Locus 8475

Sequence ID	X_DroMel_CAF1
Location	21,040,326 – 21,040,478
Length	152
Max. P	0.896199

overview

Window 5

Location	21,040,326 – 21,040,438
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.70
Mean single sequence MFE	-25.48
Consensus MFE	-23.40
Energy contribution	-23.80
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.29
Structure conservation index	0.92
SVM decision value	0.64
SVM RNA-class probability	0.808881
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21040326 112 - 22224390
UCGCACACA----CACUUAUGGCCACUAACAAAUCAUGGCUGGUCGUGCAUGUUUCAUGUCCACUUAGCCAAGAAGACGACAUAACGACAAAGUCGGCCG----CCCACCCAUAACUCCA
.........----.......((((.........((.((((((((.(..((((...))))..))).)))))).)).(((..............))))))).----................ ( -25.04)
>DroSec_CAF1 10784 112 - 1
UCGCACACA----CACUUAUGGCCACUAACAAAUCAUGGCCGGUCGUGCAUGUUUCAUGUCCACUUAGCCAAGAAGACGACAUAACGACAAAGUCGGCCG----CCCACCCAUAACUCCA
..((.....----.......(((((...........)))))(((((....((((..(((((..(((.......)))..)))))...))))....))))))----)............... ( -23.80)
>DroSim_CAF1 11274 112 - 1
UCGCACACA----CACUUAUGGCCACUAACAAAUCAUGGCCGGUCGUGCAUGUUUCAUGUCCACUUAGCCAAGAAGACGACAUAACGACAAAGUCGGCCG----CCCACCCAUAACUCCA
..((.....----.......(((((...........)))))(((((....((((..(((((..(((.......)))..)))))...))))....))))))----)............... ( -23.80)
>DroEre_CAF1 11481 116 - 1
UCGCACACACUCGCACUUAUGGCCACUAACAAAUCAUGGCUGGUCGUGCAUGUUUCAUGUCCACUUAGCCAAGAAGACGACAUAACGACAAAGUCGGCCG----CCCACCCAUAACUCCA
..((........))......((((.........((.((((((((.(..((((...))))..))).)))))).)).(((..............))))))).----................ ( -26.34)
>DroYak_CAF1 12517 120 - 1
UCGCGCACACUCGCACUUAUGGCCACUAACAAAUCAUGGCUGGUCGUGCAUGUUUCAUGUCCACUUAGCCAAGAAGACGACAUAACGACAAAGUCGGCCGCCCGCCCACCCAUAACUCCA
..((((......))......((((.........((.((((((((.(..((((...))))..))).)))))).)).(((..............)))))))))................... ( -28.44)
>consensus
UCGCACACA____CACUUAUGGCCACUAACAAAUCAUGGCUGGUCGUGCAUGUUUCAUGUCCACUUAGCCAAGAAGACGACAUAACGACAAAGUCGGCCG____CCCACCCAUAACUCCA
....................((((.........((.((((((((.(..((((...))))..))).)))))).)).(((..............)))))))..................... (-23.40 = -23.80 +   0.40)

alignment

secondary structure

dotplot

Window 6

Location	21,040,362 – 21,040,478
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.77
Mean single sequence MFE	-29.18
Consensus MFE	-24.87
Energy contribution	-25.67
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.62
Structure conservation index	0.85
SVM decision value	0.99
SVM RNA-class probability	0.896199
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21040362 116 - 22224390
AAAAAAAAUGAGAAAAACAAUAUAUGGCGGGCCGUAAGAGUCGCACACA----CACUUAUGGCCACUAACAAAUCAUGGCUGGUCGUGCAUGUUUCAUGUCCACUUAGCCAAGAAGACGA
...........................(((((((((((.((.......)----).))))))))).........((.((((((((.(..((((...))))..))).)))))).))...)). ( -29.80)
>DroSec_CAF1 10820 115 - 1
AAA-AAAAUGAGAAAAACAAUAUAUGGCGGGCCGUAAGUGUCGCACACA----CACUUAUGGCCACUAACAAAUCAUGGCCGGUCGUGCAUGUUUCAUGUCCACUUAGCCAAGAAGACGA
...-...((((((....((.....((((.((((((((((((.......)----))))))))))).....((.....))))))....))....))))))(((..(((....)))..))).. ( -32.10)
>DroSim_CAF1 11310 116 - 1
AAAAAAAAUGAGAAAAACAAUAUAUGGCGGGCCGUAAGAGUCGCACACA----CACUUAUGGCCACUAACAAAUCAUGGCCGGUCGUGCAUGUUUCAUGUCCACUUAGCCAAGAAGACGA
.......((((((....((.....((((.(((((((((.((.......)----).))))))))).....((.....))))))....))....))))))(((..(((....)))..))).. ( -27.40)
>DroEre_CAF1 11517 118 - 1
AAA--AAAUGGCAAAAACAAUAUAUGGCGGGCCGAAAGAGUCGCACACACUCGCACUUAUGGCCACUAACAAAUCAUGGCUGGUCGUGCAUGUUUCAUGUCCACUUAGCCAAGAAGACGA
...--...((((.....((.....))..((((.((((((((.......))))((((...((((((...........))))))...))))...))))..)))).....))))......... ( -27.50)
>DroYak_CAF1 12557 119 - 1
AAA-AAAAUGAGAAAAACAAUAUAUGGCGGGCCGAAAGAGUCGCGCACACUCGCACUUAUGGCCACUAACAAAUCAUGGCUGGUCGUGCAUGUUUCAUGUCCACUUAGCCAAGAAGACGA
...-...((((((...........(((((((((....).))).))).))...((((...((((((...........))))))...))))...))))))(((..(((....)))..))).. ( -29.10)
>consensus
AAA_AAAAUGAGAAAAACAAUAUAUGGCGGGCCGUAAGAGUCGCACACA____CACUUAUGGCCACUAACAAAUCAUGGCUGGUCGUGCAUGUUUCAUGUCCACUUAGCCAAGAAGACGA
...........................(((((((((((.................))))))))).........((.((((((((.(..((((...))))..))).)))))).))...)). (-24.87 = -25.67 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:04:58 2006