Locus 9929

Sequence ID 3R_DroMel_CAF1
Location 26,578,598 – 26,578,715
Length 117
Max. P 0.999924
window15828 window15829

overview

Window 8

Location 26,578,598 – 26,578,715
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.22
Mean single sequence MFE -33.47
Consensus MFE -31.50
Energy contribution -31.53
Covariance contribution 0.03
Combinations/Pair 1.03
Mean z-score -2.42
Structure conservation index 0.94
SVM decision value 3.79
SVM RNA-class probability 0.999618
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26578598 117 + 27905053
AAAAAGCAAUUUGCGGACGUGCAUGAAAAACUUUUACUGGCAGCAAAUUGAAAUUAAUGUGAAGUUUCAGUAAAAGUGGCUUAAAUGCACACACGGGCCGCAUUUGGGGAAUUGCU---G
....((((((((.(.((.((((.......((((((((((((..((.((((....)))).))..))..))))))))))(((((............))))))))))).).))))))))---. ( -33.40)
>DroPse_CAF1 208562 120 + 1
AAAAAGCAAUUUGCGGACGUGCACGGAAAACUUUUACUGGCAGCAAAUUGAAAUUAAUGUGAAGUUUCAGUAAAAGUGGCUUAAAUGCACACACGGGCCGCAUUUGGGGAAUUGCUGCUG
....((((((((.(.((.((((.......((((((((((((..((.((((....)))).))..))..))))))))))(((((............))))))))))).).)))))))).... ( -33.40)
>DroGri_CAF1 337418 117 + 1
CAAAAGCAAUUUGCGGACGUGCAUGAAAAACUUUUACUGGCAGCAAAUUGGAAUUAAUGUGAAGUUUCAGUAAAAGUGGCUUAAAUGCACACACGGGCCGCAUUUUGGGAAUUGCA---G
.....(((((((.((((.((((.......((((((((((((..((.((((....)))).))..))..))))))))))(((((............))))))))))))).))))))).---. ( -33.30)
>DroWil_CAF1 193348 114 + 1
CAAAAGCAAUUUGCGGACGUGCAUGA-AAACUUUUACUGGCAGCAAAUUGAAAUUAAUGUGAAGUUUCAGUAAAAGUGGCUUAAAUGCACACACGGGCCGCAUUUUGGGAAUUGC-----
.....(((((((.((((.((((....-..((((((((((((..((.((((....)))).))..))..))))))))))(((((............))))))))))))).)))))))----- ( -31.90)
>DroMoj_CAF1 216068 117 + 1
CAAAAGCAAUUUGCGGACGUGCAUGAAAAACUUUUACUGGCAGCAAAUUGAAAUUAAUGUGAAGCUGAAGUAAAAGUGGCUUAAAUGCACACACGGGCCGCAUUUUGGGAAUUGCA---C
.....(((((((.((((.((((.......(((((((((..((((..((((....)))).....)))).)))))))))(((((............))))))))))))).))))))).---. ( -35.40)
>DroPer_CAF1 206540 120 + 1
AAAAAGCAAUUUGCGGACGUGCACGGAAAACUUUUACUGGCAGCAAAUUGAAAUUAAUGUGAAGUUUCAGUAAAAGUGGCUUAAAUGCACACACGGGCCGCAUUUGGGGAAUUGCUGCUG
....((((((((.(.((.((((.......((((((((((((..((.((((....)))).))..))..))))))))))(((((............))))))))))).).)))))))).... ( -33.40)
>consensus
AAAAAGCAAUUUGCGGACGUGCAUGAAAAACUUUUACUGGCAGCAAAUUGAAAUUAAUGUGAAGUUUCAGUAAAAGUGGCUUAAAUGCACACACGGGCCGCAUUUGGGGAAUUGCU___G
.....(((((((((((.((((........((((((((((((..((.((((....)))).))..))..)))))))))).((......))...))))..))))).......))))))..... (-31.50 = -31.53 +   0.03)

alignment

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secondary structure

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dotplot

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Window 9

Location 26,578,598 – 26,578,715
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 94.22
Mean single sequence MFE -29.28
Consensus MFE -27.97
Energy contribution -27.91
Covariance contribution -0.06
Combinations/Pair 1.03
Mean z-score -2.73
Structure conservation index 0.96
SVM decision value 4.59
SVM RNA-class probability 0.999924
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26578598 117 - 27905053
C---AGCAAUUCCCCAAAUGCGGCCCGUGUGUGCAUUUAAGCCACUUUUACUGAAACUUCACAUUAAUUUCAAUUUGCUGCCAGUAAAAGUUUUUCAUGCACGUCCGCAAAUUGCUUUUU
.---(((((((.......(((((..(((((((((......)).((((((((((...(..((.(((......))).))..).)))))))))).....))))))).)))))))))))).... ( -29.21)
>DroPse_CAF1 208562 120 - 1
CAGCAGCAAUUCCCCAAAUGCGGCCCGUGUGUGCAUUUAAGCCACUUUUACUGAAACUUCACAUUAAUUUCAAUUUGCUGCCAGUAAAAGUUUUCCGUGCACGUCCGCAAAUUGCUUUUU
....(((((((.......(((((..((((..(((......)).((((((((((...(..((.(((......))).))..).)))))))))).....)..)))).)))))))))))).... ( -29.11)
>DroGri_CAF1 337418 117 - 1
C---UGCAAUUCCCAAAAUGCGGCCCGUGUGUGCAUUUAAGCCACUUUUACUGAAACUUCACAUUAAUUCCAAUUUGCUGCCAGUAAAAGUUUUUCAUGCACGUCCGCAAAUUGCUUUUG
.---.((((((.......(((((..(((((((((......)).((((((((((...(..((.(((......))).))..).)))))))))).....))))))).)))))))))))..... ( -28.41)
>DroWil_CAF1 193348 114 - 1
-----GCAAUUCCCAAAAUGCGGCCCGUGUGUGCAUUUAAGCCACUUUUACUGAAACUUCACAUUAAUUUCAAUUUGCUGCCAGUAAAAGUUU-UCAUGCACGUCCGCAAAUUGCUUUUG
-----((((((.......(((((..(((((((((......)).((((((((((...(..((.(((......))).))..).))))))))))..-..))))))).)))))))))))..... ( -28.41)
>DroMoj_CAF1 216068 117 - 1
G---UGCAAUUCCCAAAAUGCGGCCCGUGUGUGCAUUUAAGCCACUUUUACUUCAGCUUCACAUUAAUUUCAAUUUGCUGCCAGUAAAAGUUUUUCAUGCACGUCCGCAAAUUGCUUUUG
.---.((((((.......(((((..(((((((((......)).(((((((((.((((...................))))..))))))))).....))))))).)))))))))))..... ( -31.42)
>DroPer_CAF1 206540 120 - 1
CAGCAGCAAUUCCCCAAAUGCGGCCCGUGUGUGCAUUUAAGCCACUUUUACUGAAACUUCACAUUAAUUUCAAUUUGCUGCCAGUAAAAGUUUUCCGUGCACGUCCGCAAAUUGCUUUUU
....(((((((.......(((((..((((..(((......)).((((((((((...(..((.(((......))).))..).)))))))))).....)..)))).)))))))))))).... ( -29.11)
>consensus
C___AGCAAUUCCCAAAAUGCGGCCCGUGUGUGCAUUUAAGCCACUUUUACUGAAACUUCACAUUAAUUUCAAUUUGCUGCCAGUAAAAGUUUUUCAUGCACGUCCGCAAAUUGCUUUUG
.....((((((.......(((((..((((..(((......)).((((((((((...(..((.(((......))).))..).)))))))))).....)..)))).)))))))))))..... (-27.97 = -27.91 +  -0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:45:06 2006