGGCUUUCGCUAACACAUUGCUUUUGCAGCUUCAGAGCAACGCCAUCAUCAGUACCAUUCUUUUUGGUACUUCUUGGCUUGUCCUUACAUUCCAAAGCUUUUGCUGU
......(((((....(((......((((....))))......)))...((((.....(((((((.......)))))))...))))..)))))...................... (-23.86 = -24.43 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 957,450 – 957,559
Length 109
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 89.71
Mean single sequence MFE -28.77
Consensus MFE -23.51
Energy contribution -23.82
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -2.71
Structure conservation index 0.82
SVM decision value 1.72
SVM RNA-class probability 0.974100
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 957450 109 - 1281640
ACAGCAAAAGCUUUGGAAUGUAAGGACAAGCCAA---GUACCAAAAAGAAUGGUACUGAUGAUGGCGUUGCUCUGAAGCUGCAAAAGCAAUGUGUUAGCGAAAGCCCU-AA-AA
..((((..(((((..((.(((....))).(((((---((((((.......))))))).....)))).....))..)))))((....))....)))).((....))...-..-.. ( -30.50)
>DroSim_CAF1 17793 112 - 1
ACAGAAAAAGCUUUGGAAUGUAAGGACACGCCAAGAAGUACCAAAAAGAAUGGUACUGGUGAUGGCGUUGCUCUGAAGCUGCAAAAGCAAUGUGUUAGCGAAAGCCCU-AA-AA
(((.....(((((..((..((((.(.(((((((....((((((.......))))))))))).)).).))))))..)))))((....))..)))....((....))...-..-.. ( -33.30)
>DroEre_CAF1 23177 107 - 1
-------AAGCUUCGAAAUGUAAGGACAAGCAAAGAAGUACCAAAAAGAAUGGUACUGAUGAUGGCGUUGCUCUGAAGCUGCAAAAGCAAUGUGUUAGCAAAAGCCCUUAAAAA
-------.(((((((....((((.(.(...((....(((((((.......)))))))..))...)).))))..)))))))((....))..(((....))).............. ( -22.80)
>DroYak_CAF1 22900 113 - 1
ACAGCAAAAGCUUUGGAAUGUAAGGGCAAGACAAGAAGUACCAAAUAGGAUGGUACUGAUGAUGGCGUUGCUCUGAAGCUGCAAAAGCAAUGUGUUAGCAAAAGCCCU-AAAAA
...((...(((((..((..((((.(.((...((...(((((((.......)))))))..)).)).).))))))..)))))((....)).........)).........-..... ( -28.50)
>consensus
ACAGCAAAAGCUUUGGAAUGUAAGGACAAGCCAAGAAGUACCAAAAAGAAUGGUACUGAUGAUGGCGUUGCUCUGAAGCUGCAAAAGCAAUGUGUUAGCAAAAGCCCU_AA_AA
........(((((((((..((((.(.((........(((((((.......))))))).....)).).)))))))))))))((....)).........((....))......... (-23.51 = -23.82 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:36 2006