Locus 1737

Sequence ID 3R_DroMel_CAF1
Location 4,996,357 – 4,996,490
Length 133
Max. P 0.760464
window2856 window2857 window2858

overview

Window 6

Location 4,996,357 – 4,996,467
Length 110
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.92
Mean single sequence MFE -29.20
Consensus MFE -21.38
Energy contribution -21.68
Covariance contribution 0.31
Combinations/Pair 1.17
Mean z-score -2.52
Structure conservation index 0.73
SVM decision value 0.50
SVM RNA-class probability 0.760464
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4996357 110 + 27905053
AUUAAAGCCAAGACAAACAAACUC-----GCAAUGGGGC----GCAGACACGUGCAAAAUGAGU-UAACAAUUUGCAUGCAAAUCUGCGCCGACAAGUCGCCUAAUGUUAACCCAUUAAG
........................-----..((((((((----(((((..((((((((.((...-...)).))))))))....)))))))(((....)))...........))))))... ( -31.00)
>DroPse_CAF1 146904 103 + 1
---AAAGC-----------ACUUCGAGGGGCAG-GGGGAGGGGCUAGACACGUGCAAAAUGAGU-UAACAAUUUGCAUGUUAAUUUGCUCCGACAAGUCGCUUAAUGUUAACCCAU-GAA
---.....-----------...(((.((((((.-.(((.(((((.....(((((((((.((...-...)).)))))))))......)))))((....)).)))..)))...))).)-)). ( -29.40)
>DroSim_CAF1 106883 110 + 1
AUUAAAGCCAAGACAAACAAACUC-----GCAAUGGGGC----GCAGACACGUGCAAAAUGAGU-UAACAAUUUGCAUGCAAAUCUGCGCCGACAAGUCGCCUAAUGUUAACCCAUUAAG
........................-----..((((((((----(((((..((((((((.((...-...)).))))))))....)))))))(((....)))...........))))))... ( -31.00)
>DroEre_CAF1 103998 110 + 1
AUUAAAGCCAAGACAAACAAACUC-----GCAAUGGGGC----GCAGACACGUGCAAAAUGAGU-UAACAAUUUGCAUGCAAAUCUGCGUCGACAAGUCGCCUAAUGUUAACCCAUUAAG
........................-----..((((((((----(((((..((((((((.((...-...)).))))))))....)))))))(((....)))...........))))))... ( -29.10)
>DroYak_CAF1 105353 110 + 1
AUUAAAGCCAAGACAAACAAACUC-----GCAAUGGGGC----GCAGACACGUGCAAAAUGAGU-UAACAAUUUGCAUGCAAAUCUGCGCCGACAAGUCGCCUAAUGUUAACCCAUUAAG
........................-----..((((((((----(((((..((((((((.((...-...)).))))))))....)))))))(((....)))...........))))))... ( -31.00)
>DroAna_CAF1 97868 113 + 1
ACUACUGACAAGACAAACA--UUC-----ACACUGGGUUGCUGGCAGACACGUGCAAAAUGAGUUUAACAAUUUGUAUGUAAAUCCGCGCCGACAAGUCGCCUAAUGUUAACCCAUUAAG
...................--...-----....((((((((.(((.((((((((((((.((.......)).)))))))))...((......))...))))))....).)))))))..... ( -23.70)
>consensus
AUUAAAGCCAAGACAAACAAACUC_____GCAAUGGGGC____GCAGACACGUGCAAAAUGAGU_UAACAAUUUGCAUGCAAAUCUGCGCCGACAAGUCGCCUAAUGUUAACCCAUUAAG
...............................((((((......(((((..((((((((.((.......)).))))))))....)))))..(((....)))...........))))))... (-21.38 = -21.68 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 4,996,357 – 4,996,467
Length 110
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.92
Mean single sequence MFE -31.02
Consensus MFE -21.86
Energy contribution -22.87
Covariance contribution 1.00
Combinations/Pair 1.11
Mean z-score -1.91
Structure conservation index 0.70
SVM decision value 0.03
SVM RNA-class probability 0.546643
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4996357 110 - 27905053
CUUAAUGGGUUAACAUUAGGCGACUUGUCGGCGCAGAUUUGCAUGCAAAUUGUUA-ACUCAUUUUGCACGUGUCUGC----GCCCCAUUGC-----GAGUUUGUUUGUCUUGGCUUUAAU
......(((((((...((((((((((((.(((((((((..((.((((((.((...-...)).)))))).))))))))----))).....))-----))).)))))))..))))))).... ( -37.10)
>DroPse_CAF1 146904 103 - 1
UUC-AUGGGUUAACAUUAAGCGACUUGUCGGAGCAAAUUAACAUGCAAAUUGUUA-ACUCAUUUUGCACGUGUCUAGCCCCUCCCC-CUGCCCCUCGAAGU-----------GCUUU---
...-(((((((((((.....(((....)))..(((........)))....)))))-))))))...((((...((.((...(.....-..)...)).)).))-----------))...--- ( -21.50)
>DroSim_CAF1 106883 110 - 1
CUUAAUGGGUUAACAUUAGGCGACUUGUCGGCGCAGAUUUGCAUGCAAAUUGUUA-ACUCAUUUUGCACGUGUCUGC----GCCCCAUUGC-----GAGUUUGUUUGUCUUGGCUUUAAU
......(((((((...((((((((((((.(((((((((..((.((((((.((...-...)).)))))).))))))))----))).....))-----))).)))))))..))))))).... ( -37.10)
>DroEre_CAF1 103998 110 - 1
CUUAAUGGGUUAACAUUAGGCGACUUGUCGACGCAGAUUUGCAUGCAAAUUGUUA-ACUCAUUUUGCACGUGUCUGC----GCCCCAUUGC-----GAGUUUGUUUGUCUUGGCUUUAAU
(((((((......)))))))(((....))).(((((((..((.((((((.((...-...)).)))))).))))))))----)..(((..((-----(((....)))))..)))....... ( -31.50)
>DroYak_CAF1 105353 110 - 1
CUUAAUGGGUUAACAUUAGGCGACUUGUCGGCGCAGAUUUGCAUGCAAAUUGUUA-ACUCAUUUUGCACGUGUCUGC----GCCCCAUUGC-----GAGUUUGUUUGUCUUGGCUUUAAU
......(((((((...((((((((((((.(((((((((..((.((((((.((...-...)).)))))).))))))))----))).....))-----))).)))))))..))))))).... ( -37.10)
>DroAna_CAF1 97868 113 - 1
CUUAAUGGGUUAACAUUAGGCGACUUGUCGGCGCGGAUUUACAUACAAAUUGUUAAACUCAUUUUGCACGUGUCUGCCAGCAACCCAGUGU-----GAA--UGUUUGUCUUGUCAGUAGU
.(((.((((((.......(.(((....))).)((((((..((...((((.((.......)).))))...))))))))....))))))...)-----)).--................... ( -21.80)
>consensus
CUUAAUGGGUUAACAUUAGGCGACUUGUCGGCGCAGAUUUGCAUGCAAAUUGUUA_ACUCAUUUUGCACGUGUCUGC____GCCCCAUUGC_____GAGUUUGUUUGUCUUGGCUUUAAU
..(((((((.........(.(((....))).)((((((..((.((((((.((.......)).)))))).))))))))......))))))).............................. (-21.86 = -22.87 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 4,996,391 – 4,996,490
Length 99
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 85.35
Mean single sequence MFE -31.00
Consensus MFE -24.98
Energy contribution -25.03
Covariance contribution 0.06
Combinations/Pair 1.19
Mean z-score -2.08
Structure conservation index 0.81
SVM decision value 0.42
SVM RNA-class probability 0.727956
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4996391 99 - 27905053
-----------------CAGCGACGACAGCUUUUCACGGCCUUAAUGGGUUAACAUUAGGCGACUUGUCGGCGCAGAUUUGCAUGCAAAUUGUUA-ACUCAUUUUGCACGUGUCUGC---
-----------------...((((((..((((.....(((((....)))))......))))...))))))..((((((..((.((((((.((...-...)).)))))).))))))))--- ( -30.90)
>DroPse_CAF1 146929 101 - 1
-----------------CAACGACGACAGCUUUUCACGGCUUC-AUGGGUUAACAUUAAGCGACUUGUCGGAGCAAAUUAACAUGCAAAUUGUUA-ACUCAUUUUGCACGUGUCUAGCCC
-----------------...........(((...((((((...-(((((((((((.....(((....)))..(((........)))....)))))-))))))...)).))))...))).. ( -29.20)
>DroEre_CAF1 104032 99 - 1
-----------------CAGCGACGACAGCUUUUCACGGCCUUAAUGGGUUAACAUUAGGCGACUUGUCGACGCAGAUUUGCAUGCAAAUUGUUA-ACUCAUUUUGCACGUGUCUGC---
-----------------..(((((((..((((.....(((((....)))))......))))...)))))).)((((((..((.((((((.((...-...)).)))))).))))))))--- ( -30.90)
>DroYak_CAF1 105387 99 - 1
-----------------CAGCGACGACAGCUUUUCACGGCCUUAAUGGGUUAACAUUAGGCGACUUGUCGGCGCAGAUUUGCAUGCAAAUUGUUA-ACUCAUUUUGCACGUGUCUGC---
-----------------...((((((..((((.....(((((....)))))......))))...))))))..((((((..((.((((((.((...-...)).)))))).))))))))--- ( -30.90)
>DroAna_CAF1 97901 120 - 1
GCAGAAACUGGCAGCAACAGCGACAGAAGCUUUUCAGGGCCUUAAUGGGUUAACAUUAGGCGACUUGUCGGCGCGGAUUUACAUACAAAUUGUUAAACUCAUUUUGCACGUGUCUGCCAG
.......(((((((((...((((.....(((...((((((((.((((......))))))))..))))..)))..(..((((((.......)).))))..)...))))...)).))))))) ( -33.60)
>DroPer_CAF1 152822 102 - 1
-----------------CAACGACGACAGCUUUUCACGGCUUUAAUGGGUUAACAUUAAGCGACUUGUCGGAGCAAAUUUACAUGCAAAUUGUUA-ACUCAUUUUGCACGUGUCUAGCCC
-----------------...........(((...((((((...((((((((((((.....(((....)))..(((........)))....)))))-)))))))..)).))))...))).. ( -30.50)
>consensus
_________________CAGCGACGACAGCUUUUCACGGCCUUAAUGGGUUAACAUUAGGCGACUUGUCGGCGCAGAUUUACAUGCAAAUUGUUA_ACUCAUUUUGCACGUGUCUGC___
....................((((((..((((.....(((((....)))))......))))...))))))..((((((..((.((((((.((.......)).)))))).))))))))... (-24.98 = -25.03 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:06 2006