Locus 1566

Sequence ID	2R_DroMel_CAF1
Location	5,908,856 – 5,908,957
Length	101
Max. P	0.661350

overview

Window 5

Location	5,908,856 – 5,908,957
Length	101
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.29
Mean single sequence MFE	-32.88
Consensus MFE	-22.25
Energy contribution	-23.28
Covariance contribution	1.03
Combinations/Pair	1.24
Mean z-score	-2.26
Structure conservation index	0.68
SVM decision value	0.27
SVM RNA-class probability	0.661350
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5908856 101 + 20766785
ACCUCAGCAAACACUGCACCCGAGU-----------------GUUAGCAAAUGGAGAUCUUAUGUGCCCAUAUA--CAAGUGCGUGUGUGGGCUGGAAAUUUGUUGUCAAUUUCCGGCAA
..(((.((.((((((.......)))-----------------))).)).....)))......((((((((((((--(......))))))))))((((((((.......))))))))))). ( -32.70)
>DroSec_CAF1 50897 103 + 1
ACCUCAGCAAACACUGCACCCGAGU-----------------GUUAGCAAAUGGGCAUCUUAUGUGCCCAUAUACACAAGUGCGUGUGUGGGCUGGAAAUUUGUUGUCAAUUUCCGGUAA
(((..(((..(((((((((....((-----------------((......((((((((.....))))))))..))))..))))).))))..)))(((((((.......)))))))))).. ( -37.50)
>DroSim_CAF1 44091 103 + 1
ACCUCAGCAAACACUGCACCCGAGU-----------------GUUAGCAAAUGGGCAUCUUAUGUGCCCAUAUACGCAAGUGCGUGUGUGGGCUGGAAAUUUGUUGUCAAUUUCCGGCAA
.((.(.((.((((((.......)))-----------------))).))..((((((((.....))))))))((((((....))))))).))((((((((((.......)))))))))).. ( -41.50)
>DroEre_CAF1 43116 99 + 1
ACCUCAGCAAACACUGCACCCGAGU-----------------GUUAGUAAAUGGGCAUCUUAUGUGCCCUUAU----AAGUGCGUGUGUGGGCUGGAAAUUUGUUGUCAAUUUCCGGCAA
.((...(((..((((((((....))-----------------))........((((((.....))))))....----.))))..)))..))((((((((((.......)))))))))).. ( -33.60)
>DroYak_CAF1 43395 97 + 1
ACCUCAGCAAACACUGCACCCGAGU-----------------GUUAGUAAAUGGGUCUCUUAUGUGCCCAUAU------GUGUGUGUGUGUGCUGGAAAUUUGUUGUCAAUUUCCGGCAA
......(((.((((.((((....))-----------------))......(((((((......).))))))..------)))).)))...(((((((((((.......))))))))))). ( -28.80)
>DroAna_CAF1 50358 120 + 1
ACCUCAACAAACACUGGACCCAAUUUUCCGUAUGUGUAGUUGAUUAGUAAAUGGGCUCUUUAUAUCCUUAUGUAAGCGACAGAGUGUGUGUCCUGGAAAUUUGUUGUCAAUUUCCGGCAA
...(((((..((((((((........))))...)))).))))).......(((.(((((((((((....)))))).....))))).)))...(((((((((.......)))))))))... ( -23.20)
>consensus
ACCUCAGCAAACACUGCACCCGAGU_________________GUUAGCAAAUGGGCAUCUUAUGUGCCCAUAUA__CAAGUGCGUGUGUGGGCUGGAAAUUUGUUGUCAAUUUCCGGCAA
.......((.((((.((((.......................(....)..((((((((.....))))))))........)))))))).)).((((((((((.......)))))))))).. (-22.25 = -23.28 +   1.03)

alignment

secondary structure

dotplot

Window 6

Location	5,908,856 – 5,908,957
Length	101
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.29
Mean single sequence MFE	-30.74
Consensus MFE	-19.42
Energy contribution	-19.28
Covariance contribution	-0.14
Combinations/Pair	1.20
Mean z-score	-2.41
Structure conservation index	0.63
SVM decision value	0.17
SVM RNA-class probability	0.614812
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5908856 101 - 20766785
UUGCCGGAAAUUGACAACAAAUUUCCAGCCCACACACGCACUUG--UAUAUGGGCACAUAAGAUCUCCAUUUGCUAAC-----------------ACUCGGGUGCAGUGUUUGCUGAGGU
..((((((((((.......)))))))(((..((((..(((((((--......((((.((.........)).))))...-----------------...))))))).))))..)))..))) ( -29.00)
>DroSec_CAF1 50897 103 - 1
UUACCGGAAAUUGACAACAAAUUUCCAGCCCACACACGCACUUGUGUAUAUGGGCACAUAAGAUGCCCAUUUGCUAAC-----------------ACUCGGGUGCAGUGUUUGCUGAGGU
..((((((((((.......)))))))(((..((((..(((((((.(((.((((((((....).))))))).)))....-----------------...))))))).))))..)))..))) ( -37.10)
>DroSim_CAF1 44091 103 - 1
UUGCCGGAAAUUGACAACAAAUUUCCAGCCCACACACGCACUUGCGUAUAUGGGCACAUAAGAUGCCCAUUUGCUAAC-----------------ACUCGGGUGCAGUGUUUGCUGAGGU
..((((((((((.......)))))))(((..((((..(((((((.(((.((((((((....).))))))).)))....-----------------...))))))).))))..)))..))) ( -36.00)
>DroEre_CAF1 43116 99 - 1
UUGCCGGAAAUUGACAACAAAUUUCCAGCCCACACACGCACUU----AUAAGGGCACAUAAGAUGCCCAUUUACUAAC-----------------ACUCGGGUGCAGUGUUUGCUGAGGU
..((((((((((.......)))))))(((..((((..(((((.----....((((((....).))))).........(-----------------....)))))).))))..)))..))) ( -29.20)
>DroYak_CAF1 43395 97 - 1
UUGCCGGAAAUUGACAACAAAUUUCCAGCACACACACACAC------AUAUGGGCACAUAAGAGACCCAUUUACUAAC-----------------ACUCGGGUGCAGUGUUUGCUGAGGU
..((((((((((.......)))))))((((.((((......------..((((((........).))))).......(-----------------((....)))..)))).))))..))) ( -26.50)
>DroAna_CAF1 50358 120 - 1
UUGCCGGAAAUUGACAACAAAUUUCCAGGACACACACUCUGUCGCUUACAUAAGGAUAUAAAGAGCCCAUUUACUAAUCAACUACACAUACGGAAAAUUGGGUCCAGUGUUUGUUGAGGU
..((((((((((.......)))))))..((((.(((((.((((.(((....)))))))....(..((((.............................))))..)))))).))))..))) ( -26.65)
>consensus
UUGCCGGAAAUUGACAACAAAUUUCCAGCCCACACACGCACUUG__UAUAUGGGCACAUAAGAUGCCCAUUUACUAAC_________________ACUCGGGUGCAGUGUUUGCUGAGGU
..((((((((((.......)))))))(((..((((.............((((....))))....((((...............................))))...))))..)))..))) (-19.42 = -19.28 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:39 2006