Locus 4549

Sequence ID	3L_DroMel_CAF1
Location	13,091,419 – 13,091,556
Length	137
Max. P	0.711197

overview

Window 3

Location	13,091,419 – 13,091,525
Length	106
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.90
Mean single sequence MFE	-32.60
Consensus MFE	-21.30
Energy contribution	-21.22
Covariance contribution	-0.08
Combinations/Pair	1.17
Mean z-score	-1.60
Structure conservation index	0.65
SVM decision value	0.38
SVM RNA-class probability	0.711197
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13091419 106 + 23771897
----CAGCAGAACAAC-AACACCCUGCGUCAGUUCACGCACUGAUCCUCGA---CCUAUCGACGCAGGCAGCUGAGCAUCUAUGCUUAGU-AGUCC-----GCUGCCCAACACUGUGAUG
----((((.((.....-.....(((((((((((......)))))...((((---....))))))))))..((((((((....))))))))-..)).-----))))............... ( -31.70)
>DroPse_CAF1 68609 104 + 1
----------AACAAC-AACACCCUGCGGCAGUUCACCCACUGAUCCACGGUUGACUAUCGACGCAGGCAGCUGAGCAUCUACGCUUAGUUCGGCC-----GCUGUCCAACACUGUGAUG
----------......-..(((..((.(..((((.(((...........))).))))..)(((((.(((.(((((((......)))))))...)))-----)).)))...))..)))... ( -28.00)
>DroGri_CAF1 110258 106 + 1
----------AGCGACGAACACCUUGCGGCAAUUCACGCACUGAUCCUCGGAGCACUAUCGUCGCAGGCAGCUGAGCAUUUUUGCUUAGU-UCCUCGUCGCGUUGCC-A--ACUGUGAUG
----------.(((((((......((((((.((....((.(((.....))).))...)).))))))((.(((((((((....))))))))-))))))))))((..(.-.--...)..)). ( -40.50)
>DroYak_CAF1 78118 110 + 1
GCAGCAGCAGAACAAC-AACACACUGCGUCAGUUCACGCACUGAUCCUCGA---CCUAUCGACGCAGGCAGCUGAGCAUCUUUGCUUAGU-AGUCC-----GCUGCCCAACACUGUGAUG
...(((((........-......((((((((((......)))))...((((---....)))))))))((.((((((((....))))))))-.))..-----))))).............. ( -34.70)
>DroAna_CAF1 72834 106 + 1
----CAGCAGAACAAC-AACACCCUGCGCCAGUUCACGCACUGAUCCUCGA---CCUACCGACGCAGGCAGCUGAGUAUCUUUGCUUAGC-CCCCU-----GCUGCCCCCCACUGUGAUG
----((((((......-.....((((((.((((......))))....(((.---.....)))))))))..((((((((....))))))))-...))-----))))............... ( -32.70)
>DroPer_CAF1 44071 104 + 1
----------AACAAC-AACACCCUGCGGCAGUUCACCCACUGAUCCACGGUUGACUAUCGACGCAGGCAGCUGAGCAUCUACGCUUAGUUCGGCC-----GCUGUCCAACACUGUGAUG
----------......-..(((..((.(..((((.(((...........))).))))..)(((((.(((.(((((((......)))))))...)))-----)).)))...))..)))... ( -28.00)
>consensus
__________AACAAC_AACACCCUGCGGCAGUUCACGCACUGAUCCUCGA___ACUAUCGACGCAGGCAGCUGAGCAUCUAUGCUUAGU_CGCCC_____GCUGCCCAACACUGUGAUG
...................(((((((((.((((......)))).....(((.......))).))))))..(((((((......)))))))........................)))... (-21.30 = -21.22 +  -0.08)

alignment

secondary structure

dotplot

Window 4

Location	13,091,454 – 13,091,556
Length	102
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	78.95
Mean single sequence MFE	-22.44
Consensus MFE	-15.88
Energy contribution	-15.60
Covariance contribution	-0.28
Combinations/Pair	1.12
Mean z-score	-1.02
Structure conservation index	0.71
SVM decision value	-0.05
SVM RNA-class probability	0.507202
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13091454 102 + 23771897
CUGAUCCUCGA---CCUAUCGACGCAGGCAGCUGAGCAUCUAUGCUUAGUAGUCC-----GCUGCCCAACACUGUGAUGCCAAAACCCCC-------AAGAAGCCCACUAAAACCAC--
.......((((---....)))).((.(((.((((((((....)))))))).))).-----))...........(((..((..........-------.....)).))).........-- ( -19.16)
>DroGri_CAF1 110288 109 + 1
CUGAUCCUCGGAGCACUAUCGUCGCAGGCAGCUGAGCAUUUUUGCUUAGUUCCUCGUCGCGUUGCC-A--ACUGUGAUGCCAAAUUCUGU-------AAAUGCCCCACAACAACAAGAA
.........((.(((.....(.((.(((.(((((((((....)))))))))))))).)((((..(.-.--...)..))))..........-------...))).))............. ( -30.90)
>DroSim_CAF1 76723 102 + 1
CUGAUCCUCGA---CCUAUCGACGCAGGCAGCUGAGCAUCUAUGCUUAGUAGUCC-----GCUGCCCAACACUGUGAUGCCAAAACCCCC-------AAAAAGCCCACUAAAACCAC--
.......((((---....)))).((.(((.((((((((....)))))))).))).-----))...........(((..((..........-------.....)).))).........-- ( -19.16)
>DroEre_CAF1 75680 102 + 1
CUGAUCCUCGA---CCUAUAGACGCAGGCAGCUGAGCAUCUAUGCUUAGUAGUCC-----GCUGCCCAACACUGUGAUGCCAAAACCCCC-------AAAAAACACACUAAAACCAC--
...........---....(((..((.(((.((((((((....)))))))).))).-----))..........((((..............-------......))))))).......-- ( -17.95)
>DroYak_CAF1 78157 102 + 1
CUGAUCCUCGA---CCUAUCGACGCAGGCAGCUGAGCAUCUUUGCUUAGUAGUCC-----GCUGCCCAACACUGUGAUGCCAAAACCCCC-------AAAAAGCCCACUAAAACCAC--
.......((((---....)))).((.(((.((((((((....)))))))).))).-----))...........(((..((..........-------.....)).))).........-- ( -19.96)
>DroAna_CAF1 72869 109 + 1
CUGAUCCUCGA---CCUACCGACGCAGGCAGCUGAGUAUCUUUGCUUAGCCCCCU-----GCUGCCCCCCACUGUGAUGCCUGGUCCUGCCCCACCCUCACAUCCUGCCCCAUCCAC--
.......(((.---.....))).(((((..((((((((....))))))))..)))-----))..........(((((.(..(((.......)))..))))))...............-- ( -27.50)
>consensus
CUGAUCCUCGA___CCUAUCGACGCAGGCAGCUGAGCAUCUAUGCUUAGUAGUCC_____GCUGCCCAACACUGUGAUGCCAAAACCCCC_______AAAAAGCCCACUAAAACCAC__
......................((((((((((((((((....))))))............))))))......))))........................................... (-15.88 = -15.60 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:16 2006