Locus 7986

Sequence ID X_DroMel_CAF1
Location 19,880,115 – 19,880,350
Length 235
Max. P 0.767634
window13100 window13101

overview

Window 0

Location 19,880,115 – 19,880,233
Length 118
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 81.19
Mean single sequence MFE -37.98
Consensus MFE -22.76
Energy contribution -25.83
Covariance contribution 3.06
Combinations/Pair 1.07
Mean z-score -2.11
Structure conservation index 0.60
SVM decision value 0.52
SVM RNA-class probability 0.767634
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19880115 118 - 22224390
UAUUUUUUCCGCUCCAUGCUGCGCGUUGUUGGCGCUGUUUUGGCGUGGAUUACCAACUCAAAAAUGCGAGCAUAUGAAUGUUUG-UGUUUUUGUGUAGCCGUGGGAAAAAGGGCUGCAC
.......(((((.(((.((.((((.......)))).))..))).))))).........(((((((((((((((....)))))))-))))))))(((((((.(.......).))))))). ( -44.60)
>DroSec_CAF1 33958 118 - 1
UAUUUUUUCCGCUCCAUGCUGCGCGUUGUUGGCGCUGUUUUGGCGCGGAUUACGAACUCAAAAAUGCGAGCAUAUGAAUGCAUGUUGUUUUUGUGUAGCCGAGGGAA-AAGGGCUGCAC
..((((((((.(((...(((((.(((.(((.(((((.....))))).))).)))....((((((((((.((((....)))).)).)))))))).))))).)))))))-))))....... ( -39.80)
>DroEre_CAF1 11276 104 - 1
UAUUU-UUCCGCUCCAUGCUGCGCGUUGUUG-----------GCGCGGAUUACCAACUCAAAAAUGCGAGCAUAUGUAUGUAUG-UGUUUUUGUGCAGCCGGGG-GA-AAGGGCUGCAC
.....-.(((((.(((.((........))))-----------).))))).........((((((((((.((((....)))).))-))))))))(((((((....-..-...))))))). ( -35.00)
>DroYak_CAF1 9687 97 - 1
UAUUUUUUCCGCUCCAUGCUGCGCGUUGUUGGCGCUGUUUUGGCGCGGAUUACCAACUCAAAAAUGCGAGCAUAUGUACG--------------------AGGG-AA-AAGGGCUGCAC
..((((((((.(((.(((((.((((((.((((((((.....)))))((....))....))).)))))))))))......)--------------------))))-))-))))....... ( -32.50)
>consensus
UAUUUUUUCCGCUCCAUGCUGCGCGUUGUUGGCGCUGUUUUGGCGCGGAUUACCAACUCAAAAAUGCGAGCAUAUGAAUGUAUG_UGUUUUUGUGUAGCCGGGG_AA_AAGGGCUGCAC
...............(((((.((((((.((((((((.....)))))((....))....))).)))))))))))...................((((((((...........)))))))) (-22.76 = -25.83 +   3.06)

alignment

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secondary structure

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dotplot

Postscript

Window 1

Location 19,880,233 – 19,880,350
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.39
Mean single sequence MFE -24.12
Consensus MFE -13.76
Energy contribution -14.33
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -1.94
Structure conservation index 0.57
SVM decision value 0.30
SVM RNA-class probability 0.678227
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19880233 117 - 22224390
AAGAACAACAAUAACAUAAAUGUACGCCCUUCCGGAACGCAACUUAAAGCAGCAUU-UAAGUGCAUUUGGACAA-AACCGGAACAAUCCGA-GGGGAGAAAGCCUCUUGUUUCCAAUUAA
..((((((.....(((....))).(.((((((.(((..(((.((((((......))-))))))).(((((....-..)))))....)))))-)))).)........))))))........ ( -26.50)
>DroSec_CAF1 34076 113 - 1
AAGAACAACA---ACAGAAAUGUACCCCCUUCCGGAACGCAACU-AAAGCAGCAUU-UAAGUGCAUUUGGACAA-AACCGGAACGAUCCGA-GGGGAGAAAGCCUCUUGUUUCCAAUUAA
..((((((..---(((....)))..(((((((((((..((....-...)).((((.-...)))).))))))...-...((((....)))))-))))..........))))))........ ( -28.00)
>DroEre_CAF1 11380 91 - 1
AACAACGGG-----------------------GGGAACGCAACU-AAAGCAGCAUUUUAAGUGCAUUUGGACAA-AACCGAAACAAUCCGA----GAGAAAGCCUCUUUUUUCCAAUUAA
......(((-----------------------((((..((....-...)).((((.....)))).(((((....-..)))))....)))((----(((.....)))))..))))...... ( -17.90)
>DroYak_CAF1 9784 96 - 1
AAGAGCAAC-----------------------UGAAAUGCAACU-AAGGCAGCAUUUUAAGUGCAUUUGGACAAAAACCGGAACAAUCCGAAGGGGAGAAAGCCUCUUGUUUUCAAUUAA
....(((..-----------------------((((((((..(.-...)..))))))))..)))..(((((.......((((....))))((((((......))))))...))))).... ( -24.10)
>consensus
AAGAACAAC_______________________CGGAACGCAACU_AAAGCAGCAUU_UAAGUGCAUUUGGACAA_AACCGGAACAAUCCGA_GGGGAGAAAGCCUCUUGUUUCCAAUUAA
......................................((........)).((((.....))))..(((((.......((((....))))...(((((.....)))))...))))).... (-13.76 = -14.33 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:52:25 2006