Locus 6056

Sequence ID dm3.chr3L
Location 3,370,949 – 3,371,017
Length 68
Max. P 0.924049
window8337 window8338

overview

Window 7

Location 3,370,949 – 3,371,017
Length 68
Sequences 7
Columns 76
Reading direction forward
Mean pairwise identity 69.18
Shannon entropy 0.54402
G+C content 0.50247
Mean single sequence MFE -22.66
Consensus MFE -12.32
Energy contribution -13.19
Covariance contribution 0.86
Combinations/Pair 1.33
Mean z-score -1.52
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.30
SVM RNA-class probability 0.924049
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3370949 68 + 24543557
AUAACUCAUAGCCCCCAUUU-GGAGCUAGGCUCCGCUCAGGUCUUUGAAAGUCUU------GGGGGGCACAGUGC-
..........((((((....-(((((...)))))...((((.((.....)).)))------))))))).......- ( -26.50, z-score =  -1.95, R)
>droSim1.chr3L 2905864 68 + 22553184
AUAACUCAUAGCCCCCAUUU-GGAGCUAGGCUCCGCUCAGGUCUUUGAAAGUCUU------GGGGGGCACAGUGC-
..........((((((....-(((((...)))))...((((.((.....)).)))------))))))).......- ( -26.50, z-score =  -1.95, R)
>droSec1.super_2 3363459 68 + 7591821
AUAACUCAUAGCCCCCAUUU-GGAGCUAGGCUCCGCUCAGGUCUUUGAAAGUCUU------GGGGGGCACAGUGC-
..........((((((....-(((((...)))))...((((.((.....)).)))------))))))).......- ( -26.50, z-score =  -1.95, R)
>droYak2.chr3L 3917541 72 + 24197627
AUAACUUAUAGCCCCCAUUU-GGAGCUAGGCUCCGCUCAGGUCUUUGAAAGUCUUUGG---GGGGGGCAAAGUGAC
...((((...((((((....-(((((...))))).((((((.((.....)).).))))---))))))).))))... ( -26.80, z-score =  -1.61, R)
>droEre2.scaffold_4784 6060473 69 + 25762168
AUAACUUAUAGCCCCCAUUUUGGAGCUAGGCUCCGCUCAGGUCUUUGAAAGUCUU------GGGGGGCACAGUGC-
..........((((((.....(((((...)))))...((((.((.....)).)))------))))))).......- ( -26.50, z-score =  -2.00, R)
>dp4.chrXR_group8 5459705 73 + 9212921
AUAACUCCU--CUUGUAAAAACUGUCUUCGAUUCGCUUCUUCGUUCGAGAAGCUUAGUUCCAUGGAACGCUCUGU-
.........--.......................(((((((.....)))))))...((((....)))).......- ( -12.90, z-score =  -0.58, R)
>droPer1.super_38 573873 73 - 801819
AUAACUCCU--CUUGUAAAAACUGUCUUCGAUUCGCUUCUUCGUUCGAGAAGCUUAGUUCCAUGGAACGCUCUGU-
.........--.......................(((((((.....)))))))...((((....)))).......- ( -12.90, z-score =  -0.58, R)
>consensus
AUAACUCAUAGCCCCCAUUU_GGAGCUAGGCUCCGCUCAGGUCUUUGAAAGUCUU______GGGGGGCACAGUGC_
..........((((((.....(((((...)))))..((((....))))..............))))))........ (-12.32 = -13.19 +   0.86)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 3,370,949 – 3,371,017
Length 68
Sequences 7
Columns 76
Reading direction reverse
Mean pairwise identity 69.18
Shannon entropy 0.54402
G+C content 0.50247
Mean single sequence MFE -20.56
Consensus MFE -10.01
Energy contribution -11.36
Covariance contribution 1.35
Combinations/Pair 1.27
Mean z-score -1.38
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.61
SVM RNA-class probability 0.759697
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3370949 68 - 24543557
-GCACUGUGCCCCCC------AAGACUUUCAAAGACCUGAGCGGAGCCUAGCUCC-AAAUGGGGGCUAUGAGUUAU
-.......((((((.------......((((......)))).(((((...)))))-....)))))).......... ( -21.90, z-score =  -1.26, R)
>droSim1.chr3L 2905864 68 - 22553184
-GCACUGUGCCCCCC------AAGACUUUCAAAGACCUGAGCGGAGCCUAGCUCC-AAAUGGGGGCUAUGAGUUAU
-.......((((((.------......((((......)))).(((((...)))))-....)))))).......... ( -21.90, z-score =  -1.26, R)
>droSec1.super_2 3363459 68 - 7591821
-GCACUGUGCCCCCC------AAGACUUUCAAAGACCUGAGCGGAGCCUAGCUCC-AAAUGGGGGCUAUGAGUUAU
-.......((((((.------......((((......)))).(((((...)))))-....)))))).......... ( -21.90, z-score =  -1.26, R)
>droYak2.chr3L 3917541 72 - 24197627
GUCACUUUGCCCCCC---CCAAAGACUUUCAAAGACCUGAGCGGAGCCUAGCUCC-AAAUGGGGGCUAUAAGUUAU
...((((.((((((.---.........((((......)))).(((((...)))))-....))))))...))))... ( -23.80, z-score =  -2.35, R)
>droEre2.scaffold_4784 6060473 69 - 25762168
-GCACUGUGCCCCCC------AAGACUUUCAAAGACCUGAGCGGAGCCUAGCUCCAAAAUGGGGGCUAUAAGUUAU
-..(((..((((((.------......((((......)))).(((((...))))).....))))))....)))... ( -23.00, z-score =  -1.90, R)
>dp4.chrXR_group8 5459705 73 - 9212921
-ACAGAGCGUUCCAUGGAACUAAGCUUCUCGAACGAAGAAGCGAAUCGAAGACAGUUUUUACAAG--AGGAGUUAU
-.......((((....))))..((((((((....(.((((((............)))))).)..)--))))))).. ( -15.70, z-score =  -0.82, R)
>droPer1.super_38 573873 73 + 801819
-ACAGAGCGUUCCAUGGAACUAAGCUUCUCGAACGAAGAAGCGAAUCGAAGACAGUUUUUACAAG--AGGAGUUAU
-.......((((....))))..((((((((....(.((((((............)))))).)..)--))))))).. ( -15.70, z-score =  -0.82, R)
>consensus
_GCACUGUGCCCCCC______AAGACUUUCAAAGACCUGAGCGGAGCCUAGCUCC_AAAUGGGGGCUAUGAGUUAU
........((((((.............((((......)))).(((((...))))).....)))))).......... (-10.01 = -11.36 +   1.35)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:00:30 2011